Supplemental Data A single ancient origin for …...Supplemental Data A single ancient origin for prototypical SR splicing factors Sophie Califice, Denis Baurain , Marc Hanikenne and

Supplemental Data

A single ancient origin for prototypical SR splicing factors

Sophie Califice, Denis Baurain¶, Marc Hanikenne and Patrick Motte¶

¶To whom correspondence should be addressed.

E-mail: [email protected], [email protected]

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Table of contents

Supplemental Texts

Text S1. Detailed description of computational procedures. 4

Supplemental Table Legends. 17

Supplemental Figure Legends. 19

Supplemental References. 28

Supplemental Tables

Table S1. Taxonomic distribution of RRM-containing proteins. Table S1 File

Table S2. Hand-curated corpus of RRM-containing proteins collected in the primary literature. 30

Table S3. Qualitative comparison of the five large RRM domain trees. 56

Table S4. Summary of the groupings observed for SR protein RRM1 domains. 58

Table S5. Compositional features specific of one or more SR subfamilies. 59

Table S6. Determination key for SR families and subfamilies. 60

Table S7. Statistics for the curated inventory of SR proteins in 20 selected proteomes. 61

Supplemental Figures

Figure S1. Scheme of the analysis pipeline. 62

Figure S2. Optimization of clustering parameters for RRM domains. 63

Figure S3. Evaluation of the selection algorithm for cluster representatives. 68

Figure S4. Color key for KOG annotation. 69

Figure S5. Maximum Parsimony tree of representative RRM domains. 70

Figure S6. RAXML tree of representative RRM domains obtained under the WAG+Γ4 model. 81

Figure S7. TREEFINDER tree of representative RRM domains obtained under the WAG+Γ4 model. 92

Figure S8. RAXML tree of representative RRM domains obtained under the LG+F+Γ4 model. 103

Figure S9. RAXML tree of the enlarged RRM dataset obtained under the WAG+Γ4 model. 114

Figure S10. Qualitative consensus of phylogenetic analyses of representative RRM domains. 130

Figure S11. Mutual affinities of SR protein RRM domains in the five large trees. 131

Figure S12. RAXML tree of the largest RRM clusters obtained under the LG+F+Γ4 model. 132

Figure S13. Exhaustive RAXML tree of SR-associated RRM1 domains (WAG+Γ4 model). 133

Figure S14. Exhaustive TREEFINDER tree of SR-associated RRM1 domains (WAG+Γ4 model). 137

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Figure S15. RAXML tree of RRM1 domains from RNPS1-like proteins (WAG+Γ4 model). 141

Figure S16. TREEFINDER tree of RRM1 domains from RNPS1-like proteins (WAG+Γ4 model). 142

Figure S17. RAXML tree of RRM2 domains from dual RRM SR proteins (WAG+Γ4 model). 143

Figure S18. TREEFINDER tree of RRM2 domains from dual RRM SR proteins (WAG+Γ4 model). 147

Figure S19. RAXML tree of slowly evolving SR-associated RRM1 domains (WAG+Γ4 model). 151

Figure S20. TREEFINDER tree of slowly evolving SR-associated RRM1 domains (WAG+Γ4 model). 154

Figure S21. Sequence conservation in the first RRM domain of SR proteins. 157

Figure S22. Sequence conservation across prokaryotic RRM domains. 161

Figure S23. Sequence conservation across ZnK domains of SR proteins. 162

Figure S24. Distributions of relevant compositional features within SR subfamilies. 163

Figure S25. Architecture, conservation and compositional profile of SR subfamilies. 173

Figure S26. RAXML RRM tree of candidate SR proteins from selected proteomes (WAG+Γ4 model). 175

Figure S27. TREEFINDER RRM tree of candidate SR proteins from selected proteomes (WAG+Γ4 model). 178

Figure S28. RAXML tree of candidate SR proteins from selected proteomes (LG+F+Γ4 model). 181

Figure S29. PHYLOBAYES tree of candidate SR proteins from selected proteomes (CAT+Γ4 model). 184

Datasets

Dataset S1. HMM profiles for SR-associated RRM domains. Dataset S1 File

Dataset S2. Accessions and sequences of SR proteins identified in the inventory. Dataset S2 File

Dataset S3a. Architectures of candidate SR proteins from selected proteomes. Dataset S3 File

Dataset S3b. 1-AA word densities in candidate SR proteins from selected proteomes. Dataset S3 File

Dataset S3c. 2-AA word densities in candidate SR proteins from selected proteomes. Dataset S3 File

Dataset S3d. 3-AA word densities in candidate SR proteins from selected proteomes. Dataset S3 File

Dataset S4. Alignments in FASTA format. Dataset S4 File

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Text S1. Detailed description of computational procedures

1. RRM distribution across the Tree of Life

1.1. Data downloads

All complete prokaryotic and eukaryotic proteomes available on Ensembl and NCBI FTP servers

were downloaded in November 2007 (http://www.ncbi.nlm.nih.gov/sites/genome/). Additional

complete proteomes from photosynthetic eukaryotes were downloaded from JGI (Aureococcus

anophagefferens, Chlamydomonas reinhardtii, Ostreococcus lucimarinus, Ostreococcus tauri,

Phaeodactylum tricornutum, Physcomitrella patens, Phytophthora ramorum, Phytophthora

sojae, Thalassiosira pseudonana, and Volvox carteri; http://genome.jgi-psf.org/) and TIGR

(Ricinus communis and Zea mays; now located at http://cmr.jcvi.org/) servers. Cyanidioschyzon

merolae and Medicago truncatula complete proteomes were downloaded from their respective

project websites (http://merolae.biol.s.u-tokyo.ac.jp/ and http://medicago.org/).

1.2. Prediction of RRM domains

The PFAM (Finn et al., 2010) alignment for the RRM domain (pfam00076; 79 domain

sequences from 57 proteins) was downloaded from the NCBI Conserved Domain Database

(CDD) (Marchler-Bauer et al., 2009) and used to build a HMM profile with the HMMBUILD

component of the HMMER software package (http://hmmer.org/, see also Durbin et al., 1998).

As mentioned on the PFAM website (http://pfam.sanger.ac.uk/ family?acc=PF00076), the C-

terminal β-strand and final helix are hard to align and have been omitted in the seed alignment,

thus yielding a 72-amino-acid (AA) profile slightly truncated relative to the complete RRM

structure. RRM domains were predicted in each complete proteome with the program

HMMSEARCH (HMMER) using the HMM profile and a loose domain E-value threshold of 1e-5.

1.3. Extraction of RRM domains and RRM-containing proteins

HMMER reports were parsed to extract both the predicted RRM domains and the corresponding

full-length proteins in FASTA format. To determine the best domain E-value threshold,

sequences were repeatedly extracted using five increasingly stringent thresholds (1e-5, 1e-10,

1e-15, 1e-20, and 1e-25). Eventually, the threshold was set to 1e-10 as this value appeared to

give the best compromise between sensitivity and specificity. RRM domains were numbered

according to their N-term relative position within each protein (e.g., the second RRM domain of

any given protein is numbered RRM2). Consequently, RRM domains located downstream of at

least one unpredicted RRM domain (owing to an evolutionarily divergent sequence) were

4

http://www.ncbi.nlm.nih.gov/sites/genome/

http://genome.jgi-psf.org/

http://cmr.jcvi.org/

http://merolae.biol.s.u-tokyo.ac.jp/

http://medicago.org/

http://pfam.sanger.ac.uk/family?acc=PF00076

assigned an incorrect number. This shortcoming was taken into account during annotation and

manual analyses of RRM trees (see Sections 2.4-2.5). Finally, proteins containing more than one

predicted RRM were extracted only once to ensure accurate statistics.

1.4. Prediction of putative SR proteins

Extracted RRM-containing proteins were tagged as 'putative SR' when they met the rather crude

criterion proposed in reference (Boucher et al., 2001), i.e., having at least one occurrence of

either quadripeptide 'RSRS' or 'SRSR'. Tagging was carried out for annotation purposes only;

thus the absence of the 'SR' tag was never used to exclude a protein from subsequent analyses.

For Figure 1C, RS/SR dipeptides were counted either in the complete dataset of non-redundant

8,042 RRM-containing proteins or in a subset of 197 proteins displaying at least 95% identity to

reference sequences confirmed as SR or SRrp proteins (see Table S2 below for details).

1.5. Taxonomic distribution of RRM-containing proteins

For each domain E-value threshold, the numbers of RRM domains, RRM-containing proteins

and putative SR proteins predicted in each complete proteome were compiled, along with

proteome size and lineage, as fetched from the NCBI Taxonomy server (Benson et al., 2009;

Sayers et al., 2009). Proteomes were further categorized according to domain (Archaea,

Bacteria, or Eukaryota), complexity (unicellular vs. multicellular) and metabolism (standard vs.

capable of oxygenic photosynthesis) and the influence of these factors was assessed using F-

tests performed with the R statistical software (R Development Core Team, 2010). Though all

eukaryotic and 126 prokaryotic proteomes yielded at least a few RRM-containing proteins, most

prokaryotic and viral proteomes appeared devoid of RRM domains (Figure 1A-B and Table S1).

These were nevertheless included for completeness.

2. Origin and evolution of SR proteins

2.1. Clustering of RRM domains

To allow phylogenetic analyses, the large number of RRM domains extracted in Section 1.3

(12,023 at the 1e-10 threshold) was reduced to a more tractable dataset through a two-step

clustering based on sequence similarity.

First, exactly identical domains were consolidated and renamed after the most inclusive

taxonomic group of each cluster members (e.g., a RRM domain found in both Mus musculus

and Rattus norvegicus proteomes would be renamed 'Murinae'). Most of the time, merged

domains corresponded to orthologues of closely related organisms or to in-paralogues (i.e.,

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terminal gene duplications specific to an organism or to a small clade) or to protein isoforms.

This step roughly reduced the number of RRM domains by 50% (6,633 at the 1e-10 threshold).

Second, these unique RRM domains were more aggressively clustered by single-linkage using

the (now deprecated) BLASTCLUST component of the NCBI C toolkit (Altschul et al., 1997). Two

main parameters control the granularity of the clustering: these are the similarity threshold

(fraction of identical residues in the local pairwise alignment) and the coverage threshold

(fraction of the longest sequence covered by the alignment) that are to be reached to consider

two domains as neighbors. To ensure the best clustering (Ck), we explored the parameter space

for both thresholds (by steps of 0.05) and chose the combination of values that maximized a

composite score rewarding normalized entropy (Cover and Thomas, 2006) but penalizing the

number of singleton clusters (i.e., having only one domain) :

Sc =H(Ck )

logK− 0.8

N1

N

where

H(Ck ) = −Nk

Nk=1

K

∑ logNk

N

with N = total number of domains

K = number of clusters

Nk = number of domains in cluster k

N1 = number of singleton clusters

As shown in Figure S2, optimal parameters were as follow: similarity threshold = 0.60 and

coverage threshold = 0.85. These values held for domain E-value thresholds ranging from 1e-5

to 1e-20 and this step further reduced the cluster number by 80% (down to 1266 at the 1e-10

threshold). In the clustered datasets, each cluster was represented by the sequence of one of its

domains and names were attributed as in the first step, albeit often resulting into much higher

level taxa (e.g., Viridiplantae, Eukaryota, cellular organisms).

By default, BLASTCLUST selects the longest sequence as the cluster representative. Since longer

sequences are also more prone to be evolutionarily divergent (due to the accumulation of non-

conserved insertions), we modified BLASTCLUST to instead allow the selection of the most

slowly evolving cluster sequence. In practice, for each cluster, the domain showing the highest

average similarity with non-cluster domains was selected as the cluster representative. Our

algorithm is an independent re-implementation of the approach used in the SCAFOS software

package (Roure et al., 2007). The usefulness of this modification was evaluated by comparing

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the length of the phylogenetic trees inferred by parsimony (see Section 2.3 for details) from

three alternative datasets based on the selection strategy applied: (i) longest sequence; (ii) most

slowly evolving sequence; (iii) fastest-evolving sequence (control experiment). Out of 1266

clusters, there were 352 differences when comparing cluster representatives between strategy (i)

and (ii); 299 between (i) and (iii); and 479 between (ii) and (iii). In terms of performance, Figure

S3 shows that strategy (ii) generally yielded the shortest trees, followed by strategies (i) and (iii).

These results indicate that our algorithmic modification to BLASTCLUST should help to reduce

the occurrence of phylogenetic artifacts by actively avoiding the selection of evolutionarily

divergent sequences.

In the following, the 1266-cluster dataset built by selection of the most slowly evolving RRM

domains was used as the basis of all analyses.

2.2. Alignment of RRM domains

Due to weak conservation combined to a large number of RRM domains to consider, standard

alignment methods (e.g., CLUSTALW) led to overly wide alignments with so many gaps that they

were practically unusable (data not shown). Alternatively, RRM domains were aligned with

HMMALIGN (HMMER) against the HMM profile already used for their prediction (see Section

1.2). To control alignment width, amino acids that did not align to match states of the profile

were discarded (option -m), thus literally 'splicing' autapomorphic (and unalignable) insertions

out of longer domain sequences. Consequently, the resulting alignment had only 72 AA

positions, as many as the HMM profile. Visual inspection of the 1266 domain sequences

indicated that this alignment was suitable for large-scale analyses.

2.3. Phylogenetic analyses of RRM domains

The large alignment of RRM domains was analysed by Maximum Parsimony (MP) using PAUP*

(Swofford, 2002) (Figure S5) and by Maximum Likelihood (ML) using either TREEFINDER (Jobb et

al., 2004) with a WAG+Γ4 model (Yang, 1993; Whelan and Goldman, 2001) (Figure S7) or

RAXML with the very similar PROTMIXWAG model (Stamatakis et al., 2005) (Figure S6) or with

the LG+F+Γ4 model (Le and Gascuel, 2008) (Figure S8). SEQBOOT and CONSENSE from the

PHYLIP software package (Felsenstein, 2005) were used respectively to generate 100 bootstrap

replicates (Felsenstein, 1985) for each analysis and to compute support values. Bayesian

inference with the CAT model known to reduce phylogenetic artifacts (Lartillot and Philippe,

2004; Lartillot et al., 2009; Philippe et al., 2011) was also investigated. However, this

sophisticated model designed for phylogenomics did not yield useful results on our sequence-

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rich but position-poor dataset, even after having run two independent PHYLOBAYES chains for

more than 85,000 cycles (data not shown).

To evaluate our selection algorithm for representative cluster sequences (see Section 2.1) in a

reasonable time, PAUP* was invoked with the following options: NREPS=1;

ADDSEQ=RANDOM; SWAP=TBR; MAXTREE=10. In contrast, the tree built for phylogenetic

purposes was inferred using more time-consuming options: NREPS=10; ADDSEQ=RANDOM;

SWAP=TBR; MAXTREE=1000. As a consequence, the latter MP tree (Figure S5; 36,439

parsimony steps) was slightly shorter than the former (Figure S3; 36,617 parsimony steps).

Trees were rooted and left-ladderized using the TREEPLOT component of the MUST software

package (Philippe, 1993). Since prokaryotic (and prokaryotic-containing) clusters were mostly

concentrated in a small region of the tree, the root was set on the branch separating the bulk of

these predominantly prokaryotic clusters from eukaryote-specific clusters. Automatic

ladderization based on subtree content helped to order branches so that similarly composed

subtrees were easily recognizable by eye across analyses.

2.4. Annotation of RRM trees

Prior to manual examination, RRM trees were automatically annotated using several data

sources. To maximize the sensitivity, annotation was actually performed on the individual

proteins corresponding to the RRM domains clustered in the trees. Thus, the main challenge

was to keep track of the relationships between individual RRM domains (12,023) and RRM-

containing proteins (8,042) on one side and cluster representative RRM domains (1266) on the

other side, especially considering the two-step clustering and the taxonomic renaming of

cluster representatives (see Section 2.1). Another challenge was to efficiently summarize the

annotation of potentially numerous domains on the single tree leaf corresponding to each

cluster representative. This was addressed by adding to leaf labels all annotation pieces that

qualified at least 5% of cluster members, ordered by relevance within each data source. In

addition to this relative measurement, stretches of stars ('*') growing with the natural logarithm

of the absolute number of domains qualified by each annotation piece were included. Finally,

the color code of the most relevant (i.e., with the highest percentage) KOG annotation (see next

paragraph and Figure S4) was applied to all labels for which the information was available.

Altogether, this considerably facilitated visual comparison of the trees.

Two main data sources were used for annotation: (i) the KOG (Tatusov et al., 2003) component

of NCBI CDD and (ii) a hand-curated corpus of about 500 RRM-containing proteins collected

in the primary literature (Table S2). In preliminary experiments, other components (SMART,

PFAM, COG, and PRK) of NCBI CDD were evaluated, but KOG was ultimately selected as the

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most complete source. KOG was mined using RPS-BLAST (a variant of PSI-BLAST) (Altschul et

al., 1997) with an E-value threshold of 1e-10, whereas reference proteins were searched using

BLASTP (or TBLASTN for reference mRNAs) with an identity threshold of 75%. More stringent

thresholds (respectively 1e-25 and 95%) were also considered but eventually abandoned due to

a general lack of sensitivity that left most leafs without annotation. The flip side of adopting

such a sensitive approach was a potential lack of specificity. That is why we took the resulting

annotation with a grain of salt when analyzing the trees.

Other annotation bits added to leaf labels included: (iii) the number of domains in the cluster;

(iv) the distribution of RRM numbers in the cluster (see Section 1.3 for the caveat about

unpredicted RRM domains); (v) the amount of prokaryotic proteins; and (vi) the amount of

'putative SR' proteins. Notably, all annotation also applied to singleton clusters, except that

numbers were dropped for simplicity. Furthermore, the following typographical conventions

were enforced: (vii) prokaryotic-containing clusters in italic and (viii) clusters with domains

from more than one species in boldface.

2.5. Analyses of an enlarged RRM dataset

Phylogenetic accuracy is known to be difficult to achieve. Consequently, robustness of

phylogenetic inference is often assessed by analyzing the same alignment with multiple

reconstruction methods and/or evolutionary models. Orthogonal to this approach, it is possible

to enlarge or reduce the set of sequences included in the alignment. Experience has indeed

shown that varying 'taxon sampling' is very efficient at uncovering phylogenetic artifacts (for

reviews, see Delsuc et al., 2005; Philippe et al., 2005; Philippe et al., 2011). Here, both

strategies were used to generate five different large RRM trees that were carefully compared to

test the hypothesis of a single origin for SR splicing factors (see Section 2.6). As stated in Section

2.3, the first four trees (Figures S5-8) were inferred from the same 1266-cluster alignment. The

purpose of this section is to explain how we assembled the huge alignment used for the fifth

(even larger) tree (Figure S9).

As an alternative to complete proteomes used throughout this study, two other protein

databases were mined for RRM domains: (i) NCBI RefSeq release 26 (Pruitt et al., 2007) and (ii)

SMART 6 (Letunic et al., 2009). While RefSeq proteins were processed exactly as in Sections

1.2-1.3 (using the HMM profile for prediction), RRM domains and RRM-containing proteins

were directly downloaded through the batch interface of the SMART website (http://smart.embl-

heidelberg.de/). In both cases, the usual 1e-10 domain E-value threshold was used for

extraction, which respectively yielded 10,739 and 9,978 RRM domains (see Table S1 for

taxonomic distributions).

9

http://smart.embl-heidelberg.de/

http://smart.embl-heidelberg.de/

RRM domains from all three sources (including complete proteomes) were then merged into

one huge (yet overlapping) dataset and clustered using the same parameter values as in Section

2.1 to give a non-redundant dataset of 1831 clusters (to be compared to the 1266 clusters of

complete proteomes alone). Automated alignment with HMMALIGN resulted in an alignment that

had again 72 AA positions and that was analyzed using RAXML with the WAG+Γ4 model.

Finally, the tree was rooted on most prokaryotic domains, left-ladderized and annotated, even if

its assembly from multiple sources made the process more difficult.

2.6. Comparison of large RRM trees and phylogenetic analysis of the largest RRM clusters

The overall congruence of the large RRM trees was manually assessed by taking advantage of

the multiple annotation pieces described in Section 2.4. The primary criterion was the KOG

color coding, along with matches to RRM-containing reference proteins. The RRM number was

also heavily used for proteins with multiple (up to six) RRM domains. For practical reasons, we

mainly focused on leafs (clusters) representing a large number of RRM domains and/or

including matches to reference RRM-containing proteins. When comparing the five different

trees, two types of issues pertaining to RRM associations were examined: (i) do proteins from a

given KOG consistently group together? and (ii) do different KOG consistently group together?

These analyses allowed us to identify 88 groupings that were generally stable across the trees

(Table S3). Associations between these groupings are summarized in a qualitative consensus

tree (Figure S10). Altogether, mutual affitinities among groups of SR-associated RRM domains

suggested that most SR proteins share a single origin (Figure S11 and Table S4).

To check that SR proteins indeed derive from a common ancestor, an additional ML tree

focusing on the 152 largest multi-species RRM clusters was computed using RAXML with the

LG+F+Γ4 model (Figures 2 and S12). Briefly, the 1266-cluster RRM alignment was filtered to

discard sequences that did not represent at least 8 RRM domains. We also removed 5 more

sequences that represented larger RRM clusters, of which sequences all came from a single

species, as these corresponded to multiple in-paralogues and/or mis-predicted proteins:

Caenorhabditis@F42A6_7a_1_RRM_2, (8 domains), Caenorhabditis@Y46G5A_13_RRM_3

(10), Caenorhabditis@Y73B6BL_6a_3_RRM_2 (10), Caenorhabditis@Y73B6BL_6b_3_RRM_1

(10), and Danio @ENSDARP00000091192_RRM_1 (14). Therefore, the 152 retained sequences

represented 10,101 of the 12,023 originally retrieved RRM domains (84%). Strikingly, in this

sparser yet still unbiased tree, the RRM1 domains of most SR proteins were resolved as a single

clade, while the global phylogenetic resolution was much improved (Figures 2 and S12). This

result greatly strengthened our confidence in a single origin of main SR protein architectures.

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2.7. Phylogenetic analyses of SR-associated RRM domains

To analyze the subsequent evolution of SR proteins, we decided to focus on three subtrees

(shown in pink in Figure S6). For each subtree, RRM domains hidden behind each leaf were

extracted from the 6,633-cluster dataset obtained after the first clustering step (see Section 2.1).

Starting from this non-redundant dataset allowed us to greatly refine our sampling and to

discard any potential mis-clustering caused by the greedy single linkage algorithm of

BLASTCLUST, while ensuring that no duplicate domains were included. RRM domains were

anew aligned using the HMM profile but this time without discarding insertions to preserve as

much phylogenetic information as possible. The resulting alignments were cursorily optimized

by hand using the interactive editor ED (MUST) then analyzed by ML using both TREEFINDER and

RAXML with the WAG+Γ4 model, yielding six small RRM trees (Figures S13-18) out of three

datasets. After automatic annotation as already described, the trees computed from the RRM1 of

SR45/RNPS1 proteins (42 domains x 73 AA; Figures S15-16) and from the RRM2 of dual RRM

SR proteins (349 domains x 97 AA; Figures S17-18) were directly interpretable, whereas the

poor phylogenetic resolution of those inferred from the RRM1 of SR proteins (434 domains x 93

AA; Figures S13-14) prompted us to experiment with variations in taxon sampling.

In a first variant, we removed 130 fast-evolving domains (i.e., having long branches in the trees)

to reduce the occurrence of phylogenetic artifacts, which helps to improve resolution. The two

trees inferred from this curated dataset (304 domains x 87 AA) are shown in Figures S19-20.

Then, we produced three more variants of this curated dataset by removing domains either from

RS proteins (292 domains x 85 AA) or from dual ZnK SR proteins (297 domains x 87 AA) or

from both subfamilies at the same time (285 domains x 85 AA). The trees obtained from these

additional datasets are not shown but were used to monitor the effect of alternative samplings

on the phylogenetic resolution of the relationships among the remaining SR-protein families

and subfamilies (Table 1).

Along with RRM1/RRM2 and ZnK sequence logos (see Section 3.2), thorough comparison and

integration of 5 (+1) large and 14 small RRM trees (see Section 4.2 for 4 more small trees)

together laid the basis of our scenario for the single origin and subsequent diversification of SR

proteins into 4 natural families (Figures 2-3 and S10-11 and Tables 1 and S3-4).

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3. Profiling of sequence features in SR families

3.1. Extraction of RRM domains of SR-protein subfamilies

Based on the curated RAXML tree of SR-associated RRM domains (Figure S19), RRM1 domain

sequences corresponding to each SR-protein subfamily were extracted from the initial 12,023-

domain dataset (see Figure 3 for an up-to-date nomenclature). Subfamilies defined in this tree

were (i) SC35; (ii); SCL; (iii) SRrp; (iv) 9G8; (v) SRp20; (vi) RSZ; (vii) RS2Z; (viii) animal ASF-like;

(ix) plant ASF-like; (x) SRp40-55-75; and (xi) RS. Similarly, the two remaining small RAXML

trees were used to extract the RRM1 of (xii) SR45 and of (xiii) RNPS1 (Figure S15), as well as the

RRM2 of animal ASF-like and of SRp40-55-75 (Figure S17). Owing to its evolutionary

divergence, the RRM2 of the RS family had to be extracted from the large RAXML/WAG tree

inferred from complete proteomes (Figure S6). Furthermore, to complete our subfamily-specific

RRM domain datasets, the missed RRM2 of the plant ASF-like subfamily was predicted anew

using a very loose domain E-value threshold (0.1) directly on the corresponding proteins.

As explained in the main text, the RRM of human SRp54 was also too divergent to be detected

by the universal HMM profile. This SR protein was thus not investigated in our study as it

would have featured a very long branch prone to phylogenetic artifacts. To complicate matters,

the official SRP54 symbol actually corresponds to another protein, the signal recognition

particle 54 kDa (ENSG00000100883), which is a ribonucleoprotein belonging to the GTP-

binding SRP family and devoid of RRM domain... yet interacting with RNPS1! See

http://www.uniprot.org/uniprot/P61011 for details.

3.2. Sequence logos of aligned RRM and ZnK domains of SR-protein subfamilies

Within each subfamily, RRM1 domains were carefully aligned with ED (MUST) using the

secondary structure as a guide. To improve alignments, minor domain-specific insertions (1-2

AA) were occasionally spliced out, while a handful of divergent domains were excluded. Then,

RRM2 domains from dual RRM SR subfamilies were separately aligned. Finally, subfamilies

were aligned with each other based on their consensus sequences to yield a high-quality

structural alignment including RRM1 and RRM2 domains from all SR-protein subfamilies. Using

different excerpts of this alignment, sequence logos (Schneider and Stephens, 1990) for each

subfamily (Figure 4; see also Figure S21) were computed with WEBLOGO (Crooks et al., 2004)

after enabling the correction for small samples.

Two overlapping strategies were used to sample prokaryotic RRM domains: (i) either all

prokaryotic domains found in the initial dataset or (ii) only those located in the mainly

prokaryotic subtrees used to root the large RAXML/WAG tree (Figure S6). The resulting

12

http://www.uniprot.org/uniprot/P61011

prokaryotic RRM datasets (cleared of potential eukaryotic contaminants) were processed as SR-

protein subfamilies to generate the corresponding sequence logos (Figure S22).

To predict ZnK domains, a HMM profile was built from the PFAM alignment for the zf-CCHC

domain (pfam00098; 182 domain sequences from 109 proteins). As for RRM domains before,

ZnK domains were predicted in all complete proteomes. However, only those corresponding to

single RRM ZnK-like SR subfamilies were actually extracted, thus resulting in four small

datasets: 9G8, RSZ, RS2Z (left) and RS2Z (right). To increase the sampling for RSZ and RS2Z,

ZnK domains from SR proteins identified in the inventory of additional proteomes (see Sections

4.1-4.4) were also included. Alignments and logos were easy to obtain due to the apparent

constraint on size characterizing these domains (Figure S23).

3.3. Profiling of compositional features in SR-protein subfamilies

Full-length proteins corresponding to subfamily datasets used for RRM logos were collected and

submitted to blind compositional analyses. First, a 24-AA sliding window was moved (1 AA at a

time) along every individual protein. At each step, the numbers of occurrences for all possible

overlapping unordered words of size 1 to 3 AA were recorded. Unordered means that

occurrences of, e.g., SR and RS dipeptides were consolidated, while overlapping means that,

e.g., the SRR tripeptide was counted as either (i) 1xS and 2xR or (ii) 1xRS/SR and 1xRR or (iii)

1xRRS/RSR/SRR, depending on word size. These word densities were then plotted for all

proteins of each subfamily (data not shown, but see Dataset S3b-d for an illustration of a similar

procedure). To avoid unnecessary clutter, density curves that did not reach a predefined

threshold (1 AA: 8; 2-3 AA: 6) for any protein within a subfamily were discarded. After visual

inspection of the resulting graphs, a series of words were identified as potentially useful for

discriminating the different SR subfamilies (Table S5). Second, this preselection was refined by

comparing the distribution (across all proteins of a given subfamily) of each word between

subfamilies. Since we were mostly interested in inter-domain compositional features, promising

words were tracked in particular protein regions: (i) before the first domain; (ii) between the first

and the second domain; and (iii) after the last domain. This process led to one graph per

word/region combination, each displaying the distribution of the compositional feature in every

SR subfamily (Figure S24). Third, one representative protein was selected out of each subfamily,

except for SRp40-55-75 and animal ASF-like, from which were selected three (SRp40, SRp55,

SRp75) and two (ASF/SF2 and SRp30c) representatives, respectively. These proteins were used

to graphically summarize the results of the compositional profiling (Figures 5 and S25).

13

3.4. Profiling of conservation in SR-protein subfamilies

The same full-length protein datasets were automatically aligned with CLUSTALW (Thompson et

al., 1994). Alignments were then analyzed with the program PLOTCON (EMBOSS software

package, Rice et al., 2000) to profile sequence conservation in every subfamily. Briefly,

conservation along aligned proteins was computed by averaging all possible pairwise scores

(using the EBLOSUM62 similarity matrix) at each position within a 24-AA sliding window. To

allow a perfect juxtaposition with composition profiles, subfamily alignments were first cleared

of sequence insertions relative to the representative proteins selected in Section 3.3. In practice,

columns corresponding to positions missing in these proteins were removed from the

alignments using the program NET (MUST), which implies that, for each subfamily, PLOTCON

actually analyzed an alignment of exactly the same length as the protein representing the

subfamily (Figures 5 and S25).

3.5. Development of a determination key for classifying SR proteins

To help classifying uncharacterized SR proteins, a determination key was developed by

integrating most of our analyses: (i) protein architecture; (ii) conserved motifs in RRM domains;

and (iii) compositional features (Table S6). This key was validated on candidate SR proteins

identified in Sections 4.1-4.4.

4. Inventory of SR proteins in selected organisms

4.1. Optimized prediction of SR-associated RRM1 domains

Our original HMM profile for the RRM domain was deliberately universal in order to sample as

much functional diversity as possible. This allowed us to investigate the origin and evolution of

SR proteins using the ubiquitous RRM domain as a proxy for whole proteins. However, for

uncharacterized proteomes, directly predicting domains that belong to SR proteins is more

advantageous. To this end, six new HMM profiles optimized for the prediction of SR-associated

RRM1 domains were computed from our alignments. The first three profiles were built from two

sequence-rich but automatically HMM-aligned RRM1 subtrees (Figures S12,14; outgroups

excluded), whereas the three remaining profiles were derived from RRM1 sequence logos

(Figure S21), which had been structurally aligned by hand but lacked fast-evolving sequences.

These six new profiles were then tested on 20 selected proteomes: 13 model organisms already

used in the previous analyses and 7 recently sequenced photosynthetic species (downloaded in

June 2009; see Tables 2 and S7 for species list). HMMSEARCH was run with the same loose

domain E-value threshold as in Section 1.2 (1e-5) but each HMMER report (6 x 20 = 120) was

14

individually examined to determine the optimal threshold. In practice, we set the threshold in

the valley between the best hits (normally derived from SR proteins) and the remaining (non-SR)

hits. For most reports, this task was rather easy to perform as the valley was unambiguous

(except for Aspergillus fumigatus that did not yield any obvious SR-associated RRM1 domain).

After consolidation of duplicates (i.e., predicted by more than one profile), a total of 247

candidate SR proteins were retained out of 19 proteomes.

4.2. Phylogenetic analyses of candidate SR protein RRM domains

RRM1 (and RRM2) domains from candidate SR proteins were extracted and automatically

aligned on our structural alignment of SR-protein subfamily consensus sequences (see Section

3.2). This was carried out with the BABA component of the MUST software package, which also

affiliated each candidate RRM domain to the most appropriate SR-protein subfamily.

The resulting high-quality alignment was then analyzed as in Section 2.3 (with both TREEFINDER

and RAXML heuristics, as well as with PHYLOBAYES). Again, different variants of the dataset

were considered: (i) with or without RRM2 domains; (ii) including or excluding positions

corresponding to subfamily-specific insertions. Finally, we settled on a dataset containing all

SR-associated RRM1 domains, along with RRM2 domains from plant RS proteins to test the

duplication hypothesis (see main text), but no outgroup domains to minimize phylogenetic

artifacts (Philippe et al., 2011). The trees, which eventually excluded subfamily-specific

insertions, were rooted on the SR45/RNPS1 RRM domains (for convenience) and automatically

annotated (Figures S26-29; see also Table 1 for the phylogenetic resolution of relationships

among SR-protein families and subfamilies).

4.3. Architectural and compositional analyses of candidate SR proteins

The architecture of every candidate SR protein was elucidated by scripting the NCBI Conserved

Domain Database web server (http://www.ncbi.nlm.nih.gov/cdd/). Consequently, domain

identification was not restricted to RRM and ZnK domains but took advantage of the full

breadth of domains available in CDD (Dataset S3a).

In parallel, candidate SR proteins were submitted to the blind compositional analyses already

described, except that all candidate SR proteins were processed at the same time, rather than

subfamily by subfamily as when selecting discriminating features (Dataset S3b-d).

15

http://www.ncbi.nlm.nih.gov/cdd/

4.4. Curation of candidate SR proteins

To assemble our curated inventory of SR proteins, candidates were validated by integrating the

results of all aforementioned analyses. At the domain level, we considered the subfamily

attributed by the alignment procedure as well as the phylogenetic position of the RRM1 domain

in the last trees (Figures S26-29). At the protein level, we applied our determination key (Table

S6) based on the architectural and compositional profiling of candidates (Dataset S3a-d). For

dubious cases, confirmatory searches were conducted on the NCBI BLAST website

(http://blast.ncbi.nlm.nih.gov/). This stepwise validation led to the confirmation of 192 proteins

as genuine SR proteins along with 52 isoforms, of which the overwhelming majority could be

classified into one of the previously identified subfamilies (Table 2; see also Table S7).

16

http://blast.ncbi.nlm.nih.gov/

Table S1. Taxonomic distribution of RRM-containing proteins. The three Excel sheets

summarize the statistics for RRM domain, RRM-containing and putative SR protein content per

proteome for each data source: (i) complete proteomes; (ii) NCBI RefSeq; and (iii) SMART

database. Statistics are given for the five domain E-value thresholds (1e-5, 1e-10, 1e-15, 1e-20

and 1e-25) used in the prediction of RRM domains. Proteomes are sorted by taxonomic lineage,

except that proteomes devoid of RRM domains are listed at the bottom.

Table S2. Hand-curated corpus of RRM-containing proteins collected in the primary

literature. Reference proteins are organized by family. For convenience, an independent

bibliography is provided at the end of the corresponding file.

Table S3. Qualitative comparison of the five large RRM domain trees. The Table is a

companion to Figure S10. Node numbers match those given in tree annotations (Figures S5-9)

and in other comparative display elements (Figures S10-11 and Table S4). Unstable subgroups

are enclosed in brackets. RRM#: RRM number; KOG#: abridged KOG number and name; MP:

1266-cluster parsimony tree; RW: 1266-cluster RAXML (WAG+Γ4) tree; TW: 1266-cluster

TREEFINDER (WAG+Γ4) tree; RL: 1266-cluster RAXML (LG+F+Γ4) tree; mRX: 1831-cluster RAXML

tree; y/n: does/does not exist in the corresponding tree.

Table S4. Summary of the groupings observed for SR protein RRM1 domains. The Table is a

companion to Figure S11. Datasets are described in the text. Node numbers are as in Figure

S10 and Table S3: (16) RRM1 domains of dual RRM SR proteins; (17) RRM1 domains of single

RRM ZnK-like SR proteins; (22-23) RRM1 domains of single RRM SR proteins; (26-27) RRM1

domains of the atypical RNPS1/SR45 proteins.

Table S5. Compositional features specific of one or more SR subfamilies. For each subfamily,

discriminating features used in the SR determination key and secondary features are listed.

Features correspond to single, unordered 2-AA or 3-AA words, respectively. The SRp40-55-75

(SRSF5-6-4) and animal ASF-like (SRSF1-ASF/SF2 and SRSF9/SRp30c) subfamilies were split in

their individual component proteins thus resulting in 16 rows in the Table.

Table S6. Determination key for SR families and subfamilies. The key was constructed by

integrating architectural and compositional features that are specific either of SR natural

families or subfamilies.

17

Table S7. Statistics for the curated inventory of SR proteins in 20 selected proteomes. The

Table is a companion to Table 2 found in the main text. It provides detailed numbers for the

stepwise validation of candidate SR proteins from RRM prediction to phylogenetic analysis and

determination key classification. cand: candidate SR proteins; rej: candidates rejected as non-

SR proteins; iso: isoforms of confirmed SR proteins (mis-modeling or alternative splicing); conf:

candidates confirmed as SR proteins; key: confirmed candidates correctly classified by the

determination key; trunc: truncated candidates (mis-modeling or alternative splicing) that were

incorrectly classified by the determination key. The 7 recently sequenced photosynthetic added

for the inventory are shown in boldface.

18

Figure S1. Scheme of the analysis pipeline. The four sections of the main text results are shown

by discontinuous shaded areas (labeled 1 to 4). Within an area, each colored box corresponds

to a logical analysis step (e.g., program execution followed by processing of its output). For

simplicity, data and execution flows are confounded in the same arrows. Input data sources

and pipeline outputs are symbolized by distinct icons. Both main and Supplemental Figure and

Table numbers are indicated on the corresponding icons. See Text S1 for detailed methods and

technical results.

Figure S2. Optimization of clustering parameters for RRM domains. Non-redundant RRM

domains were clustered by single-linkage based on sequence similarity (fraction of identical

residues). The parameter space for both similarity and coverage thresholds was explored to

determine the combination that maximized a composite score rewarding normalized entropy

but penalizing the number of singleton clusters. The analysis was conducted for each of the five

non-redundant RRM datasets that were obtained at the following domain E-value thresholds:

(A) 1e-5, (B) 1e-10, (C) 1e-15, (D) 1e-20 and (E) 1e-25.

Figure S3. Evaluation of the selection algorithm for cluster representatives. Three clustered

datasets were assembled using either of the following selection criteria for cluster

representatives: (i) longest sequence (orange); (ii) most slowly evolving sequence (green); (iii)

fastest-evolving sequence (red). For each dataset, the corresponding tree was inferred by

Maximum Parsimony along with 100 bootstrap replicates. The resulting tree lengths (in

parsimony steps) are plotted either as a vertical line for the original tree or as a cumulative

distribution for bootstrap replicates.

Figure S4. Color key for KOG annotation. A unique combination of background and text color

has been attributed to each KOG, which are listed by descending occurrence count in the

RRM-containing protein dataset.

Figure S5. Maximum Parsimony tree of representative RRM domains. The tree was obtained

using PAUP* from the analysis of 72 aligned amino acid positions across 1266 sequences and

rooted using prokaryotic RRM domains as outgroups. The length of the tree is 36,439

parsimony steps. Leaves were automatically annotated and colored based on cluster content

using (i) KOG annotation and (ii) reference RRM-containing proteins (Figure S4 and Table S2).

Furthermore, the following information is provided: (iii) the number of domains in the cluster;

(iv) the distribution of RRM numbers in the clusters; (v) the amount of prokaryotic proteins; and

19

(vi) the amount of putative SR proteins. All numbers are given as percentages as well as

logarithmic estimates represented as stretches of stars (*). Clusters that contain domains from

more than one species or at least one prokaryotic RRM are shown in bold and italic,

respectively. Stable groupings are indicated and follow the numbering of Figure S10 and Table

S3. Bootstrap proportions >50% are shown. The scale bar at the bottom gives the number of

substitutions per site.

Figure S6. RAXML tree of representative RRM domains obtained under the WAG+Γ4 model.

The tree was actually obtained under the very similar PROTMIXWAG model from the analysis

of 72 aligned amino acid positions across 1266 sequences and rooted using prokaryotic RRM

domains as outgroups. Leaves were automatically annotated and colored based on cluster

content using (i) KOG annotation and (ii) reference RRM-containing proteins (Figure S4 and

Table S2). Furthermore, the following information is provided: (iii) the number of domains in

the cluster; (iv) the distribution of RRM numbers in the clusters; (v) the amount of prokaryotic

proteins; and (vi) the amount of putative SR proteins. All numbers are given as percentages as

well as logarithmic estimates represented as stretches of stars (*). Clusters that contain domains

from more than one species or at least one prokaryotic RRM are shown in bold and italic,


S3. SR-associated subtrees that were further analyzed are shown in pink. Subtrees prok-1 to

prok-3 used to compute prokaryotic RRM logos are also indicated. Bootstrap proportions >50%

are shown. The scale bar at the bottom gives the number of substitutions per site.

Figure S7. TREEFINDER tree of representative RRM domains obtained under the WAG+Γ4

model. The tree was obtained from the analysis of 72 aligned amino acid positions across 1266

sequences and rooted using prokaryotic RRM domains as outgroups. Leaves were automatically

annotated and colored based on cluster content using (i) KOG annotation and (ii) reference

RRM-containing proteins (Figure S4 and Table S2). Furthermore, the following information is

provided: (iii) the number of domains in the cluster; (iv) the distribution of RRM numbers in the

clusters; (v) the amount of prokaryotic proteins; and (vi) the amount of putative SR proteins. All

numbers are given as percentages as well as logarithmic estimates represented as stretches of

stars (*). Clusters that contain domains from more than one species or at least one prokaryotic

RRM are shown in bold and italic, respectively. Stable groupings are indicated and follow the

numbering of Figure S10 and Table S3. Bootstrap proportions >50% are shown. The scale bar

at the bottom gives the number of substitutions per site.

20

Figure S8. RAXML tree of representative RRM domains obtained under the LG+F+Γ4 model.

The tree was obtained from the analysis of 72 aligned amino acid positions across 1266

sequences and rooted using prokaryotic RRM domains as outgroups. Leaves were automatically

annotated and colored based on cluster content using (i) KOG annotation and (ii) reference

RRM-containing proteins (Figure S4 and Table S2). Furthermore, the following information is

provided: (iii) the number of domains in the cluster; (iv) the distribution of RRM numbers in the

clusters; (v) the amount of prokaryotic proteins; and (vi) the amount of putative SR proteins. All

numbers are given as percentages as well as logarithmic estimates represented as stretches of

stars (*). Clusters that contain domains from more than one species or at least one prokaryotic

RRM are shown in bold and italic, respectively. Stable groupings are indicated and follow the

numbering of Figure S10 and Table S3. Bootstrap proportions >50% are shown. The scale bar

at the bottom gives the number of substitutions per site.

Figure S9. RAXML tree of the enlarged RRM dataset obtained under the WAG+Γ4 model. The

tree was actually obtained under the very similar PROTMIXWAG model from the analysis of 72

aligned amino acid positions across 1831 sequences and rooted using prokaryotic RRM

domains as outgroups. Leaves were automatically annotated and colored based on cluster

content using (i) KOG annotation and (ii) reference RRM-containing proteins (Figure S4 and

Table S2). Furthermore, the following information is provided: (iii) the number of domains in

the cluster; (iv) the distribution of RRM numbers in the clusters; (v) the amount of prokaryotic


well as logarithmic estimates represented as stretches of stars (*). Clusters that contain domains

from more than one species or at least one prokaryotic RRM are shown in bold and italic,


S3. Bootstrap proportions >50% are shown. The scale bar at the bottom gives the number of


Figure S10. Qualitative consensus of phylogenetic analyses of representative RRM domains.

The consensus is based on a manual comparison of the 5 large trees (Figures S5-9). Recurrent

nodes across analyses were uniquely numbered by descending grouping level. Unstable

subgroups are enclosed in brackets. Notes about individual nodes and trees can be found in

companion Table S3. Simple terminal branches correspond to functionally homogenous

groupings, whereas open triangles represent mixed functionality. SR-associated subtrees are

indicated by shaded boxes and the corresponding branches are color-coded to match Figures 2,

3 and S11: RRM1 of single RRM SR proteins (green); RRM1 of single RRM ZnK-like SR proteins

21

(blue); RRM1 of dual RRM SR proteins (red); RRM1 of RNPS1/SR45 proteins (orange); RRM2 of

non-plant dual RRM SR proteins (violet); RRM2 of the plant-specific ‘RS’ group of SR proteins

(brown). Note that node names are based on automated KOG annotation without manual

curation, hence the presence of occasional inaccuracies (e.g., node 83 labelled as 'splicing

factor RNPS1' while it actually includes PABP proteins; see Table S3).

Figure S11. Mutual affinities of SR protein RRM domains in the five large trees. Cartoons (A)

to (E) summarize the trees given in Figures S5 to S9, respectively, and leaf node numbers are

described in Figure S10 and Table S3. Simple terminal branches correspond to functionally

homogenous groupings, whereas open triangles represent mixed functionality. SR-associated

RRM domains are color-coded as in Figures 2, 3 and S10, while outgroup RRM domains are

shown in black. Companion Table S4 summarizes the groupings observed in each tree for the

RRM1 domains of SR splicing factors.

Figure S12. RAXML tree of the largest RRM clusters obtained under the LG+F+Γ4 model. The

tree was obtained from the analysis of 72 aligned amino acid positions across 152 slowly

evolving RRM sequences representative of all multi-species RRM clusters with ≥ 8 member

domains (i.e., 10,101 out of 12,023 retrieved domains), and rooted using prokaryotic RRM

clusters as outgroups (in italic). Leaves were automatically annotated and colored based on

cluster content using (i) KOG annotation and (ii) reference RRM-containing proteins (Figure S4

and Table S2). Furthermore, the following information is provided: (iii) the number of domains

in the cluster; (iv) the distribution of RRM numbers in the clusters; (v) the amount of prokaryotic


well as logarithmic estimates represented as stretches of stars (*). Stable groupings are indicated

and follow the numbering of Figure S10 and Table S3. All non-zero bootstrap proportions are

shown. The scale bar at the bottom gives the number of substitutions per site.

Figure S13. Exhaustive RAXML tree of SR-associated RRM1 domains (WAG+Γ4 model). The


aligned amino acid positions across 434 sequences and was left unrooted as 'outgroups' are not

monophyletic. Leaves correspond to unique domain sequences belonging to clusters present in

the 'RRM1 of SR proteins' subtree (in pink in Figure S6). Annotation is as described for Figures

S5-9. Bootstrap proportions >50% are shown. The scale bar at the bottom gives the number of


22

Figure S14. Exhaustive TREEFINDER tree of SR-associated RRM1 domains (WAG+Γ4 model).

The unrooted tree was obtained from the analysis of 93 aligned amino acid positions across

434 sequences and was left unrooted as 'outgroups' are not monophyletic. Leaves correspond

to unique domain sequences belonging to clusters present in the 'RRM1 of SR proteins' subtree

(in pink in Figure S6). Annotation is as described for Figures S5-9. Bootstrap proportions >50%

are shown. The scale bar at the bottom gives the number of substitutions per site.

Figure S15. RAXML tree of RRM1 domains from RNPS1-like proteins (WAG+Γ4 model). The


aligned amino acid positions across 42 sequences and rooted between RNPS1 and SR45

domains. Leaves correspond to unique domain sequences belonging to clusters present in the

'RRM1 of SR45/RNPS1' subtree (in pink in Figure S6). Annotation is as described for Figures S5-

9. Bootstrap proportions >50% are shown. The scale bar at the bottom gives the number of


Figure S16. TREEFINDER tree of RRM1 domains from RNPS1-like proteins (WAG+Γ4 model).

The unrooted tree was obtained from the analysis of 73 aligned amino acid positions across 42

sequences and rooted between RNPS1 and SR45 domains. Leaves correspond to unique

domain sequences belonging to clusters present in the 'RRM1 of SR45/RNPS1' subtree (in pink

in Figure S6). Annotation is as described for Figures S5-9. Bootstrap proportions >50% are


Figure S17. RAXML tree of RRM2 domains from dual RRM SR proteins (WAG+Γ4 model). The


aligned amino acid positions across 349 sequences and rooted between SR-associated and

outgroup domains. Leaves correspond to unique domain sequences belonging to clusters

present in the 'RRM2 of dual RRM SR proteins' subtree (in pink in Figure S6). Annotation is as

described for Figures S5-9. Bootstrap proportions >50% are shown. The scale bar at the bottom

gives the number of substitutions per site.

Figure S18. TREEFINDER tree of RRM2 domains from dual RRM SR proteins (WAG+Γ4 model).

The unrooted tree was obtained from the analysis of 97 aligned amino acid positions across

349 sequences and rooted between SR-associated and outgroup domains. Leaves correspond to

unique domain sequences belonging to clusters present in the 'RRM2 of dual RRM SR proteins'

23

subtree (in pink in Figure S6). Annotation is as described for Figures S5-9. Bootstrap proportions

>50% are shown. The scale bar at the bottom gives the number of substitutions per site.

Figure S19. RAXML tree of slowly evolving SR-associated RRM1 domains (WAG+Γ4 model).

The tree was actually obtained under the very similar PROTMIXWAG model from the analysis

of 87 aligned amino acid positions across 304 sequences and was left unrooted as 'outgroups'

are not monophyletic. Leaves correspond to unique domain sequences belonging to clusters

present in the 'RRM1 of SR proteins' subtree (in pink in Figure S6), of which 130 fast-evolving

(i.e., long-branched) sequences have been removed. Annotation is as described for Figures S5-

9. Bootstrap proportions >50% are shown. The scale bar at the bottom gives the number of


Figure S20. TREEFINDER tree of slowly evolving SR-associated RRM1 domains (WAG+Γ4

model). The tree was obtained from the analysis of 87 aligned amino acid positions across 304

sequences and was left unrooted as 'outgroups' are not monophyletic. Leaves correspond to

unique domain sequences belonging to clusters present in the 'RRM1 of SR proteins' subtree (in

pink in Figure S6), of which 130 fast-evolving (i.e., long-branched) sequences have been

removed. Annotation is as described for Figures S5-9. Bootstrap proportions >50% are shown.

The scale bar at the bottom gives the number of substitutions per site.

Figure S21. Sequence conservation in the first RRM domain of SR proteins. RRM sequence

logos are aligned based on secondary structure (bottom). At a given position, the height of any

residue is proportional to its frequency while overall stack height corresponds to sequence

conservation. Error bars reflects the uncertainty of conservation estimates. Small sample sizes

lead to conservatively downscaled letters (e.g., RS2Z subfamily and SR45). RNP1 and RNP2

motifs are shaded, as are conserved aromatic residues in these motifs. β1-4, α1-2 and L1-5

respectively stand for β-sheets, α-helices and linkers of the RRM secondary structure. The

Figure contains four panels, one for each natural family of SR proteins: (A) single RRM; (B)

single RRM ZnK-like; (C) dual RRM; and (D) RNPS1-like. In (C), RS2Z proteins were grouped

with other ZnK-containing proteins even if their RRM is quite different, including RNP motifs.

Figure S22. Sequence conservation across prokaryotic RRM domains. RRM sequence logos are

aligned based on secondary structure (bottom). At a given position, the height of any residue is

proportional to its frequency while overall stack height corresponds to sequence conservation.

Error bars reflects the uncertainty of conservation estimates. RNP1 and RNP2 motifs are shaded,

24

as are conserved aromatic residues in these motifs. β1-4, α1-2 and L1-5 respectively stand for

β-sheets, α-helices and linkers of the RRM secondary structure. The 2 upper logos respectively

include all prokaryotic or cyanobacterial RRM domains independently of their actual position

in the phylogenetic tree (Figure S6). The 3 lower logos each correspond to one of the mainly

prokaryotic subtrees used as outgroups, of which non-prokaryotic domains were excluded.

Grey boxes highlight motifs specific of the discrete cyanobacterial subtree (middle).

Figure S23. Sequence conservation across ZnK domains of SR proteins. Thanks to their very

constraint size, ZnK sequence logos were easily aligned by hand. At a given position, the height

of any residue is proportional to its frequency while overall stack height corresponds to

sequence conservation. Error bars reflects the uncertainty of conservation estimates. To increase

sampling for RSZ and RS2Z logos, ZnK domains from SR proteins identified in the inventory of

the seven additional photosynthetic proteomes were also included. Left and right ZnK domains

from RS2Z proteins were considered separately in an attempt to determine their respective

ancestry by comparison with SRSF7/9G8 and RSZ homologues (grey boxes). However, this

analysis proved inconclusive due to the short size of ZnKs. Universally conserved CCHC motifs

(yellow) and glycine residues (orange) are also shaded. ZnKs of the CCHC family have amino

acid arrangements with the consensus sequence 'C-ϕ-X-C-G-±-X-G-H-X3-δ-C,' where X is a

variable amino acid, ϕ is an aromatic amino acid, (±) is a charged amino acid, and δ is a

carbonyl-containing residue (Green and Berg, 1989; Cavaloc et al., 1994; Cavaloc et al., 1999;

Armas et al., 2008).

Figure S24. Distributions of relevant compositional features within SR subfamilies. Each panel

corresponds to the distributions of the density of a particular word (1, 2 or 3 unordered

residues) in a specific region across all subfamilies. Regions are bounded by RRM and ZnK

domains and defined as follows: (i) before the first domain; (ii) between the first and the second

domain; and (iii) after the last domain (e.g., RS/SR before RRM1 or GG between RRM1 and

ZnK1). For a given word/region combination, density is computed as the number of

overlapping word occurrences in a sliding-window of 24 amino acid residues scanning the

region in each protein. Maximal word densities (i.e., highest peaks) are then pooled by

subfamily to allow joint plotting of resulting distributions on a single graph. Numbers in panel

legends indicate the number of analyzed proteins in each subfamily. This number can vary

between word/region combinations because of (i) mis-modeled proteins lacking one or more

canonical domains of the family and (ii) non-prediction of divergent domains. Similarly, not all

25

combinations can be analyzed for every subfamily, e.g., single RRM SR proteins do not possess

an interdomain region.

Figure S25. Architecture, conservation and compositional profile of SR subfamilies. Within

each panel, an individual protein was selected as representative for compositional profiling

while conservation was computed on the alignment of all subfamily sequences. The SRp40-55-

75 (SRSF5-6-4) and animal ASF-like (SRSF1-ASF/SF2 and SRSF9/SRp30c) subfamilies were split

in their individual component proteins thus resulting in 16 panels. In these cases, a single

subfamily alignment was used for conservation profiling in respectively three (K, L, M) and two

(H, I) panels. Only informative features (Table S5) are shown, with discriminating features used

in the key (Table S6) in plain style and secondary features in dashed style. (A) SC35: human

SRSF2/SC35 (ENSP00000293233); (B) SCL: Arabidopsis At-SCL33 (NP_001031195); (C) SRrp:

mouse SRSF10/SRrp40 (ENSMUSP00000030437); (D) 9G8: human SRSF7/9G8

(ENSP00000325905); (E) SRp20: human SRSF3/SRp20 (ENSP00000362820); (F) RSZ:

Arabidopsis At-RSZ21 (NP_564208); (G) RS2Z: rice Os-RS2Z36 (NP_001054489); (H)

ASF/SF2: human SRSF1-ASF/SF2 (ENSP00000258962); (I) SRp30c: human SRSF9/SRp30c

(ENSP00000229390); (J) ASF-like: rice Os-SR32 (NP_001050082); (K) SRp40: human

SRSF5/SRp40 (ENSP00000342294); (L) SRp55: human SRSF6/SRp55 (ENSP00000244020); (M)

SRp75: human SRSF4/SRp75 (ENSP00000362900); (N) RS: Arabidopsis At-RS41 (NP_200017);

(O) SR45: Arabidopsis SR45 (NP_173107); (P) RNPS1: human RNPS1 (ENSP00000380275).

Figure S26. RAXML RRM tree of candidate SR proteins from selected proteomes (WAG+Γ4

model). The tree was actually obtained under the very similar PROTMIXWAG model from the

analysis of 64 unambiguously aligned amino acid positions across 270 sequences and

arbitrarily rooted using RNPS1-like proteins. Positions corresponding to subfamily-specific

insertions were discarded from the full alignment (82 amino acid positions) prior to analysis.

RRM2 domains from RS proteins were also included to test the duplication hypothesis (see

main text). Annotation was limited to KOG identifiers and reference RRM-containing proteins,

supplemented with a subfamily code added during automatic alignment on subfamily

consensus (e.g., asflkpl stands for plant ASF-like). Bootstrap proportions >50% are shown. The

scale bar at the bottom gives the number of substitutions per site.

Figure S27. TREEFINDER RRM tree of candidate SR proteins from selected proteomes (WAG+Γ4

model). The tree was obtained from the analysis of 64 unambiguously aligned amino acid

positions across 270 sequences and arbitrarily rooted using RNPS1-like proteins. Positions

26

corresponding to subfamily-specific insertions were discarded from the full alignment (82

amino acid positions) prior to analysis. RRM2 domains from RS proteins were also included to

test the duplication hypothesis. Annotation was limited to KOG identifiers and reference RRM-

containing proteins, supplemented with a subfamily code added during automatic alignment on

subfamily consensus (e.g., asflkpl stands for plant ASF-like). Bootstrap proportions >50% are


Figure S28. RAXML tree of candidate SR proteins from selected proteomes (LG+F+Γ4 model).

The tree was obtained from the analysis of 64 unambiguously aligned amino acid positions

across 270 sequences and arbitrarily rooted using RNPS1-like proteins. Positions corresponding

to subfamily-specific insertions were discarded from the full alignment (82 amino acid

positions) prior to analysis. RRM2 domains from RS proteins were also included to test the

duplication hypothesis. Annotation was limited to KOG identifiers and reference RRM-

containing proteins, supplemented with a subfamily code added during automatic alignment on

subfamily consensus (e.g., asflkpl stands for plant ASF-like). Bootstrap proportions >50% are


Figure S29. PHYLOBAYES tree of candidate SR proteins from selected proteomes (CAT+Γ4

model). The tree was obtained from the analysis of 64 unambiguously aligned amino acid

positions across 270 sequences. It is the consensus of two independent chains ran for 55,000

cycles (burn-in = 5000 cycles; one tree sampled every 100 cycles) and is arbitrarily rooted

using RNPS1-like proteins. Positions corresponding to subfamily-specific insertions were

discarded from the full alignment (82 amino acid positions) prior to analysis. RRM2 domains

from RS proteins were also included to test the duplication hypothesis. Annotation was limited

to KOG identifiers and reference RRM-containing proteins, supplemented with a subfamily

code added during automatic alignment on subfamily consensus (e.g., asflkpl stands for plant

ASF-like). Posterior probabilities (PP) >50% are shown (whereas nodes with PP <5% are

collapsed). The scale bar at the bottom gives the number of substitutions per site.

27

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29

i

organism name description accession #RRM references

. ARRS — acidic rich RS protein (RRM and RS domains)

Mus musculus Psc1 – AAS19274 1 Kavanagh et al. (2005)

Mus musculus ARRS – BAC34721 1 Kavanagh et al. (2005)

Homo sapiens KIAA1311 – BAA92549 1 Kavanagh et al. (2005)

Homo sapiens Se70-2 – AAH41655 1 Kavanagh et al. (2005)

Xenopus laevis RBM26 – AAH43744 1 Kavanagh et al. (2005)

Drosophila melanogaster ARRS – NP_609976 1 Kavanagh et al. (2005)

Anopheles gambiae ARRS – XP_318628 1 Kavanagh et al. (2005)

Caenorhabditis elegans ARRS – NP_498234 1 Kavanagh et al. (2005)

Dictyostelium discoideum ARRS – AA051188 1 Kavanagh et al. (2005)

Homo sapiens RBM 26 – NP_071401 2 Kavanagh et al. (2005)

Homo sapiens RBM 27 – NP_061862 1 Kavanagh et al. (2005)

. Bruno — CUG-BP1 and ETR-3 like factors (CELF)/BRUNO-like proteins

Homo sapiens CUGBP 1 CUG triplet repeat, RNA-binding protein 1 NP_006551 3 Timchenko et al. (1996)

Homo sapiens CUGBP 2 ETR-3 NP_001020247 3 Lu et al. (1999)

Homo sapiens CELF 3 Bruno-like 3 NP_064565 3 Ladd et al. (2001)

Homo sapiens CELF 4 Bruno-like 4 Q9BZC1 3 Ladd et al. (2001)



Mus musculus CUGBP 1 – NP_059064 3 Timchenko et al. (2006)

Mus musculus BRUNOL-4 – NP_573458 3 Meins et al. (2002)

Mus musculus BRUNOL-6 – NP_780444 3 McKee et al. (2005)

Gallus gallus CUGBP 1 – NP_001012539 3 Brimacombe and Ladd (2007)

Rattus norvegicus CUGBP 1 – NP_001020592 3 Karagiannides et al. (2006)

Danio rerio CUGBP 1 – NP_571688 3 Hashimoto et al. (2006)

Xenopus laevis EDEN-BP embryo deadenylation element binding protein NP_001084196 3 Paillard et al. (1998)

. CAPER — coactivator of activating protein-1 (AP-1) and estrogen receptors (Ers)

Homo sapiens CAPER – NP_909122 3 Jung et al. (2002)

Mus musculus CAPER – NP_573505 3 Jung et al. (2002)

. CPEB — cytoplasmic polyadenylation element binding protein

Homo sapiens CPEB 1 – NP_085097 2 Welk et al. (2001)

Homo sapiens CPEB 2 – NP_872587 2 Hagele et al. (2008)

Homo sapiens CPEB 3 – NP_055727 2 Salehi-Ashtiani et al. (2006)

Homo sapiens CPEB 4 – NP_085130 2 Kurihara et al. (2003)

Table S2

30

ii


Xenopus laevis CPEB – NP_001084072 2 Paris et al. (1991)

Mus musculus CPEB 1 – NP_031781 2 Gebauer and Richter (1996)

Mus musculus CPEB 2 – NP_787951 2 Kurihara et al. (2003)

Mus musculus CPEB 3 – NP_938042 2 Theis et al. (2003)

Mus musculus CPEB 4 – NP_080528 2 Theis et al. (2003)

Rattus norvegicus CPEB 1 – NP_001099746 2 Wu et al. (1998)

. Dazap — Deleted in azoospermia-associated protein

Homo sapiens Dazap1 DAZ associated protein 1 NP_061832 2 Tsui et al. (2000)

Mus musculus Dazap1 DAZ associated protein 1 NP_573451 2 Dai et al. (2001)

Mus musculus Dazap1 DAZ associated protein 1 NP_001116077 2 Dai et al. (2001)

Rattus norvegicus Dazap1 DAZ associated protein 1 NP_001020913 2 Pan et al. (2005)

Xenopus laevis Dazap1 DAZ associated protein 1 and Prrp (proline-rich RNA binding protein) Q98SJ2 2 Zhao et al. (2001)

. ELAV — embryonic lethal, abnormal vision, Drosophila-like 1/Hu

Mus musculus ELAVL 1/HuR Hu antigen R NP_034615 3 Atasoy et al. (1998)

Mus musculus ELAVL 2 Hu antigen B NP_034616 3 Abe et al. (1996b)

Mus musculus ELAVL 3 Hu antigen C NP_034617 3 Okano and Darnell (1997)

Mus musculus ELAVL 4 Hu antigen D NP_034618 3 Abe et al. (1994)

Homo sapiens ELAVL 1/HuR Hu antigen R NP_001410 3 Ma et al. (1996)

Homo sapiens ELAVL 2/HuB Hu antigen B NP_004423 3 Levine et al. (1993)

Homo sapiens ELAVL 3 Hu antigen C NP_001411 3 Van Tine et al. (1998)

Homo sapiens ELAVL 4 Hu antigen D NP_068771 3 Szabo et al. (1991)

Gallus gallus ELAVL 4 Hu antigen D NP_990161 3 Wakamatsu and Weston (1997)

Gallus gallus ELAVL 1/HuR Hu antigen R NP_990164 3 Wakamatsu and Weston (1997)

Rattus norvegicus ELAVL 1/HuR Hu antigen R NP_001102318 3 Tang et al. (2002)

Rattus norvegicus ELAVL 2/HuB Hu antigen B NP_775431 3 Fornaro et al. (2007)

Rattus norvegicus ELAVL 3 Hu antigen C NP_758827 3 Abe et al. (1996a)

Rattus norvegicus ELAVL 4 Hu antigen D NP_001071119 3 Steller et al. (1996)

. FCAFPA — other Arabidopsis RRM proteins FCA and FPA

Arabidopsis thaliana FCA – CAB10407 2 Macknight et al. (1997)

Arabidopsis thaliana FCA-like – AAB63831 2 Lorkovic and Barta (2002)

Arabidopsis thaliana FPA – AAB64314 3 Schomburg et al. (2001)

Arabidopsis thaliana AtY14 – AAG52616 1 Park and Muench (2007)

Arabidopsis thaliana AtREF – NP_200803 1 Lorkovic and Barta (2002)

Arabidopsis thaliana AtREF – AAG51767 1 Lorkovic and Barta (2002)

Arabidopsis thaliana AtREF – CAB85990 1 Lorkovic and Barta (2002)

Table S2

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Arabidopsis thaliana AtREF – NP_198588 1 Lorkovic and Barta (2002)

. FOX — Feminizing locus on X

Caenorhabditis elegans Fox-1 – NP_508446 1 Hodgkin et al. (1994)

Homo sapiens Fox-1 ataxin 2-binding protein 1 NP_665898 1 Shibata et al. (2000)

Homo sapiens Fox-2 RBM 9 NP_001076045 1 Lieberman et al. (2001)

Homo sapiens Fox-3 hexaribonucleotide binding protein NP_001076044 1 Underwood et al. (2005)

Mus musculus Fox-1 ataxin 2-binding protein NP_067452 1 Kiehl et al. (2001)

Mus musculus Fox-2 RBM 9 NP_444334 1 Lieberman et al. (2001)

Danio rerio Fox-1 ataxin 2-binding protein-like NP_999940 1 Jin et al. (2003)

. G3BP — Ras-GTPase-activating protein SH3-domain-binding protein

Homo sapiens G3BP 1 – NP_938405 1 Parker et al. (1996)

Homo sapiens G3BP 2 – NP_987100 1 Prigent et al. (2000)

Mus musculus G3BP 1 – NP_038744 1 Kennedy et al. (1996)

. GRSRBP — Glycine-Rich-RNA Binding (GR-RBP) and small RNA-binding protein (S-RBP)

Arabidopsis thaliana GR-RBP1 – AAD22311 1 Lorkovic and Barta (2002)

Arabidopsis thaliana GR-RBP2 – CAB36849 1 Lorkovic and Barta (2002)

Arabidopsis thaliana GR-RBP3 – BAB10366 1 Lorkovic and Barta (2002)

Arabidopsis thaliana GR-RBP4 – BAB03001 1 Lorkovic and Barta (2002)

Arabidopsis thaliana GR-RBP5 – AAG52402 1 Lorkovic and Barta (2002)

Arabidopsis thaliana GR-RBP6 – AAF98412 1 Lorkovic and Barta (2002)

Arabidopsis thaliana GR-RBP7 – AAD23639 1 Heintzen et al. (1997)

Arabidopsis thaliana GR-RBP8 – CAB43641 1 Carpenter et al. (1994)

Arabidopsis thaliana AtRZ-1a – BAB02203 1 Lorkovic and Barta (2002)

Arabidopsis thaliana AtRZ-1b – AAB71977 1 Lorkovic and Barta (2002)

Arabidopsis thaliana AtRZ-1c – NP_196048 1 Lorkovic and Barta (2002)

Arabidopsis thaliana AtRZ-1-like – AAG51392 1 Lorkovic and Barta (2002)

Arabidopsis thaliana S-RBP1 – CAB78428 1 Lorkovic and Barta (2002)

Zea mays GRP – NP_001105707 1 Didierjean et al. (1992)

Nicotiana sylvestris RZ-1 – BAA06012 1 Hanano et al. (1996)

Homo sapiens GRSF 1 G-rich RNA sequence binding factor 1 NP_002083 3 Qian and Wilusz (1994)

Homo sapiens RBM3 – NP_006734 1 Danno et al. (1997)

Homo sapiens CIRP – NP_001271 1 Nishiyama et al. (1997)

Mus musculus CIRP – NP_031731 1 Nishiyama et al. (1997)

Table S2

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. IGF2BP — insulin-like growth factor 2 RNA binding protein

Homo sapiens IGF2BP 1 – NP_006537 2 Nielsen et al. (1999)



. LA — LA

Homo sapiens La – NP_003133 1 Maraia and Intine (2001)

Homo sapiens Larp 7 – NP_056269 1 Krueger et al. (2008)

Mus musculus Ssb Sjogren syndrome antigen B NP_001103615 1 Maraia and Intine (2001)

Mus musculus Larp7 – NP_613059 1 Krueger et al. (2008)

Arabidopsis thaliana La1 – NP_001031777 1 Fleurdepine et al. (2007)

Arabidopsis thaliana La – NP_178106 2 Fleurdepine et al. (2007)





Oryza sativa La – BAD19607 2 Fleurdepine et al. (2007)

Oryza sativa La – CAE03115 2 Fleurdepine et al. (2007)

Schizosaccharomyces pombe la1 – NP_593315 1 Van Horn et al. (1997)

Saccharomyces cerevisiae Lhp1 – NP_010232 1 Yoo and Wolin (1994)

Drosophila melanogaster La – NP_724257 1 Yoo and Wolin (1994)

. LARK — LARK

Homo sapiens RBM4 LARK NP_002887 2 Markus and Morris (2006)

Mus musculus RBM4 LARK NP_033058 2 Kojima et al. (2007)

Drosophila melanogaster LARK – NP_523957 2 McNeil et al. (2001)

Bombyx mori LARK – NP_001037293 2 Wang et al. (2005)

. Musashi — Musashi

Homo sapiens musashi 1 neural-specific RNA binding protein NP_002433 2 Good et al. (1998)

Homo sapiens musashi 2 neural-specific RNA binding protein NP_620412 2 Barbouti et al. (2003)

Mus musculus Musashi 1 neural-specific RNA binding protein homolog 1 NP_032655 2 Sakakibara et al. (1996)

Mus musculus Musashi 2 neural-specific RNA binding protein homolog 2 NP_473384 2 Sakakibara et al. (2001)

Xenopus laevis nrp-1B neural-specific RNA binding protein NP_001084040 2 Richter et al. (1990)

Caenorhabditis elegans Musashi-1 neural-specific RNA binding protein NP_497799 2 Yoda et al. (2000)

Ciona intestinalis Musashi neural-specific RNA binding protein NP_001027721 2 Kawashima et al. (2000)

Halocynthia roretzi Musashi neural-specific RNA binding protein BAA82622 2 Kawashima et al. (2000)

Table S2

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. NTF — RRM proteins containing the NTF domain

Arabidopsis thaliana NTF-RRM1 – AAF20222 2 Lorkovic and Barta (2002)

Arabidopsis thaliana NTF-RRM2 – AAD20086 1 Lorkovic and Barta (2002)



Arabidopsis thaliana NTF-RRM5 – BAB09056 1 Lorkovic and Barta (2002)





. P54nrb — 54 kD nuclear RNA-binding protein/ non-POU domain containing, octamer-binding

Homo sapiens p54nrb – NP_031389 2 Dong et al. (1993)

Mus musculus NonO – NP_075633 2 Yang et al. (1993)

Rattus norvegicus NonO/p54nrb – NP_001020442 2 Too et al. (1998)

Rattus norvegicus NonO – NP_001012356 2 Brown et al. (2005)

Xenopus laevis P54nrb – NP_001080735 2 Takahashi et al. (2005)

Drosophila melanogaster NonA no on or off transient A NP_523367 2 Jones and Rubin (1990)

. PABP — poly(A)-binding proteins

Homo sapiens PABPC1 – NP_002559 4 Hosoda et al. (2006)

Homo sapiens PABP2 – NP_004634 1 Wahle (1991)

Homo sapiens PABPC3 – NP_112241 3 Feral et al. (2001)

Homo sapiens PABPC4 – NP_003810 4 Yang et al. (1995)

Homo sapiens PABPC5 – NP_543022 4 Blanco et al. (2001)

Mus musculus PAPB2 – NP_001007463 1 Cosson et al. (2004)

Mus musculus PABP1 – NP_032800 4 Wang et al. (1992)

Mus musculus PABP2 – NP_035163 4 Kleene et al. (1998)

Mus musculus PABPC5 – NP_444344 4 Blanco et al. (2001)

Rattus norvegicus PABP1 – NP_599180 4 Lim et al. (2006)

Drosophila melanogaster PABPC1 – NP_725750 4 Behm-Ansmant et al. (2007)

Drosophila melanogaster PABPN1 – NP_476902 1 Behm-Ansmant et al. (2007)

Xenopus laevis PABPC1 – NP_001080204 4 Voeltz et al. (2001)

Xenopus laevis ePAB – NP_001082094 4 Voeltz et al. (2001)

Bos taurus PABPN1 – NP_776994 1 Kuhn et al. (2003)

Arabidopsis thaliana PABP1 – NP_174676 3 Belostotsky (2003)



Table S2

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vi








Arabidopsis thaliana PABN1 – NP_568751 1 Forbes et al. (2006)

Chlamydomonas reinhardtii RB57 – XP_001689671 4 Yohn et al. (1998)

Saccharomyces cerevisiae Pab1p – NP_011092 4 Otero et al. (1999)

Saccharomyces cerevisiae Rbp29 – NP_012266 1 Winstall et al. (2000)

Schizosaccharomyces pombe Pab2 – CAB16904 1 Perreault et al. (2007)

. PDIP — DNA polymerase delta interacting protein 3

Homo sapiens PDIP3 PDIP46 NP_115687 1 Smyk et al. (2006)

Mus musculus PDIP3 – NP_848742 1 Liu et al. (2003)

. PSF — polypyrimidine tract binding protein associated, splicing factor proline/glutamine rich

Homo sapiens PSF sfpq NP_005057 2 Gozani et al. (1994)

Mus musculus PSF sfpq NP_076092 2 Shav-Tal et al. (2001)

Danio rerio PSF sfpq NP_998443 2 Lowery et al. (2007)

. PSP1 — paraspeckle protein

Homo sapiens PSP1 paraspeckle protein 1 NP_001035879 2 Fox et al. (2002)

Mus musculus PSP1 paraspeckle protein 1 NP_079958 2 Myojin et al. (2004)

. PTBP — polypyrimidine tract-binding protein

Homo sapiens PTBP1 – NP_114368 4 Gil et al. (1991)

Homo sapiens PTBP2 – NP_067013 4 Markovtsov et al. (2000)

Mus musculus PTBP1 – NP_032982 4 Bothwell et al. (1991)

Mus musculus PTBP2 brPTB NP_062423 4 Polydorides et al. (2000)

Rattus norvegicus PTBP1 PTB4 NP_071961 4 Gooding et al. (2003)

Rattus norvegicus PTBP smPTB NP_877970 4 Gooding et al. (2003)

Rattus norvegicus PTBP2 nPTB NP_001005555 4 Gooding et al. (2003)

. RALYL — RALY RNA binding protein and RALY-like

Homo sapiens RALYL – NP_776247 1 Ji et al. (2003)

Homo sapiens RALY hnRNP-associated with lethal yellow NP_031393 1 Khrebtukova et al. (1999)

Table S2

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Mus musculus RALY hnRNP-associated with lethal yellow NP_075619 1 Khrebtukova et al. (1999)

. RBM — RNA Binding Motif proteins

Homo sapiens RBM1 RNPC1 NP_906270 1 Shu et al. (2006)

Homo sapiens RBM5 – NP_005769 2 Shu et al. (2007)

Homo sapiens RBM6 – NP_005768 2 Wang et al. (2007b)

Homo sapiens RBM8A – NP_005096 1 Salicioni et al. (2000)

Homo sapiens RBM8B – AAG16782 1 Salicioni et al. (2000)

Homo sapiens RBM10 – NP_690595 2 Inoue et al. (1996)

Rattus norvegicus RBM10 – NP_690600 2 Inoue et al. (1996)

Homo sapiens RBM12 – NP_690051 4 Stover et al. (2001)

Pongo pygmaeus RBM12 – Q5RBM8 4 GenBank

Macaca mulatta RBM12 – Q8SQ27 4 GenBank

Mus musculus RBM12 – Q8R4X3 4 GenBank

Homo sapiens RBM14 – NP_006319 2 Iwasaki et al. (2001)

Homo sapiens RBM15 – NP_073605 3 Ma et al. (2001)

Mus musculus RBM15 – NP_001039272 3 Ma et al. (2007)

Homo sapiens RBM22 – NP_060517 1 Montaville et al. (2006)

Homo sapiens RBM25 – NP_067062 1 Fortes et al. (2007)

Homo sapiens RBM28 – NP_060547 4 Damianov et al. (2006)

Homo sapiens RBM40 – Q96LT9 2 Zhao et al. (2003)

Mus musculus RBM40 – Q3UZ01 2 Zhao et al. (2003)

Rattus norvegicus RBM40 – Q4G055 2 GenBank

Homo sapiens RBM45 – NP_694453 4 Tamada et al. (2002)

Mus musculus RBM45 – NP_700454 4 Tamada et al. (2002)

. RBMS — RNA binding motif, single stranded interacting protein

Homo sapiens RBMS1 scr2/MSSP1 NP_002888 2 Kanaoka and Nojima (1994) ; Negishi et al. (1994)

Homo sapiens RBMS2 scr3 NP_002889 2 Kanaoka and Nojima (1994)

Homo sapiens RBMS3 – NP_001003792 2 Penkov et al. (2000) ; Fritz and Stefanovic (2007)

Mus musculus RBMS1 – NP_064692 2 Fujimoto et al. (2000)

Mus musculus RBMS2 – NP_062685 2 Fujimoto et al. (2000)

Gallus gallus RBMS1 – NP_990355 2 Kimura et al. (1998)

. RBMY — RNA binding motif protein, Y-linked, family 1

Homo sapiens RBMY A1 – NP_005049 1 Chai et al. (1998)

Homo sapiens RBMY B – NP_001006121 1 Chai et al. (1998)

Homo sapiens RBMY D – NP_001006120 1 Chai et al. (1998)

Table S2

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Homo sapiens RBMY E – NP_001006118 1 Chai et al. (1998)

Homo sapiens RBMY F – NP_689798 1 Chai et al. (1998)

Homo sapiens RBMY J – NP_001006117 1 Chai et al. (1998)

. RDM1 — RAD52 motif 1

Homo sapiens RDM1 – NP_663629 1 Hamimes et al. (2005)

Gallus gallus RDM1 – NP_989877 1 Hamimes et al. (2005)

Mus musculus RDM1 – NP_079930 1 Hamimes et al. (2005)

. RNPS1 — RNA-binding protein S1

Homo sapiens RNPS1 – NP_006702 1 Badolato et al. (1995)

Mus musculus RNPS1 – NP_033096 1 Schmidt and Werner (1993)

. SART3 — squamous cell carcinoma antigen recognized by T cells 3

Homo sapiens SART 3 – NP_055521 2 Harada et al. (2001)

Mus musculus SART 3 – NP_058622 2 Harada et al. (2000)

Danio rerio SART 3 – NP_001025289 2 Trede et al. (2007)

Rattus norvegicus SART 3 – NP_001100626 2 GenBank

. SR — SR proteins

Homo sapiens SRp20 – P84103 1 Zahler et al. (1992)

Homo sapiens SC35 – NP_003007 1 Fu and Maniatis (1992)

Homo sapiens SRp30c – AAA93069 2 Screaton et al. (1995)

Homo sapiens 9G8 – NP_001026854 1 Cavaloc et al. (1994)

Homo sapiens ASF/SF2 – NP_008855 2 Krainer et al. (1990) ; Ge and Manley (1990)

Homo sapiens SRp40 – NP_008856 2 Screaton et al. (1995)

Homo sapiens SRp46 – NP_115285 1 Soret et al. (1998)

Homo sapiens SRp55 – Q13247 2 Screaton et al. (1995)

Homo sapiens SRp54 – NP_004759 1 Zhang and Wu (1996)

Homo sapiens SRp75 – Q08170 2 Zahler et al. (1993)

Arabidopsis thaliana SRp30 – NP_172386 2 Lopato et al. (1999b)

Arabidopsis thaliana SR1/SRp34 – O22315 2 Lazar et al. (1995)

Arabidopsis thaliana SRp34a – NP_190512 2 Lorkovic and Barta (2002)

Arabidopsis thaliana SRp34b – NP_567235 2 Lorkovic and Barta (2002)

Arabidopsis thaliana RSp31 – P92964 2 Lopato et al. (1996)

Arabidopsis thaliana RSp31a – NP_182184 2 Kalyna and Barta (2004)

Arabidopsis thaliana RSp40/SRp35 – P92965 2 Lopato et al. (1996)

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Arabidopsis thaliana RSp41 – P92966 2 Lopato et al. (1996)

Arabidopsis thaliana SRZ21/RSZ21 – AAD12770 1 Golovkin and Reddy (1998)

Arabidopsis thaliana SRZ22/RSZ22 – NP_194886 1 Golovkin and Reddy (1998)

Arabidopsis thaliana RSZ22a – NP_180035 1 Lopato et al. (1999a)

Arabidopsis thaliana RSZ32 – NP_190918 1 Lopato et al. (2002)

Arabidopsis thaliana RSZ33 – CAC03605 1 Lopato et al. (2002)

Arabidopsis thaliana SC35 – NP_201225 1 Lopato et al. (2002)

Arabidopsis thaliana SR33/SCL33 – NP_564685 1 Golovkin and Reddy (1999)

Arabidopsis thaliana SCL30 – NP_567021 1 Lopato et al. (2002)

Arabidopsis thaliana SCL30a – NP_187966 1 Lopato et al. (2002)

Arabidopsis thaliana SCL28 – NP_197382 1 Lopato et al. (2002)

Arabidopsis thaliana SR45 – Q9SEE9 1 Golovkin and Reddy (1999)

Oryza sativa SRp32 – AK061903 2 Isshiki et al. (2006)

Oryza sativa SRp33a – AK106176 2 Isshiki et al. (2006)

Oryza sativa SRp33b – AK071503 2 Isshiki et al. (2006)

Oryza sativa SR20 – AK103534 2 Isshiki et al. (2006)

Oryza sativa SC35a – AK103676 1 Isshiki et al. (2006)

Oryza sativa SC35b – AK070292 1 Isshiki et al. (2006)

Oryza sativa SC35c – AK073057 1 Isshiki et al. (2006)

Oryza sativa SCL25 – AK073451 1 Isshiki et al. (2006)

Oryza sativa SCL30a – AK062577 1 Isshiki et al. (2006)

Oryza sativa SCL30b – AK065531 1 Isshiki et al. (2006)

Oryza sativa RSZp21a – AK063879 1 Isshiki et al. (2006)

Oryza sativa RSZp21b – AK073210 1 Isshiki et al. (2006)

Oryza sativa RSZp23 – AK060088 1 Isshiki et al. (2006)

Oryza sativa RSp29 – AK102071 2 Isshiki et al. (2006)

Oryza sativa RSp33 – AK121372 2 Isshiki et al. (2006)

Oryza sativa RSZ36 – AK103897 1 Isshiki et al. (2006)

Oryza sativa RSZ37a – AK060171 1 Isshiki et al. (2006)

Oryza sativa RSZ37b – AK073348 1 Isshiki et al. (2006)

Oryza sativa RSZ39 – AK063518 1 Isshiki et al. (2006)

Zea mays SRp30 – AAU29331 2 Gao et al. (2004)

Zea mays SRp30’ – Q64HB9 2 Gao et al. (2004)

Zea mays SRp31 – Q64HB5 2 Gao et al. (2004)

Zea mays SRp31" – Q64HB8 2 Gao et al. (2004)

Zea mays SRp32 – AAU29328 2 Gao et al. (2004)

Zea mays SRp32’ – Q64HC2 2 Gao et al. (2004)

Caenorhabditis elegans CeSRp75/rsp-1 – Q23121 2 Longman et al. (2000)

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Caenorhabditis elegans CeSF2/ASF/rsp-3 – Q9NEW6 2 Longman et al. (2000)

Caenorhabditis elegans CeSC35/rsp-4 – Q09511 1 Longman et al. (2000)

Caenorhabditis elegans CeSC35-2/rsp-5 – Q10021 1 Longman et al. (2000)


Caenorhabditis elegans Cep54/rsp-7 – O01159 2 Longman et al. (2000)

Drosophila melanogaster SC35 – NP_652612 1 Allemand et al. (2001)

Drosophila melanogaster 9G8 – AAF43414 1 Allemand et al. (2001)

Drosophila melanogaster SRp55 – CAA41556 2 Roth et al. (1991)

Schizosaccharomyces pombe Srp1 – AAC49909 1 Gross et al. (1998)

Chironomus tentans Hrp45 – Z54163 2 Alzhanova-Ericsson et al. (1996)

. SRrp — SR related protein

Homo sapiens SRp40 – AAL57514 1 Cowper et al. (2001)

Homo sapiens SRrp35 – Q8WXF0 1 Cowper et al. (2001)

Homo sapiens SRrp86 – NP_001070667 2 Barnard and Patton (2000)

Homo sapiens SRp38 – NP_473357 1 Shin et al. (2004)

. TARDBP — TAR DNA binding protein

Homo sapiens TARDBP – NP_031401 2 Ou et al. (1995)

Mus musculus TARDBP – NP_663531 2 Buratti and Baralle (2008)

. TIATIAR — T-cell internal antigen-1 (TIA-1) and TIA-1-related protein (TIAR)

Homo sapiens TIAR – NP_003243 3 Kawakami et al. (1992)

Homo sapiens TIA-1 – NP_071320 3 Tian et al. (1991)

Mus musculus TIA-1 – NP_035715 3 Lowin et al. (1996)

Gallus gallus TIA-1 – NP_989687 3 Le Guiner et al. (2003)

Bombyx mori TIA-1 – NP_001036895 3 Kotani et al. (2003)

Rattus norvegicus TIA-1 – NP_001012096 3 GenBank

Mus musculus TiaL1 – NP_033409 3 Beck et al. (1996)

Rattus norvegicus TiaL1 – NP_001013211 3 GenBank

. TIF3 — Translation initiation factor 3

Arabidopsis thaliana TIF3 – AAG51445 1 Lorkovic and Barta (2002)

Arabidopsis thaliana TIF3 – BAB10805 1 Lorkovic and Barta (2002)

Table S2

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. UMH — Proteins with the UHM domain (RRM variant)

Homo sapiens KIS kinase interacting stathmin NP_787062 1 Bieche et al. (2003)

Mus musculus KIS kinase interacting stathmin NP_034763 1 Maucuer et al. (1995)

Rattus norvegicus KIS kinase interacting stathmin NP_058989 1 Maucuer et al. (1997)

Homo sapiens PUF60 poly-U binding splicing factor 60KDa NP_510965 3 Page-McCaw et al. (1999)

Drosophila melanogaster PUF60 poly-U binding splicing factor 60KDa NP_525123 2 Van Buskirk and Schupbach (2002)

Mus musculus PUF60 poly-U binding splicing factor 60KDa AAH10601 2 Kielkopf et al. (2004)

Danio rerio PUF60 poly-U binding splicing factor 60KDa CAD61099 2 Kielkopf et al. (2004)

Anopheles gambiae PUF60 poly-U binding splicing factor 60KDa EAA09944 2 Kielkopf et al. (2004)

Caenorhabditis elegans PUF60 poly-U binding splicing factor 60KDa AAF60676 2 Kielkopf et al. (2004)

Homo sapiens SPF45 RBM17 NP_116294 1 Sampath et al. (2003)

Mus musculus SPF45 RBM17 NP_690037 1 Kielkopf et al. (2004)

Danio rerio SPF45 – AAH45473 1 Kielkopf et al. (2004)

Anopheles gambiae SPF45 – EAA15153 1 Kielkopf et al. (2004)

Drosophila melanogaster SPF45 – EAA46008 1 Chaouki and Salz (2006)

Caenorhabditis elegans SPF45 – CAA97799 1 Kielkopf et al. (2004)

Homo sapiens Tat-SF1 – AAB18823 1 Zhou and Sharp (1996)

Mus musculus Tat-SF1 – AAH37711 1 Kielkopf et al. (2004)

Danio rerio Tat-SF1 – AAH55565 1 Kielkopf et al. (2004)

Drosophila melanogaster Tat-SF1 – AAF51719 1 Kielkopf et al. (2004)

Anopheles gambiae Tat-SF1 – EAA10753 1 Kielkopf et al. (2004)

Caenorhabditis elegans Tat-SF1 – AAK29956 1 Kielkopf et al. (2004)

Homo sapiens HCC1 Hepatocellular carcinoma protein 1 Q14498 2 Imai et al. (1993)

Mus musculus HCC1 – Q8VH51 2 Kielkopf et al. (2004)

Danio rerio HCC1 – AAH44487 2 Kielkopf et al. (2004)

Drosophila melanogaster HCC1 – AAF52478 2 Kielkopf et al. (2004)

Anopheles gambiae HCC1 – EAA12873 2 Kielkopf et al. (2004)

Caenorhabditis elegans HCC1 – AAM97977 2 Kielkopf et al. (2004)

Arabidopsis thaliana HCC1 – AAM20703 2 Kielkopf et al. (2004)

. ZCRB1 — zinc finger CCHC-type and RNA binding motif

Homo sapiens ZCRB1 – NP_149105 1 Wang et al. (2007a)

Mus musculus ZCRB1 – NP_080301 1 Wang et al. (2007a)

. cpRNP — chloroplast RRM containing proteins

Arabidopsis thaliana cpRNP28 – AAD14476 2 Lorkovic and Barta (2002)

Arabidopsis thaliana cpRNP28b – AAF26472 2 Lorkovic and Barta (2002)

Arabidopsis thaliana cpRNP29 – CAB67653 2 Ohta et al. (1995)

Table S2

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Arabidopsis thaliana cpRNP29b – AAC98043 2 Lorkovic and Barta (2002)

Arabidopsis thaliana cpRNP31 – CAA22986 2 Ohta et al. (1995)

Arabidopsis thaliana cpRNP31b – BAB09396 2 Lorkovic and Barta (2002)

Arabidopsis thaliana cpRNP33 – CAB43448 2 Ohta et al. (1995)

Arabidopsis thaliana cpRNP33b – AAC36180 2 Lorkovic and Barta (2002)

. cyclophilin — cyclophilins

Arabidopsis thaliana AtCyp59 – NP_175776 1 Gullerova et al. (2006)

Rattus norvegicus CypE – NP_001041333 1 GenBank

Caenorhabditis elegans cyp-13 – NP_503034 1 Zorio and Blumenthal (1999)

Mus musculus Cyp-33 – Q9QZH3 1 Anderson et al. (2002)

Drosophila melanogaster Cyp-33 – Q9V3G3 1 Anderson et al. (2002)

Homo sapiens Cyp-33 – Q9UNP9 1 Mi et al. (1996)

Homo sapiens PPIL4 – Q8WUA2 1 Zeng et al. (2001)

Mus musculus PPIL4 – Q9CXG3 1 Zeng et al. (2001)

Schizosaccharomyces pombe PPIL4 – Q9UUE4 1 Pemberton and Kay (2005)

Haemonchus contortus CYP – AAW82658 1 Valle et al. (2005)

. eIF4B — eukaryotic translation initiation factor 4B

Homo sapiens eIF-4B – NP_001408 1 Milburn et al. (1990)

Mus musculus eIF-4B – NP_663600 1 Shahbazian et al. (2006)

. hnRNP — Heterogeneous nuclear ribonucleoprotein

Arabidopsis thaliana AtRNP A/B1 – CAB10209 2 Lorkovic et al. (2000b)

Arabidopsis thaliana AtRNP A/B2 – AAB80680 2 Lorkovic et al. (2000b)

Arabidopsis thaliana AtRNP A/B3 – BAB08572 2 Lorkovic et al. (2000b)

Arabidopsis thaliana AtRNP A/B4 – CAB43861 2 Lorkovic et al. (2000b)

Arabidopsis thaliana AtRNP A/B5 – BAB09088 2 Lorkovic et al. (2000b)

Arabidopsis thaliana AtRNP A/B6 – AAF21191 2 Lorkovic et al. (2000b)

Arabidopsis thaliana AtRNP H/F1 – BAB10406 2 Lorkovic et al. (2000b)

Arabidopsis thaliana AtRNP H/F2 – BAB02497 2 Lorkovic et al. (2000b)

Arabidopsis thaliana AtRNP I/PTB – BAB08421 2 Lorkovic et al. (2000b)

Arabidopsis thaliana AtRNP I/PTB – AAF26159 2 Lorkovic and Barta (2002)

Arabidopsis thaliana AtRNP I/PTB – NP_175010 4 Lorkovic and Barta (2002)

Homo sapiens hnRNP A2/B1 – NP_112533 2 Burd et al. (1989)

Homo sapiens hnRNP A1/A1 – NP_002127 2 Buvoli et al. (1988)

Homo sapiens hnRNP A/B – NP_112556 2 Khan et al. (1991)

Homo sapiens hnRNP A0 – NP_006796 2 Myer and Steitz (1995)

Table S2

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Homo sapiens hnRNP C1/C2 – AAH07052 1 Swanson et al. (1987)

Homo sapiens hnRNP C – NP_001070910 1 Swanson et al. (1987)

Homo sapiens hnRNP D – NP_112737 2 Park et al. (2007)

Homo sapiens hnRNP F – NP_001091676 3 Matunis et al. (1994)

Homo sapiens hnRNP G – P38159 1 Soulard et al. (1993)

Homo sapiens hnRNP H3 – NP_036339 2 Mahe et al. (1997)

Homo sapiens hnRNP L – NP_001524 4 Pinol-Roma et al. (1989)

Homo sapiens hnRNP L-like – NP_612403 3 Shur et al. (2004)

Homo sapiens hnRNP R – NP_005817 3 Hassfeld et al. (1998)

Rattus norvegicus hnRNP A2/B1 – NP_001098083 2 Kamma et al. (1999)

Rattus norvegicus hnRNP M – NP_001103381 3 Kafasla et al. (2000)

Chironomus tentans Hrp59 protein – CAH05070 3 Kiesler et al. (2005)

Mus musculus HNRP A/B – NP_034578 2 Inoue et al. (2001)

Mus musculus HNRP L – NP_796275 3 Costain and Mishra (2003)

Mus musculus HNRP M – NP_084080 3 Mahe et al. (2000)

Drosophila melanogaster Hrp36 – CAA44502 2 Matunis et al. (1992)

. nucleolin — nucleolins

Arabidopsis thaliana nucleolin AtNUC-L1 NP_175322 2 Pontvianne et al. (2007)

Arabidopsis thaliana nucleolin AtNUC-L2 NP_188491 2 Pontvianne et al. (2007)

Homo sapiens nucleolin/C23 – NP_005372 4 Srivastava et al. (1989)

Rattus norvegicus nucleolin/C23 – NP_036881 4 Bourbon et al. (1988b)

Schizosaccharomyces pombe GAR2 – NP_593531 2 Gulli et al. (1995)

Saccharomyces cerevisiae NSR1 – NP_011675 2 Edwards et al. (2000)

Xenopus laevis NCL – P20397 4 Heine et al. (1993)

Mus musculus NCL – NP_035010 4 Bourbon et al. (1988a)

. oligoU — oligouridylated-specific RRM proteins (UBP1, RBP45, RBP47, UBA1 et UBA2)

Arabidopsis thaliana RBP45b – NP_172630 3 Lorkovic et al. (2000a)

Arabidopsis thaliana RBP47a – AAG13046 3 Lorkovic et al. (2000a)

Arabidopsis thaliana RBP47b – BAB02953 3 Lorkovic et al. (2000a)

Arabidopsis thaliana RBP47c – AAD46038 3 Lorkovic et al. (2000a)

Arabidopsis thaliana RBP47c’ – AAD46037 3 Lorkovic et al. (2000a)

Nicotiana plumbaginifolia RBP45 – CAC01237 3 Lorkovic et al. (2000a)

Arabidopsis thaliana UBP1a – AAD25780 3 Lambermon et al. (2000)

Arabidopsis thaliana UBP1b – AAF79492 3 Lambermon et al. (2000)

Arabidopsis thaliana UBP1c – BAB02974 3 Lambermon et al. (2000)

Nicotiana plumbaginifolia UBP1 – CAB75429 3 Lambermon et al. (2000)

Table S2

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Arabidopsis thaliana UBA2a – NP_850711 2 Lorkovic and Barta (2002)

Arabidopsis thaliana UBA2b – NP_001078035 2 Lorkovic and Barta (2002)

Arabidopsis thaliana UBA2c – BAA97064 2 Lorkovic and Barta (2002)

Arabidopsis thaliana UBA1a – AAD25815 1 Lorkovic and Barta (2002)

Arabidopsis thaliana UBA1b – AAD25814 1 Lorkovic and Barta (2002)

Arabidopsis thaliana UBA1c – AAC16468 1 Lorkovic and Barta (2002)

Arabidopsis thaliana S-RBP2 – BAB09544 1 Lorkovic and Barta (2002)

Arabidopsis thaliana S-RBP3 – AAC61284 1 Lorkovic and Barta (2002)



Arabidopsis thaliana S-RBP7 – AAG51218 1 Lorkovic and Barta (2002)

Arabidopsis thaliana S-RBP8 – AAD20390 1 Lorkovic and Barta (2002)

Arabidopsis thaliana S-RBP9 – AAC23648 1 Lorkovic and Barta (2002)

Arabidopsis thaliana S-RBP10 – AAF21210 1 Lorkovic and Barta (2002)




Arabidopsis thaliana S-RBP14 – AAB88654 1 Lorkovic and Barta (2002)


. snRNP — small nuclear ribonucleoprotein (snRNP)

Solanum tuberosum U1A – CAA90282 2 Simpson et al. (1995)

Homo sapiens U1A – NP_004587 2 Sillekens et al. (1987)

Mus musculus U1A – NP_056597 2 Bennett et al. (1993)

Xenopus laevis U1A – CAA41021 2 Scherly et al. (1991)

Solanum tuberosum U2B” – AAA33847 2 Simpson et al. (1991)

Arabidopsis thaliana U1A – NP_182280 2 Simpson et al. (1995)

Arabidopsis thaliana U170K – CAB62436 1 Golovkin and Reddy (1996)

Arabidopsis thaliana U2B – NP_180585 2 Simpson et al. (1995)

Arabidopsis thaliana U2B – AAF82223 2 Simpson et al. (1991)

Arabidopsis thaliana U2AF65a – CAB80335 2 Domon et al. (1998)

Arabidopsis thaliana U2AF65b – AAG51641 3 Domon et al. (1998)

Arabidopsis thaliana U2SF3b53a – AAD12222 2 Lorkovic and Barta (2002)

Arabidopsis thaliana U2SF3b53b – AAD15475 2 Lorkovic and Barta (2002)

Arabidopsis thaliana U11-35kD – AAB64330 1 Lorkovic and Barta (2002)

Arabidopsis thaliana U2AF35 – BAB10638 1 Domon et al. (1998)

Nicotiana plumbaginifolia U2AF65 – CAA77136 3 Domon et al. (1998)

Zea mays U170K – AAT64945 1 Gupta et al. (2006)

Table S2

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Danio rerio U170K – Q6DRE8 1 Amsterdam et al. (2004)

Mus musculus U11/U1235K – Q9D384 1 GenBank

Homo sapiens U2AF35 – NP_006749 1 Zhang et al. (1992)

Mus musculus U2AF35 – Q9D883 1 Pacheco et al. (2004)

Danio rerio U2AF35 – AAM34646 1 Pacheco et al. (2004)

Drosophila melanogaster U2AF35 – AAB17271 1 Rudner et al. (1996)

Caenorhabditis elegans U2AF35 – CAB55137 1 Zorio and Blumenthal (1999)

Gallus gallus U2AF35 – NP_989986 1 Pacheco et al. (2004)

Schizosaccharomyces pombe U2AF23 – AAC49805 1 Wentz-Hunter and Potashkin (1996)

Homo sapiens U2AF65 – NP_009210 3 Zamore et al. (1992)

Mus musculus U2AF65 – NP_598432 3 Sailer et al. (1992)

Danio rerio U2AF65 – AAH65869 3 Kielkopf et al. (2004)

Caenorhabditis elegans U2AF65 – AAC26982 3 Zorio et al. (1997)

Homo sapiens U11/U12 35K – NP_073208 1 Will et al. (2004)

Mus musculus U2AF1-rs 1 – NP_035793 1 Kitagawa et al. (1995)

Homo sapiens U2A1L3 – Q8WU68 1 Shepard et al. (2002)

Homo sapiens U2AF1L4 – NP_001035515 1 Shepard et al. (2002)

. 30kRRM — 30K-RRM proteins

Arabidopsis thaliana 30K-RRM1 – CAB77597 1 Lorkovic and Barta (2002)

Arabidopsis thaliana 30K-RRM2 – AAF27001 1 Lorkovic and Barta (2002)

Arabidopsis thaliana 30K-RRM3 – AAD30604 1 Lorkovic and Barta (2002)

Arabidopsis thaliana 30K-RRM4 – AAG51948 1 Lorkovic and Barta (2002)



Arabidopsis thaliana 30K-RRM7 – AAC33496 1 Lorkovic and Barta (2002)

Arabidopsis thaliana 30K-RRM8 – AAK32921 1 Lorkovic and Barta (2002)

Table S2

44

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Q. Zhou and P. A. Sharp. Tat-SF1: cofactor for stimula-tion of transcriptional elongation by HIV-1 Tat. Science,274:605–10, 1996.

D. A. Zorio and T. Blumenthal. U2AF35 is encoded

by an essential gene clustered in an operon withRRM/cyclophilin in Caenorhabditis elegans. Rna, 5:487–94, 1999.

D. A. Zorio, K. Lea, and T. Blumenthal. Cloning ofCaenorhabditis U2AF65: an alternatively spliced RNAcontaining a novel exon. Mol Cell Biol, 17:946–53,1997.

Table S2

55

i

node RRM# (KOG#) KOG name reference sequences MP RW TW RL mRW

1 RRM1 (0110) RBP – y y y y1 y

2 RRM1 (0117) hnRNPr hnRNP (excl. flowering plants) y2 y y y y1

3 RRM1 (0123) PABP PABP y3 y y1 y y

4RRM2 (0123) PABP

RRM2 (0131) splicing factor 2b

[RRM2 (0115) RBP p54 nrb]

PABP

– (fungi)

p54 nrb/PSP1/PSF

y4 y5 y4 y4 y5

5 RRM3 (0123) PABP PABP (minor subgroup) y3 y y y y

6 RRM4 (0123) PABP PABP y3 y y y y

7 RRM1 (0144) BRUNOBRUNO

FCAFPA (land plants)y2 y y y y

8 RRM2 (0144) BRUNOBRUNO

FCAFPA (land plants)y2 y y y y

9 RRM3 (0144) BRUNO BRUNO y3 y y y y

10 RRM1 (0145) ELAV/HU ELAV y3 y y y y

11 RRM2 (0145) ELAV/HU ELAV/RBMS y3 y y y y

12 RRM3 (0145) ELAV/HU ELAV y3 y y y y

13 [RRM1 (0151) predicted splicing regulator] – y3 y y1 y1 y1

14 [RRM1 (0153) RBP] RBM y3 y y1 y1 y1

15 – – n6 y y n6 y

16RRM1 (0105) ASF/SF2RRM1 (0106) SRp55/B52/SRp75

dual RRM SR proteins y y y y y

17 [RRM1 (0107) SRp20/9G8] single RRM Zn-K SR proteins y y y y y

18 – see footnote [7] n y n y y

19 [RRM1 (0111) cyclophilin-type PPCTI8] cyclophilin y9 y y9 y9 y

20 [RRM1 (0130) RBP RBM810] RBM y9 y y9 y y

21 – – n n n n y

22 RRM1 (4207) predicted SR protein single RRM SR proteins y y y y y

23 RRM1 (0111) cyclophilin-type PPCTI8 SRrp y y y y y

24 [RRM1 (0121) CBP20] – y y y y y9

25 – – y y y y n11

26 RRM1 (-) SR45 (green plants) y y y y y

27 RRM1 (4209) splicing factor RNPS1 RNPS1 y y y y y

28 – – y y y y y

29RRM2 (0105) ASF/SF2RRM2 (0106) SRp55/B52/SRp75

dual RRM SR proteins (excl. plants) y y y y y

30RRM1/2/3 (4212) hnRNPm

[RRM1 (0533) RRM-containing protein]

hnRNP

PDIP/FCAFPAy12 y13 y13 y12 y12

31 RRM1 (0117) hnRNPr – (flowering plants) y y y y y

32 RRM3 (0110) RBP – y14 y y y y

33 [RRM1 (0115) RBP p54 nrb] p54 nrb-PSP1-PSF n y n n y

34 RRM1 (2277) CID1 – y y y15 y15 y

35RRM1 (0116) Rasputin

RRM1 (0149) SEB4

RRM1/2 (4205) HRP1

G3BP

RBM/30KRRM

hnRNP/Musashi/Dazap/TARDBP/OligoU

y16 y n y16 y

36 RRM1 (0113) U1 snRNP snRNP y15 y y y y

37 RRM2 (0128) SART3 SART3 y15 y y y17 y17

38 [RRM1 (0415) PPCTI8] cyclophilin y15 y15 y y y

39 – – n6 n18 y19 y20 y20

40 RRM1 (4206) U1A/U2B snRNP snRNP y y y y y

41 RRM2 (4206) U1A/U2B snRNP snRNP y y y y y

42 RRM1 (4660) Mei2 – y y y y y

43 RRM2 (4660) Mei2 – y y y y y

44 [RRM1 (0114) RBP] – y y y y y

45 – – n21 n22 n23 n24 n24

46 RRM1 (0131) splicing factor 2b see footnote [25] y y y y y

47 RRM1 (4454) RBP – y y y y y

48 [RRM1 (2193) IGF2BP] IGF2BP y y y y y

Table S3

56

ii

node RRM# (KOG#) KOG name reference sequences MP RW TW RL mRW

49 – – y y n26 y n26

50 RRM1 (0109) LARK LARK y y y y y

51 RRM2 (0109) LARK LARK y y y y y

52 – – n y y n y

53 RRM2 (0112) RBP RBM y y y y y27

54 RRM3 (0112) RBP – y y y y y27

55 – – n y y y y

56 RRM2 (0106) SRp55/B52/SRp75 plant-specific RS group of SR proteins y y y y y

57 RRM1 (0108) RNA15 ZCRB1 y y y y y

58 RRM1 (0108) RNA15 GRSRBP/hnRNP/RBMY y y y y y

59 RRM4/5 (0110) RBP – y y y y y

60 RRM4/5/6 (0110) RBP – y y y y y

61 RRM4 (0112) RBP – y y y y y

62 RRM1 (0117) hnRNPr – (land plants) y y y y y

63 RRM3 (0117) hnRNPr hnRNP n28 y y n28 n28

64 RRM2 (0120) U2AF snRNP y y y y y

65 RRM1 (0122) TIF3 (eIF3) – y y y y y

66 RRM3 (0123) PABP PABP (major subgroup) y29 y y y2930 y30

67RRM2 (0124) PUF60

RRM2 (0147) CAPER/UMH

[RRM1 (0124) PUF60]

UMH

UMH

UMH

y31 y31 y32 y32 y32

68RRM1 (0125) ataxin-2 binding protein

RRM1 (0127) fibrillarin

RRM1 (4661) SAF-B

FOX

– (land plants)

–

n y y y y

69 RRM1 (0126) RBP – y y y y y

70 RRM1 (0127) fibrillarin RBM y y y y y



73 RRM1 (0128) SART3 SART3 (excl. green plants) y y y y y

74 RRM1 (0128) SART3 – (green plants) y y y y y

75 RRM1 (0147) CAPER/UMH CAPER/UMH y y y y y

76 RRM1 (0148) TIA1/TIAR TIATIAR/OligoU y n6 y y y

77RRM2 (0148) TIA1/TIAR

RRM1 (0226) RBP

TIATIAR/OligoU

–y y y y y

78 RRM3 (0148) TIA1/TIAR OligoU y y y y y

79 RRM3 (0148) TIA1/TIAR TIATIAR/OligoU n6 y y y y

80RRM? (1365) fusillin

RRM2 (4211) hnRNPf

–

hnRNPy y y y y

81 RRM1 (1855) predicted RBP La y y y y y

82 RRM1 (4208) NIFK – y y y y y

83 RRM1 (4209) splicing factor RNPS1 PABP (26%) y y y y y

84 RRM1 (4213) RBP La La y y y y y

85 RRM2 (4676) splicing factor SR rich SRrp y y y y y

86 RRM1 (–) hnRNP/RALYL y y y y y

87 RRM1 (–) eIF4b y y y y y

88 RRM1 (0108)33 prokaryotic RRMs n6 y y y y

1not associated to node (15); 2also associated in MP tree but independently of node (15); 3forming a mini node in MP tree (15); 4RRM2 of

p54 nrb not associated to the group; 5RRM2 of p54 nrb associated to the group; 6split; 79G8 and SC35/SCL groups associated in TF and MP

trees; 8PPCTI: peptidyl-propyl cis-trans isomerase; 9not associated to SR proteins; 10always associated to 9G8 SR proteins; 11RRM1 of CBP20

not associated to the group; 12RRM1 of KOG0533 not associated to the group; 13RRM1 of KOG0533 associated to the group; 14fungal RBP

missing from the group; 15not associated to the group; 16RRM1 of Rasputin not associated to the group; 17more distantly related to the group;18nodes (36, 37) associated; 19nodes (36, 37, 38) associated; 20nodes (36, 37) + (38) associated; 214 groups: nodes (42, 44), node (40), node

(41), and node (43); 222 groups: nodes (41, 42, 43, 44) and node (40); 232 groups: nodes (40, 41, 43, 44) and node (42); 244 groups: nodes (40,

43), node (41), node (42), and node (44); 25snRNPs represent 8% of group proteins; 26RRM1 of IGF2BP not associated to the group; 27nodes

(53) and (54) merged; 28split into plant and animal groups; 29associated to node (5); 30associated to node (6); 31RRM1 of PUF60 not associated

to the group; 32RRM1 of PUF60 associated to the group; 33mostly KOG0108, but also a lower % of KOG0116 and KOG0145

Table S3

57

dataset seq#/AA# meth. heuristic model tree node associations

original 1266x72 MP PAUP* – Fig. S5 [16] vs. [17+(22-23)+(26-27)]

original 1266x72 ML RAxML WAG+G4 Fig. S6 [16+17+(22-23)] vs. [(26-27)]

original 1266x72 ML TreeFinder WAG+G4 Fig. S7 [16] vs. [17+(22-23)] vs. [(26-27)]

original 1266x72 ML RAxML LG+F+G4 Fig. S8 [16+17+(26-27)] vs. [(22-23)]

enlarged 1831x72 ML RAxML WAG+G4 Fig. S9 [16+17+(26-27)] vs. [(22-23)]

Table S4

58

SR subfamily key features secondary features

SC35 K P S KS R RS

SCL P R GR RS E G S

SRrp K P R S KS RS

9G8 R RS S

SRp20 G P R S RS

RSZ G GG GR P R S RS

RS2Z G P R S GR RS

ASF/SF2 G P R S RS

SRp30c G P R S RS

ASF-like (plants) G KS RS SS R S

SRp40 G K S KS R RS

SRp55 G K S KS R RS

SRp75 G K S KS R RS

RS E P R S RS

SR45 K P R S PP RS SS SSS

RNPS1 P R S PP RS SS ST SSS

Table S5

59

step criteria result

1 one RRM domain step 2

two RRM domains step 9

2 2 Zn knuckles . RS2Z1 Zn knuckle step 3

no Zn knuckle step 4

3 enriched in G, GG, GR, GGG between RRM and ZnK . RSZenriched in R, RS between RRM and ZnK . 9G8

4 enriched in P, R, RS before RRM step 5

otherwise step 7

5 enriched in GR before RRM . SCLenriched in S, GS, SS before RRM and P, PP, PPP after RRM step 6

6 enriched in R, ST, SSS before RRM . RNPS1enriched in K, SSS after RRM . SR45

7 enriched in K, KS after RRM and P, S before RRM step 8

enriched G before RRM . SRp208 enriched in R before RRM . SRrp

otherwise . SC359 second RRM lacks SWKDLKD motif . RS

enriched in G between RRMs step 10

10 enriched in KS after second RRM step 11

enriched in G before first RRM . ASF/SF2, SRp30c11 enriched in RS, SS before RRM . ASF-like (plant)

enriched in S, K, KS after last domain . SRp40-55-75

Table S6

60

organism lineage cand rej iso conf key trunc

Homo sapiens Eutheria 23 0 11 12 11 0

Mus musculus Eutheria 26 1 13 12 12 0

Drosophila melanogaster Insecta 15 0 6 9 5 0

Caenorhabditis elegans Nematoda 14 0 7 7 4 0

Aspergillus fumigatus Ascomycota 0 0 0 0 0 0

Arabidopsis thaliana eudicotyledons 29 0 10 19 18 0

Populus trichocarpa eudicotyledons 30 0 0 30 21 6

Oryza sativa Liliopsida 23 1 0 22 17 0

Sorghum bicolor Liliopsida 21 0 0 21 15 4

Selaginella moellendorfii Lycopodiophyta 15 0 5 10 4 4

Physcomitrella patens Bryophyta 12 0 0 12 11 0

Chlamydomonas reinhardtii Chlorophyta 9 0 0 9 4 3

Volvox carteri Chlorophyta 8 1 0 7 1 1

Chlorella sp. NC64A Chlorophyta 7 0 0 7 3 1

Micromonas pusilla CCMP1545 Chlorophyta 3 0 0 3 0 3

Micromonas pusilla RCC299 Chlorophyta 3 0 0 3 1 1

Ostreococcus sp. RCC809 Chlorophyta 3 0 0 3 0 3

Ostreococcus lucimarinus Chlorophyta 3 0 0 3 0 3

Ostreococcus tauri Chlorophyta 1 0 0 1 0 1

Cyanidioschyzon merolae Rhodophyta 2 0 0 2 1 0

Total 247 3 52 192 128 30

Table S7

61

CDD/KOGNCBI Taxonomy

refs fromliterature

CDD/Pfam~700 completeproteomes fromEnsembl, NCBI, JGI...

me

S2

SMART

NCBI RefSeq

CDD/Pfam 20 selected (7 new)complete proteomes

S13

S15

CDD/KOGNCBI Taxonomy

refs fromliterature

S2

Tab. 2S7, DS2

DS3b-d

DS3a

S26-29

Fig. 5

S25S1

S5-9

S13-20

S19

S15S17, S6

S23

Fig. 4

S21

S2-3

S5-6

S24Fig. 1

S22

Fig. 2

S10-12

Tab. 1S3-4

Fig. 3S4

S21

S21

curatedstructuralalignments

exhaustiveHMM profile

alignments

Build HMM profile for

RRM domain

PredictRRM domains using profile

Extractpredicted

RRM domains

Extractpredicted

RRM proteins

Predict putative

SR proteins

Analyzetaxonomic distribution

ClusterRRM domainsby similarity

HMM alignRRM domains using profile

Infer trees of RRM domains

Annotate RRM trees

PruneSR-associated

subtrees

Develop evolutionary

scenario

Draw RRM logos for

SR families

ExtractSR-associatedRRM domains

Prune subtrees forSR families

Extract RRMdomains of SR families

Profile composition of SR families

Extract proteins ofSR families

Build HMM profile for

ZnK domain

PredictZnK domains using profile

Extract ZnKdomains of SR families

Align ZnK domains

Draw ZnK logos for

SR families

Structurally align RRM domains

Profile conservation of SR families

Build RRM profiles for SR proteins

PredictRRM domainsusing profiles

Extract predicted

RRM domains

Extract predicted

RRM proteins

BLAST align RRM domains

using logos

AnalyzeRRM protein architecture

Analyze RRM protein composition

Infer trees of RRM domains

Assemble inventory of SR proteins

Annotate RRM trees

Developkey for SR families

Analyzeprotein

composition

Compare RRM trees

1

2

34

DS1

Fig. S1

62

A. E-value threshold = 1E-05 / # RRM domains = 8471

0

0.5

1

Identity0

0.5

1

Coverage

0

0.5

1

Score

0.75

0.80

0.85

0.90

0.95

1.00

Fig. S2

63

B. E-value threshold = 1E-10 / # RRM domains = 6633

0

0.5

1

Identity0

0.5

1

Coverage

0

0.5

1

Score

0.75

0.80

0.85

0.90

0.95

1.00

Fig. S2

64

C. E-value threshold = 1E-15 / # RRM domains = 4523

0

0.5

1

Identity0

0.5

1

Coverage

0

0.5

1

Score

0.75

0.80

0.85

0.90

0.95

1.00

Fig. S2

65

D. E-value threshold = 1E-20 / # RRM domains = 2311

0

0.5

1

Identity0

0.5

1

Coverage

0

0.5

1

Score

0.75

0.80

0.85

0.90

0.95

1.00

Fig. S2

66

E. E-value threshold = 1E-25 / # RRM domains = 597

0

0.5

1

Identity0

0.5

1

Coverage

0

0.5

1

Score

0.75

0.80

0.85

0.90

0.95

1.00

Fig. S2

67

0

10

20

30

40

50

60

70

80

90

100

30,000 32,000 34,000 36,000 38,000 40,000

Tre

e ra

nk

Tree length (parsimony steps)

slowest sequencefastest sequencelongest sequence

Fig. S3

68

[KOG3208] 1 [Intracellular trafficking, secretion, and vesicular transport] SNARE protein GS28

[KOG4198] 1 [General function prediction only] RNA-binding Ran Zn-finger protein and related proteins

[KOG2490] 1 [Function unknown] Predicted membrane protein

[KOG1611] 1 [General function prediction only] Predicted short chain-type dehydrogenase

[KOG0307] 1 [Intracellular trafficking, secretion, and vesicular transport] Vesicle coat complex COPII, subunit SEC31

[KOG1337] 1 [General function prediction only] N-methyltransferase

[KOG0161] 1 [Cytoskeleton] Myosin class II heavy chain

[KOG1267] 1 [Transcription, General function prediction only] Mitochondrial transcription termination factor, mTERF

[KOG2553] 1 [Translation, ribosomal structure and biogenesis] Pseudouridylate synthase

[KOG0474] 1 [Inorganic ion transport and metabolism] Cl- channel CLC-7 and related proteins (CLC superfamily)

[KOG4246] 1 [General function prediction only] Predicted DNA-binding protein, contains SAP domain

[KOG0197] 1 [Signal transduction mechanisms] Tyrosine kinases

[KOG0475] 1 [Inorganic ion transport and metabolism] Cl- channel CLC-3 and related proteins (CLC superfamily)

[KOG1311] 1 [General function prediction only] DHHC-type Zn-finger proteins

[KOG0591] 1 [Cell cycle control, cell division, chromosome partitioning] NIMA (never in mitosis)-related G2-specific serine/threonine protein kinase

[KOG0687] 1 [Posttranslational modification, protein turnover, chaperones] 26S proteasome regulatory complex, subunit RPN7/PSMD6

[KOG0585] 1 [Signal transduction mechanisms] Ca2+/calmodulin-dependent protein kinase kinase beta and related serine/threonine protein kinases

[KOG0433] 1 [Translation, ribosomal structure and biogenesis] Isoleucyl-tRNA synthetase

[KOG1924] 1 [Signal transduction mechanisms, Cytoskeleton] RhoA GTPase effector DIA/Diaphanous

[KOG0462] 1 [Translation, ribosomal structure and biogenesis] Elongation factor-type GTP-binding protein

[KOG4177] 1 [Cell wall/membrane/envelope biogenesis] Ankyrin

[KOG2029] 1 [Function unknown] Uncharacterized conserved protein

[KOG0941] 1 [Posttranslational modification, protein turnover, chaperones] E3 ubiquitin protein ligase

[KOG0899] 1 [Translation, ribosomal structure and biogenesis] Mitochondrial/chloroplast ribosomal protein S19

[KOG2186] 1 [Cell cycle control, cell division, chromosome partitioning] Cell growth-regulating nucleolar protein

[KOG1860] 1 [Intracellular trafficking, secretion, and vesicular transport, Cell cycle control, cell division, chromosome partitioning] Nuclear protein export factor

[KOG2476] 1 [Function unknown] Uncharacterized conserved protein

[KOG2087] 1 [Signal transduction mechanisms] Glycoprotein hormone receptor

[KOG1178] 2 [Secondary metabolites biosynthesis, transport and catabolism] Non-ribosomal peptide synthetase/alpha-aminoadipate reductase and related enzymes

[KOG1832] 2 [Cell cycle control, cell division, chromosome partitioning] HIV-1 Vpr-binding protein

[KOG1274] 2 [General function prediction only] WD40 repeat protein

[KOG1457] 2 [General function prediction only] RNA binding protein (contains RRM repeats)

[KOG3766] 2 [Transcription] Polycomb group protein SCM/L(3)MBT (tumor-supressor in Drosophila and humans)

[KOG0331] 2 [RNA processing and modification] ATP-dependent RNA helicase

[KOG3070] 2 [Translation, ribosomal structure and biogenesis] Predicted RNA-binding protein containing PIN domain and invovled in translation or RNA processing

[KOG4307] 2 [General function prediction only] RNA binding protein RBM12/SWAN

[KOG3001] 2 [Chromatin structure and dynamics, Transcription] Dosage compensation regulatory complex/histone acetyltransferase complex, subunit MSL-3/MRG15/EAF3, and related CHROMO domain-containing proteins

[KOG2141] 2 [Signal transduction mechanisms] Protein involved in high osmolarity signaling pathway

[KOG1833] 2 [Nuclear structure, Intracellular trafficking, secretion, and vesicular transport] Nuclear pore complex, gp210 component

[KOG3257] 2 [Translation, ribosomal structure and biogenesis] Mitochondrial/chloroplast ribosomal protein L11

[KOG0055] 3 [Secondary metabolites biosynthesis, transport and catabolism] Multidrug/pheromone exporter, ABC superfamily

[KOG1144] 3 [Translation, ribosomal structure and biogenesis] Translation initiation factor 5B (eIF-5B)

[KOG4849] 3 [RNA processing and modification] mRNA cleavage factor I subunit/CPSF subunit

[KOG2248] 3 [Replication, recombination and repair] 3'-5' exonuclease

[KOG1984] 3 [Intracellular trafficking, secretion, and vesicular transport] Vesicle coat complex COPII, subunit SFB3

[KOG4574] 4 [General function prediction only] RNA-binding protein (contains RRM and Pumilio-like repeats)

[KOG0598] 4 [General function prediction only, Signal transduction mechanisms] Ribosomal protein S6 kinase and related proteins

[KOG1365] 4 [RNA processing and modification, General function prediction only] RNA-binding protein Fusilli, contains RRM domain

[KOG0576] 4 [Signal transduction mechanisms] Mitogen-activated protein kinase kinase kinase kinase (MAP4K), germinal center kinase family

[KOG2044] 4 [Replication, recombination and repair, RNA processing and modification] 5'-3' exonuclease HKE1/RAT1

[KOG1548] 4 [Transcription] Transcription elongation factor TAT-SF1

[KOG3702] 5 [RNA processing and modification] Nuclear polyadenylated RNA binding protein

[KOG1240] 5 [Signal transduction mechanisms] Protein kinase containing WD40 repeats

[KOG2277] 6 [Cell cycle control, cell division, chromosome partitioning] S-M checkpoint control protein CID1 and related nucleotidyltransferases

[KOG1080] 6 [Chromatin structure and dynamics, Transcription] Histone H3 (Lys4) methyltransferase complex, subunit SET1 and related methyltransferases

[KOG0119] 6 [RNA processing and modification] Splicing factor 1/branch point binding protein (RRM superfamily)

[KOG1015] 6 [Transcription] Transcription regulator XNP/ATRX, DEAD-box superfamily

[KOG0670] 7 [RNA processing and modification] U4/U6-associated splicing factor PRP4

[KOG2193] 8 [RNA processing and modification, General function prediction only] IGF-II mRNA-binding protein IMP, contains RRM and KH domains

[KOG0154] 8 [General function prediction only] RNA-binding protein RBM5 and related proteins, contain G-patch and RRM domains

[KOG2253] 8 [RNA processing and modification] U1 snRNP complex, subunit SNU71 and related PWI-motif proteins

[KOG0548] 9 [Posttranslational modification, protein turnover, chaperones] Molecular co-chaperone STI1

[KOG4210] 13 [Transcription] Nuclear localization sequence binding protein

[KOG4368] 19 [General function prediction only] Predicted RNA binding protein, contains SWAP, RPR and G-patch domains

[KOG1190] 19 [RNA processing and modification] Polypyrimidine tract-binding protein

[KOG4213] 19 [RNA processing and modification] RNA-binding protein La

[KOG3598] 21 [Transcription] Thyroid hormone receptor-associated protein complex, subunit TRAP230

[KOG0132] 22 [RNA processing and modification, Transcription] RNA polymerase II C-terminal domain-binding protein RA4, contains RPR and RRM domains

[KOG1855] 34 [General function prediction only] Predicted RNA-binding protein

[KOG4454] 34 [General function prediction only] RNA binding protein (RRM superfamily)

[KOG4660] 34 [Cell cycle control, cell division, chromosome partitioning] Protein Mei2, essential for commitment to meiosis, and related proteins

[KOG4676] 39 [RNA processing and modification] Splicing factor, arginine/serine-rich

[KOG0153] 42 [General function prediction only] Predicted RNA-binding protein (RRM superfamily)

[KOG0921] 44 [Transcription] Dosage compensation complex, subunit MLE

[KOG0151] 53 [General function prediction only] Predicted splicing regulator, contains RRM, SWAP and RPR domains

[KOG0130] 56 [General function prediction only] RNA-binding protein RBM8/Tsunagi (RRM superfamily)


[KOG4207] 58 [RNA processing and modification] Predicted splicing factor, SR protein superfamily

[KOG1995] 66 [General function prediction only] Conserved Zn-finger protein

[KOG0121] 74 [RNA processing and modification] Nuclear cap-binding protein complex, subunit CBP20 (RRM superfamily)

[KOG0226] 76 [General function prediction only] RNA-binding proteins

[KOG0415] 77 [Posttranslational modification, protein turnover, chaperones] Predicted peptidyl prolyl cis-trans isomerase

[KOG4208] 77 [General function prediction only] Nucleolar RNA-binding protein NIFK

[KOG0120] 86 [RNA processing and modification] Splicing factor U2AF, large subunit (RRM superfamily)


[KOG4661] 93 [Transcription] Hsp27-ERE-TATA-binding protein/Scaffold attachment factor (SAF-B)

[KOG0533] 94 [RNA processing and modification] RRM motif-containing protein

[KOG0112] 97 [General function prediction only] Large RNA-binding protein (RRM superfamily)

[KOG0122] 102 [Translation, ribosomal structure and biogenesis] Translation initiation factor 3, subunit g (eIF-3g)

[KOG0128] 106 [RNA processing and modification] RNA-binding protein SART3 (RRM superfamily)

[KOG4206] 107 [RNA processing and modification] Spliceosomal protein snRNP-U1A/U2B

[KOG0107] 113 [RNA processing and modification] Alternative splicing factor SRp20/9G8 (RRM superfamily)

[KOG0113] 123 [RNA processing and modification] U1 small nuclear ribonucleoprotein (RRM superfamily)

[KOG4211] 135 [RNA processing and modification] Splicing factor hnRNP-F and related RNA-binding proteins

[KOG0111] 140 [Posttranslational modification, protein turnover, chaperones] Cyclophilin-type peptidyl-prolyl cis-trans isomerase

[KOG0124] 144 [RNA processing and modification] Polypyrimidine tract-binding protein PUF60 (RRM superfamily)

[KOG4209] 145 [RNA processing and modification] Splicing factor RNPS1, SR protein superfamily

[KOG0116] 149 [Signal transduction mechanisms] RasGAP SH3 binding protein rasputin, contains NTF2 and RRM domains

[KOG0106] 164 [RNA processing and modification] Alternative splicing factor SRp55/B52/SRp75 (RRM superfamily)

[KOG0125] 167 [General function prediction only] Ataxin 2-binding protein (RRM superfamily)

[KOG0149] 178 [General function prediction only] Predicted RNA-binding protein SEB4 (RRM superfamily)

[KOG0109] 199 [RNA processing and modification, General function prediction only] RNA-binding protein LARK, contains RRM and retroviral-type Zn-finger domains

[KOG0147] 203 [Transcription] Transcriptional coactivator CAPER (RRM superfamily)

[KOG0131] 205 [RNA processing and modification] Splicing factor 3b, subunit 4

[KOG0115] 209 [RNA processing and modification] RNA-binding protein p54nrb (RRM superfamily)

[KOG0110] 233 [General function prediction only] RNA-binding protein (RRM superfamily)

[KOG0127] 246 [RNA processing and modification] Nucleolar protein fibrillarin NOP77 (RRM superfamily)

[KOG0105] 292 [RNA processing and modification] Alternative splicing factor ASF/SF2 (RRM superfamily)

[KOG0146] 297 [RNA processing and modification] RNA-binding protein ETR-3 (RRM superfamily)

[KOG4212] 328 [RNA processing and modification] RNA-binding protein hnRNP-M

[KOG0108] 359 [RNA processing and modification] mRNA cleavage and polyadenylation factor I complex, subunit RNA15

[KOG0144] 435 [RNA processing and modification] RNA-binding protein CUGBP1/BRUNO (RRM superfamily)

[KOG0117] 515 [RNA processing and modification] Heterogeneous nuclear ribonucleoprotein R (RRM superfamily)

[KOG0148] 534 [RNA processing and modification, Translation, ribosomal structure and biogenesis] Apoptosis-promoting RNA-binding protein TIA-1/TIAR (RRM superfamily)

[KOG0145] 972 [RNA processing and modification] RNA-binding protein ELAV/HU (RRM superfamily)

[KOG0123] 1303 [RNA processing and modification, Translation, ribosomal structure and biogenesis] Polyadenylate-binding protein (RRM superfamily)

[KOG4205] 1554 [RNA processing and modification] RNA-binding protein musashi/mRNA cleavage and polyadenylation factor I complex, subunit HRP1

identifier count process description

Fig. S4

69

61

60

59

66

54

57

50

75

62

70

75

81

Plasmodium falciparum 3D7@XP 001352039[RRM1][KOG0144]Cryptosporidium parvum_Iowa_II@XP_628599[RRM1][KOG4205]Viridiplantae@29631_m001006[3][RRM1:100%*][put-sr:33%][KOG0108:67%][.KOG2253:33%]Euteleostomi@ENSGACP00000016390[7][RRM1:100%*][put-sr:86%*][RBM:14%][KOG2253:100%*]

Thalassiosira pseudonana@jgi_Thaps3_20887[RRM1]Phaeodactylum tricornutum@jgi_Phatr2_44468[RRM1]

Coelomata@XP_001182806[39][RRM1:100%***][KOG0108:13%*][.KOG0116:8%*][.KOG0921:5%]Sordariomycetes@XP_956776[2][RRM1:100%][put-sr:50%]

Trypanosomatidae@XP_827554[2][RRM1:50%][.RRM2:50%][put-sr:50%]Ashbya gossypii_ATCC_10895@NP_983970[RRM1]

Yarrowia lipolytica@XP_504609[RRM1]Pichia stipitis_CBS_6054@XP_001384729[RRM1]

Dictyostelium discoideum_AX4@XP_643642[RRM2][KOG0148]Thalassiosira pseudonana@jgi_Thaps3_24369[RRM1]

Phytophthora@jgi_Phyra1_1_76845[2][RRM1:100%][KOG0123:100%]Phaeodactylum tricornutum@jgi_Phatr2_44442[RRM1][KOG4211]

Ciona@ENSCSAVP00000001842[2][RRM1:100%]Euteleostomi@ENSSARP00000000775[28][RRM1:100%***][eIF4B:54%**]

Drosophila melanogaster@CG10837-PA[3][RRM1:100%*]Anopheles gambiae@AGAP000525-PA[RRM1]

Coelomata@ENSDARP00000093407[32][RRM2:88%***][.RRM1:12%*][KOG0108:12%*][.KOG3001:6%][.KOG0123:6%][.KOG0126:6%]Phaeodactylum tricornutum@jgi_Phatr2_46145[RRM2]

Apis mellifera@XP_394565[RRM2][KOG0147]Ascomycota@XP_505055[6][RRM1:83%*][.RRM2:17%]

Dictyostelium discoideum_AX4@XP_635997[RRM2]Caenorhabditis elegans@F11A10_7[RRM2][KOG0131]

Magnoliophyta@30054_m000807[2][RRM2:100%][KOG1267:50%]Ostreococcus@jgi_Ostta4_30189[2][RRM1:50%][.RRM2:50%][put-sr:50%]

Volvox carteri@jgi_Volca1_118759[RRM2]Dictyostelium discoideum_AX4@XP_642758[RRM1]

Aureococcus anophagefferens@jgi_Auran1_17171[RRM1][KOG0108]Phytophthora@jgi_Phyra1_1_83430[2][RRM1:100%]

Ostreococcus@jgi_Ost9901_3_31221[2][RRM1:100%][KOG0128:100%]Magnoliophyta@29609_m000574[4][RRM1:100%*][KOG0128:100%*]

Physcomitrella patens@jgi_Phypa1_1_135986[RRM1][KOG0128]Schizosaccharomyces pombe_972h-@NP_595728[RRM1]

Ustilago maydis_521@XP_762237[RRM1]Aspergillus fumigatus_Af293@XP_755976[RRM1]

Apocrita@XP_001602363[2][RRM1:100%][KOG1832:50%]Schizosaccharomyces pombe_972h-@NP_596033[RRM1]Phytophthora@jgi_Physo1_1_136292[2][RRM1:100%]

Phaeodactylum tricornutum@jgi_Phatr2_32836[RRM1]Cryptococcus neoformans_var._neoformans_JEC21@XP_570477[RRM1]Sordariomycetes@XP_389032[2][RRM1:100%]

Neurospora crassa_OR74A@XP_964518[RRM1]Takifugu rubripes@SINFRUP00000134535[RRM1][KOG0123]

Kluyveromyces lactis@XP_451368[RRM3][KOG0123]Ashbya gossypii_ATCC_10895@NP_984845[RRM3][KOG0123]

Saccharomyces cerevisiae@YFR023W[RRM3][KOG0123]Saccharomyces cerevisiae@YHR015W[RRM3][KOG0123]

Candida glabrata_CBS138@XP_447635[RRM3][KOG0123]Arabidopsis thaliana@NP_175125[7][RRM1:43%*][.RRM2:29%][.RRM4:14%][.RRM3:14%][PABP:29%][KOG0123:100%*]

Dictyostelium discoideum_AX4@XP_646584[RRM1][KOG0127]Chlamydomonadales@jgi_Chlre3_186870[2][RRM1:100%][KOG0127:100%]

Magnoliophyta@NP_565513[6][RRM1:100%*][KOG0127:100%*]Physcomitrella patens@jgi_Phypa1_1_201182[RRM1][KOG0127]

Tetraodontidae@GSTENP00014994001[2][RRM1:50%][.RRM3:50%][KOG0123:50%]Euteleostomi@GSTENP00022906001[41][RRM3:83%***][.RRM2:10%*][.RRM1:7%*][nucleolin:54%***][KOG0123:93%***]

Euteleostomi@ENSMODP00000021210[32][RRM2:97%***][nucleolin:59%**][KOG0123:100%***]Ciona@ENSCINP00000008105[4][RRM1:100%*][KOG0116:50%][.KOG2141:25%]Dictyostelium discoideum_AX4@XP_638463[RRM1][KOG0110]

Caenorhabditis elegans@T23F6_4_1[2][RRM1:100%][KOG0110:100%]Euteleostomi@GSTENP00029551001[21][RRM1:100%***][put-sr:10%][KOG0110:100%***]

Saccharomycetaceae@XP_001386803[2][RRM1:100%][KOG0110:100%]Ustilago maydis_521@XP_758493[RRM1][KOG0110]

Cyanidioschyzon merolae@gnl_CMER_CMO246C[RRM1][KOG0110]Viridiplantae@jgi_Phypa1_1_207810[3][RRM1:100%*][KOG0110:100%*]

Arabidopsis thaliana@NP_196191[RRM1][KOG0110]Drosophila melanogaster@CG3335-PA[RRM1][KOG0110]Apocrita@XP_624611[2][RRM1:100%][KOG0110:100%]

Culicidae@AGAP005249-PA[2][RRM1:100%][KOG0110:100%]Schizosaccharomyces pombe_972h-@NP_595599[RRM1][KOG0110]

Deuterostomia@ENSMODP00000011218[78][RRM1:100%****][G3BP:82%****][KOG0116:100%****]Ciona@ENSCINP00000009845[4][RRM1:100%*][KOG0116:100%*]

Tribolium castaneum@XP_975463[RRM1][KOG0116]Apis mellifera@XP_623996[RRM1][KOG0116]

Leptospira@YP_001385[4][RRM1:100%*][PROK:100%*]Coelomata@ENSXETP00000008271[74][RRM1:100%****][LARK:61%***][KOG0109:97%****]

Dictyostelium discoideum_AX4@XP_638767[RRM1][KOG0123]Ciona intestinalis@ENSCINP00000017840[RRM1][KOG0109]

Gammaproteobacteria@YP_113294[2][RRM1:100%][PROK:100%]Euteleostomi@ENSDNOP00000012760[63][RRM2:94%****][.RRM1:6%*][LARK:65%***][.RBM:21%**][KOG0109:97%****]

Ciona intestinalis@ENSCINP00000017840[RRM2][KOG0109]Endopterygota@CG8597-PE[8][RRM2:100%**][LARK:62%*][KOG0109:100%**]

Danio rerio@ENSDARP00000065401[RRM2][KOG0109]Ciona savignyi@ENSCSAVP00000008315[4][RRM1:100%*][KOG0108:100%*]

Theileria parva_strain_Muguga@XP_765374[RRM1]Cryptosporidium parvum_Iowa_II@XP_001388131[RRM1][KOG1015]

Dictyostelium discoideum_AX4@XP_643642[RRM1][KOG0148]Saccharomycetales@YHL034C[2][RRM1:100%]

Pichia stipitis_CBS_6054@XP_001387063[RRM1]Schizosaccharomyces pombe_972h-@NP_593427[RRM1][KOG0123]

Kluyveromyces lactis@XP_454447[RRM3][KOG0128]Embryophyta@28180_m000395[3][RRM1:100%*][KOG0124:100%*]

Arabidopsis thaliana@NP_191094[RRM1][KOG4205]Theileria parva_strain_Muguga@XP_765374[RRM2]

Yarrowia lipolytica@XP_504884[RRM3][KOG0123]Aedes aegypti@AAEL010807-PA[RRM1][put-sr][KOG1080]

Euteleostomi@ENSORLP00000016244[7][RRM1:100%*][KOG1080:57%*]Saccharomyces cerevisiae@YOR319W[RRM2][KOG0131]

51 - LARK

part of 35 - G3BP

RBM

30K RRM

hnRNP

Musashi

Dazap

TARDBP

OligoU

1

74

87 - eIF-4B

Fig. S5

70

59

67 52

63

99

100

55

65

83

64

64

62

60

59

57

65

94

98 70

82

54

68

63

75

61

Ostreococcus lucimarinus@jgi Ost9901 3 8794[RRM1][KOG0105]Plasmodium falciparum_3D7@XP_001351730[RRM1][put-sr][KOG0105]Phytophthora@jgi_Physo1_1_140403[2][RRM1:100%][put-sr:100%][KOG0127:100%]

Cyanidioschyzon merolae@gnl_CMER_CMO009C[RRM2]Yarrowia lipolytica@XP_500797[RRM1][put-sr]

Ustilago maydis_521@XP_758616[RRM1]Schizosaccharomyces pombe_972h-@NP_596398[RRM1][put-sr][SR]

Cryptosporidium parvum_Iowa_II@XP_627232[RRM1][put-sr][KOG0105]Eukaryota@ENSTBEP00000007356[92][RRM1:100%****][put-sr:82%****][SR:65%****][KOG0105:100%****]

Phytophthora@jgi_Physo1_1_138982[2][RRM1:100%][KOG0105:100%]Theileria parva_strain_Muguga@XP_766386[RRM1][put-sr][KOG0105]

Ciona intestinalis@ENSCINP00000016525[RRM1][put-sr][KOG0106]Cavia porcellus@ENSCPOP00000010577[RRM1][put-sr][SR][KOG0106]

Eukaryota@ENSOANP00000021053[127][RRM1:100%****][put-sr:91%****][SR:61%****][KOG0106:55%****][.KOG0105:37%***]Aedes aegypti@AAEL012621-PA[RRM1][put-sr][KOG0105]

Caenorhabditis elegans@T28D9_2a[3][RRM1:100%*][put-sr:100%*][SR:100%*][KOG0106:100%*]Strongylocentrotus purpuratus@XP_001185906[2][RRM1:100%][KOG0107:100%]

Dictyostelium discoideum_AX4@XP_001134500[RRM1][put-sr][KOG0147]Cryptococcus neoformans_var._neoformans_JEC21@XP_567562[RRM1][KOG0106]

Schizosaccharomyces pombe_972h-@NP_594570[RRM1][put-sr][KOG0106]Neurospora crassa_OR74A@XP_960334[RRM1][put-sr][KOG0105]

Phytophthora@jgi_Physo1_1_129427[2][RRM2:100%][KOG0110:100%]Caenorhabditis elegans@T23F6_4_1[2][RRM3:100%][KOG0110:100%]

Ustilago maydis_521@XP_758493[RRM2][KOG0110]Aureococcus anophagefferens@jgi_Auran1_1296[RRM1][KOG0110]

Neurospora crassa_OR74A@XP_965014[RRM2][KOG0110]Phaeodactylum tricornutum@jgi_Phatr2_20740[RRM2][KOG0110]

Cryptococcus neoformans_var._neoformans_JEC21@XP_569873[RRM2][KOG0110]Saccharomycetales@NP_984131[7][RRM2:100%*][KOG0110:100%*]

Aspergillus fumigatus_Af293@XP_750233[RRM2][KOG0110]Schizosaccharomyces pombe_972h-@NP_595599[RRM2][KOG0110]

Strongylocentrotus purpuratus@XP_783689[2][RRM2:100%][KOG0127:100%]Oryza sativa_japonica_cultivar-group@NP_001053839[RRM1][KOG0110]

Phytophthora sojae@jgi_Physo1_1_132702[RRM4][KOG0127]Phytophthora ramorum@jgi_Phyra1_1_79608[2][RRM4:100%][KOG0127:100%]

Chlamydomonas reinhardtii@jgi_Chlre3_181993[RRM1]Geobacter uraniumreducens_Rf4@YP_001230384[RRM1][PROK][KOG0108]

Bacillariophyta@jgi_Phatr2_8451[2][RRM1:100%][KOG0108:100%]Oryza sativa_japonica_cultivar-group@NP_001058465[RRM1][KOG0108]

Aureococcus anophagefferens@jgi_Auran1_23269[RRM1][KOG0108]Saccharomycetaceae@XP_001383390[2][RRM1:100%][KOG0108:100%]

Cryptococcus neoformans_var._neoformans_JEC21@XP_572946[RRM1][KOG0108]Neurospora crassa_OR74A@XP_965346[RRM2][KOG0110]

Aspergillus fumigatus_Af293@XP_747328[RRM2][KOG0110]Yarrowia lipolytica@XP_505184[RRM1]Phaeodactylum tricornutum@jgi_Phatr2_44395[RRM1]

Yarrowia lipolytica@XP_499736[RRM2][KOG4205]Schizosaccharomyces pombe_972h-@NP_594970[RRM2][KOG4210]

Saccharomycetales@NP_982813[6][RRM2:100%*][KOG4210:100%*]Aspergillus fumigatus_Af293@XP_755020[RRM2]

Saccharomycetales@XP_001385462[7][RRM3:100%*][KOG0127:100%*]Basidiomycota@XP_756663[3][RRM4:67%][.RRM3:33%][KOG0127:100%*]

Schizosaccharomyces pombe_972h-@NP_596114[RRM3][KOG0127]Sordariomycetes@XP_962933[2][RRM3:100%][KOG0127:100%]

Aspergillus fumigatus_Af293@XP_752199[RRM3][KOG0127]Phaeodactylum tricornutum@jgi_Phatr2_8457[RRM1][KOG0122]

Physcomitrella patens@jgi_Phypa1_1_201182[RRM3][KOG0127]Physcomitrella patens@jgi_Phypa1_1_204078[RRM1][KOG0116]

Magnoliophyta@NP_001052571[5][RRM1:100%*][KOG0116:100%*]Arabidopsis thaliana@NP_189151[RRM1][NTF][KOG0116]

Saccharomycetales@NP_986417[7][RRM1:100%*][KOG0127:100%*]Phytophthora@jgi_Physo1_1_132702[3][RRM1:100%*][KOG0127:100%*]

Ostreococcus@jgi_Ostta4_19569[2][RRM3:100%][KOG0127:100%]Chlamydomonadales@jgi_Volca1_87629[2][RRM3:100%][KOG0127:100%]

Magnoliophyta@30131_m007093[6][RRM3:83%*][.RRM2:17%][KOG0127:100%*]Dictyostelium discoideum_AX4@XP_646584[RRM3][KOG0127]

Ostreococcus tauri@jgi_Ostta4_19569[RRM1][KOG0127]Ostreococcus lucimarinus@jgi_Ost9901_3_26255[RRM1][KOG0127]

Embryophyta@NP_001062111[8][RRM1:100%**][put-sr:62%*][KOG4849:38%*][.KOG4246:12%][.KOG0113:12%][.KOG4676:12%]Ostreococcus lucimarinus@jgi_Ost9901_3_26750[RRM1]

Aureococcus anophagefferens@jgi_Auran1_67810[RRM1][put-sr][KOG0120]Aureococcus anophagefferens@jgi_Auran1_60739[RRM1][put-sr][KOG1860]

Cryptosporidium parvum_Iowa_II@XP_627975[RRM1][KOG0108]Theileria parva_strain_Muguga@XP_766096[RRM1]Plasmodium falciparum_3D7@XP_001352196[RRM1][KOG0108]

Culicidae@AAEL001997-PA[2][RRM1:100%]Drosophila melanogaster@CG3594-PA[RRM1][KOG0110]

Saccharomycetaceae@XP_001385249[2][RRM1:100%][KOG0113:100%]Saccharomycetales@NP_984033[3][RRM1:100%*][KOG0113:100%*]Kluyveromyces lactis@XP_452557[RRM1][KOG0113]

Yarrowia lipolytica@XP_503802[RRM1][KOG0113]Euteleostomi@ENSGALP00000013474[20][RRM5:85%**][.RRM4:5%][.RRM3:5%][.RRM2:5%][put-sr:10%][KOG0110:100%**]

Culicidae@AAEL004075-PA[3][RRM5:67%][.RRM1:33%][KOG0110:100%*]Ostreococcus@jgi_Ost9901_3_710[2][RRM4:100%][KOG0110:100%]Magnoliophyta@NP_193696[2][RRM3:100%][KOG0110:100%]

Apocrita@XP_001605134[2][RRM5:100%][KOG0110:100%]Phytophthora sojae@jgi_Physo1_1_129427[RRM4][KOG0110]Cryptococcus neoformans_var._neoformans_JEC21@XP_569873[RRM4][KOG0110]

Thalassiosira pseudonana@jgi_Thaps3_268689[RRM4][KOG0110]Phaeodactylum tricornutum@jgi_Phatr2_20740[RRM4][KOG0110]

Ascomycota@XP_001386803[10][RRM4:90%**][.RRM2:10%][KOG0110:100%**]Cryptosporidium parvum_Iowa_II@XP_627799[RRM4][KOG0110]

Deuterostomia@XP_001178221[30][RRM1:100%***][put-sr:63%**][snRNP:70%***][KOG0113:100%***]Ciona@ENSCSAVP00000001345[2][RRM1:100%][KOG0113:100%]

Embryophyta@29657_m000467[4][RRM1:100%*][put-sr:50%][snRNP:25%][KOG0113:100%*]Tribolium castaneum@XP_966565[RRM1][KOG0113]

Cryptosporidium parvum_Iowa_II@XP_627471[RRM1][KOG0113]Phytophthora@jgi_Phyra1_1_44765[2][RRM1:100%][put-sr:50%][KOG0113:100%]

Coelomata@AAEL011340-PB[2][RRM1:100%][put-sr:50%][KOG0113:100%]Rattus norvegicus@ENSRNOP00000048879[RRM1][snRNP][KOG0113]

Felis catus@ENSFCAP00000006212[RRM1][put-sr][KOG0113]Ostreococcus@jgi_Ostta4_11066[2][RRM1:100%][KOG0113:100%]Eukaryota@jgi_Physo1_1_143842[43][RRM1:100%***][put-sr:47%**][snRNP:14%*][KOG0113:100%***]

Aureococcus anophagefferens@jgi_Auran1_34517[2][RRM1:100%][put-sr:50%][KOG0113:100%]Schizosaccharomyces pombe_972h-@NP_593779[RRM1][KOG0113]Sordariomycetes@XP_959061[2][RRM1:100%][KOG0113:100%]

Aspergillus fumigatus_Af293@XP_753306[RRM1][KOG0113]Trypanosomatidae@XP_001463723[2][RRM1:100%][KOG0110:100%]

Drosophila melanogaster@CG2050-PA[RRM2]Theileria parva_strain_Muguga@XP_765501[RRM1][KOG0127]

Percomorpha@ENSGACP00000011877[6][RRM1:100%*][KOG0123:100%*]Gallus gallus@ENSGALP00000012472[2][RRM1:100%][KOG0123:100%]


Encephalitozoon cuniculi_GB-M1@NP_597583[RRM1][KOG4205]Cryptosporidium parvum_Iowa_II@XP_001388131[RRM2][KOG1015]

Schizosaccharomyces pombe_972h-@NP_596518[RRM1][KOG0116]Dictyostelium discoideum_AX4@XP_638767[RRM2][KOG0123]

Aedes aegypti@AAEL012119-PA[RRM1]Plasmodium falciparum_3D7@XP_001352039[RRM1][KOG0144]

36 - snRNP

59

16 - dual-RRM

SR proteins

Fungal SR (SpSrp1)

Fungal SR (SpSrp2)

Fig. S5

71

100

99

79

84

51

57

79

85

62

62

53

63

58

99

98

50

60

89

96

65

76

Phytophthora ramorum@jgi Phyra1 1 73884[RRM1][KOG4205]Bilateria@ENSRNOP00000022054[326][RRM1:100%*****][hnRNP:54%*****][KOG4205:100%*****]

Cryptosporidium parvum_Iowa_II@XP_628599[RRM2][KOG4205]Plasmodium falciparum_3D7@XP_001352039[RRM2][KOG0144]

Cryptosporidium parvum_Iowa_II@XP_626158[RRM2][KOG0144]Ciona intestinalis@ENSCINP00000029053[RRM1][KOG4205]

Ciona intestinalis@ENSCINP00000006182[RRM1][KOG4205]Strongylocentrotus purpuratus@XP_001176409[2][RRM1:100%][KOG4205:100%]

Strongylocentrotus purpuratus@XP_001189292[2][RRM1:100%][KOG4205:100%]Aureococcus anophagefferens@jgi_Auran1_6078[RRM1][KOG4205]

Coelomata@SINFRUP00000146060[58][RRM1:100%****][TARDBP:72%***][KOG4205:98%****]Strongylocentrotus purpuratus@XP_789716[2][RRM1:100%][KOG4205:100%]

Oryctolagus cuniculus@ENSOCUP00000001170[RRM1][hnRNP][KOG4205]Myotis lucifugus@ENSMLUP00000003070[RRM1][hnRNP][KOG4205]

Chlamydomonadales@jgi_Volca1_107445[2][RRM1:100%][KOG4205:100%]Cyanidioschyzon merolae@gnl_CMER_CMR392C[RRM1][KOG4205]Ciona@ENSCINP00000012771[9][RRM1:100%**][put-sr:11%][KOG4205:100%**]

Eukaryota@jgi_Ostta4_3181[66][RRM1:100%****][put-sr:47%***][cyclophilin:32%***][KOG0415:97%****]Debaryomyces hansenii_CBS767@XP_459815[RRM1][KOG0415]

Chlamydomonadales@jgi_Chlre3_181880[2][RRM2:100%][KOG4205:100%]Drosophila melanogaster@CG9654-PA[RRM1][KOG4205]

Cryptosporidium parvum_Iowa_II@XP_001388284[RRM1][KOG4205]Ustilago maydis_521@XP_758567[RRM2][KOG4205]

Thalassiosira pseudonana@jgi_Thaps3_25203[2][RRM1:100%][KOG4205:100%]Phaeodactylum tricornutum@jgi_Phatr2_41450[RRM1][KOG4205]

Strongylocentrotus purpuratus@NP_999784[3][RRM1:100%*][KOG4205:100%*]Embryophyta@jgi_Phypa1_1_112860[6][RRM2:100%*][put-sr:17%][KOG4205:100%*]

Chlamydomonadales@jgi_Chlre3_105806[2][RRM2:100%][KOG4205:100%]Embryophyta@jgi_Phypa1_1_156290[6][RRM1:100%*][put-sr:17%][KOG4205:100%*]

Phaeodactylum tricornutum@jgi_Phatr2_21039[RRM2][KOG4205]Embryophyta@28611_m000102[4][RRM2:100%*][put-sr:75%*][KOG0154:100%*]

Anopheles gambiae@AGAP007689-PA[RRM1]Aedes aegypti@AAEL010101-PA[RRM1]

Saccharomycetaceae@XP_458658[2][RRM1:100%][KOG0921:100%]Aureococcus anophagefferens@jgi_Auran1_6342[RRM2][KOG0123]

Eukaryota@jgi_Phatr2_8132[54][RRM1:100%***][KOG0114:100%***]Theileria parva_strain_Muguga@XP_766722[RRM1][KOG0144]

Plasmodium falciparum_3D7@XP_001349292[RRM1][KOG0146]Pichia stipitis_CBS_6054@XP_001384763[RRM3][KOG0123]

Apocrita@XP_623710[2][RRM1:100%]Euteleostomi@ENSOANP00000024755[113][RRM1:100%****][hnRNP:36%***][.RALYL:15%**]

Leishmania infantum_JPCM5@XP_001468615[RRM1]Dictyostelium discoideum_AX4@XP_647083[RRM1]

Cryptococcus neoformans_var._neoformans_JEC21@XP_567374[RRM1][KOG0307]Embryophyta@30128_m008555[15][RRM1:100%**][KOG4660:100%**]

Chlamydomonas reinhardtii@jgi_Chlre3_152680[RRM1][KOG4660]Eukaryota@NP_001053839[55][RRM6:42%***][.RRM5:35%**][.RRM4:11%*][.RRM3:9%*][KOG0110:100%****]

Cyanidioschyzon merolae@gnl_CMER_CMO246C[RRM5][KOG0110]Encephalitozoon cuniculi_GB-M1@NP_597181[RRM3][KOG0110]

Plasmodium falciparum_3D7@XP_001350574[RRM3][KOG0110]Cryptosporidium parvum_Iowa_II@XP_627799[RRM5][KOG0110]

Saccharomycetales@YNL016W[6][RRM3:100%*][put-sr:33%][KOG0148:83%*][.KOG0123:17%]Tribolium castaneum@XP_967803[2][RRM1:100%][KOG0117:100%]Eutheria@ENSCPOP00000011171[3][RRM1:100%*][hnRNP:67%][KOG0117:100%*]Bilateria@ENSGALP00000025475[210][RRM1:100%*****][hnRNP:33%****][KOG0117:100%*****]Rattus norvegicus@ENSRNOP00000053644[RRM1][KOG0117]

Aedes aegypti@AAEL015050-PA[2][RRM1:100%][KOG0117:100%]Eutheria@ENSBTAP00000025092[6][RRM1:100%*][KOG0117:100%*]

Gasterosteus aculeatus@ENSGACP00000025947[RRM1][KOG0117]Anopheles gambiae@AGAP002326-PA[RRM1]

Clupeocephala@ENSORLP00000002364[10][RRM2:100%**][KOG0109:100%**]Phaeodactylum tricornutum@jgi_Phatr2_16633[RRM1][KOG0125]

Neurospora crassa_OR74A@XP_958552[RRM3][KOG0128]Phytophthora@jgi_Phyra1_1_75647[2][RRM1:100%]

Ciona@ENSCSAVP00000017501[2][RRM1:50%][.RRM2:50%][KOG0109:50%]Saccharomycetales@XP_446998[3][RRM1:100%*][KOG0122:100%*]Saccharomycetaceae@XP_001388004[2][RRM1:100%][KOG0122:100%]

Yarrowia lipolytica@XP_503515[RRM1][KOG0122]Caenorhabditis elegans@F22B5_2[RRM1][KOG0122]

Cryptococcus neoformans_var._neoformans_JEC21@XP_567824[RRM1][KOG0122]Eukaryota@NP_187747[49][RRM1:100%***][KOG0122:98%***]

Medicago truncatula@IMGA_AC144431_18_2[RRM1][KOG0122]Apicomplexa@XP_001388056[3][RRM1:100%*][KOG0122:100%*]

Cyanidioschyzon merolae@gnl_CMER_CMH159C[RRM1][KOG0122]Eukaryota@NP_001063859[35][RRM1:100%***][ZCRB1:69%***][KOG0108:40%**][.KOG0122:9%*][.KOG0117:6%][.KOG0107:6%]

Phytophthora ramorum@jgi_Phyra1_1_94226[RRM1][put-sr][KOG0941]Drosophila melanogaster@CG5213-PA[RRM2][KOG0145]

Chlamydomonadales@jgi_Volca1_72841[2][RRM3:50%][.RRM2:50%][KOG0144:100%]Chlamydomonadales@jgi_Chlre3_99329[2][RRM1:50%][.RRM2:50%][KOG0144:100%]

Volvox carteri@jgi_Volca1_72841[RRM1][KOG0144]Embryophyta@30076_m004622[9][RRM1:100%**][FCAFPA:22%][KOG0144:100%**]

Medicago truncatula@IMGA_AC155099_2_2[2][RRM1:100%][KOG0144:100%]Arabidopsis thaliana@NP_850472[RRM1][FCAFPA][KOG0144]

Poaceae@11320_m000014_AZM5_6848[3][RRM1:100%*][KOG0144:100%*]Dictyostelium discoideum_AX4@XP_635247[RRM1][KOG0144]

Physcomitrella patens@jgi_Phypa1_1_107590[2][RRM1:100%][KOG0144:100%]Cryptosporidium parvum_Iowa_II@XP_628265[RRM1][KOG0144]Chlamydomonadales@jgi_Volca1_118581[3][RRM2:67%][.RRM4:33%][KOG0144:67%][.KOG1240:33%]

Volvox carteri@jgi_Volca1_88093[RRM4][KOG1240]Thalassiosira pseudonana@jgi_Thaps3_261541[RRM1][KOG0144]

Phaeodactylum tricornutum@jgi_Phatr2_42828[RRM1][KOG0144]Phytophthora@jgi_Phyra1_1_82644[2][RRM1:100%][KOG0144:100%]

Coelomata@XP_782270[24][RRM1:100%***][Bruno:42%**][KOG0144:100%***]Bilateria@ENSXETP00000031370[81][RRM1:100%****][Bruno:42%***][KOG0146:84%****][.KOG0144:16%**]

Cryptosporidium parvum_Iowa_II@XP_001388078[RRM1][put-sr][KOG0144]Theileria parva_strain_Muguga@XP_766017[RRM1][KOG0144]

Plasmodium falciparum_3D7@XP_001350299[RRM1][KOG0144]Trypanosomatidae@XP_827838[2][RRM1:100%][KOG0144:100%]

Trypanosomatidae@XP_845656[2][RRM1:100%][KOG0131:50%]Trypanosomatidae@XP_001468238[3][RRM1:100%*][KOG0144:100%*]

Leishmania infantum_JPCM5@XP_001468236[RRM1]Aconoidasida@XP_766017[2][RRM2:100%][KOG0144:100%]

Plasmodium falciparum_3D7@XP_001348269[RRM2][KOG0144]Cryptosporidium parvum_Iowa_II@XP_001388078[RRM2][put-sr][KOG0144]Embryophyta@jgi_Phypa1_1_115029[9][RRM2:100%**][KOG0144:100%**]

Bilateria@AGAP009477-PA[250][RRM2:73%*****][.RRM1:27%****][Bruno:59%****][KOG0144:56%****][.KOG0146:44%****]Trypanosomatidae@XP_001468777[2][RRM2:100%][KOG0144:100%]

Cryptosporidium parvum_Iowa_II@XP_628265[RRM2][KOG0144]Embryophyta@29889_m003323[11][RRM2:100%**][FCAFPA:18%][KOG0144:100%**]

Arabidopsis thaliana@NP_850472[RRM2][FCAFPA][KOG0144]Phytophthora@jgi_Physo1_1_133760[2][RRM2:100%][KOG0144:100%]

Thalassiosira pseudonana@jgi_Thaps3_261541[RRM2][KOG0144]Dictyostelium discoideum_AX4@XP_646268[RRM2][KOG0146]

Dictyostelium discoideum_AX4@XP_635247[RRM2][KOG0144]Chlamydomonadales@jgi_Volca1_88093[2][RRM1:100%][KOG1240:100%]

Chlamydomonas reinhardtii@jgi_Chlre3_174860[RRM2][KOG1240]Gammaproteobacteria@YP_561253[27][RRM1:100%***][PROK:100%***][KOG0108:96%***]Alkalilimnicola ehrlichei_MLHE-1@YP_741458[RRM1][PROK]Embryophyta@NP_194280[13][RRM1:100%**][put-sr:77%**][SR:62%**][KOG0106:100%**]

Ostreococcus lucimarinus@jgi_Ost9901_3_8794[RRM1][KOG0105]

8 - Bruno

FCA FPA

7 - Bruno

FCA FPA

65

2 - hnRNP

60

45

38 - cyclophilin

86 - hnRNP

RALYL44

42

57 - ZCRB1

g ( p p )

Fig. S5

72

68

72

72

71

59

94

96

94

97

60

60

Pezizomycotina@XP 961985[2][RRM1:100%][KOG0116:50%]Aureococcus anophagefferens@jgi_Auran1_69134[RRM1][put-sr]

Caenorhabditis elegans@C50B8_1[RRM1]Embryophyta@jgi_Phypa1_1_44443[2][RRM2:100%][KOG0149:100%]

Embryophyta@29900_m001607[13][RRM2:100%**][oligoU:38%*][KOG4205:77%**][.KOG0149:23%*]Caenorhabditis elegans@C07A4_1[RRM2][KOG0148]

Coelomata@CG4787-PA[102][RRM3:74%****][.RRM2:16%**][.RRM1:11%**][TIATIAR:75%****][KOG0148:100%****]Caenorhabditis elegans@Y46G5A_13[10][RRM2:80%**][.RRM3:20%][KOG0148:100%**]

Diptera@AGAP003899-PA[15][RRM2:100%**][KOG0145:100%**]Coelomata@XP_974651[54][RRM2:83%***][.RRM1:17%**][put-sr:87%***][RBM:37%**][KOG0112:100%***]

Saccharomyces cerevisiae@YMR302C[RRM1]Nasonia vitripennis@XP_001604488[RRM1]

Ascomycota@YDL224C[8][RRM1:88%*][.RRM2:12%][KOG3598:12%][.KOG1457:12%]Chlamydomonas reinhardtii@jgi_Chlre3_145376[RRM2]Methanomicrobiales@YP_503016[5][RRM1:100%*][PROK:100%*][KOG0108:40%][.KOG0125:20%][.KOG0116:20%]Cryptococcus neoformans_var._neoformans_JEC21@XP_568231[RRM1][put-sr][KOG0147]

Physcomitrella patens@jgi_Phypa1_1_161310[RRM3][KOG3598]Embryophyta@NP_001063403[14][RRM1:100%**][KOG0148:100%**]

Endopterygota@XP_974444[2][RRM1:100%][KOG0144:100%]Clupeocephala@ENSORLP00000016619[5][RRM1:100%*][KOG0131:60%*][.KOG0123:40%]

Phaeodactylum tricornutum@jgi_Phatr2_38474[RRM1]Ustilago maydis_521@XP_760296[RRM1]

Cryptococcus neoformans_var._neoformans_JEC21@XP_572996[RRM1]Ricinus communis@30169_m006629[RRM1][KOG0123]

Euteleostomi@ENSOANP00000013028[22][RRM1:100%***]Endopterygota@XP_967886[3][RRM1:100%*]

Drosophila melanogaster@CG14414-PB[RRM1]Chlamydomonadales@jgi_Volca1_43575[2][RRM3:100%][KOG4205:100%]Embryophyta@NP_001067623[8][RRM1:100%**][KOG0117:100%**]

Dictyostelium discoideum_AX4@XP_640243[RRM1][KOG0117]Eukaryota@AAEL002461-PA[78][RRM1:100%****][put-sr:29%***][KOG0126:100%****]

Saccharomycetaceae@XP_459205[2][RRM1:100%][KOG0126:100%]Ustilago maydis_521@XP_760864[RRM1][KOG0126]

Caenorhabditis elegans@Y73B6BL_6a_3[10][RRM2:100%**][KOG4205:100%**]Ciona@ENSCSAVP00000016637[3][RRM2:100%*][KOG4205:100%*]

Ciona@ENSCINP00000028810[2][RRM2:100%][KOG4205:100%]Euteleostomi@ENSSTOP00000002923[18][RRM1:100%**][KOG4205:11%]

Strongylocentrotus purpuratus@XP_001188704[2][RRM1:100%][KOG0149:100%]Phaeodactylum tricornutum@jgi_Phatr2_49481[RRM1][KOG1337]

Strongylocentrotus purpuratus@XP_789716[2][RRM2:100%][KOG4205:100%]Strongylocentrotus purpuratus@XP_780859[2][RRM2:100%][KOG4205:100%]

Oryza sativa_japonica_cultivar-group@NP_001058805[RRM1][KOG4205]Chlamydomonadales@jgi_Chlre3_105806[2][RRM1:100%][KOG4205:100%]

Aureococcus anophagefferens@jgi_Auran1_9576[RRM1][KOG0149]Ricinus communis@28976_m000161[RRM1][KOG4205]

Ricinus communis@30170_m013671[RRM1][KOG4205]Arabidopsis thaliana@NP_176143[RRM1][KOG4205]

Zea mays@14684_m000016_AZM5_14964[RRM1][KOG4205]Oryza sativa_japonica_cultivar-group@NP_001051402[RRM1][KOG0149]

Phytophthora sojae@jgi_Physo1_1_139371[RRM2][KOG4205]Cyanidioschyzon merolae@gnl_CMER_CMR392C[RRM2][KOG4205]

Ostreococcus tauri@jgi_Ostta4_33731[RRM2]Ostreococcus tauri@jgi_Ostta4_33731[RRM1]

Oryza sativa_japonica_cultivar-group@NP_001064224[RRM1][KOG0117]Magnoliophyta@29709_m001182[6][RRM1:100%*][put-sr:17%][KOG0117:100%*]

Ricinus communis@30072_m000974[RRM1][KOG0117]Physcomitrella patens@jgi_Phypa1_1_140180[3][RRM1:100%*][KOG0117:100%*]

Phytophthora sojae@jgi_Physo1_1_139371[RRM1][KOG4205]Oryza sativa_japonica_cultivar-group@NP_001054022[RRM1][KOG4205]

Magnoliophyta@NP_001042672[10][RRM1:100%**][oligoU:50%*][KOG4205:80%**][.KOG0149:20%]Arabidopsis thaliana@NP_850021[4][RRM1:100%*][oligoU:100%*][KOG0149:75%*][.KOG2186:25%]

Takifugu rubripes@SINFRUP00000163373[RRM1][KOG0149]Takifugu rubripes@SINFRUP00000145256[RRM1][KOG0149]

Arabidopsis thaliana@NP_187353[RRM1][30kRRM][KOG0149]Eukaryota@NP_001058102[93][RRM1:100%****][RBM:52%***][.30kRRM:13%**][KOG0149:96%****]Arabidopsis thaliana@NP_200183[2][RRM1:100%][oligoU:100%][KOG0149:100%]

Dictyostelium discoideum_AX4@XP_629598[RRM2][KOG4205]Dictyostelium discoideum_AX4@XP_643377[RRM1][KOG3598]

Caenorhabditis elegans@F56D1_7[RRM1]Euteleostomi@ENSEEUP00000005436[64][RRM1:95%****]Coelomata@AAEL001684-PA[39][RRM1:100%***][KOG0125:21%**]

Takifugu rubripes@SINFRUP00000155469[RRM1]Tupaia belangeri@ENSTBEP00000015084[RRM1]

Spermophilus tridecemlineatus@ENSSTOP00000003171[RRM1]Strongylocentrotus purpuratus@XP_798256[2][RRM1:100%][KOG2277:100%]

Oryzias latipes@ENSORLP00000005442[2][RRM1:100%][KOG2277:100%]Xenopus tropicalis@ENSXETP00000012439[RRM1][KOG2277]

Oryctolagus cuniculus@ENSOCUP00000014792[RRM1][KOG2277]Ostreococcus lucimarinus@jgi_Ost9901_3_24530[RRM1][KOG4205]Oryza sativa_japonica_cultivar-group@NP_001067093[RRM1][KOG4177]

Strongylocentrotus purpuratus@NP_999784[3][RRM2:100%*][KOG4205:100%*]Endopterygota@AAEL008257-PA[8][RRM2:100%**][KOG4205:100%**]

Cryptococcus neoformans_var._neoformans_JEC21@XP_568675[RRM2][KOG4205]Embryophyta@IMGA_AC144431_42_2[6][RRM3:100%*][put-sr:17%][KOG4205:100%*]

Theileria parva_strain_Muguga@XP_766400[RRM1][put-sr][KOG4205]Plasmodium falciparum_3D7@XP_001351452[RRM2][KOG4205]

Plasmodium falciparum_3D7@XP_001347758[RRM2][KOG0149]Plasmodium falciparum_3D7@XP_001347758[RRM1][KOG0149]

Euteleostomi@ENSDARP00000005968[129][RRM2:95%****][.RRM1:5%*][hnRNP:57%****][KOG4205:100%****]Eukaryota@AGAP006656-PA[121][RRM2:88%****][.RRM1:12%**][Musashi:36%***][.Dazap:21%***][.hnRNP:10%**][KOG4205:100%****]

Ciona@ENSCSAVP00000001921[3][RRM2:100%*][Musashi:67%][KOG4205:100%*]Phytophthora ramorum@jgi_Phyra1_1_73884[RRM2][KOG4205]

Endopterygota@XP_001121454[19][RRM2:100%**][KOG4205:100%**]Strongylocentrotus purpuratus@XP_001176409[2][RRM2:100%][KOG4205:100%]

Viridiplantae@NP_851001[17][RRM2:100%**][put-sr:12%][KOG4205:94%**][.KOG1833:6%]Cryptococcus neoformans_var._neoformans_JEC21@XP_566745[2][RRM1:100%]

Endopterygota@CG16901-PC[19][RRM1:100%**][KOG4205:100%**]Bacillariophyta@jgi_Phatr2_21039[2][RRM1:100%][KOG4205:100%]

Kluyveromyces lactis@XP_453971[RRM1]Strongylocentrotus purpuratus@XP_001183095[2][RRM2:100%][KOG4205:100%]

Caenorhabditis elegans@Y73B6BL_6b_3[10][RRM1:100%**][KOG4205:100%**]Plasmodium falciparum_3D7@XP_001351452[RRM1][KOG4205]

Coelomata@CG6354-PB[373][RRM2:95%*****][hnRNP:53%*****][KOG4205:100%*****]Drosophila melanogaster@CG9654-PA[RRM2][KOG4205]

Caenorhabditis elegans@F42A6_7a_1[8][RRM2:100%**][KOG4205:100%**]Sorex araneus@ENSSARP00000008097[RRM2][hnRNP][KOG4205]

Ciona@ENSCINP00000008394[8][RRM2:100%**][KOG4205:100%**]Ciona intestinalis@ENSCINP00000012771[RRM2][put-sr][KOG4205]

Cryptosporidium parvum_Iowa_II@XP_626025[RRM1][KOG4205]Chlamydomonadales@jgi_Volca1_107445[2][RRM2:100%][KOG4205:100%]

Ascomycota@XP_961230[5][RRM2:100%*][put-sr:20%][KOG4205:100%*]Encephalitozoon cuniculi_GB-M1@NP_597487[RRM1][KOG4205]

Saccharomycetales@XP_449511[7][RRM2:100%*][KOG4205:100%*]Ricinus communis@28976_m000161[RRM2][KOG4205]

Cryptosporidium parvum_Iowa_II@XP_001388284[RRM2][KOG4205]Physcomitrella patens@jgi_Phypa1_1_19696[RRM1][KOG4205]

Cryptosporidium parvum_Iowa_II@XP_626579[RRM2][KOG4205]Cryptosporidium parvum_Iowa_II@XP_626025[RRM2][KOG4205]

Eukaryota@ENSMODP00000031317[289][RRM1:100%*****][hnRNP:28%****][.Musashi:13%***][.Dazap:9%***][KOG4205:99%*****]Phytophthora ramorum@jgi_Phyra1_1_73884[RRM1][KOG4205]

34

35 - G3BP

RBM

30K-RRM

hnRNP

Musashi

Dazap

TARDBP

OligoU

62

62

69

53 - RBM

79 - TIA TIAR

OligoU

Fig. S5

73

53

51

100

99

97

97

Eukaryota@8925 m000027 AZM5 1178[67][RRM1:100%****][put sr:84%****][SR:61%***][KOG4207:61%***][ KOG4368:24%**]Bacillariophyta@jgi_Thaps3_23196[2][RRM1:100%][KOG4207:50%]

Phytophthora sojae@jgi_Physo1_1_138511[RRM1][put-sr]Ostreococcus@jgi_Ostta4_7793[2][RRM1:100%][KOG0108:100%]

Ostreococcus lucimarinus@jgi_Ost9901_3_8174[RRM1][KOG4207]Yarrowia lipolytica@XP_500351[RRM1][KOG0123]Chlamydomonadales@jgi_Volca1_90315[3][RRM2:67%][.RRM3:33%][KOG0123:67%]

Thalassiosira pseudonana@jgi_Thaps3_33709[RRM1][KOG0111]Bacillariophyta@jgi_Thaps3_19374[2][RRM1:100%][KOG0121:100%]

Encephalitozoon cuniculi_GB-M1@NP_597585[RRM1][KOG0121]Theileria parva_strain_Muguga@XP_766484[RRM1][KOG0121]

Cryptosporidium parvum_Iowa_II@XP_627536[RRM1][KOG0121]Trypanosomatidae@XP_001466901[2][RRM1:100%][KOG0121:100%]

Eukaryota@ENSMODP00000034858[66][RRM1:100%****][KOG0121:100%****]Plasmodium falciparum_3D7@XP_001351463[RRM1][KOG0121]

Dictyostelium discoideum_AX4@XP_641373[RRM1][put-sr]Aureococcus anophagefferens@jgi_Auran1_17018[RRM1][KOG0111]Encephalitozoon cuniculi_GB-M1@NP_586226[RRM1][put-sr][KOG0123]

Dictyostelium discoideum_AX4@XP_641568[RRM3][KOG3598]Trypanosomatidae@XP_827855[2][RRM1:100%]

Tribolium castaneum@XP_969873[RRM1]Theileria parva_strain_Muguga@XP_766728[RRM1][KOG0124]

Theileria parva_strain_Muguga@XP_765867[RRM1][KOG0111]Trypanosoma brucei_TREU927@XP_951655[RRM2][put-sr][KOG0109]

Leishmania infantum_JPCM5@XP_001466413[RRM2][put-sr][KOG0147]Trypanosomatidae@XP_847474[2][RRM1:100%]Trypanosomatidae@XP_001467105[2][RRM1:100%][KOG4209:100%]Culicidae@AGAP003171-PA[3][RRM2:100%*][KOG0148:33%]

Drosophila melanogaster@CG12288-PA[RRM2]Candida glabrata_CBS138@XP_446891[RRM3][KOG0128]

Plasmodium falciparum_3D7@XP_001352080[RRM2]Apis mellifera@XP_394565[RRM1][KOG0147]

Coelomata@ENSMUSP00000057332[45][RRM1:100%***][put-sr:100%***][RNPS1:64%***][KOG4209:87%***]Cryptococcus neoformans_var._neoformans_JEC21@XP_569824[RRM1][put-sr]

Sordariomycetes@XP_001522188[3][RRM1:100%*][put-sr:67%]Schizosaccharomyces pombe_972h-@NP_596549[RRM1][put-sr]

Dictyostelium discoideum_AX4@XP_636445[RRM1][put-sr]Viridiplantae@jgi_Phypa1_1_105411[8][RRM1:100%**][put-sr:100%**][SR:25%][KOG0117:12%][.KOG0462:12%]

Caenorhabditis elegans@K02F3_11_2[2][RRM1:100%][put-sr:100%][KOG4209:100%]Schizosaccharomyces pombe_972h-@NP_595090[RRM1]

Physcomitrella patens@jgi_Phypa1_1_120016[RRM2][KOG4205]Aureococcus anophagefferens@jgi_Auran1_17068[RRM1][KOG4207]

Viridiplantae@NP_001046448[23][RRM1:100%***][put-sr:91%***][SR:35%**][KOG4207:13%*][.KOG0127:13%*][.KOG0110:9%]Phytophthora@jgi_Physo1_1_136528[2][RRM1:100%][put-sr:50%][KOG3208:50%]Chordata@ENSETEP00000001114[45][RRM1:100%***][put-sr:96%***][SRrp:82%***][KOG0111:29%**][.KOG0415:13%*]

Chlamydomonadales@jgi_Volca1_121229[2][RRM1:100%][put-sr:100%][KOG0415:50%]Cryptosporidium parvum_Iowa_II@XP_628282[2][RRM1:100%][put-sr:100%][KOG0111:50%][.KOG4207:50%]

Plasmodium falciparum_3D7@XP_001351591[RRM1]Plasmodium falciparum_3D7@XP_001347950[RRM1][KOG4207]

Murinae@ENSMUSP00000078984[3][RRM1:100%*][KOG4207:100%*]Dictyostelium discoideum_AX4@XP_628876[RRM1]

Strongylocentrotus purpuratus@XP_001178467[2][RRM1:100%][put-sr:100%]Strongylocentrotus purpuratus@XP_001180596[2][RRM1:100%][put-sr:100%]Eukaryota@ENSGALP00000022397[157][RRM1:100%*****][put-sr:75%****][SR:59%****][KOG0107:66%****]Endopterygota@CG5655-PA[5][RRM1:100%*][put-sr:100%*][KOG0107:80%*][.KOG0921:20%]

Bilateria@ENSLAFP00000012959[197][RRM3:93%*****][.RRM2:5%**][hnRNP:36%****][KOG0117:100%*****]Dictyostelium discoideum_AX4@XP_646584[RRM2][KOG0127]

Embryophyta@jgi_Phypa1_1_201182[6][RRM2:100%*][KOG0127:100%*]Chlamydomonas reinhardtii@jgi_Chlre3_186870[RRM2][KOG0127]

Ostreococcus@jgi_Ost9901_3_26255[2][RRM2:100%][KOG0127:100%]Drosophila melanogaster@CG4806-PA[RRM1][KOG0127]Aedes aegypti@AAEL008572-PA[RRM1][KOG0127]

Chordata@ENSOGAP00000005376[31][RRM2:90%***][.RRM3:6%][RBM:39%**][KOG0127:100%***]Embryophyta@IMGA_AC141435_12_2[17][RRM2:76%**][.RRM1:24%*][KOG4660:100%**]

Drosophila melanogaster@CG2050-PA[RRM3]Schizosaccharomyces pombe_972h-@NP_596114[RRM2][KOG0127]

Saccharomycetales@XP_459044[4][RRM2:100%*][KOG0127:100%*]Pezizomycotina@XP_962933[3][RRM2:100%*][KOG0127:100%*]

Yarrowia lipolytica@XP_499726[RRM2][KOG0127]Ustilago maydis_521@XP_757329[RRM2][KOG0145]

Eukaryota@IMGA_AC144483_30_2[123][RRM2:83%****][.RRM1:17%***][TIATIAR:58%****][.oligoU:6%*][KOG0148:99%****]Strongylocentrotus purpuratus@XP_001183631[2][RRM2:100%][KOG0148:100%]

Ciona intestinalis@ENSCINP00000004384[RRM2][KOG0148]Oryza sativa_japonica_cultivar-group@NP_001062811[RRM1][KOG1190]

Physcomitrella patens@jgi_Phypa1_1_137240[2][RRM1:100%][KOG3598:50%]Ricinus communis@30005_m001243[RRM1]Ricinus communis@29577_m000447[RRM1][KOG0123]

Arabidopsis thaliana@NP_181869[4][RRM1:100%*][FCAFPA:100%*][KOG0117:100%*]Volvox carteri@jgi_Volca1_88720[RRM3]

Chlamydomonas reinhardtii@jgi_Chlre3_148816[RRM2][KOG3598]Oryza sativa_japonica_cultivar-group@NP_001063671[RRM2][KOG0123]rosids@NP_001078046[5][RRM2:100%*][FCAFPA:80%*][KOG0117:80%*][.KOG0123:20%]

Physcomitrella patens@jgi_Phypa1_1_161310[RRM2][KOG3598]Gasterosteus aculeatus@ENSGACP00000006521[RRM1][KOG0548]

Danio rerio@ENSDARP00000075089[2][RRM1:100%][KOG0548:100%]Schizosaccharomyces pombe_972h-@NP_595389[RRM1][KOG4574]

Cryptococcus neoformans_var._neoformans_JEC21@XP_570411[RRM2][KOG4574]Yarrowia lipolytica@XP_500252[RRM1][KOG4574]

Neurospora crassa_OR74A@XP_962915[RRM1][KOG4574]Embryophyta@jgi_Phypa1_1_28366[17][RRM1:100%**][put-sr:76%**][KOG0127:29%*][.KOG0125:12%][.KOG4661:6%][.KOG0147:6%]Phytophthora@jgi_Physo1_1_137237[2][RRM1:100%][put-sr:100%][KOG0125:50%][.KOG0148:50%]

Plasmodium falciparum_3D7@XP_001347313[RRM1][KOG0127]Schizosaccharomyces pombe_972h-@NP_001018280[RRM1][KOG0145]

Chlamydomonas reinhardtii@jgi_Chlre3_152139[RRM1][KOG0117]Cryptococcus neoformans_var._neoformans_JEC21@XP_570425[RRM1][put-sr][KOG0145]

Pezizomycotina@XP_960722[3][RRM1:100%*][put-sr:33%][KOG0113:33%]Yarrowia lipolytica@XP_499712[RRM1][KOG0145]

Basidiomycota@XP_757472[3][RRM1:100%*][put-sr:33%][KOG0122:33%]Dictyostelium discoideum_AX4@XP_642304[RRM1][KOG0415]

Coelomata@AGAP006798-PA[81][RRM1:100%****][put-sr:99%****][KOG0122:26%***][.KOG0125:25%**][.KOG0147:14%**][.KOG0108:9%*]Caenorhabditis elegans@C18D11_4_1[2][RRM1:100%][put-sr:100%][KOG0921:100%]

Aedes aegypti@AAEL004293-PA[RRM1][put-sr]Drosophila melanogaster@CG10128-PC[6][RRM1:100%*][put-sr:100%*]

Eutheria@ENSMLUP00000005283[2][RRM1:100%][put-sr:100%]Spermophilus tridecemlineatus@ENSSTOP00000006011[RRM1][put-sr]

Magnoliophyta@NP_001062073[4][RRM1:100%*][KOG0110:75%*][.KOG0127:25%]Poaceae@8373_m000321_c0161G04[2][RRM1:100%][KOG4205:50%][.KOG4211:50%]

Trypanosoma brucei_TREU927@XP_829716[RRM1]Saccharomycetales@XP_455897[3][RRM1:100%*][KOG0123:67%]

Debaryomyces hansenii_CBS767@XP_460681[RRM3][KOG0128]Aspergillus fumigatus_Af293@XP_750045[RRM1]

Ustilago maydis_521@XP_758439[RRM3][KOG0123]Xenopus tropicalis@ENSXETP00000056096[RRM1][KOG0109]

Mammalia@ENSTBEP00000003150[16][RRM1:100%**][RBM:94%**][KOG0109:100%**]Clupeocephala@ENSGACP00000025151[11][RRM1:100%**][KOG0109:100%**]

Ciona intestinalis@ENSCINP00000023722[RRM1][KOG0109]Culicidae@AAEL001131-PA[2][RRM1:100%][KOG0113:100%]

Zea mays@11279_m000026_AZM5_6772[RRM1][put-sr][KOG0117]Oryza sativa_japonica_cultivar-group@NP_001067112[RRM2][put-sr][KOG0117]

Pezizomycotina@XP_961985[2][RRM1:100%][KOG0116:50%]

71 - RBM

17 - single-RRM

Zn-K SR proteins

43

50 - LARK

63 - hnRNP

23 - SRrp

22 - single-RRM SR proteins

27 - RNPS1

27 - RNPS126 - SR45

25

28

24

22 - single-RRM SR proteins

Fungal SpRnps1

Fig. S5

74

53

58

96

88

52

52

59

56

65

Magnoliophyta@NP 001060859[5][RRM1:100%*][cpRNP:40%][KOG0110:40%][ KOG0148:40%]Leishmania infantum_JPCM5@XP_001466659[RRM1][KOG0145]

Leishmania infantum_JPCM5@XP_001466665[RRM1][KOG0110]Trypanosoma brucei_TREU927@XP_843985[3][RRM1:100%*][put-sr:33%][KOG0110:100%*]

Leishmania infantum_JPCM5@XP_001466666[RRM1][KOG0145]Leishmania infantum_JPCM5@XP_001464836[RRM1][KOG0145]

Leishmania infantum_JPCM5@XP_001464835[2][RRM1:100%][KOG0145:100%]Ostreococcus@jgi_Ost9901_3_27365[2][RRM1:100%][KOG0123:50%]

Desulfuromonadales@NP_952377[4][RRM1:100%*][PROK:100%*][KOG0108:50%][.KOG0145:25%]Pelobacter carbinolicus_DSM_2380@YP_357907[RRM1][PROK][KOG0145]

Magnoliophyta@NP_001058927[3][RRM1:100%*][cpRNP:33%][KOG0131:67%]rosids@30054_m000821[3][RRM1:100%*][cpRNP:33%][KOG0127:100%*]

Oryza sativa_japonica_cultivar-group@NP_001053710[RRM1][KOG0127]Ostreococcus tauri@jgi_Ostta4_10328[RRM1][KOG2476]

Phytophthora sojae@jgi_Physo1_1_139998[RRM1]Aureococcus anophagefferens@jgi_Auran1_71372[2][RRM3:50%][.RRM2:50%][put-sr:100%][KOG1178:100%]

Phytophthora@jgi_Phyra1_1_77488[2][RRM1:100%][KOG4205:100%]Volvox carteri@jgi_Volca1_90315[RRM1]Ostreococcus tauri@jgi_Ostta4_34258[RRM2]

Caenorhabditis elegans@W02D3_11b[2][RRM1:100%][KOG4211:100%]Danio rerio@ENSDARP00000069459[RRM2][KOG4211]

Coelomata@ENSCINP00000003632[126][RRM2:70%****][.RRM1:30%***][hnRNP:37%***][.GRSRBP:15%**][KOG4211:100%****]Physcomitrella patens@jgi_Phypa1_1_162342[RRM3][KOG1365]

Oryzias latipes@ENSORLP00000025180[RRM2][put-sr][KOG4307]Volvox carteri@jgi_Volca1_117772[RRM1][KOG1365]

Plasmodium falciparum_3D7@XP_001347519[RRM1][KOG1365]Caenorhabditis elegans@Y73B6BL_33[RRM1][KOG4211]

Arabidopsis thaliana@NP_188725[RRM2][hnRNP][KOG1365]Thalassiosira pseudonana@jgi_Thaps3_5686[RRM2][KOG4211]

Ciona savignyi@ENSCSAVP00000001587[RRM5][KOG4307]Ustilago maydis_521@XP_761797[RRM1][put-sr][KOG3257]

Schizosaccharomyces pombe_972h-@NP_596114[RRM1][KOG0127]Basidiomycota@XP_568669[3][RRM1:100%*][KOG0127:100%*]

Euteleostomi@ENSOANP00000001262[28][RRM1:100%***][RBM:46%**][KOG0127:100%***]Sordariomycetes@XP_382687[2][RRM1:100%][KOG0127:100%]

Aspergillus fumigatus_Af293@XP_752199[RRM1][KOG0127]Magnoliophyta@10511_m000028_AZM5_5258[15][RRM1:100%**][cpRNP:33%*][KOG0127:53%**][.KOG0131:27%*][.KOG0145:13%][.KOG0108:7%]

Magnoliophyta@NP_001062760[4][RRM1:100%*][KOG0124:50%][.KOG0131:50%]Embryophyta@jgi_Phypa1_1_134646[11][RRM1:100%**][cpRNP:9%][KOG0123:45%*][.KOG0127:36%*][.KOG2029:9%]

Syntrophobacter fumaroxidans_MPOB@YP_844222[RRM1][PROK][KOG0108]Synechococcus@YP_473618[2][RRM1:100%][PROK:100%][KOG0108:100%]

Candida glabrata_CBS138@XP_445637[RRM1]Chordata@ENSETEP00000010530[36][RRM1:50%**][.RRM2:50%**][put-sr:100%***][SRrp:75%***][KOG4676:100%***]

Caenorhabditis elegans@R09B3_3[3][RRM1:100%*][KOG0108:100%*]Caenorhabditis elegans@B0035_12_2[2][RRM2:100%][KOG0128:100%]

Ostreococcus lucimarinus@jgi_Ost9901_3_28918[RRM1]Volvox carteri@jgi_Volca1_103724[RRM1][put-sr][KOG0591]

Arabidopsis thaliana@NP_180012[RRM1]Physcomitrella patens@jgi_Phypa1_1_167236[RRM1][KOG4209]

Magnoliophyta@IMGA_AC160842_25_1[6][RRM1:100%*][KOG3702:83%*][.KOG4209:17%]Ciona@ENSCSAVP00000010162[2][RRM1:100%][KOG4209:100%]Eukaryota@ENSCSAVP00000003369[89][RRM1:100%****][put-sr:17%**][PABP:26%***][KOG4209:100%****]

Dictyostelium discoideum_AX4@XP_642788[RRM1][KOG4209]Caenorhabditis elegans@T08B6_5[RRM1][KOG4209]Caenorhabditis elegans@EEED8_12[2][RRM1:100%][KOG4209:100%]

Strongylocentrotus purpuratus@XP_001180991[4][RRM1:100%*]Cyanidioschyzon merolae@gnl_CMER_CMO334C[RRM2][KOG0126]


Magnoliophyta@29675_m000389[3][RRM2:100%*][KOG0123:67%][.KOG1015:33%]Arabidopsis thaliana@NP_188491[RRM2][nucleolin][KOG4210]

Tribolium castaneum@XP_972538[RRM1][KOG0128]Ciona intestinalis@ENSCINP00000019832[3][RRM1:100%*][KOG0128:100%*]

Culicidae@AAEL011961-PA[3][RRM1:100%*][KOG0128:100%*]Encephalitozoon cuniculi_GB-M1@NP_597167[RRM1][KOG0108]

Apocrita@XP_001602582[2][RRM1:100%][KOG0128:100%]Strongylocentrotus purpuratus@XP_781643[RRM1][KOG0128]

Ostreococcus@jgi_Ostta4_33150[2][RRM2:100%][KOG0108:50%]Euteleostomi@ENSSTOP00000002132[31][RRM1:100%***][SART3:68%***][KOG0128:100%***]

Ciona intestinalis@ENSCINP00000023563[RRM1][KOG0108]Strongylocentrotus purpuratus@XP_001198098[2][RRM1:100%][put-sr:100%][KOG0147:100%]

Ostreococcus@jgi_Ost9901_3_42846[2][RRM1:100%][put-sr:50%][KOG0147:100%]Volvox carteri@jgi_Volca1_84128[2][RRM1:100%][put-sr:50%][KOG0147:100%]


Phytophthora@jgi_Physo1_1_157186[2][RRM1:100%][KOG0147:100%]Dictyostelium discoideum_AX4@XP_638966[RRM1][KOG0147]

Eukaryota@ENSMLUP00000011758[47][RRM1:100%***][put-sr:91%***][UMH:64%***][.CAPER:15%*][KOG0147:100%***]Ascomycota@NP_594422[4][RRM1:100%*][put-sr:100%*][KOG0147:100%*]

Yarrowia lipolytica@XP_504318[RRM1][KOG0147]Eukaryota@ENSDARP00000064611[84][RRM1:100%****][KOG0108:99%****]

Chlamydomonadales@jgi_Volca1_48801[2][RRM1:100%][KOG0120:100%]Schizosaccharomyces pombe_972h-@NP_595396[RRM1][put-sr][KOG0120]Plasmodium falciparum_3D7@XP_001348830[RRM2][put-sr][KOG0120]

Pezizomycotina@XP_387225[3][RRM1:67%][.RRM2:33%][put-sr:100%*][KOG0120:100%*]Yarrowia lipolytica@XP_503754[RRM1][KOG0120]

Eukaryota@jgi_Volca1_82970[75][RRM2:91%****][.RRM1:9%*][put-sr:80%****][snRNP:53%***][KOG0120:100%****]Phaeodactylum tricornutum@jgi_Phatr2_11145[RRM2][KOG0120]

Euteleostomi@ENSXETP00000044031[49][RRM2:76%***][.RRM1:24%**][KOG0145:41%**][.KOG0123:14%*][.KOG0110:14%*]Ciona@ENSCSAVP00000018820[2][RRM2:100%][KOG0145:100%]

Volvox carteri@jgi_Volca1_107013[RRM3][KOG0117]Dictyostelium discoideum_AX4@XP_635793[RRM2][KOG0145]

Tribolium castaneum@XP_969008[RRM2][KOG0331]Plasmodium falciparum_3D7@XP_001352162[RRM1]

Plasmodium falciparum_3D7@XP_001351468[RRM1]Saccharomycetales@XP_462132[6][RRM1:100%*][KOG0533:100%*]

Mammalia@ENSETEP00000003776[19][RRM1:100%**][LA:95%**][KOG4213:100%**]Sordariomycetes@XP_956471[2][RRM1:100%][KOG0533:100%]

Schizosaccharomyces pombe_972h-@NP_595715[RRM1][KOG0533]Ustilago maydis_521@XP_760032[RRM1][KOG0533]

Cryptococcus neoformans_var._neoformans_JEC21@XP_572037[RRM1][KOG0533]Cyanidioschyzon merolae@gnl_CMER_CMH135C[RRM1]

Phytophthora@jgi_Phyra1_1_97175[2][RRM1:100%][put-sr:50%][KOG0533:100%]Euteleostomi@ENSTBEP00000009485[3][RRM1:100%*][PDIP:33%][KOG0533:33%]Endopterygota@CG6961-PA[7][RRM1:100%*][KOG0533:29%]Chlamydomonadales@jgi_Volca1_90392[2][RRM1:100%][KOG0533:100%]

Eukaryota@GSTENP00007343001[69][RRM1:100%****][FCAFPA:10%*][KOG0533:99%****]Ostreococcus tauri@jgi_Ostta4_36431[RRM1][KOG0533]

Dictyostelium discoideum_AX4@XP_638266[RRM1][KOG0533]Pezizomycotina@XP_958422[3][RRM1:100%*][put-sr:33%][KOG0533:100%*]

Yarrowia lipolytica@XP_505140[RRM1][KOG0533]Ustilago maydis_521@XP_757147[RRM1][KOG0533]

Theileria parva_strain_Muguga@XP_764636[RRM1]Plasmodium falciparum_3D7@XP_966143[RRM1][KOG0533]

Cryptosporidium parvum_Iowa_II@XP_626158[RRM1][KOG0144]Chlamydomonadales@jgi_Volca1_120471[2][RRM1:100%][KOG0108:100%]

Ornithorhynchus anatinus@ENSOANP00000022523[3][RRM1:67%][.RRM2:33%][KOG2248:100%*]Chlamydomonadales@jgi_Volca1_107765[2][RRM1:100%][KOG0145:100%]Cyanidioschyzon merolae@gnl_CMER_CML202C[RRM1][put-sr]

Eukaryota@8925_m000027_AZM5_1178[67][RRM1:100%****][put-sr:84%****][SR:61%***][KOG4207:61%***][.KOG4368:24%**]

84 - La

s g e S p ote s

30 - hnRNP

PDIP

FCA FPA

64 - snRNP

75 - CAPER

UMH

73 - SART3

83 - PABP

85 - SRrp

70 - RBM

80 - hnRNP

Fig. S5

75

64

56

96

97

Aureococcus anophagefferens@jgi Auran1 9434[RRM1]Chlamydomonadales@jgi_Chlre3_184151[2][RRM1:100%][KOG0921:50%][.KOG0116:50%]

Coxiella_burnetii@YP_001424629[2][RRM1:100%][PROK:100%][KOG0108:100%]Aspergillus fumigatus_Af293@XP_747328[RRM1][KOG0110]

Ostreococcus lucimarinus@jgi_Ost9901_3_34965[RRM1][KOG4212]Physcomitrella patens@jgi_Phypa1_1_96043[RRM1]

Volvox carteri@jgi_Volca1_103054[RRM2][KOG0055]Trypanosoma brucei_TREU927@XP_823301[RRM1][KOG0921]

Cryptosporidium parvum_Iowa_II@XP_628165[RRM2][KOG4212]Eukaryota@jgi_Volca1_109965[18][RRM1:78%**][.RRM2:22%*][put-sr:22%*][KOG4212:61%**][.KOG0123:39%*]

Ostreococcus lucimarinus@jgi_Ost9901_3_27365[RRM2][KOG0123]Saccharomycetales@XP_446962[5][RRM1:100%*][put-sr:60%*][KOG0127:60%*][.KOG0123:40%]

Saccharomycetaceae@XP_462023[2][RRM1:100%][put-sr:100%][KOG0123:100%]Phytophthora@jgi_Phyra1_1_75500[2][RRM3:100%][KOG0123:100%]


Strongylocentrotus purpuratus@XP_786244[2][RRM3:100%][put-sr:100%][KOG4212:100%]Volvox carteri@jgi_Volca1_109965[RRM2][KOG4212]Chlamydomonadales@jgi_Volca1_78979[2][RRM1:100%][KOG3070:100%]

Phytophthora ramorum@jgi_Phyra1_1_84100[RRM2][KOG0105]Theileria parva_strain_Muguga@XP_766386[RRM2][put-sr][KOG0105]

Plasmodium falciparum_3D7@XP_001347501[RRM2][put-sr][KOG0105]Phytophthora@jgi_Physo1_1_136493[2][RRM2:100%][put-sr:100%][KOG0105:100%]Fungi/Metazoa_group@AGAP004592-PA[123][RRM2:81%****][.RRM1:18%***][put-sr:100%****][SR:60%****][KOG0105:50%****][.KOG0106:46%****]Bilateria@XP_967263[73][RRM2:78%****][.RRM1:22%**][put-sr:79%****][SR:75%****][KOG0105:100%****]

Ostreococcus lucimarinus@jgi_Ost9901_3_34965[RRM2][KOG4212]Saccharomyces cerevisiae@YNL004W[RRM2][KOG0127]

Saccharomycetaceae@XP_453283[2][RRM1:50%][.RRM2:50%][KOG0123:50%][.KOG0127:50%]Candida glabrata_CBS138@XP_446962[RRM2][put-sr][KOG0127]

Saccharomycetales@XP_001386572[3][RRM2:67%][.RRM1:33%][put-sr:67%][KOG0123:67%][.KOG4212:33%]Cryptococcus neoformans_var._neoformans_JEC21@XP_572539[4][RRM2:100%*][KOG4212:100%*]

Basidiomycota@XP_758699[7][RRM1:71%*][.RRM2:29%][put-sr:14%][KOG4212:100%*]Saccharomycetales@XP_445179[2][RRM2:100%][put-sr:100%][KOG0123:100%]Cyanidioschyzon merolae@gnl_CMER_CMM078C[RRM2][KOG4212]

Cryptococcus neoformans_var._neoformans_JEC21@XP_568231[RRM2][put-sr][KOG0147]Pezizomycotina@XP_751108[2][RRM2:100%][put-sr:100%][KOG4212:100%]

Trypanosomatidae@XP_001465100[2][RRM1:100%][KOG4212:100%]Schizosaccharomyces pombe_972h-@NP_594207[RRM2][KOG4212]

Dikarya@XP_568231[5][RRM3:100%*][put-sr:80%*][KOG4212:80%*][.KOG0147:20%]Yarrowia lipolytica@XP_503927[RRM3][put-sr][KOG4212]

Saccharomycetales@XP_888678[3][RRM3:67%][.RRM2:33%][put-sr:67%][KOG0123:67%][.KOG4212:33%]Saccharomycetales@YNL004W[4][RRM3:100%*][put-sr:50%][KOG0123:50%][.KOG0127:50%]

Kluyveromyces lactis@XP_453283[RRM2][KOG0123]Coelomata@ENSMLUP00000006206[100][RRM2:88%****][.RRM1:12%**][put-sr:5%*][hnRNP:28%***][KOG4212:98%****]

Caenorhabditis elegans@C25A1_4_2[2][RRM2:100%][put-sr:100%][KOG4212:100%]Chordata@ENSOGAP00000002890[91][RRM3:80%****][.RRM2:13%**][.RRM1:7%*][hnRNP:37%***][KOG4212:100%****]

Chlamydomonadales@jgi_Chlre3_184854[2][RRM1:100%][KOG0055:50%]Bacillariophyta@jgi_Phatr2_7426[2][RRM1:100%]Endopterygota@CG9373-PA[4][RRM3:100%*][KOG4212:100%*]

Plasmodium falciparum_3D7@XP_001347353[RRM2][KOG4212]Theileria parva_strain_Muguga@XP_766728[RRM2][KOG0124]

Plasmodium falciparum_3D7@XP_001347332[RRM2][put-sr][KOG0105]Eukaryota@XP_391240[27][RRM2:67%**][.RRM1:33%**][cpRNP:19%*][KOG0127:48%**][.KOG0108:22%*][.KOG0131:15%*][.KOG0149:7%][.KOG0145:7%]

Volvox carteri@jgi_Volca1_36996[RRM1][KOG0116]Tribolium castaneum@XP_970765[RRM1][KOG0127]

Dictyostelium discoideum_AX4@XP_643856[3][RRM1:100%*][KOG0149:100%*]Chlamydomonadales@jgi_Volca1_103054[2][RRM3:50%][.RRM2:50%][KOG0055:50%]

Ostreococcus lucimarinus@jgi_Ost9901_3_27365[RRM3][KOG0123]Aureococcus anophagefferens@jgi_Auran1_31715[RRM1][KOG0149]

Embryophyta@jgi_Phypa1_1_217831[15][RRM3:93%**][.RRM1:7%][KOG0117:100%**]Ustilago maydis_521@XP_756401[RRM1]

Oryza sativa_japonica_cultivar-group@NP_001054296[RRM5][KOG0123]Embryophyta@jgi_Phypa1_1_189930[7][RRM1:100%*][KOG0119:86%*][.KOG0307:14%]

Oryza sativa_japonica_cultivar-group@NP_001054296[RRM6][KOG0123]Oryza sativa_japonica_cultivar-group@NP_001054296[RRM2][KOG0123]

Magnoliophyta@NP_189032[4][RRM1:100%*][put-sr:100%*][KOG0670:100%*]Ostreococcus tauri@jgi_Ostta4_24260[RRM1]

Caenorhabditis elegans@ZC404_8_2[2][RRM1:100%][KOG0125:100%]Bilateria@ENSORLP00000014121[125][RRM1:100%****][FOX:75%****][KOG0125:100%****]

Felis catus@ENSFCAP00000007638[RRM1][KOG0125]Saccharomycetales@XP_456900[7][RRM2:100%*][nucleolin:14%][KOG0148:57%*][.KOG0131:29%][.KOG4210:14%]

Pezizomycotina@XP_754840[2][RRM2:100%][KOG0127:50%][.KOG0148:50%]Schizosaccharomyces pombe_972h-@NP_593531[RRM2][nucleolin][KOG0147]

Ustilago maydis_521@XP_762340[RRM2][KOG0148]Cryptococcus neoformans_var._neoformans_JEC21@XP_566835[RRM2][KOG0148]

Ostreococcus lucimarinus@jgi_Ost9901_3_32831[RRM1]Aureococcus anophagefferens@jgi_Auran1_8214[RRM1]Phytophthora@jgi_Physo1_1_136329[2][RRM2:100%][KOG0123:100%]

Aspergillus fumigatus_Af293@XP_754657[RRM1]Eukaryota@jgi_Phypa1_1_37849[169][RRM1:100%*****][put-sr:5%**][GRSRBP:33%****][.hnRNP:18%***][.RBMY:15%***][KOG0108:23%***][.KOG0111:23%***][.KOG0149:18%***][.KOG0117:11%**][.KOG0116:9%**]

Magnoliophyta@NP_001059075[6][RRM1:100%*][put-sr:17%][GRSRBP:50%*][KOG0108:50%*][.KOG0148:33%][.KOG0111:17%]Arabidopsis thaliana@NP_173298[RRM1][GRSRBP][KOG0149]

Magnoliophyta@NP_181287[9][RRM1:100%**][oligoU:22%][KOG0148:56%*][.KOG0127:22%][.KOG0145:11%][.KOG0113:11%]Magnoliophyta@9946_m000021_AZM5_3995[2][RRM1:100%][KOG0111:50%][.KOG0113:50%]

Magnoliophyta@29930_m000611[5][RRM1:100%*][KOG0113:100%*]Ricinus communis@30055_m001598[RRM1][KOG0149]Arabidopsis thaliana@NP_565646[RRM1][KOG0149]

Magnoliophyta@NP_001052753[3][RRM1:100%*][oligoU:33%][KOG0108:33%][.KOG0149:33%][.KOG0127:33%]rosids@29154_m000213[5][RRM1:100%*][oligoU:40%][KOG0122:40%][.KOG0113:20%][.KOG0148:20%]

Medicago truncatula@IMGA_AC122162_7_2[RRM1][KOG0149]Legionella_pneumophila@YP_001249669[3][RRM1:100%*][PROK:100%*][put-sr:100%*][KOG0149:100%*]

eurosids_I@IMGA_CT963106_6_1[2][RRM1:100%][KOG0117:50%]Arabidopsis thaliana@NP_567594[RRM1][KOG0117]

Eukaryota@IMGA_AC183923_6_1[34][RRM3:74%***][.RRM1:15%*][.RRM2:12%*][put-sr:6%][KOG0110:100%***]Thalassiosira pseudonana@jgi_Thaps3_268689[RRM2][KOG0110]

Plasmodium falciparum_3D7@XP_966276[RRM2]Plasmodium falciparum_3D7@XP_001348607[RRM1]

Dikarya@NP_596771[2][RRM1:100%][KOG0108:50%]Aedes aegypti@AAEL006876-PA[RRM1][KOG2193]

Drosophila melanogaster@CG3312-PA[2][RRM1:100%][KOG0128:100%]Encephalitozoon cuniculi_GB-M1@NP_597181[RRM1][KOG0110]

Euteleostomi@ENSOCUP00000014007[29][RRM2:97%***][SART3:69%**][KOG0128:100%***]Ciona intestinalis@ENSCINP00000019833[3][RRM2:100%*][KOG0128:100%*]Apocrita@XP_001602582[2][RRM2:100%][KOG0128:100%]

Tribolium castaneum@XP_972538[RRM2][KOG0128]Culicidae@AAEL011963-PA[3][RRM2:100%*][KOG0128:100%*]

Strongylocentrotus purpuratus@XP_781643[RRM2][KOG0128]Phaeodactylum tricornutum@jgi_Phatr2_8270[RRM1][KOG4207]

Thalassiosira pseudonana@jgi_Thaps3_20266[RRM1][KOG4207]Bacillariophyta@jgi_Thaps3_20223[2][RRM1:100%][KOG0108:100%]

Cryptosporidium parvum_Iowa_II@XP_626081[RRM1][KOG0122]Aureococcus anophagefferens@jgi_Auran1_9375[2][RRM1:100%][KOG0122:100%]

Ostreococcus@jgi_Ost9901_3_12693[2][RRM2:100%][KOG0127:100%]Ostreococcus tauri@jgi_Ostta4_19468[RRM1][KOG0127]

Aureococcus anophagefferens@jgi_Auran1_9018[RRM1]Trypanosomatidae@XP_001465100[2][RRM2:100%][KOG4212:100%]

Dictyostelium discoideum_AX4@XP_629578[RRM1][KOG0122]Endopterygota@CG7903-PA[5][RRM1:100%*][KOG0109:80%*]

Tribolium castaneum@XP_971700[RRM1]Magnoliophyta@NP_001060859[5][RRM1:100%*][cpRNP:40%][KOG0110:40%][.KOG0148:40%]

39

32

3133 - p54nrb

PSP1

PSF

58 - GRSRBP

hnRNP

RBMYpart of 68 - FOX

30 - hnRNP

PDIP

FCA FPA

29 - dual-RRM

SR proteins

part of 63 - hnRNP

Fig. S5

76

82

88

52

66

56

61

67

70

80

73

58

65

52

56

53

63

73

Euteleostomi@ENSGACP00000016696[19][RRM3:79%**][ RRM4:11%][ RRM1:11%][RBM:58%**][KOG0127:100%**]Oryzias latipes@ENSORLP00000012079[RRM3][KOG0127]

Trypanosoma brucei_TREU927@XP_845376[RRM3][KOG0148]Cryptococcus neoformans_var._neoformans_JEC21@XP_569209[RRM2][KOG0144]

Endopterygota@CG10328-PA[9][RRM1:100%**][P54nrb:33%*][KOG0115:100%**]Deuterostomia@ENSDNOP00000008593[94][RRM1:100%****][P54nrb:28%***][.PSP1:21%**][.PSF:18%**][KOG0115:99%****]Caenorhabditis elegans@F25B5_7d[2][RRM1:100%][KOG0115:100%]

Neurospora crassa_OR74A@XP_965346[RRM1][KOG0110]Physcomitrella patens@jgi_Phypa1_1_93324[RRM1]

Apis mellifera@XP_623573[RRM1][KOG0113]Oryza sativa_japonica_cultivar-group@NP_001045556[RRM1][KOG0108]

Coelomata@ENSTBEP00000005385[105][RRM2:86%****][.RRM1:14%**][P54nrb:30%***][.PSP1:24%***][.PSF:21%***][KOG0115:100%****]Volvox carteri@jgi_Volca1_116517[RRM2][KOG1984]Dictyostelium discoideum_AX4@XP_646802[RRM2][KOG0145]

Dictyostelium discoideum_AX4@XP_641568[RRM2][KOG3598]Saccharomycetales@XP_445844[3][RRM2:100%*][KOG0123:33%]

Kluyveromyces lactis@XP_455897[RRM2][KOG0123]Pichia stipitis_CBS_6054@XP_001384462[RRM2]

Debaryomyces hansenii_CBS767@XP_460517[RRM2][KOG0117]Phaeodactylum tricornutum@jgi_Phatr2_49387[RRM1]

Dictyostelium discoideum_AX4@XP_645848[RRM1][put-sr]Dictyostelium discoideum_AX4@XP_638672[RRM1][put-sr][KOG0147]Dictyostelium discoideum_AX4@XP_629950[RRM1][KOG0128]

Dictyostelium discoideum_AX4@XP_643007[RRM1]Dictyostelium discoideum_AX4@XP_638262[RRM1][put-sr][KOG0670]

Eukaryota@ENSFCAP00000006163[84][RRM2:88%****][.RRM1:12%**][put-sr:86%****][UMH:39%***][.CAPER:8%*][KOG0147:100%****]Bilateria@Y47G6A_20a[64][RRM1:100%****][UMH:73%***][KOG0124:100%****]

Ostreococcus tauri@jgi_Ostta4_31925[RRM1][KOG0117]Phytophthora ramorum@jgi_Phyra1_1_81440[2][RRM1:100%][KOG0124:100%]

Neurospora crassa_OR74A@XP_964541[RRM1]Aspergillus fumigatus_Af293@XP_748929[RRM1]

Leishmania infantum_JPCM5@XP_001464648[RRM1][KOG0113]Viridiplantae@jgi_Chlre3_99594[25][RRM1:100%***][KOG0123:8%]

Ostreococcus@jgi_Ost9901_3_7913[3][RRM1:100%*][KOG0131:33%]Trypanosoma brucei_TREU927@XP_829593[RRM1]

Plasmodium falciparum_3D7@XP_966051[RRM1]Encephalitozoon cuniculi_GB-M1@XP_965888[RRM1][KOG4209]

Saccharomyces cerevisiae@YMR268C[RRM1][KOG0128]Pichia stipitis_CBS_6054@XP_001384763[RRM1][KOG0123]

Neurospora crassa_OR74A@XP_958552[RRM1][KOG0128]Neurospora crassa_OR74A@XP_960450[RRM1]

Magnoliophyta@15974_m000013_AZM5_17589[3][RRM2:67%][.RRM1:33%]Plasmodium falciparum_3D7@XP_966051[RRM2]

Cryptosporidium parvum_Iowa_II@XP_627780[RRM2][KOG0131]Eukaryota@jgi_Physo1_1_108557[316][RRM2:91%*****][.RRM1:9%***][PABP:46%****][KOG0123:79%*****][.KOG0131:21%****]

Saccharomycetaceae@XP_001385635[2][RRM2:100%][KOG0131:100%]Yarrowia lipolytica@XP_503979[RRM2][KOG0131]

Physcomitrella patens@jgi_Phypa1_1_176266[RRM1][KOG1924]Dictyostelium discoideum_AX4@XP_001134510[RRM4][KOG0123]

Dictyostelium discoideum_AX4@XP_645848[RRM2][put-sr]Cryptococcus neoformans_var._neoformans_JEC21@XP_566572[RRM1][KOG0111]

Coelomata@ENSORLP00000008206[18][RRM1:100%**][snRNP:83%**][KOG4206:100%**]Sordariomycetes@XP_962704[2][RRM1:100%][put-sr:50%][KOG4206:100%]

Pichia stipitis_CBS_6054@XP_001382592[RRM1][KOG4206]Tetrapoda@ENSXETP00000004736[17][RRM2:59%**][.RRM1:41%*][PTBP:94%**][KOG1190:100%**]


Ciona intestinalis@ENSCINP00000027768[RRM1][KOG0548]Dictyostelium discoideum_AX4@XP_629218[RRM2][KOG0151]

Euteleostomi@ENSMODP00000018834[25][RRM1:100%***][put-sr:64%**][KOG0147:48%**][.KOG0132:12%*]Tribolium castaneum@XP_971953[RRM1]Strongylocentrotus purpuratus@XP_001185731[2][RRM1:100%]

Ciona@ENSCSAVP00000015853[4][RRM2:100%*][KOG0145:100%*]Dictyostelium discoideum_AX4@XP_629639[RRM2][KOG0145]

Plasmodium falciparum_3D7@XP_001348072[RRM1][KOG0144]Schizosaccharomyces pombe_972h-@NP_593427[RRM2][KOG0123]

Schizosaccharomyces pombe_972h-@NP_001018242[RRM3][KOG0123]Saccharomycetaceae@XP_451236[2][RRM1:100%][KOG0144:100%]

Saccharomyces cerevisiae@YGR250C[RRM1][KOG0108]Pichia stipitis_CBS_6054@XP_001386002[RRM2][KOG0148]

Debaryomyces hansenii_CBS767@XP_461354[RRM2][KOG0148]Yarrowia lipolytica@XP_501542[RRM2][KOG0131]

Cryptococcus neoformans_var._neoformans_JEC21@XP_571861[RRM1][KOG0226]Eukaryota@XP_964958[72][RRM1:100%****][KOG0226:100%****]

Nasonia vitripennis@XP_001603091[RRM1][KOG0226]Dictyostelium discoideum_AX4@XP_635179[RRM1][KOG0148]

Aureococcus anophagefferens@jgi_Auran1_28594[RRM2][KOG0148]Endopterygota@AAEL011988-PA[5][RRM2:100%*][KOG0144:80%*][.KOG0145:20%]

Dictyostelium discoideum_AX4@XP_641688[RRM1][KOG0117]Ustilago maydis_521@XP_761797[RRM2][put-sr][KOG3257]

Ciona intestinalis@ENSCINP00000008726[RRM1][put-sr][KOG2193]Thalassiosira pseudonana@jgi_Thaps3_18991[RRM1][KOG0226]

Phaeodactylum tricornutum@jgi_Phatr2_13402[RRM1][KOG0226]Saccharomycetales@XP_455748[4][RRM2:100%*][KOG0148:75%*][.KOG0145:25%]

Eukaryota@ENSMUSP00000030730[72][RRM2:85%****][.RRM1:15%**][oligoU:10%*][KOG0148:58%***][.KOG0123:25%**][.KOG0131:14%**]Saccharomycetales@XP_460477[6][RRM1:67%*][.RRM2:33%][KOG0148:67%*][.KOG3598:17%][.KOG0145:17%]

Ciona@ENSCSAVP00000020066[4][RRM1:50%][.RRM2:50%][KOG0131:50%]cellular_organisms@YP_001113853[137][RRM1:100%****][PROK:99%****][KOG0108:58%****][.KOG0116:14%**][.KOG0921:7%**][.KOG0149:7%**][.KOG0111:6%**]

Magnoliophyta@IMGA_AC119413_25_2[4][RRM2:100%*][cpRNP:25%][KOG0127:100%*]Carboxydothermus hydrogenoformans_Z-2901@YP_359251[RRM1][PROK][KOG0108]

rosids@NP_171616[3][RRM2:100%*][cpRNP:67%][KOG0148:67%][.KOG0110:33%]Oryza sativa_japonica_cultivar-group@NP_001060859[RRM2][KOG0110]

Schizosaccharomyces pombe_972h-@NP_596721[RRM3][KOG0128]Aspergillus fumigatus_Af293@XP_749317[RRM3][KOG0128]

Physcomitrella patens@jgi_Phypa1_1_167900[3][RRM1:100%*][KOG0123:33%][.KOG4210:33%][.KOG1015:33%]Cyanidioschyzon merolae@gnl_CMER_CMT598C[RRM1][KOG0148]

Embryophyta@jgi_Phypa1_1_161416[4][RRM1:100%*][put-sr:75%*][KOG0154:75%*][.KOG0147:25%]Dictyostelium discoideum_AX4@XP_646990[RRM1][put-sr][KOG0147]

Magnoliophyta@NP_001048500[5][RRM2:100%*][cpRNP:20%][KOG0123:100%*]Strongylocentrotus purpuratus@XP_792521[4][RRM1:100%*][put-sr:100%*][KOG0109:100%*]

Diptera@AAEL008317-PA[3][RRM1:100%*][KOG0149:100%*]Diptera@AAEL006645-PA[2][RRM1:100%][KOG0149:100%]

Poaceae@19213_m000022_AZM5_85721[2][RRM1:50%][.RRM2:50%][KOG0127:50%]Ricinus communis@29908_m006094[RRM2][KOG0110]

Arabidopsis thaliana@NP_192643[2][RRM2:100%][KOG0110:100%]Chlamydomonadales@jgi_Volca1_54847[2][RRM1:100%][KOG0108:100%]

Aureococcus anophagefferens@jgi_Auran1_64341[RRM2][KOG0108]stramenopiles@jgi_Auran1_17857[4][RRM1:50%][.RRM2:50%][KOG0108:50%][.KOG4205:50%]

Ostreococcus lucimarinus@jgi_Ost9901_3_92667[RRM1]Ostreococcus tauri@jgi_Ostta4_32569[RRM2]

Phytophthora@jgi_Physo1_1_141766[2][RRM2:100%][KOG0148:100%]Embryophyta@28180_m000395[6][RRM2:100%*][KOG0124:50%*][.KOG4205:33%][.KOG4211:17%]

Magnoliophyta@NP_001053909[5][RRM1:100%*][nucleolin:40%][KOG0123:40%][.KOG4210:40%][.KOG1015:20%]Neurospora crassa_OR74A@XP_963862[RRM1][KOG0127]

Saccharomycetales@XP_456900[6][RRM1:100%*][nucleolin:17%][KOG0148:50%*][.KOG0131:33%][.KOG4210:17%]Schizosaccharomyces pombe_972h-@NP_593531[RRM1][nucleolin][KOG0147]

Aspergillus fumigatus_Af293@XP_754840[RRM1][KOG0148]Basidiomycota@XP_566835[2][RRM1:100%][KOG0148:100%]

Yarrowia lipolytica@XP_505375[RRM1][KOG0148]Aureococcus anophagefferens@jgi_Auran1_9434[RRM1]

88 - prokaryotic RRMs

77 - TIA TIAR

OligoU

40 - snRNP

4 - PABP

p54nrb

PSP1

PSF

67 - UMH

33 - p54nrb

PSP1

PSF

part of 4

- PABP

p54nrb

PSP1

Fig. S5

77

50

52

74

75

70

51

63

59

50

60

69

57

66

83

82

52

76

52 50

70

88

Strongylocentrotus purpuratus@XP 001185821[2][RRM1:100%][KOG0670:100%]Trypanosomatidae@XP_827358[2][RRM2:100%][KOG0123:100%]Eukaryota@ENSETEP00000015606[204][RRM3:85%*****][.RRM2:11%***][PABP:66%****][KOG0123:100%*****]

Echinops telfairi@ENSETEP00000008100[RRM3][PABP][KOG0123]Aureococcus anophagefferens@jgi_Auran1_9354[RRM1]Dikarya@XP_960425[12][RRM3:100%**][PABP:17%][KOG0123:100%**]

Phytophthora@jgi_Physo1_1_108322[2][RRM3:100%][KOG0123:100%]Thalassiosira pseudonana@jgi_Thaps3_13224[RRM3][KOG0123]

Phaeodactylum tricornutum@jgi_Phatr2_23959[RRM3][KOG0123]Yarrowia lipolytica@XP_501289[RRM3][KOG0123]

Embryophyta@jgi_Phypa1_1_140180[4][RRM3:100%*][KOG0117:100%*]Strongylocentrotus purpuratus@XP_793277[2][RRM3:100%][KOG0117:100%]

Embryophyta@NP_188026[13][RRM1:100%**][oligoU:38%*][KOG0148:100%**]rosids@NP_001030849[6][RRM1:100%*][KOG0117:100%*]

Oryza sativa_japonica_cultivar-group@NP_001066102[RRM1][KOG0117]Dictyostelium discoideum_AX4@XP_644288[RRM1][KOG3598]

Aedes aegypti@AAEL010888-PA[RRM2]Phaeodactylum tricornutum@jgi_Phatr2_10122[RRM1][KOG0153]

Arabidopsis thaliana@NP_179762[RRM1][oligoU]Physcomitrella patens@jgi_Phypa1_1_170658[RRM1]Encephalitozoon cuniculi_GB-M1@NP_584552[RRM3][KOG0123]

Encephalitozoon cuniculi_GB-M1@NP_586099[RRM2][KOG0131]Oryza sativa_japonica_cultivar-group@NP_001054954[2][RRM1:100%][KOG0108:100%]

Chlamydomonadales@jgi_Volca1_107658[2][RRM1:100%][KOG4205:50%][.KOG0474:50%]Ciona intestinalis@ENSCINP00000024280[RRM1][KOG0113]

rosids@NP_568388[3][RRM1:100%*][KOG0125:33%][.KOG0148:33%]Physcomitrella patens@jgi_Phypa1_1_151460[4][RRM1:100%*][KOG0108:75%*][.KOG0149:25%]

Ostreococcus lucimarinus@jgi_Ost9901_3_7602[RRM1][KOG0145]Trypanosomatidae@XP_847111[2][RRM1:100%]

Leishmania infantum_JPCM5@XP_001465764[RRM1]Phytophthora@jgi_Phyra1_1_84416[2][RRM1:100%][KOG0148:100%]

Trypanosoma brucei_TREU927@XP_951655[RRM3][put-sr][KOG0109]Physcomitrella patens@jgi_Phypa1_1_12664[RRM1]

rosids@30155_m001644[2][RRM1:100%][KOG0116:50%]Aureococcus anophagefferens@jgi_Auran1_66158[RRM1][put-sr][KOG0149]

Phytophthora@jgi_Phyra1_1_50314[2][RRM3:100%][KOG0148:100%]Aureococcus anophagefferens@jgi_Auran1_28594[RRM3][KOG0148]

Eukaryota@YHR086W[51][RRM3:76%***][.RRM2:20%**][oligoU:10%*][KOG0148:90%***]Schizosaccharomyces pombe_972h-@NP_594243[RRM3][KOG0148]

Trypanosoma brucei_TREU927@XP_844190[RRM1][KOG0144]Dictyostelium discoideum_AX4@XP_645138[RRM1]

Ricinus communis@28452_m000049[RRM1][KOG1457]Medicago truncatula@IMGA_CU012061_4_1[RRM1]

Euteleostomi@ENSDARP00000069729[82][RRM1:100%****][KOG1995:77%****][.KOG0921:16%**][.KOG2044:5%*]Endopterygota@XP_624681[6][RRM1:100%*][put-sr:17%][KOG0921:67%*][.KOG1548:33%]

Strongylocentrotus purpuratus@XP_001196853[2][RRM1:100%][KOG1995:100%]Arabidopsis thaliana@NP_564565[RRM1][put-sr][KOG1995]

Apis mellifera@XP_393878[RRM1][put-sr][KOG2193]Theileria parva_strain_Muguga@XP_766466[RRM3][KOG0123]

Plasmodium falciparum_3D7@XP_001350640[RRM3][KOG0123]Clupeocephala@ENSORLP00000009616[3][RRM1:100%*][KOG0548:100%*]

Strongylocentrotus purpuratus@XP_001188888[2][RRM1:100%][KOG0548:100%]Aedes aegypti@AAEL010890-PA[RRM1][put-sr][KOG0132]

Eutheria@ENSETEP00000000464[10][RRM1:100%**][put-sr:100%**][KOG0132:100%**]Endopterygota@CG4266-PA[5][RRM1:100%*][put-sr:100%*][KOG0132:100%*]

Saccharomyces cerevisiae@YMR268C[RRM2][KOG0128]Debaryomyces hansenii_CBS767@XP_460681[RRM2][KOG0128]

Pezizomycotina@XP_749317[2][RRM2:100%][KOG0128:100%]Schizosaccharomyces pombe_972h-@NP_596721[RRM2][KOG0128]

Phytophthora@jgi_Physo1_1_140019[2][RRM1:100%][KOG0116:100%]Cryptosporidium parvum_Iowa_II@XP_626331[RRM1][KOG0146]

Thalassiosira pseudonana@jgi_Thaps3_2206[RRM1]Encephalitozoon cuniculi_GB-M1@NP_584580[RRM1][KOG0114]

Debaryomyces hansenii_CBS767@XP_458197[RRM1][KOG0114]Ciona@ENSCSAVP00000005375[4][RRM2:75%*][.RRM1:25%][KOG0116:75%*][.KOG2141:25%]

Saccharomycetales@XP_454821[4][RRM1:100%*][KOG3598:50%][.KOG1984:25%]Coelomata@ENSMMUP00000010529[37][RRM3:54%**][.RRM2:41%**][.RRM1:5%][put-sr:92%***][KOG0112:84%***][.KOG3598:8%*]Strongylocentrotus purpuratus@XP_001184502[2][RRM2:100%][put-sr:100%][KOG1144:100%]

Plasmodium falciparum_3D7@XP_001347332[RRM1][put-sr][KOG0105]Saccharomyces cerevisiae@YLL046C[RRM1]


Saccharomycetales@XP_454345[4][RRM1:100%*][KOG0148:75%*][.KOG0123:25%]Bilateria@ENSSARP00000011721[82][RRM1:100%****][TIATIAR:80%****][KOG0148:100%****]

Saccharomycetaceae@XP_001383142[2][RRM1:100%][put-sr:100%][KOG0148:100%]Yarrowia lipolytica@XP_501542[RRM1][KOG0131]Sordariomycetes@XP_385593[2][RRM1:100%][KOG0148:100%]Cryptococcus neoformans_var._neoformans_JEC21@XP_570577[RRM1][KOG0148]

Trypanosoma brucei_TREU927@XP_845742[RRM1][KOG0126]Phytophthora ramorum@jgi_Phyra1_1_77702[RRM1][KOG0154]

Theileria parva_strain_Muguga@XP_766553[RRM1][KOG4208]Cyanidioschyzon merolae@gnl_CMER_CMI122C[RRM1][KOG4208]


Eukaryota@CG6937-PA[73][RRM1:100%****][put-sr:5%*][KOG4208:99%****]Caenorhabditis elegans@T04A8_6[RRM1][KOG4208]

Dictyostelium discoideum_AX4@XP_643547[RRM1]Anopheles gambiae@AGAP006090-PA[RRM1]

Euteleostomi@GSTENP00013801001[29][RRM1:100%***][LA:59%**][KOG1855:100%***]Euteleostomi@ENSORLP00000006283[2][RRM1:100%][LA:50%][KOG1855:100%]

Apocrita@XP_001600355[2][RRM1:100%][KOG1855:100%]Tribolium castaneum@XP_974730[RRM1][KOG1855]Embryophyta@29727_m000492[13][RRM3:92%**][.RRM2:8%][oligoU:46%*][KOG0148:100%**]Dikarya@XP_570577[4][RRM3:100%*][KOG0148:100%*]

Bacillariophyta@jgi_Phatr2_20857[2][RRM2:100%][put-sr:100%][KOG0147:100%]Aedes aegypti@AAEL006197-PA[RRM1][KOG0108]

Percomorpha@ENSGACP00000007987[5][RRM1:100%*][IGF2BP:80%*][KOG2193:100%*]Dictyostelium discoideum_AX4@XP_641693[RRM1][KOG0122]

Caenorhabditis elegans@Y37D8A_21_1[2][RRM1:100%][KOG4454:100%]Deuterostomia@ENSXETP00000012868[47][RRM1:100%***][KOG4454:60%***][.KOG0131:40%**]

Magnoliophyta@NP_001055607[4][RRM1:100%*][put-sr:25%][KOG0131:100%*]Endopterygota@AGAP002256-PA[4][RRM1:100%*][KOG4454:75%*][.KOG0131:25%]Drosophila melanogaster@CG11454-PA[RRM1][KOG4454]

Ashbya gossypii_ATCC_10895@NP_982888[RRM1][KOG0131]Saccharomyces cerevisiae@YOR319W[RRM1][KOG0131]Candida glabrata_CBS138@XP_447678[RRM1][KOG0131]Saccharomycetaceae@XP_001385635[2][RRM1:100%][KOG0131:100%]

Dictyostelium discoideum_AX4@XP_647248[RRM1][KOG0131]Eukaryota@NP_001064759[59][RRM1:100%****][snRNP:8%*][KOG0131:100%****]


Coxiella_burnetii@YP_001424503[2][RRM1:100%][PROK:100%][KOG0113:100%]Cryptosporidium parvum_Iowa_II@XP_627799[RRM2][KOG0110]

Thalassiosira pseudonana@jgi_Thaps3_263845[RRM1][KOG0108]Drosophila melanogaster@CG4806-PA[RRM2][KOG0127]

Endopterygota@XP_001605703[3][RRM2:67%][.RRM3:33%][KOG0127:100%*]Aedes aegypti@AAEL008572-PA[RRM2][KOG0127]

Caenorhabditis elegans@R05H10_2[RRM2][KOG0127]Ciona intestinalis@ENSCINP00000018774[2][RRM3:100%][KOG0127:100%]

Euteleostomi@ENSGACP00000016696[19][RRM3:79%**][.RRM4:11%][.RRM1:11%][RBM:58%**][KOG0127:100%**]

72 - RBMPSF UMH

46

47

49

48 - IGF2BP

part of 79 - TIA TIAR

OligoU81 - La

82

76 - TIA TIAR

OligoU

54

78 - OligoU

Fig. S5

78

67

77

72

73 98

100

86

80

70

73

83

85

73

70

69

Ostreococcus tauri@jgi Ostta4 31833[RRM2][KOG0148]Saccharomyces cerevisiae@YMR268C[RRM3][KOG0128]


Trypanosomatidae@XP_829274[2][RRM1:100%][KOG0145:50%]Leishmania infantum_JPCM5@XP_001463468[RRM1]

Trypanosoma brucei_TREU927@XP_829272[RRM1][KOG0145]Leishmania infantum_JPCM5@XP_001463465[RRM1][KOG0122]

Encephalitozoon cuniculi_GB-M1@NP_586226[RRM2][put-sr][KOG0123]Ashbya gossypii_ATCC_10895@NP_984845[RRM2][KOG0123]

Cyanidioschyzon merolae@gnl_CMER_CMG025C[RRM1][KOG1080]Leishmania infantum_JPCM5@XP_001466041[RRM2][KOG0123]

rosids@30146_m003481[2][RRM2:100%][PABP:50%][KOG0123:100%]rosids@30078_m002213[3][RRM2:100%*][PABP:33%][KOG0123:100%*]

Arabidopsis thaliana@NP_174676[RRM1][PABP][KOG0123]Theileria parva_strain_Muguga@XP_765501[RRM2][KOG0127]

Oryza sativa_japonica_cultivar-group@NP_001049727[RRM2][KOG0123]Dictyostelium discoideum_AX4@XP_638262[RRM2][put-sr][KOG0670]

Bilateria@ENSCSAVP00000007991[62][RRM2:95%****][.RRM1:5%*][UMH:74%***][KOG0124:100%****]Phytophthora@jgi_Phyra1_1_84640[3][RRM2:67%][.RRM1:33%][KOG0124:67%][.KOG0120:33%]

Cryptosporidium parvum_Iowa_II@XP_628096[RRM2][put-sr][KOG0124]Leishmania infantum_JPCM5@XP_001466413[RRM3][put-sr][KOG0147]Dictyostelium discoideum_AX4@XP_638966[RRM2][KOG0147]Ostreococcus@jgi_Ost9901_3_41266[2][RRM1:100%][KOG0153:100%]

Embryophyta@jgi_Phypa1_1_185655[7][RRM1:100%*][KOG0153:100%*]Ciona@ENSCSAVP00000015574[2][RRM1:100%][KOG0153:100%]

Encephalitozoon cuniculi_GB-M1@NP_585779[RRM1]Coelomata@XP_975014[28][RRM1:100%***][RBM:86%***][KOG0153:100%***]

Caenorhabditis elegans@T11G6_8_1[2][RRM1:100%][KOG0153:100%]Encephalitozoon cuniculi_GB-M1@NP_584552[RRM1][KOG0123]

Plasmodium falciparum_3D7@XP_001349948[RRM1][KOG0111]Eukaryota@ENSGALP00000021793[59][RRM1:100%****][cyclophilin:59%***][KOG0111:98%****]Eutheria@ENSEEUP00000009324[3][RRM1:100%*][cyclophilin:100%*][KOG0111:100%*]Otolemur garnettii@ENSOGAP00000003225[RRM1][KOG0111]


Pezizomycotina@XP_755630[3][RRM1:100%*][KOG0111:100%*]Phytophthora ramorum@jgi_Phyra1_1_76171[2][RRM1:100%][KOG0111:100%]

Caenorhabditis elegans@Y55F3AM_3c_1[3][RRM2:100%*][put-sr:33%][UMH:100%*][KOG0147:100%*]Schizosaccharomyces pombe_972h-@NP_595190[RRM1][KOG0111]

Cryptococcus neoformans_var._neoformans_JEC21@XP_571060[RRM2][KOG0147]Ustilago maydis_521@XP_756311[RRM2][put-sr][KOG0147]

Cryptosporidium parvum_Iowa_II@XP_628096[RRM1][put-sr][KOG0124]Ascomycota@XP_385341[4][RRM2:100%*][put-sr:100%*][KOG0147:100%*]

Yarrowia lipolytica@XP_504318[RRM2][KOG0147]Phytophthora@jgi_Phyra1_1_94266[2][RRM2:100%][KOG0147:100%]

Plasmodium falciparum_3D7@XP_001349956[RRM2][KOG0147]Leishmania infantum_JPCM5@XP_001467067[2][RRM1:100%][KOG0144:100%]

Bilateria@CG3151-PE[218][RRM2:92%*****][.RRM1:7%**][ELAV:84%*****][KOG0145:100%*****]Ustilago maydis_521@XP_759141[RRM2][KOG0145]

Gammaproteobacteria@YP_001083500[11][RRM1:100%**][PROK:100%**][KOG0145:27%*][.KOG0108:18%][.KOG0144:9%][.KOG0122:9%]Vibrio fischeri_ES114@YP_206444[RRM1][PROK][KOG0145]

Phytophthora@jgi_Phyra1_1_74707[2][RRM3:100%][KOG0110:100%]Volvox carteri@jgi_Volca1_63158[RRM2][KOG0110]Schizosaccharomyces pombe_972h-@NP_594609[RRM1][KOG4660]

Saccharomycetales@NP_984279[4][RRM1:100%*][KOG0921:75%*][.KOG0106:25%]Encephalitozoon cuniculi_GB-M1@NP_586226[RRM3][put-sr][KOG0123]

Ricinus communis@30146_m003481[RRM3][KOG0123]Euteleostomi@ENSGALP00000012472[36][RRM4:89%***][.RRM2:8%*][nucleolin:56%**][KOG0123:100%***]

Trypanosomatidae@XP_843886[2][RRM1:100%][KOG0145:100%]Trypanosomatidae@XP_828145[5][RRM1:100%*][KOG0145:100%*]

Trypanosoma brucei_TREU927@XP_845996[RRM1][KOG0122]Trypanosomatidae@XP_847495[2][RRM1:100%][KOG0110:50%][.KOG0127:50%]


Aconoidasida@XP_001349292[3][RRM2:100%*][KOG0146:67%][.KOG0144:33%]Plasmodium falciparum_3D7@XP_001350320[RRM3][KOG0123]

Cryptosporidium parvum_Iowa_II@XP_001388078[RRM3][put-sr][KOG0144]Eukaryota@ENSOANP00000006980[251][RRM3:67%*****][.RRM2:24%****][.RRM1:10%***][Bruno:50%****][KOG0144:55%****][.KOG0146:45%****]

Theileria parva_strain_Muguga@XP_766017[RRM3][KOG0144]Plasmodium falciparum_3D7@XP_001350320[RRM2][KOG0123]

Bilateria@ENSORLP00000004891[130][RRM1:100%****][RBMS:72%****][KOG0145:99%****]Ciona@ENSCINP00000023191[4][RRM3:75%*][.RRM1:25%][KOG0145:100%*]

Dictyostelium discoideum_AX4@XP_635793[RRM3][KOG0145]Coelomata@ENSTBEP00000015452[229][RRM3:88%*****][.RRM2:9%**][ELAV:82%*****][KOG0145:100%*****]

Caenorhabditis elegans@F35H8_5[RRM3][KOG0145]Theria@ENSMODP00000002817[2][RRM1:100%]

Yarrowia lipolytica@XP_505724[RRM1][KOG4198]Trypanosomatidae@XP_001469326[2][RRM4:100%][KOG0123:100%]

Trypanosomatidae@XP_001469222[2][RRM4:100%][KOG0123:100%]Ustilago maydis_521@XP_759458[RRM2][KOG0123]

Cryptococcus neoformans_var._neoformans_JEC21@XP_569319[RRM1][KOG0123]Pezizomycotina@XP_750167[2][RRM4:100%][KOG0123:100%]

Eukaryota@ENSDNOP00000002400[249][RRM4:82%*****][.RRM3:11%***][.RRM2:6%**][PABP:54%****][KOG0123:100%*****]Leishmania infantum_JPCM5@XP_001466041[RRM4][KOG0123]

Arabidopsis thaliana@NP_188259[RRM4][PABP][KOG0123]Drosophila melanogaster@CG4612-PA[RRM2][KOG0123]

Cryptosporidium parvum_Iowa_II@XP_001388334[RRM3][KOG0123]Yarrowia lipolytica@XP_500351[RRM3][KOG0123]Aedes aegypti@AAEL007013-PA[RRM1][KOG0123]


Ustilago maydis_521@XP_757329[RRM1][KOG0145]Volvox carteri@jgi_Volca1_84128[RRM2][KOG0147]Oryza sativa_japonica_cultivar-group@NP_001054296[RRM4][KOG0123]

Volvox carteri@jgi_Volca1_106063[RRM2]Dictyostelium discoideum_AX4@XP_636266[RRM3][KOG3598]

Dictyostelium discoideum_AX4@XP_635793[RRM1][KOG0145]Nasonia vitripennis@XP_001604889[RRM2][KOG0144]

Dictyostelium discoideum_AX4@XP_636266[RRM1][KOG3598]Endopterygota@CG1316-PA[5][RRM1:100%*][KOG0144:80%*][.KOG0148:20%]

Euteleostomi@ENSDNOP00000001522[23][RRM1:100%***][RBM:61%**][KOG0144:87%**][.KOG0145:13%*]Strongylocentrotus purpuratus@XP_001199679[4][RRM1:100%*][KOG0145:50%]

Dictyostelium discoideum_AX4@XP_629639[RRM1][KOG0145]Bilateria@ENSORLP00000021434[219][RRM1:100%*****][ELAV:79%*****][KOG0145:100%*****]

Diptera@AAEL011150-PA[15][RRM1:100%**][KOG0145:100%**]Drosophila melanogaster@CG5213-PA[RRM1][KOG0145]


Felis catus@ENSFCAP00000004622[RRM3][PABP][KOG0123]Caenorhabditis elegans@Y106G6H_2a_4[7][RRM3:71%*][.RRM2:29%][KOG0123:100%*]

Caenorhabditis elegans@F18H3_3b[5][RRM3:100%*][KOG0123:100%*]Trypanosoma brucei_TREU927@XP_827358[RRM3][KOG0123]

Leishmania infantum_JPCM5@XP_001469222[RRM3][KOG0123]Ciona@ENSCINP00000018772[3][RRM1:100%*][KOG0127:100%*]

Trypanosoma brucei_TREU927@XP_827237[RRM3][KOG0123]Chlamydomonadales@jgi_Volca1_82578[2][RRM3:100%][PABP:100%][KOG0123:100%]

Strongylocentrotus purpuratus@XP_001177782[4][RRM3:50%][.RRM2:50%][KOG0123:100%*]Dictyostelium discoideum_AX4@XP_629007[RRM3][KOG0123]

Strongylocentrotus purpuratus@XP_001185821[2][RRM1:100%][KOG0670:100%]5 - PABP

+

66 - PABP

10 - ELAV

6 - PABP

12 - ELAV

5 - PABP

11 - ELAV

RBMS

19 - cyclophilin

14 - RBM

part of 67 - UMH

Fungal SR (ScNp13) ?

Fig. S5

79

15.0

51

51

51

59

51

63

79

83

56

65

50

Campylobacter@YP_001467322[2][RRM1:100%][PROK:100%][KOG0148:100%]Candidatus Protochlamydia_amoebophila_UWE25@YP_007892[RRM1][PROK][KOG0149]

Leptospira@YP_000459[4][RRM1:100%*][PROK:100%*][KOG0108:100%*]Syntrophobacter fumaroxidans_MPOB@YP_845575[RRM1][PROK]

Treponema pallidum_subsp._pallidum_str._Nichols@NP_218796[RRM1][PROK][KOG0149]Bacteroidales@YP_213478[13][RRM1:100%**][PROK:100%**][KOG0108:69%**][.KOG0125:31%*]

Bacteroides@YP_001298723[3][RRM1:100%*][PROK:100%*][KOG0108:100%*]Bacteroidales@YP_001302325[2][RRM1:100%][PROK:100%][KOG0123:50%][.KOG0122:50%]

Nitrosococcus oceani_ATCC_19707@YP_344746[RRM1][PROK][KOG0148]Magnoliophyta@29333_m001057[3][RRM2:67%][.RRM1:33%][cpRNP:33%][KOG0131:67%][.KOG0148:33%]

Pezizomycotina@XP_961985[2][RRM2:100%][KOG0116:50%]Schizosaccharomyces pombe_972h-@NP_595090[RRM2]

Magnoliophyta@NP_566958[6][RRM2:67%*][.RRM1:33%][KOG0123:33%][.KOG0124:33%][.KOG0131:33%]Synechococcus_elongatus@YP_399809[2][RRM1:100%][PROK:100%][KOG0108:100%]Cyanobacteria@NP_898344[17][RRM1:100%**][PROK:100%**][KOG0108:65%**]

Ostreococcus@jgi_Ost9901_3_34381[2][RRM1:100%][KOG0145:100%]Cyanobacteria@YP_476186[8][RRM1:100%**][PROK:100%**][KOG0108:38%*][.KOG0122:12%]

Anopheles gambiae@AGAP000921-PA[3][RRM1:100%*]Coelomata@ENSORLP00000004891[62][RRM2:94%****][.RRM1:6%*][RBMS:79%***][KOG0145:100%****]

Tribolium castaneum@XP_971197[RRM1][KOG4661]Coelomata@ENSTBEP00000011040[87][RRM1:98%****][put-sr:16%**][KOG4661:100%****]

Tribolium castaneum@XP_969134[RRM1]Phaeodactylum tricornutum@jgi_Phatr2_33658[RRM1]

Chlamydomonas reinhardtii@jgi_Chlre3_194261[RRM1][KOG0123]Leishmania infantum_JPCM5@XP_001463160[RRM2][put-sr]

Trypanosoma brucei_TREU927@XP_846161[RRM2]Trypanosoma brucei_TREU927@XP_846161[RRM1]

Phytophthora@jgi_Physo1_1_134615[2][RRM1:100%]Aureococcus anophagefferens@jgi_Auran1_66158[RRM2][put-sr][KOG0149]

Strongylocentrotus purpuratus@XP_793862[2][RRM2:100%][KOG0144:100%]Aureococcus anophagefferens@jgi_Auran1_8994[RRM1][KOG0149]

Aureococcus anophagefferens@jgi_Auran1_17889[RRM1][KOG4207]Tribolium castaneum@XP_970765[RRM2][KOG0127]

Encephalitozoon cuniculi_GB-M1@NP_597583[RRM2][KOG4205]Encephalitozoon cuniculi_GB-M1@NP_585962[RRM2][KOG0123]

Strongylocentrotus purpuratus@XP_786044[2][RRM1:100%][KOG0117:100%]Cyanidioschyzon merolae@gnl_CMER_CMO246C[RRM2][KOG0110]

Nasonia vitripennis@XP_001605703[RRM1][KOG0127]Apis mellifera@XP_624495[RRM1][KOG0127]

Tribolium castaneum@XP_974350[RRM1][KOG0127]Nasonia vitripennis@XP_001605703[RRM2][KOG0127]

Phytophthora@jgi_Physo1_1_132702[3][RRM3:100%*][KOG0127:100%*]Bacillariophyta@jgi_Phatr2_47737[2][RRM1:100%][put-sr:50%]

Embryophyta@29742_m001371[15][RRM2:80%**][.RRM1:20%*][put-sr:87%**][SR:67%**][KOG0106:100%**]Chlamydomonas reinhardtii@jgi_Chlre3_80366[RRM2][KOG0106]

Chlamydomonas reinhardtii@jgi_Chlre3_120019[RRM2][KOG0106]Saccharomyces cerevisiae@YBR119W[RRM1]Volvox carteri@jgi_Volca1_120369[RRM1][put-sr][KOG0147]

Pezizomycotina@XP_753458[2][RRM2:100%][put-sr:50%][KOG4206:100%]Schizosaccharomyces pombe_972h-@NP_596424[RRM2][KOG4206]


Eukaryota@ENSGACP00000013006[79][RRM2:96%****][snRNP:30%***][KOG4206:100%****]Cryptococcus neoformans_var._neoformans_JEC21@XP_568533[RRM2][KOG4206]

Arabidopsis thaliana@NP_974808[2][RRM1:100%][KOG0123:50%][.KOG0148:50%]rosids@30078_m002213[3][RRM1:100%*][PABP:33%][KOG0123:100%*]

Ricinus communis@30146_m003481[RRM1][KOG0123]Arabidopsis thaliana@NP_188259[RRM1][PABP][KOG0123]

Trypanosomatidae@XP_001469326[2][RRM1:100%][KOG0123:100%]Leishmania infantum_JPCM5@XP_001466041[RRM1][KOG0123]

Oryza sativa_japonica_cultivar-group@NP_001049727[RRM1][KOG0123]Trypanosomatidae@XP_001469222[2][RRM1:100%][KOG0123:100%]

Eukaryota@ENSXETP00000023927[236][RRM1:100%*****][PABP:55%****][KOG0123:100%*****]Tetraodon nigroviridis@GSTENP00024897001[RRM1][PABP][KOG0123]

rosids@30078_m002213[3][RRM3:100%*][PABP:33%][KOG0123:100%*]Oryza sativa_japonica_cultivar-group@NP_001049727[RRM3][KOG0123]

Arabidopsis thaliana@NP_195978[RRM1][KOG0123]Cyanidioschyzon merolae@gnl_CMER_CMS187C[RRM1][KOG0123]

Saccharomycetaceae@YFR023W[4][RRM1:100%*][KOG0123:100%*]Candida glabrata_CBS138@XP_447635[RRM1][KOG0123]

Danio rerio@ENSDARP00000091192[14][RRM1:100%**][put-sr:100%**][KOG0123:100%**]Myotis lucifugus@ENSMLUP00000003020[RRM3][PTBP][KOG1190]

Dictyostelium discoideum_AX4@XP_639372[RRM1][KOG0670]Eukaryota@jgi_Volca1_104604[49][RRM1:100%***][put-sr:78%***][KOG0151:100%***]

Plasmodium falciparum_3D7@XP_001348201[RRM1][KOG0151]Cryptococcus neoformans_var._neoformans_JEC21@XP_571608[RRM1][put-sr][KOG0151]

Yarrowia lipolytica@XP_500351[RRM2][KOG0123]Theileria parva_strain_Muguga@XP_766400[RRM2][put-sr][KOG4205]

Amniota@ENSMODP00000004174[11][RRM4:55%*][.RRM3:36%*][.RRM2:9%][put-sr:100%**][KOG0112:100%**]Cryptococcus neoformans_var._neoformans_JEC21@XP_569809[RRM1][KOG0130]

Eukaryota@jgi_Thaps3_18841[52][RRM1:100%***][put-sr:56%***][RBM:42%***][KOG0130:100%***]Phaeodactylum tricornutum@jgi_Phatr2_20716[RRM1][KOG0130]

Plasmodium falciparum_3D7@XP_001348230[RRM1][KOG0130]Yarrowia lipolytica@XP_503462[RRM1][put-sr][KOG0130]Ustilago maydis_521@XP_760711[RRM1][put-sr][KOG0687]

Saccharomycetaceae@XP_453677[2][RRM1:100%][KOG4209:100%]Saccharomyces cerevisiae@YIR001C[RRM1][PABP][KOG4209]

Candida glabrata_CBS138@XP_447800[RRM1][KOG4209]Phytophthora@jgi_Physo1_1_138873[2][RRM1:100%][put-sr:100%][KOG1611:50%]Trypanosomatidae@XP_843959[2][RRM3:100%]

Aedes aegypti@AAEL010887-PA[RRM6][put-sr][KOG1984]Plasmodium falciparum_3D7@XP_001347479[RRM1]

Coelomata@ENSOGAP00000009767[86][RRM1:100%****][hnRNP:34%***][KOG4212:100%****]Strongylocentrotus purpuratus@XP_001187716[4][RRM1:100%*][put-sr:100%*][KOG4212:50%][.KOG4661:50%]

Schizosaccharomyces pombe_972h-@NP_588373[RRM1]Ostreococcus tauri@jgi_Ostta4_31833[RRM2][KOG0148]

3 - PABP

41 - snRNP

56 - green plant-specific

RS group of SR proteins

part of 68 - FOX


13

Fig. S5

80

74 75

79 52

71

95

57

77

85

Bilateria@Y47G6A 20a[64][RRM1:100%****][UMH:73%***][KOG0124:100%****]Phaeodactylum tricornutum@jgi_Phatr2_10122[RRM1][KOG0153]

Phytophthora@jgi_Physo1_1_140403[2][RRM1:100%][put-sr:100%][KOG0127:100%]Dictyostelium discoideum_AX4@XP_641373[RRM1][put-sr]

Strongylocentrotus purpuratus@XP_001185906[2][RRM1:100%][KOG0107:100%]Dictyostelium discoideum_AX4@XP_001134500[RRM1][put-sr][KOG0147]

Yarrowia lipolytica@XP_500797[RRM1][put-sr]Schizosaccharomyces pombe_972h-@NP_596398[RRM1][put-sr][SR]

Ustilago maydis_521@XP_758616[RRM1]Volvox carteri@jgi_Volca1_72841[RRM1][KOG0144]

Bilateria@ENSSARP00000011721[82][RRM1:100%****][TIATIAR:80%****][KOG0148:100%****]Chlamydomonadales@jgi_Volca1_107765[2][RRM1:100%][KOG0145:100%]

Chlamydomonadales@jgi_Volca1_48801[2][RRM1:100%][KOG0120:100%]Eukaryota@jgi_Volca1_82970[75][RRM2:91%****][.RRM1:9%*][put-sr:80%****][snRNP:53%***][KOG0120:100%****]

Phaeodactylum tricornutum@jgi_Phatr2_11145[RRM2][KOG0120]Plasmodium falciparum_3D7@XP_001348830[RRM2][put-sr][KOG0120]

Schizosaccharomyces pombe_972h-@NP_595396[RRM1][put-sr][KOG0120]Pezizomycotina@XP_387225[3][RRM1:67%][.RRM2:33%][put-sr:100%*][KOG0120:100%*]

Yarrowia lipolytica@XP_503754[RRM1][KOG0120]Aspergillus fumigatus_Af293@XP_747328[RRM1][KOG0110]

Eukaryota@NP_001063859[35][RRM1:100%***][ZCRB1:69%***][KOG0108:40%**][.KOG0122:9%*][.KOG0117:6%][.KOG0107:6%]Aedes aegypti@AAEL006197-PA[RRM1][KOG0108]

Phytophthora ramorum@jgi_Phyra1_1_94226[RRM1][put-sr][KOG0941]Volvox carteri@jgi_Volca1_107013[RRM3][KOG0117]


Dictyostelium discoideum_AX4@XP_643547[RRM1]Thalassiosira pseudonana@jgi_Thaps3_18198[RRM1][KOG4208]

Phaeodactylum tricornutum@jgi_Phatr2_45356[RRM1][KOG4208]Caenorhabditis elegans@T04A8_6[RRM1][KOG4208]

Eukaryota@CG6937-PA[73][RRM1:100%****][put-sr:5%*][KOG4208:99%****]Anopheles gambiae@AGAP006090-PA[RRM1]


Aedes aegypti@AAEL010887-PA[RRM6][put-sr][KOG1984]Dictyostelium discoideum_AX4@XP_642758[RRM1]

Strongylocentrotus purpuratus@XP_001185731[2][RRM1:100%]Tribolium castaneum@XP_971953[RRM1]

Euteleostomi@ENSMODP00000018834[25][RRM1:100%***][put-sr:64%**][KOG0147:48%**][.KOG0132:12%*]Plasmodium falciparum_3D7@XP_001348230[RRM1][KOG0130]

Phaeodactylum tricornutum@jgi_Phatr2_20716[RRM1][KOG0130]Eukaryota@jgi_Thaps3_18841[52][RRM1:100%***][put-sr:56%***][RBM:42%***][KOG0130:100%***]


Yarrowia lipolytica@XP_503462[RRM1][put-sr][KOG0130]Cryptococcus neoformans_var._neoformans_JEC21@XP_569824[RRM1][put-sr]

Schizosaccharomyces pombe_972h-@NP_596549[RRM1][put-sr]Sordariomycetes@XP_001522188[3][RRM1:100%*][put-sr:67%]

Caenorhabditis elegans@K02F3_11_2[2][RRM1:100%][put-sr:100%][KOG4209:100%]Coelomata@ENSMUSP00000057332[45][RRM1:100%***][put-sr:100%***][RNPS1:64%***][KOG4209:87%***]


Phytophthora@jgi_Physo1_1_138873[2][RRM1:100%][put-sr:100%][KOG1611:50%]Eukaryota@AAEL002461-PA[78][RRM1:100%****][put-sr:29%***][KOG0126:100%****]

Ustilago maydis_521@XP_760864[RRM1][KOG0126]Saccharomycetaceae@XP_459205[2][RRM1:100%][KOG0126:100%]

Trypanosoma brucei_TREU927@XP_845742[RRM1][KOG0126]Apis mellifera@XP_394565[RRM1][KOG0147]

Schizosaccharomyces pombe_972h-@NP_593427[RRM1][KOG0123]Drosophila melanogaster@CG3312-PA[2][RRM1:100%][KOG0128:100%]

Saccharomyces cerevisiae@YLL046C[RRM1]Mammalia@ENSETEP00000003776[19][RRM1:100%**][LA:95%**][KOG4213:100%**]

Anopheles gambiae@AGAP007689-PA[RRM1]Aedes aegypti@AAEL010101-PA[RRM1]Tribolium castaneum@XP_969873[RRM1]

Strongylocentrotus purpuratus@XP_001185821[2][RRM1:100%][KOG0670:100%]Euteleostomi@ENSOANP00000024755[113][RRM1:100%****][hnRNP:36%***][.RALYL:15%**]

Apocrita@XP_623710[2][RRM1:100%]Saccharomycetales@XP_454821[4][RRM1:100%*][KOG3598:50%][.KOG1984:25%]

Dictyostelium discoideum_AX4@XP_638672[RRM1][put-sr][KOG0147]Plasmodium falciparum_3D7@XP_001347332[RRM1][put-sr][KOG0105]

Pichia stipitis_CBS_6054@XP_001384462[RRM2]Debaryomyces hansenii_CBS767@XP_460517[RRM2][KOG0117]

Saccharomycetales@XP_445844[3][RRM2:100%*][KOG0123:33%]Kluyveromyces lactis@XP_455897[RRM2][KOG0123]

Coxiella_burnetii@YP_001424629[2][RRM1:100%][PROK:100%][KOG0108:100%]Legionella_pneumophila@YP_001249669[3][RRM1:100%*][PROK:100%*][put-sr:100%*][KOG0149:100%*]

Ostreococcus lucimarinus@jgi_Ost9901_3_7602[RRM1][KOG0145]Dictyostelium discoideum_AX4@XP_641568[RRM2][KOG3598]

Deuterostomia@ENSDNOP00000008593[94][RRM1:100%****][P54nrb:28%***][.PSP1:21%**][.PSF:18%**][KOG0115:99%****]Caenorhabditis elegans@F25B5_7d[2][RRM1:100%][KOG0115:100%]

Endopterygota@CG10328-PA[9][RRM1:100%**][P54nrb:33%*][KOG0115:100%**]Cyanidioschyzon merolae@gnl_CMER_CMO246C[RRM2][KOG0110]

Trypanosomatidae@XP_001463723[2][RRM1:100%][KOG0110:100%]Phytophthora@jgi_Physo1_1_129427[2][RRM2:100%][KOG0110:100%]

Oryza sativa_japonica_cultivar-group@NP_001053839[RRM1][KOG0110]Bilateria@ENSORLP00000004891[130][RRM1:100%****][RBMS:72%****][KOG0145:99%****]

Schizosaccharomyces pombe_972h-@NP_595599[RRM2][KOG0110]Saccharomycetales@NP_984131[7][RRM2:100%*][KOG0110:100%*]

Aspergillus fumigatus_Af293@XP_750233[RRM2][KOG0110]Caenorhabditis elegans@T23F6_4_1[2][RRM3:100%][KOG0110:100%]


Phaeodactylum tricornutum@jgi_Phatr2_20740[RRM2][KOG0110]Ustilago maydis_521@XP_758493[RRM2][KOG0110]

Aureococcus anophagefferens@jgi_Auran1_1296[RRM1][KOG0110]Eukaryota@IMGA_AC183923_6_1[34][RRM3:74%***][.RRM1:15%*][.RRM2:12%*][put-sr:6%][KOG0110:100%***]

Thalassiosira pseudonana@jgi_Thaps3_268689[RRM2][KOG0110]Arabidopsis thaliana@NP_567594[RRM1][KOG0117]

eurosids_I@IMGA_CT963106_6_1[2][RRM1:100%][KOG0117:50%]

>>> RRM1 of SR45/RNPS1

86 - hnRNP/RALYL

84 - La

31

32

33 - p54nrb

PSP1

PSF

69

20 - RBM

27 - RNPS1

26 - SR45

28

82

57 - ZCRB1

64 - snRNP

76 - TIA TIAR

OligoU

67 - UMH

PROK

Fungal SR (SpSrp1)

Fungal SpRnps1

Fig. S6

81

82

78

68

83

61

69

55

56

67

57

72

99

76

62

Debaryomyces hansenii CBS767@XP 459815[RRM1][KOG0415]Eukaryota@jgi_Ostta4_3181[66][RRM1:100%****][put-sr:47%***][cyclophilin:32%***][KOG0415:97%****]

Leishmania infantum_JPCM5@XP_001463468[RRM1]Trypanosomatidae@XP_829274[2][RRM1:100%][KOG0145:50%]


Encephalitozoon cuniculi_GB-M1@NP_586099[RRM2][KOG0131]Phaeodactylum tricornutum@jgi_Phatr2_44468[RRM1]

Thalassiosira pseudonana@jgi_Thaps3_20887[RRM1]Encephalitozoon cuniculi_GB-M1@NP_586226[RRM2][put-sr][KOG0123]

Ashbya gossypii_ATCC_10895@NP_984845[RRM2][KOG0123]Schizosaccharomyces pombe_972h-@NP_001018242[RRM3][KOG0123]

Schizosaccharomyces pombe_972h-@NP_593427[RRM2][KOG0123]Leishmania infantum_JPCM5@XP_001466041[RRM2][KOG0123]Arabidopsis thaliana@NP_174676[RRM1][PABP][KOG0123]

Oryza sativa_japonica_cultivar-group@NP_001049727[RRM2][KOG0123]rosids@30078_m002213[3][RRM2:100%*][PABP:33%][KOG0123:100%*]

rosids@30146_m003481[2][RRM2:100%][PABP:50%][KOG0123:100%]Phytophthora sojae@jgi_Physo1_1_139371[RRM2][KOG4205]

Eukaryota@jgi_Volca1_104604[49][RRM1:100%***][put-sr:78%***][KOG0151:100%***]Plasmodium falciparum_3D7@XP_001348201[RRM1][KOG0151]

Cryptococcus neoformans_var._neoformans_JEC21@XP_571608[RRM1][put-sr][KOG0151]Ostreococcus tauri@jgi_Ostta4_31833[RRM2][KOG0148]

Eukaryota@YHR086W[51][RRM3:76%***][.RRM2:20%**][oligoU:10%*][KOG0148:90%***]Schizosaccharomyces pombe_972h-@NP_594243[RRM3][KOG0148]

Aureococcus anophagefferens@jgi_Auran1_28594[RRM3][KOG0148]Phytophthora@jgi_Phyra1_1_50314[2][RRM3:100%][KOG0148:100%]

Coelomata@XP_975014[28][RRM1:100%***][RBM:86%***][KOG0153:100%***]Caenorhabditis elegans@T11G6_8_1[2][RRM1:100%][KOG0153:100%]Ciona@ENSCSAVP00000015574[2][RRM1:100%][KOG0153:100%]

Ostreococcus@jgi_Ost9901_3_41266[2][RRM1:100%][KOG0153:100%]Embryophyta@jgi_Phypa1_1_185655[7][RRM1:100%*][KOG0153:100%*]

Encephalitozoon cuniculi_GB-M1@NP_584552[RRM3][KOG0123]Theria@ENSMODP00000002817[2][RRM1:100%]

Theileria parva_strain_Muguga@XP_764943[RRM1][KOG4206]Pichia stipitis_CBS_6054@XP_001382592[RRM1][KOG4206]

Coelomata@ENSORLP00000008206[18][RRM1:100%**][snRNP:83%**][KOG4206:100%**]Sordariomycetes@XP_962704[2][RRM1:100%][put-sr:50%][KOG4206:100%]

Endopterygota@CG4266-PA[5][RRM1:100%*][put-sr:100%*][KOG0132:100%*]Eutheria@ENSETEP00000000464[10][RRM1:100%**][put-sr:100%**][KOG0132:100%**]

Ciona intestinalis@ENSCINP00000027768[RRM1][KOG0548]Dictyostelium discoideum_AX4@XP_635179[RRM2][KOG0148]

Strongylocentrotus purpuratus@XP_001188888[2][RRM1:100%][KOG0548:100%]Clupeocephala@ENSORLP00000009616[3][RRM1:100%*][KOG0548:100%*]

Gasterosteus aculeatus@ENSGACP00000006521[RRM1][KOG0548]Danio rerio@ENSDARP00000075089[2][RRM1:100%][KOG0548:100%]

Physcomitrella patens@jgi_Phypa1_1_161310[RRM3][KOG3598]Saccharomyces cerevisiae@YMR302C[RRM1]

Physcomitrella patens@jgi_Phypa1_1_137240[2][RRM1:100%][KOG3598:50%]Arabidopsis thaliana@NP_181869[4][RRM1:100%*][FCAFPA:100%*][KOG0117:100%*]

Ricinus communis@29577_m000447[RRM1][KOG0123]Ricinus communis@30005_m001243[RRM1]


Dictyostelium discoideum_AX4@XP_644288[RRM2][KOG3598]Schizosaccharomyces pombe_972h-@NP_588373[RRM1]

Physcomitrella patens@jgi_Phypa1_1_176266[RRM1][KOG1924]Oryza sativa_japonica_cultivar-group@NP_001063671[RRM2][KOG0123]rosids@NP_001078046[5][RRM2:100%*][FCAFPA:80%*][KOG0117:80%*][.KOG0123:20%]


Dictyostelium discoideum_AX4@XP_629218[RRM2][KOG0151]Volvox carteri@jgi_Volca1_88720[RRM3]

Chlamydomonas reinhardtii@jgi_Chlre3_148816[RRM2][KOG3598]Schizosaccharomyces pombe_972h-@NP_595389[RRM1][KOG4574]

Yarrowia lipolytica@XP_500252[RRM1][KOG4574]Cryptococcus neoformans_var._neoformans_JEC21@XP_570411[RRM2][KOG4574]

Neurospora crassa_OR74A@XP_962915[RRM1][KOG4574]Dictyostelium discoideum_AX4@XP_638262[RRM2][put-sr][KOG0670]

Cryptosporidium parvum_Iowa_II@XP_628096[RRM2][put-sr][KOG0124]Bilateria@ENSCSAVP00000007991[62][RRM2:95%****][.RRM1:5%*][UMH:74%***][KOG0124:100%****]

Phytophthora@jgi_Phyra1_1_84640[3][RRM2:67%][.RRM1:33%][KOG0124:67%][.KOG0120:33%]Dictyostelium discoideum_AX4@XP_638262[RRM1][put-sr][KOG0670]

Dictyostelium discoideum_AX4@XP_643007[RRM1]Eukaryota@ENSFCAP00000006163[84][RRM2:88%****][.RRM1:12%**][put-sr:86%****][UMH:39%***][.CAPER:8%*][KOG0147:100%****]

Bacillariophyta@jgi_Phatr2_20857[2][RRM2:100%][put-sr:100%][KOG0147:100%]Volvox carteri@jgi_Volca1_84128[RRM2][KOG0147]

Phytophthora@jgi_Phyra1_1_94266[2][RRM2:100%][KOG0147:100%]Plasmodium falciparum_3D7@XP_001349956[RRM2][KOG0147]

Ascomycota@XP_385341[4][RRM2:100%*][put-sr:100%*][KOG0147:100%*]Cryptococcus neoformans_var._neoformans_JEC21@XP_571060[RRM2][KOG0147]

Caenorhabditis elegans@Y55F3AM_3c_1[3][RRM2:100%*][put-sr:33%][UMH:100%*][KOG0147:100%*]Ustilago maydis_521@XP_756311[RRM2][put-sr][KOG0147]

Cryptosporidium parvum_Iowa_II@XP_628096[RRM1][put-sr][KOG0124]Phytophthora ramorum@jgi_Phyra1_1_81440[2][RRM1:100%][KOG0124:100%]

Yarrowia lipolytica@XP_504318[RRM2][KOG0147]Volvox carteri@jgi_Volca1_106063[RRM2]

Dictyostelium discoideum_AX4@XP_636266[RRM3][KOG3598]Encephalitozoon cuniculi_GB-M1@NP_585962[RRM2][KOG0123]

Aspergillus fumigatus_Af293@XP_749317[RRM3][KOG0128]Schizosaccharomyces pombe_972h-@NP_596721[RRM3][KOG0128]


Schizosaccharomyces pombe_972h-@NP_593531[RRM2][nucleolin][KOG0147]Ustilago maydis_521@XP_762340[RRM2][KOG0148]

Cryptococcus neoformans_var._neoformans_JEC21@XP_566835[RRM2][KOG0148]Saccharomycetales@XP_456900[7][RRM2:100%*][nucleolin:14%][KOG0148:57%*][.KOG0131:29%][.KOG4210:14%]Pezizomycotina@XP_754840[2][RRM2:100%][KOG0127:50%][.KOG0148:50%]

Aspergillus fumigatus_Af293@XP_754657[RRM1]Yarrowia lipolytica@XP_500351[RRM1][KOG0123]

Neurospora crassa_OR74A@XP_964541[RRM1]Aspergillus fumigatus_Af293@XP_748929[RRM1]

Aureococcus anophagefferens@jgi_Auran1_69134[RRM1][put-sr]Pezizomycotina@XP_961985[2][RRM1:100%][KOG0116:50%]

Theileria parva_strain_Muguga@XP_765501[RRM1][KOG0127]Candida glabrata_CBS138@XP_445637[RRM1]

Ashbya gossypii_ATCC_10895@NP_983970[RRM1]Ciona intestinalis@ENSCINP00000008726[RRM1][put-sr][KOG2193]

Apis mellifera@XP_393878[RRM1][put-sr][KOG2193]Takifugu rubripes@SINFRUP00000134535[RRM1][KOG0123]

Aspergillus fumigatus_Af293@XP_750045[RRM1]Ostreococcus lucimarinus@jgi_Ost9901_3_32831[RRM1]

Debaryomyces hansenii_CBS767@XP_460681[RRM3][KOG0128]Plasmodium falciparum_3D7@XP_001347479[RRM1]

Saccharomyces cerevisiae@YMR268C[RRM3][KOG0128]Candida glabrata_CBS138@XP_446891[RRM3][KOG0128]

Aedes aegypti@AAEL010888-PA[RRM2]Dictyostelium discoideum_AX4@XP_646584[RRM2][KOG0127]

Coxiella_burnetii@YP_001424503[2][RRM1:100%][PROK:100%][KOG0113:100%]Bilateria@Y47G6A_20a[64][RRM1:100%****][UMH:73%***][KOG0124:100%****]

67 - UMH

40 - snRNP

14 - RBM

78 - OligoU

13

38 - Cyclophilin

PROK

Fig. S6

82

55

80

77

94

62

85

76

66 60

83

53

78

81

51

82

Leishmania infantum JPCM5@XP 001466041[RRM4][KOG0123]Drosophila melanogaster@CG4612-PA[RRM2][KOG0123]

Aedes aegypti@AAEL007013-PA[RRM1][KOG0123]Arabidopsis thaliana@NP_188259[RRM4][PABP][KOG0123]

Eukaryota@ENSDNOP00000002400[249][RRM4:82%*****][.RRM3:11%***][.RRM2:6%**][PABP:54%****][KOG0123:100%*****]Pezizomycotina@XP_750167[2][RRM4:100%][KOG0123:100%]

Strongylocentrotus purpuratus@XP_001177782[4][RRM3:50%][.RRM2:50%][KOG0123:100%*]Dictyostelium discoideum_AX4@XP_629007[RRM3][KOG0123]

Chlamydomonadales@jgi_Volca1_82578[2][RRM3:100%][PABP:100%][KOG0123:100%]Dikarya@XP_960425[12][RRM3:100%**][PABP:17%][KOG0123:100%**]

Yarrowia lipolytica@XP_501289[RRM3][KOG0123]Trypanosoma brucei_TREU927@XP_827237[RRM3][KOG0123]


Felis catus@ENSFCAP00000004622[RRM3][PABP][KOG0123]Caenorhabditis elegans@Y106G6H_2a_4[7][RRM3:71%*][.RRM2:29%][KOG0123:100%*]

Caenorhabditis elegans@F18H3_3b[5][RRM3:100%*][KOG0123:100%*]Echinops telfairi@ENSETEP00000008100[RRM3][PABP][KOG0123]

Phytophthora@jgi_Physo1_1_108322[2][RRM3:100%][KOG0123:100%]Thalassiosira pseudonana@jgi_Thaps3_13224[RRM3][KOG0123]

Phaeodactylum tricornutum@jgi_Phatr2_23959[RRM3][KOG0123]Aureococcus anophagefferens@jgi_Auran1_60739[RRM1][put-sr][KOG1860]

Trypanosomatidae@XP_847111[2][RRM1:100%]Leishmania infantum_JPCM5@XP_001465764[RRM1]


Leishmania infantum_JPCM5@XP_001463160[RRM2][put-sr]Trypanosomatidae@XP_001469326[2][RRM1:100%][KOG0123:100%]

Leishmania infantum_JPCM5@XP_001466041[RRM1][KOG0123]Trypanosomatidae@XP_001469222[2][RRM1:100%][KOG0123:100%]

Eukaryota@ENSXETP00000023927[236][RRM1:100%*****][PABP:55%****][KOG0123:100%*****]Tetraodon nigroviridis@GSTENP00024897001[RRM1][PABP][KOG0123]Saccharomycetaceae@YFR023W[4][RRM1:100%*][KOG0123:100%*]

Candida glabrata_CBS138@XP_447635[RRM1][KOG0123]Danio rerio@ENSDARP00000091192[14][RRM1:100%**][put-sr:100%**][KOG0123:100%**]

rosids@30078_m002213[3][RRM1:100%*][PABP:33%][KOG0123:100%*]Oryza sativa_japonica_cultivar-group@NP_001049727[RRM1][KOG0123]


Dictyostelium discoideum_AX4@XP_645138[RRM1]Chlamydomonas reinhardtii@jgi_Chlre3_181993[RRM1]

Theileria parva_strain_Muguga@XP_766466[RRM3][KOG0123]Cryptosporidium parvum_Iowa_II@XP_001388334[RRM3][KOG0123]

Embryophyta@jgi_Phypa1_1_140180[4][RRM3:100%*][KOG0117:100%*]Trypanosoma brucei_TREU927@XP_844190[RRM1][KOG0144]

Ascomycota@YDL224C[8][RRM1:88%*][.RRM2:12%][KOG3598:12%][.KOG1457:12%]Medicago truncatula@IMGA_CU012061_4_1[RRM1]

Ricinus communis@28452_m000049[RRM1][KOG1457]Plasmodium falciparum_3D7@XP_001350640[RRM3][KOG0123]

Encephalitozoon cuniculi_GB-M1@NP_584552[RRM1][KOG0123]Debaryomyces hansenii_CBS767@XP_460681[RRM2][KOG0128]

Saccharomyces cerevisiae@YMR268C[RRM2][KOG0128]Schizosaccharomyces pombe_972h-@NP_596721[RRM2][KOG0128]

Pezizomycotina@XP_749317[2][RRM2:100%][KOG0128:100%]Dictyostelium discoideum_AX4@XP_638966[RRM2][KOG0147]Plasmodium falciparum_3D7@XP_001347876[RRM1][KOG0105]

Dictyostelium discoideum_AX4@XP_645848[RRM2][put-sr]Saccharomycetales@XP_454345[4][RRM1:100%*][KOG0148:75%*][.KOG0123:25%]

Yarrowia lipolytica@XP_501542[RRM1][KOG0131]Saccharomycetaceae@XP_001383142[2][RRM1:100%][put-sr:100%][KOG0148:100%]

Sordariomycetes@XP_385593[2][RRM1:100%][KOG0148:100%]Cryptococcus neoformans_var._neoformans_JEC21@XP_570577[RRM1][KOG0148]

Embryophyta@NP_188026[13][RRM1:100%**][oligoU:38%*][KOG0148:100%**]Ustilago maydis_521@XP_757329[RRM1][KOG0145]

Aureococcus anophagefferens@jgi_Auran1_31715[RRM1][KOG0149]Oryza sativa_japonica_cultivar-group@NP_001054296[RRM5][KOG0123]

Oryza sativa_japonica_cultivar-group@NP_001054296[RRM4][KOG0123]Embryophyta@jgi_Phypa1_1_189930[7][RRM1:100%*][KOG0119:86%*][.KOG0307:14%]



Culicidae@AAEL001131-PA[2][RRM1:100%][KOG0113:100%]Ciona@ENSCSAVP00000018820[2][RRM2:100%][KOG0145:100%]

Euteleostomi@ENSXETP00000044031[49][RRM2:76%***][.RRM1:24%**][KOG0145:41%**][.KOG0123:14%*][.KOG0110:14%*]Dictyostelium discoideum_AX4@XP_635793[RRM1][KOG0145]


Trypanosomatidae@XP_001468777[2][RRM2:100%][KOG0144:100%]Trypanosomatidae@XP_847495[2][RRM1:100%][KOG0110:50%][.KOG0127:50%]

Nasonia vitripennis@XP_001604889[RRM2][KOG0144]Dictyostelium discoideum_AX4@XP_636266[RRM1][KOG3598]

Endopterygota@CG1316-PA[5][RRM1:100%*][KOG0144:80%*][.KOG0148:20%]Strongylocentrotus purpuratus@XP_001199679[4][RRM1:100%*][KOG0145:50%]

Euteleostomi@ENSDNOP00000001522[23][RRM1:100%***][RBM:61%**][KOG0144:87%**][.KOG0145:13%*]Leishmania infantum_JPCM5@XP_001464836[RRM1][KOG0145]

Leishmania infantum_JPCM5@XP_001464835[2][RRM1:100%][KOG0145:100%]Leishmania infantum_JPCM5@XP_001466666[RRM1][KOG0145]

Trypanosoma brucei_TREU927@XP_843985[3][RRM1:100%*][put-sr:33%][KOG0110:100%*]Leishmania infantum_JPCM5@XP_001466665[RRM1][KOG0110]

Leishmania infantum_JPCM5@XP_001466659[RRM1][KOG0145]Embryophyta@NP_001063403[14][RRM1:100%**][KOG0148:100%**]

Endopterygota@XP_974444[2][RRM1:100%][KOG0144:100%]Clupeocephala@ENSORLP00000016619[5][RRM1:100%*][KOG0131:60%*][.KOG0123:40%]

Dictyostelium discoideum_AX4@XP_639372[RRM1][KOG0670]Embryophyta@NP_001062111[8][RRM1:100%**][put-sr:62%*][KOG4849:38%*][.KOG4246:12%][.KOG0113:12%][.KOG4676:12%]

Ostreococcus lucimarinus@jgi_Ost9901_3_26750[RRM1]Trypanosomatidae@XP_843886[2][RRM1:100%][KOG0145:100%]

Trypanosomatidae@XP_828145[5][RRM1:100%*][KOG0145:100%*]Trypanosoma brucei_TREU927@XP_845996[RRM1][KOG0122]

Drosophila melanogaster@CG5213-PA[RRM1][KOG0145]Diptera@AAEL011150-PA[15][RRM1:100%**][KOG0145:100%**]

Dictyostelium discoideum_AX4@XP_629639[RRM1][KOG0145]Bilateria@ENSORLP00000021434[219][RRM1:100%*****][ELAV:79%*****][KOG0145:100%*****]Dictyostelium discoideum_AX4@XP_644081[RRM1][KOG0123]


Ciona@ENSCINP00000023191[4][RRM3:75%*][.RRM1:25%][KOG0145:100%*]Coelomata@ENSTBEP00000015452[229][RRM3:88%*****][.RRM2:9%**][ELAV:82%*****][KOG0145:100%*****]

Dictyostelium discoideum_AX4@XP_635793[RRM3][KOG0145]Caenorhabditis elegans@F35H8_5[RRM3][KOG0145]

Aconoidasida@XP_001349292[3][RRM2:100%*][KOG0146:67%][.KOG0144:33%]Plasmodium falciparum_3D7@XP_001350320[RRM3][KOG0123]


Cryptosporidium parvum_Iowa_II@XP_001388078[RRM3][put-sr][KOG0144]Eukaryota@ENSOANP00000006980[251][RRM3:67%*****][.RRM2:24%****][.RRM1:10%***][Bruno:50%****][KOG0144:55%****][.KOG0146:45%****]

Cryptosporidium parvum_Iowa_II@XP_626331[RRM1][KOG0146]Cyanidioschyzon merolae@gnl_CMER_CMS187C[RRM1][KOG0123]

Debaryomyces hansenii_CBS767@XP_459815[RRM1][KOG0415] 38 Cyclophilin

9 - Bruno

12 - ELAV

10 - ELAV

3 - PABP

5 - PABP

6 - PABP

associated to node 76

in 3 other trees

Fig. S6

83

70 63

68

92

71

66

52

62

91

72

94

60 73

99

70

83

Magnoliophyta@29709 m001182[6][RRM1:100%*][put sr:17%][KOG0117:100%*]Ricinus communis@30072_m000974[RRM1][KOG0117]

Oryza sativa_japonica_cultivar-group@NP_001064224[RRM1][KOG0117]Cyanidioschyzon merolae@gnl_CMER_CMG025C[RRM1][KOG1080]

Ricinus communis@30169_m006629[RRM1][KOG0123]Euteleostomi@ENSOANP00000013028[22][RRM1:100%***]

Drosophila melanogaster@CG14414-PB[RRM1]Endopterygota@XP_967886[3][RRM1:100%*]

Cryptococcus neoformans_var._neoformans_JEC21@XP_572996[RRM1]Ustilago maydis_521@XP_760296[RRM1]


Nasonia vitripennis@XP_001604488[RRM1]Oryza sativa_japonica_cultivar-group@NP_001067112[RRM2][put-sr][KOG0117]

Zea mays@11279_m000026_AZM5_6772[RRM1][put-sr][KOG0117]Coelomata@XP_974651[54][RRM2:83%***][.RRM1:17%**][put-sr:87%***][RBM:37%**][KOG0112:100%***]

Drosophila melanogaster@CG2050-PA[RRM3]Coelomata@ENSMMUP00000010529[37][RRM3:54%**][.RRM2:41%**][.RRM1:5%][put-sr:92%***][KOG0112:84%***][.KOG3598:8%*]

Strongylocentrotus purpuratus@XP_001184502[2][RRM2:100%][put-sr:100%][KOG1144:100%]Strongylocentrotus purpuratus@XP_786044[2][RRM1:100%][KOG0117:100%]

Neurospora crassa_OR74A@XP_958552[RRM1][KOG0128]Dictyostelium discoideum_AX4@XP_641568[RRM3][KOG3598]

Aedes aegypti@AAEL010890-PA[RRM1][put-sr][KOG0132]Theileria parva_strain_Muguga@XP_766728[RRM1][KOG0124]

Trypanosomatidae@XP_827358[2][RRM2:100%][KOG0123:100%]Plasmodium falciparum_3D7@XP_001352162[RRM1]

Plasmodium falciparum_3D7@XP_001351468[RRM1]Encephalitozoon cuniculi_GB-M1@NP_597181[RRM1][KOG0110]

Schizosaccharomyces pombe_972h-@NP_595599[RRM1][KOG0110]Saccharomycetaceae@XP_001386803[2][RRM1:100%][KOG0110:100%]

Viridiplantae@jgi_Phypa1_1_207810[3][RRM1:100%*][KOG0110:100%*]Dictyostelium discoideum_AX4@XP_638463[RRM1][KOG0110]

Ustilago maydis_521@XP_758493[RRM1][KOG0110]Cyanidioschyzon merolae@gnl_CMER_CMO246C[RRM1][KOG0110]

Arabidopsis thaliana@NP_196191[RRM1][KOG0110]Apocrita@XP_624611[2][RRM1:100%][KOG0110:100%]

Drosophila melanogaster@CG3335-PA[RRM1][KOG0110]Caenorhabditis elegans@T23F6_4_1[2][RRM1:100%][KOG0110:100%]

Culicidae@AGAP005249-PA[2][RRM1:100%][KOG0110:100%]Euteleostomi@GSTENP00029551001[21][RRM1:100%***][put-sr:10%][KOG0110:100%***]

Drosophila melanogaster@CG5213-PA[RRM2][KOG0145]Diptera@AGAP003899-PA[15][RRM2:100%**][KOG0145:100%**]

Ustilago maydis_521@XP_759141[RRM2][KOG0145]Coelomata@ENSORLP00000004891[62][RRM2:94%****][.RRM1:6%*][RBMS:79%***][KOG0145:100%****]

Bilateria@CG3151-PE[218][RRM2:92%*****][.RRM1:7%**][ELAV:84%*****][KOG0145:100%*****]Ciona@ENSCSAVP00000015853[4][RRM2:100%*][KOG0145:100%*]


Aconoidasida@XP_766017[2][RRM2:100%][KOG0144:100%]Plasmodium falciparum_3D7@XP_001348269[RRM2][KOG0144]

Cryptosporidium parvum_Iowa_II@XP_001388078[RRM2][put-sr][KOG0144]Thalassiosira pseudonana@jgi_Thaps3_261541[RRM2][KOG0144]Chlamydomonadales@jgi_Chlre3_99329[2][RRM1:50%][.RRM2:50%][KOG0144:100%]Chlamydomonadales@jgi_Volca1_88093[2][RRM1:100%][KOG1240:100%]

Embryophyta@jgi_Phypa1_1_115029[9][RRM2:100%**][KOG0144:100%**]Arabidopsis thaliana@NP_850472[RRM2][FCAFPA][KOG0144]

Embryophyta@29889_m003323[11][RRM2:100%**][FCAFPA:18%][KOG0144:100%**]Phytophthora@jgi_Physo1_1_133760[2][RRM2:100%][KOG0144:100%]Bilateria@AGAP009477-PA[250][RRM2:73%*****][.RRM1:27%****][Bruno:59%****][KOG0144:56%****][.KOG0146:44%****]


Trypanosomatidae@XP_845656[2][RRM1:100%][KOG0131:50%]Leishmania infantum_JPCM5@XP_001468236[RRM1]Trypanosomatidae@XP_001468238[3][RRM1:100%*][KOG0144:100%*]

Chlamydomonadales@jgi_Volca1_72841[2][RRM3:50%][.RRM2:50%][KOG0144:100%]Trypanosomatidae@XP_827838[2][RRM1:100%][KOG0144:100%]

Cryptosporidium parvum_Iowa_II@XP_628265[RRM2][KOG0144]Volvox carteri@jgi_Volca1_88093[RRM4][KOG1240]

Chlamydomonadales@jgi_Volca1_118581[3][RRM2:67%][.RRM4:33%][KOG0144:67%][.KOG1240:33%]Saccharomycetales@YNL016W[6][RRM3:100%*][put-sr:33%][KOG0148:83%*][.KOG0123:17%]

Embryophyta@30076_m004622[9][RRM1:100%**][FCAFPA:22%][KOG0144:100%**]Arabidopsis thaliana@NP_850472[RRM1][FCAFPA][KOG0144]

Medicago truncatula@IMGA_AC155099_2_2[2][RRM1:100%][KOG0144:100%]Dictyostelium discoideum_AX4@XP_635247[RRM1][KOG0144]

Dictyostelium discoideum_AX4@XP_646268[RRM1][KOG0146]Physcomitrella patens@jgi_Phypa1_1_107590[2][RRM1:100%][KOG0144:100%]

Poaceae@11320_m000014_AZM5_6848[3][RRM1:100%*][KOG0144:100%*]Phaeodactylum tricornutum@jgi_Phatr2_42828[RRM1][KOG0144]

Thalassiosira pseudonana@jgi_Thaps3_261541[RRM1][KOG0144]Cryptosporidium parvum_Iowa_II@XP_628265[RRM1][KOG0144]


Cryptosporidium parvum_Iowa_II@XP_001388078[RRM1][put-sr][KOG0144]Chlamydomonas reinhardtii@jgi_Chlre3_174860[RRM2][KOG1240]

Phytophthora@jgi_Phyra1_1_82644[2][RRM1:100%][KOG0144:100%]Bilateria@ENSXETP00000031370[81][RRM1:100%****][Bruno:42%***][KOG0146:84%****][.KOG0144:16%**]

Coelomata@XP_782270[24][RRM1:100%***][Bruno:42%**][KOG0144:100%***]Rattus norvegicus@ENSRNOP00000053644[RRM1][KOG0117]

Eutheria@ENSCPOP00000011171[3][RRM1:100%*][hnRNP:67%][KOG0117:100%*]Bilateria@ENSGALP00000025475[210][RRM1:100%*****][hnRNP:33%****][KOG0117:100%*****]

Tribolium castaneum@XP_967803[2][RRM1:100%][KOG0117:100%]Eutheria@ENSBTAP00000025092[6][RRM1:100%*][KOG0117:100%*]

Gasterosteus aculeatus@ENSGACP00000025947[RRM1][KOG0117]Aedes aegypti@AAEL015050-PA[2][RRM1:100%][KOG0117:100%]

Anopheles gambiae@AGAP002326-PA[RRM1]Saccharomycetales@NP_984279[4][RRM1:100%*][KOG0921:75%*][.KOG0106:25%]

Plasmodium falciparum_3D7@XP_001348072[RRM1][KOG0144]Trypanosomatidae@XP_001469326[2][RRM4:100%][KOG0123:100%]

Trypanosomatidae@XP_001469222[2][RRM4:100%][KOG0123:100%]Dictyostelium discoideum_AX4@XP_629639[RRM2][KOG0145]

Ricinus communis@30146_m003481[RRM3][KOG0123]rosids@30078_m002213[3][RRM3:100%*][PABP:33%][KOG0123:100%*]

Arabidopsis thaliana@NP_195978[RRM1][KOG0123]Oryza sativa_japonica_cultivar-group@NP_001049727[RRM3][KOG0123]

Dictyostelium discoideum_AX4@XP_001134510[RRM4][KOG0123]Ustilago maydis_521@XP_759458[RRM2][KOG0123]Cryptococcus neoformans_var._neoformans_JEC21@XP_569319[RRM1][KOG0123]

Saccharomycetaceae@XP_001385635[2][RRM2:100%][KOG0131:100%]Yarrowia lipolytica@XP_503979[RRM2][KOG0131]

Eukaryota@jgi_Physo1_1_108557[316][RRM2:91%*****][.RRM1:9%***][PABP:46%****][KOG0123:79%*****][.KOG0131:21%****]Cryptosporidium parvum_Iowa_II@XP_627780[RRM2][KOG0131]

Saccharomyces cerevisiae@YOR319W[RRM2][KOG0131]Volvox carteri@jgi_Volca1_116517[RRM2][KOG1984]

Coelomata@ENSTBEP00000005385[105][RRM2:86%****][.RRM1:14%**][P54nrb:30%***][.PSP1:24%***][.PSF:21%***][KOG0115:100%****]Dictyostelium discoideum_AX4@XP_646802[RRM2][KOG0145]

Leishmania infantum_JPCM5@XP_001467067[2][RRM1:100%][KOG0144:100%]Saccharomycetaceae@XP_451236[2][RRM1:100%][KOG0144:100%]

Saccharomyces cerevisiae@YGR250C[RRM1][KOG0108]Yarrowia lipolytica@XP_500351[RRM3][KOG0123]

Leishmania infantum_JPCM5@XP_001466041[RRM4][KOG0123]

4 - PABP

p54rnb

PSP1

PSF

2 - hnRNP

7 - Bruno

FCA FPA

8 - Bruno

FCA FPA

11 - ELAV

RBMS

1

54 5553 - RBM

15


Fig. S6

84

73

83

74

95

51

70

58

75

Phytophthora ramorum@jgi Phyra1 1 73884[RRM2][KOG4205]Ricinus communis@28976_m000161[RRM2][KOG4205]

Ascomycota@XP_961230[5][RRM2:100%*][put-sr:20%][KOG4205:100%*]Saccharomycetales@XP_449511[7][RRM2:100%*][KOG4205:100%*]Eukaryota@AGAP006656-PA[121][RRM2:88%****][.RRM1:12%**][Musashi:36%***][.Dazap:21%***][.hnRNP:10%**][KOG4205:100%****]

Ciona@ENSCSAVP00000001921[3][RRM2:100%*][Musashi:67%][KOG4205:100%*]Strongylocentrotus purpuratus@NP_999784[3][RRM1:100%*][KOG4205:100%*]


Cryptosporidium parvum_Iowa_II@XP_626579[RRM2][KOG4205]Theileria parva_strain_Muguga@XP_766400[RRM1][put-sr][KOG4205]

Plasmodium falciparum_3D7@XP_001351452[RRM2][KOG4205]Myotis lucifugus@ENSMLUP00000003070[RRM1][hnRNP][KOG4205]

Oryctolagus cuniculus@ENSOCUP00000001170[RRM1][hnRNP][KOG4205]Bacillariophyta@jgi_Phatr2_21039[2][RRM1:100%][KOG4205:100%]

Endopterygota@CG16901-PC[19][RRM1:100%**][KOG4205:100%**]Strongylocentrotus purpuratus@XP_001176409[2][RRM2:100%][KOG4205:100%]

Strongylocentrotus purpuratus@XP_001183095[2][RRM2:100%][KOG4205:100%]Caenorhabditis elegans@F42A6_7a_1[8][RRM2:100%**][KOG4205:100%**]

Coelomata@CG6354-PB[373][RRM2:95%*****][hnRNP:53%*****][KOG4205:100%*****]Sorex araneus@ENSSARP00000008097[RRM2][hnRNP][KOG4205]


Ustilago maydis_521@XP_758567[RRM2][KOG4205]Dictyostelium discoideum_AX4@XP_629598[RRM2][KOG4205]

Cyanidioschyzon merolae@gnl_CMER_CMR392C[RRM2][KOG4205]Ostreococcus tauri@jgi_Ostta4_33731[RRM2]

Ostreococcus tauri@jgi_Ostta4_33731[RRM1]Drosophila melanogaster@CG9654-PA[RRM2][KOG4205]

Caenorhabditis elegans@Y73B6BL_6b_3[10][RRM1:100%**][KOG4205:100%**]Strongylocentrotus purpuratus@XP_798256[2][RRM1:100%][KOG2277:100%]

Oryzias latipes@ENSORLP00000005442[2][RRM1:100%][KOG2277:100%]Xenopus tropicalis@ENSXETP00000012439[RRM1][KOG2277]

Oryctolagus cuniculus@ENSOCUP00000014792[RRM1][KOG2277]Viridiplantae@NP_851001[17][RRM2:100%**][put-sr:12%][KOG4205:94%**][.KOG1833:6%]

Theileria parva_strain_Muguga@XP_766400[RRM2][put-sr][KOG4205]Ostreococcus lucimarinus@jgi_Ost9901_3_24530[RRM1][KOG4205]

Oryza sativa_japonica_cultivar-group@NP_001067093[RRM1][KOG4177]Plasmodium falciparum_3D7@XP_001351452[RRM1][KOG4205]

Cryptococcus neoformans_var._neoformans_JEC21@XP_568675[RRM2][KOG4205]Endopterygota@AAEL008257-PA[8][RRM2:100%**][KOG4205:100%**]

Chlamydomonadales@jgi_Volca1_107445[2][RRM2:100%][KOG4205:100%]Physcomitrella patens@jgi_Phypa1_1_19696[RRM1][KOG4205]

Endopterygota@XP_001121454[19][RRM2:100%**][KOG4205:100%**]Euteleostomi@ENSDARP00000005968[129][RRM2:95%****][.RRM1:5%*][hnRNP:57%****][KOG4205:100%****]

Physcomitrella patens@jgi_Phypa1_1_120016[RRM2][KOG4205]Caenorhabditis elegans@Y73B6BL_6a_3[10][RRM2:100%**][KOG4205:100%**]

Ciona@ENSCSAVP00000016637[3][RRM2:100%*][KOG4205:100%*]Ciona@ENSCINP00000028810[2][RRM2:100%][KOG4205:100%]

Ornithorhynchus anatinus@ENSOANP00000022523[3][RRM1:67%][.RRM2:33%][KOG2248:100%*]Plasmodium falciparum_3D7@XP_001347758[RRM2][KOG0149]

Plasmodium falciparum_3D7@XP_001347758[RRM1][KOG0149]Strongylocentrotus purpuratus@XP_789716[2][RRM2:100%][KOG4205:100%]

Strongylocentrotus purpuratus@XP_780859[2][RRM2:100%][KOG4205:100%]Chlamydomonadales@jgi_Volca1_43575[2][RRM3:100%][KOG4205:100%]

Encephalitozoon cuniculi_GB-M1@NP_597487[RRM1][KOG4205]Embryophyta@IMGA_AC144431_42_2[6][RRM3:100%*][put-sr:17%][KOG4205:100%*]

Embryophyta@jgi_Phypa1_1_112860[6][RRM2:100%*][put-sr:17%][KOG4205:100%*]Chlamydomonadales@jgi_Chlre3_105806[2][RRM2:100%][KOG4205:100%]

Ostreococcus lucimarinus@jgi_Ost9901_3_27365[RRM2][KOG0123]Eukaryota@XP_391240[27][RRM2:67%**][.RRM1:33%**][cpRNP:19%*][KOG0127:48%**][.KOG0108:22%*][.KOG0131:15%*][.KOG0149:7%][.KOG0145:7%]


Ostreococcus@jgi_Ost9901_3_34381[2][RRM1:100%][KOG0145:100%]Aureococcus anophagefferens@jgi_Auran1_9354[RRM1]


Cryptosporidium parvum_Iowa_II@XP_626158[RRM2][KOG0144]Oryza sativa_japonica_cultivar-group@NP_001045556[RRM1][KOG0108]

rosids@29154_m000213[5][RRM1:100%*][oligoU:40%][KOG0122:40%][.KOG0113:20%][.KOG0148:20%]Magnoliophyta@NP_001052753[3][RRM1:100%*][oligoU:33%][KOG0108:33%][.KOG0149:33%][.KOG0127:33%]

Magnoliophyta@29930_m000611[5][RRM1:100%*][KOG0113:100%*]Magnoliophyta@9946_m000021_AZM5_3995[2][RRM1:100%][KOG0111:50%][.KOG0113:50%]

Arabidopsis thaliana@NP_974808[2][RRM1:100%][KOG0123:50%][.KOG0148:50%]Cryptococcus neoformans_var._neoformans_JEC21@XP_566745[2][RRM1:100%]

Medicago truncatula@IMGA_AC122162_7_2[RRM1][KOG0149]Arabidopsis thaliana@NP_565646[RRM1][KOG0149]

Ricinus communis@30055_m001598[RRM1][KOG0149]Eukaryota@jgi_Phypa1_1_37849[169][RRM1:100%*****][put-sr:5%**][GRSRBP:33%****][.hnRNP:18%***][.RBMY:15%***][KOG0108:23%***][.KOG0111:23%***][.KOG0149:18%***][.KOG0117:11%**][.KOG0116:9%**]

Magnoliophyta@NP_001059075[6][RRM1:100%*][put-sr:17%][GRSRBP:50%*][KOG0108:50%*][.KOG0148:33%][.KOG0111:17%]rosids@NP_568388[3][RRM1:100%*][KOG0125:33%][.KOG0148:33%]

Physcomitrella patens@jgi_Phypa1_1_151460[4][RRM1:100%*][KOG0108:75%*][.KOG0149:25%]Magnoliophyta@NP_181287[9][RRM1:100%**][oligoU:22%][KOG0148:56%*][.KOG0127:22%][.KOG0145:11%][.KOG0113:11%]

Arabidopsis thaliana@NP_173298[RRM1][GRSRBP][KOG0149]Euteleostomi@ENSGALP00000012472[36][RRM4:89%***][.RRM2:8%*][nucleolin:56%**][KOG0123:100%***]

Yarrowia lipolytica@XP_505375[RRM1][KOG0148]Saccharomycetales@XP_456900[6][RRM1:100%*][nucleolin:17%][KOG0148:50%*][.KOG0131:33%][.KOG4210:17%]

Schizosaccharomyces pombe_972h-@NP_593531[RRM1][nucleolin][KOG0147]Basidiomycota@XP_566835[2][RRM1:100%][KOG0148:100%]

Aspergillus fumigatus_Af293@XP_754840[RRM1][KOG0148]Neurospora crassa_OR74A@XP_963862[RRM1][KOG0127]

Cryptosporidium parvum_Iowa_II@XP_626158[RRM1][KOG0144]Embryophyta@29900_m001607[13][RRM2:100%**][oligoU:38%*][KOG4205:77%**][.KOG0149:23%*]

Embryophyta@jgi_Phypa1_1_44443[2][RRM2:100%][KOG0149:100%]Chordata@ENSOGAP00000005376[31][RRM2:90%***][.RRM3:6%][RBM:39%**][KOG0127:100%***]


Nasonia vitripennis@XP_001605703[RRM2][KOG0127]Nasonia vitripennis@XP_001605703[RRM1][KOG0127]

Aedes aegypti@AAEL008572-PA[RRM1][KOG0127]Drosophila melanogaster@CG4806-PA[RRM1][KOG0127]

Strongylocentrotus purpuratus@XP_793277[2][RRM3:100%][KOG0117:100%]Bilateria@ENSLAFP00000012959[197][RRM3:93%*****][.RRM2:5%**][hnRNP:36%****][KOG0117:100%*****]

Embryophyta@jgi_Phypa1_1_217831[15][RRM3:93%**][.RRM1:7%][KOG0117:100%**]Embryophyta@29742_m001371[15][RRM2:80%**][.RRM1:20%*][put-sr:87%**][SR:67%**][KOG0106:100%**]

Chlamydomonas reinhardtii@jgi_Chlre3_80366[RRM2][KOG0106]Chlamydomonas reinhardtii@jgi_Chlre3_120019[RRM2][KOG0106]Bacillariophyta@jgi_Phatr2_47737[2][RRM1:100%][put-sr:50%]

Cyanidioschyzon merolae@gnl_CMER_CMO009C[RRM2]Saccharomycetales@XP_455897[3][RRM1:100%*][KOG0123:67%]

Caenorhabditis elegans@C07A4_1[RRM2][KOG0148]Caenorhabditis elegans@Y46G5A_13[10][RRM2:80%**][.RRM3:20%][KOG0148:100%**]

Coelomata@CG4787-PA[102][RRM3:74%****][.RRM2:16%**][.RRM1:11%**][TIATIAR:75%****][KOG0148:100%****]Embryophyta@29727_m000492[13][RRM3:92%**][.RRM2:8%][oligoU:46%*][KOG0148:100%**]

Dikarya@XP_570577[4][RRM3:100%*][KOG0148:100%*]Embryophyta@NP_001067623[8][RRM1:100%**][KOG0117:100%**]

Oryza sativa_japonica_cultivar-group@NP_001066102[RRM1][KOG0117]rosids@NP_001030849[6][RRM1:100%*][KOG0117:100%*]

Physcomitrella patens@jgi_Phypa1_1_140180[3][RRM1:100%*][KOG0117:100%*]Magnoliophyta@29709_m001182[6][RRM1:100%*][put-sr:17%][KOG0117:100%*]

62

79 - TIA TIAR

OligoU



63 - hnRNP

71 - RBM

35 - G3BP

RBM

58 - GSRBP

hnRNP

RBMY

34

Fig. S6

85

5158

74

54

70

83

63

76 75

56

61 53

86

55

65 66

99

77

61

95

83

54

Saccharomycetaceae@XP 453677[2][RRM1:100%][KOG4209:100%]Candida glabrata_CBS138@XP_447800[RRM1][KOG4209]

Saccharomyces cerevisiae@YIR001C[RRM1][PABP][KOG4209]Eukaryota@ENSCSAVP00000003369[89][RRM1:100%****][put-sr:17%**][PABP:26%***][KOG4209:100%****]

Dictyostelium discoideum_AX4@XP_642788[RRM1][KOG4209]Caenorhabditis elegans@T08B6_5[RRM1][KOG4209]

Caenorhabditis elegans@EEED8_12[2][RRM1:100%][KOG4209:100%]Ciona@ENSCSAVP00000010162[2][RRM1:100%][KOG4209:100%]

Volvox carteri@jgi_Volca1_103724[RRM1][put-sr][KOG0591]Physcomitrella patens@jgi_Phypa1_1_167236[RRM1][KOG4209]

Arabidopsis thaliana@NP_180012[RRM1]Magnoliophyta@IMGA_AC160842_25_1[6][RRM1:100%*][KOG3702:83%*][.KOG4209:17%]

Aspergillus fumigatus_Af293@XP_755976[RRM1]Sordariomycetes@XP_956776[2][RRM1:100%][put-sr:50%]

Schizosaccharomyces pombe_972h-@NP_595728[RRM1]Ustilago maydis_521@XP_762237[RRM1]


Physcomitrella patens@jgi_Phypa1_1_135986[RRM1][KOG0128]Yarrowia lipolytica@XP_504609[RRM1]

Coelomata@XP_001182806[39][RRM1:100%***][KOG0108:13%*][.KOG0116:8%*][.KOG0921:5%]Phytophthora@jgi_Phyra1_1_83430[2][RRM1:100%]

Pichia stipitis_CBS_6054@XP_001384729[RRM1]Ciona@ENSCSAVP00000001842[2][RRM1:100%]Euteleostomi@ENSSARP00000000775[28][RRM1:100%***][eIF4B:54%**]

Anopheles gambiae@AGAP000525-PA[RRM1]Drosophila melanogaster@CG10837-PA[3][RRM1:100%*]

Yarrowia lipolytica@XP_505724[RRM1][KOG4198]Schizosaccharomyces pombe_972h-@NP_595090[RRM2]

Pezizomycotina@XP_961985[2][RRM2:100%][KOG0116:50%]Caenorhabditis elegans@ZC404_8_2[2][RRM1:100%][KOG0125:100%]

Felis catus@ENSFCAP00000007638[RRM1][KOG0125]Bilateria@ENSORLP00000014121[125][RRM1:100%****][FOX:75%****][KOG0125:100%****]

Dictyostelium discoideum_AX4@XP_629578[RRM1][KOG0122]Phytophthora@jgi_Physo1_1_137237[2][RRM1:100%][put-sr:100%][KOG0125:50%][.KOG0148:50%]

Plasmodium falciparum_3D7@XP_001347313[RRM1][KOG0127]Embryophyta@jgi_Phypa1_1_28366[17][RRM1:100%**][put-sr:76%**][KOG0127:29%*][.KOG0125:12%][.KOG4661:6%][.KOG0147:6%]

Coelomata@ENSTBEP00000011040[87][RRM1:98%****][put-sr:16%**][KOG4661:100%****]Tribolium castaneum@XP_971197[RRM1][KOG4661]

Tribolium castaneum@XP_969134[RRM1]Cryptococcus neoformans_var._neoformans_JEC21@XP_570425[RRM1][put-sr][KOG0145]

Yarrowia lipolytica@XP_499712[RRM1][KOG0145]Pezizomycotina@XP_960722[3][RRM1:100%*][put-sr:33%][KOG0113:33%]

Schizosaccharomyces pombe_972h-@NP_001018280[RRM1][KOG0145]Chlamydomonas reinhardtii@jgi_Chlre3_152139[RRM1][KOG0117]

Cryptococcus neoformans_var._neoformans_JEC21@XP_569209[RRM2][KOG0144]Ustilago maydis_521@XP_761797[RRM1][put-sr][KOG3257]Leptospira@YP_001385[4][RRM1:100%*][PROK:100%*]

Oryza sativa_japonica_cultivar-group@NP_001054954[2][RRM1:100%][KOG0108:100%]Chlamydomonas reinhardtii@jgi_Chlre3_194261[RRM1][KOG0123]


Encephalitozoon cuniculi_GB-M1@NP_586226[RRM1][put-sr][KOG0123]Amniota@ENSMODP00000004174[11][RRM4:55%*][.RRM3:36%*][.RRM2:9%][put-sr:100%**][KOG0112:100%**]

Ciona intestinalis@ENSCINP00000024280[RRM1][KOG0113]Chlamydomonadales@jgi_Volca1_107658[2][RRM1:100%][KOG4205:50%][.KOG0474:50%]

Dictyostelium discoideum_AX4@XP_640243[RRM1][KOG0117]Strongylocentrotus purpuratus@NP_999784[3][RRM2:100%*][KOG4205:100%*]

Ciona@ENSCINP00000009845[4][RRM1:100%*][KOG0116:100%*]Deuterostomia@ENSMODP00000011218[78][RRM1:100%****][G3BP:82%****][KOG0116:100%****]

Apis mellifera@XP_623996[RRM1][KOG0116]Tribolium castaneum@XP_975463[RRM1][KOG0116]

Dictyostelium discoideum_AX4@XP_643377[RRM1][KOG3598]Euteleostomi@ENSEEUP00000005436[64][RRM1:95%****]

Takifugu rubripes@SINFRUP00000155469[RRM1]Coelomata@AAEL001684-PA[39][RRM1:100%***][KOG0125:21%**]

Caenorhabditis elegans@F56D1_7[RRM1]Spermophilus tridecemlineatus@ENSSTOP00000003171[RRM1]

Tupaia belangeri@ENSTBEP00000015084[RRM1]Arabidopsis thaliana@NP_179762[RRM1][oligoU]

Phytophthora@jgi_Phyra1_1_84416[2][RRM1:100%][KOG0148:100%]Phytophthora@jgi_Physo1_1_134615[2][RRM1:100%]

Oryza sativa_japonica_cultivar-group@NP_001051402[RRM1][KOG0149]Zea mays@14684_m000016_AZM5_14964[RRM1][KOG4205]

Dictyostelium discoideum_AX4@XP_643856[3][RRM1:100%*][KOG0149:100%*]Euteleostomi@ENSSTOP00000002923[18][RRM1:100%**][KOG4205:11%]

Caenorhabditis elegans@C50B8_1[RRM1]Strongylocentrotus purpuratus@XP_001188704[2][RRM1:100%][KOG0149:100%]

Diptera@AAEL006645-PA[2][RRM1:100%][KOG0149:100%]Diptera@AAEL008317-PA[3][RRM1:100%*][KOG0149:100%*]

Aureococcus anophagefferens@jgi_Auran1_66158[RRM2][put-sr][KOG0149]Arabidopsis thaliana@NP_187353[RRM1][30kRRM][KOG0149]

Eukaryota@NP_001058102[93][RRM1:100%****][RBM:52%***][.30kRRM:13%**][KOG0149:96%****]Arabidopsis thaliana@NP_200183[2][RRM1:100%][oligoU:100%][KOG0149:100%]

Phytophthora sojae@jgi_Physo1_1_139371[RRM1][KOG4205]Oryza sativa_japonica_cultivar-group@NP_001054022[RRM1][KOG4205]


Aureococcus anophagefferens@jgi_Auran1_6078[RRM1][KOG4205]Aureococcus anophagefferens@jgi_Auran1_9576[RRM1][KOG0149]

Phytophthora ramorum@jgi_Phyra1_1_73884[RRM1][KOG4205]Ciona intestinalis@ENSCINP00000006182[RRM1][KOG4205]

Ciona intestinalis@ENSCINP00000029053[RRM1][KOG4205]Eukaryota@ENSMODP00000031317[289][RRM1:100%*****][hnRNP:28%****][.Musashi:13%***][.Dazap:9%***][KOG4205:99%*****]

Bilateria@ENSRNOP00000022054[326][RRM1:100%*****][hnRNP:54%*****][KOG4205:100%*****]Strongylocentrotus purpuratus@XP_001189292[2][RRM1:100%][KOG4205:100%]

Strongylocentrotus purpuratus@XP_001176409[2][RRM1:100%][KOG4205:100%]Chlamydomonadales@jgi_Chlre3_105806[2][RRM1:100%][KOG4205:100%]


Cyanidioschyzon merolae@gnl_CMER_CMR392C[RRM1][KOG4205]Chlamydomonadales@jgi_Volca1_107445[2][RRM1:100%][KOG4205:100%]

Phaeodactylum tricornutum@jgi_Phatr2_41450[RRM1][KOG4205]Thalassiosira pseudonana@jgi_Thaps3_25203[2][RRM1:100%][KOG4205:100%]Embryophyta@jgi_Phypa1_1_156290[6][RRM1:100%*][put-sr:17%][KOG4205:100%*]

Phaeodactylum tricornutum@jgi_Phatr2_21039[RRM2][KOG4205]Ciona@ENSCINP00000012771[9][RRM1:100%**][put-sr:11%][KOG4205:100%**]

Oryza sativa_japonica_cultivar-group@NP_001058805[RRM1][KOG4205]Ricinus communis@28976_m000161[RRM1][KOG4205]Ricinus communis@30170_m013671[RRM1][KOG4205]Arabidopsis thaliana@NP_176143[RRM1][KOG4205]

Takifugu rubripes@SINFRUP00000163373[RRM1][KOG0149]Takifugu rubripes@SINFRUP00000145256[RRM1][KOG0149]


Cryptosporidium parvum_Iowa_II@XP_626025[RRM1][KOG4205]Chlamydomonadales@jgi_Chlre3_181880[2][RRM2:100%][KOG4205:100%]Cryptosporidium parvum_Iowa_II@XP_001388284[RRM1][KOG4205]

Drosophila melanogaster@CG9654-PA[RRM1][KOG4205]Phytophthora ramorum@jgi_Phyra1_1_73884[RRM2][KOG4205]

30K-RRM

hnRNP

Musashi

Dazap

TARDBP

OligoU

61

68 - FOX

87 - eIF-4B

74

83 - PABP

Fig. S6

86

63 88

84

58

64

59

52

76

52

86

75

58

Tetraodontidae@GSTENP00014994001[2][RRM1:50%][ RRM3:50%][KOG0123:50%]Embryophyta@jgi_Phypa1_1_201182[6][RRM2:100%*][KOG0127:100%*]

Ostreococcus@jgi_Ost9901_3_26255[2][RRM2:100%][KOG0127:100%]Chlamydomonas reinhardtii@jgi_Chlre3_186870[RRM2][KOG0127]Leishmania infantum_JPCM5@XP_001466413[RRM3][put-sr][KOG0147]

Trypanosoma brucei_TREU927@XP_951655[RRM3][put-sr][KOG0109]Trypanosoma brucei_TREU927@XP_951655[RRM2][put-sr][KOG0109]

Leishmania infantum_JPCM5@XP_001466413[RRM2][put-sr][KOG0147]Thalassiosira pseudonana@jgi_Thaps3_1374[RRM2][KOG0116]

Aureococcus anophagefferens@jgi_Auran1_8214[RRM1]Phytophthora@jgi_Physo1_1_136329[2][RRM2:100%][KOG0123:100%]

Physcomitrella patens@jgi_Phypa1_1_93324[RRM1]Ustilago maydis_521@XP_761797[RRM2][put-sr][KOG3257]

Dictyostelium discoideum_AX4@XP_638767[RRM2][KOG0123]Phaeodactylum tricornutum@jgi_Phatr2_44442[RRM2][KOG4211]

Physcomitrella patens@jgi_Phypa1_1_96043[RRM1]Physcomitrella patens@jgi_Phypa1_1_204078[RRM1][KOG0116]

Magnoliophyta@NP_001052571[5][RRM1:100%*][KOG0116:100%*]Arabidopsis thaliana@NP_189151[RRM1][NTF][KOG0116]

Phaeodactylum tricornutum@jgi_Phatr2_8457[RRM1][KOG0122]Ostreococcus@jgi_Ostta4_19569[2][RRM3:100%][KOG0127:100%]

Chlamydomonadales@jgi_Volca1_87629[2][RRM3:100%][KOG0127:100%]Dictyostelium discoideum_AX4@XP_646584[RRM3][KOG0127]

Caenorhabditis elegans@B0035_12_2[2][RRM2:100%][KOG0128:100%]Magnoliophyta@30131_m007093[6][RRM3:83%*][.RRM2:17%][KOG0127:100%*]

Physcomitrella patens@jgi_Phypa1_1_201182[RRM3][KOG0127]Theileria parva_strain_Muguga@XP_765501[RRM2][KOG0127]

Saccharomycetales@XP_001385462[7][RRM3:100%*][KOG0127:100%*]Basidiomycota@XP_756663[3][RRM4:67%][.RRM3:33%][KOG0127:100%*]


Aspergillus fumigatus_Af293@XP_752199[RRM3][KOG0127]Ciona intestinalis@ENSCINP00000018774[2][RRM3:100%][KOG0127:100%]

Caenorhabditis elegans@R05H10_2[RRM2][KOG0127]Oryzias latipes@ENSORLP00000012079[RRM3][KOG0127]

Euteleostomi@ENSGACP00000016696[19][RRM3:79%**][.RRM4:11%][.RRM1:11%][RBM:58%**][KOG0127:100%**]Strongylocentrotus purpuratus@XP_783689[2][RRM2:100%][KOG0127:100%]

Endopterygota@XP_001605703[3][RRM2:67%][.RRM3:33%][KOG0127:100%*]Drosophila melanogaster@CG4806-PA[RRM2][KOG0127]

Aedes aegypti@AAEL008572-PA[RRM2][KOG0127]Schizosaccharomyces pombe_972h-@NP_596518[RRM1][KOG0116]

Yarrowia lipolytica@XP_505184[RRM1]Dictyostelium discoideum_AX4@XP_643642[RRM1][KOG0148]

Ciona intestinalis@ENSCINP00000023563[RRM1][KOG0108]Caenorhabditis elegans@R09B3_3[3][RRM1:100%*][KOG0108:100%*]

Chordata@ENSETEP00000010530[36][RRM1:50%**][.RRM2:50%**][put-sr:100%***][SRrp:75%***][KOG4676:100%***]Saccharomycetaceae@XP_001383390[2][RRM1:100%][KOG0108:100%]

Cryptococcus neoformans_var._neoformans_JEC21@XP_572946[RRM1][KOG0108]Oryza sativa_japonica_cultivar-group@NP_001058465[RRM1][KOG0108]

Aureococcus anophagefferens@jgi_Auran1_23269[RRM1][KOG0108]Bacillariophyta@jgi_Phatr2_8451[2][RRM1:100%][KOG0108:100%]


Eukaryota@ENSDARP00000064611[84][RRM1:100%****][KOG0108:99%****]Encephalitozoon cuniculi_GB-M1@NP_597167[RRM1][KOG0108]

Ostreococcus tauri@jgi_Ostta4_31925[RRM1][KOG0117]Euteleostomi@ENSGACP00000016390[7][RRM1:100%*][put-sr:86%*][RBM:14%][KOG2253:100%*]

Viridiplantae@29631_m001006[3][RRM1:100%*][put-sr:33%][KOG0108:67%][.KOG2253:33%]Ciona savignyi@ENSCSAVP00000008315[4][RRM1:100%*][KOG0108:100%*]

Cryptosporidium parvum_Iowa_II@XP_001388131[RRM1][KOG1015]Theileria parva_strain_Muguga@XP_765374[RRM1]

Physcomitrella patens@jgi_Phypa1_1_12664[RRM1]rosids@30155_m001644[2][RRM1:100%][KOG0116:50%]

Tribolium castaneum@XP_969008[RRM2][KOG0331]Euteleostomi@ENSDARP00000069729[82][RRM1:100%****][KOG1995:77%****][.KOG0921:16%**][.KOG2044:5%*]

Endopterygota@XP_624681[6][RRM1:100%*][put-sr:17%][KOG0921:67%*][.KOG1548:33%]Arabidopsis thaliana@NP_564565[RRM1][put-sr][KOG1995]

Strongylocentrotus purpuratus@XP_001196853[2][RRM1:100%][KOG1995:100%]Ostreococcus tauri@jgi_Ostta4_34258[RRM2]

Thalassiosira pseudonana@jgi_Thaps3_24369[RRM1]Phaeodactylum tricornutum@jgi_Phatr2_44442[RRM1][KOG4211]

Phytophthora@jgi_Phyra1_1_76845[2][RRM1:100%][KOG0123:100%]Phaeodactylum tricornutum@jgi_Phatr2_44395[RRM1]

Poaceae@8373_m000321_c0161G04[2][RRM1:100%][KOG4205:50%][.KOG4211:50%]Volvox carteri@jgi_Volca1_90315[RRM1]

Embryophyta@28180_m000395[3][RRM1:100%*][KOG0124:100%*]Arabidopsis thaliana@NP_191094[RRM1][KOG4205]Ostreococcus tauri@jgi_Ostta4_10328[RRM1][KOG2476]

Phytophthora sojae@jgi_Physo1_1_139998[RRM1]Phytophthora@jgi_Phyra1_1_77488[2][RRM1:100%][KOG4205:100%]

Aureococcus anophagefferens@jgi_Auran1_71372[2][RRM3:50%][.RRM2:50%][put-sr:100%][KOG1178:100%]Caenorhabditis elegans@W02D3_11b[2][RRM1:100%][KOG4211:100%]

Oryzias latipes@ENSORLP00000025180[RRM2][put-sr][KOG4307]Coelomata@ENSCINP00000003632[126][RRM2:70%****][.RRM1:30%***][hnRNP:37%***][.GRSRBP:15%**][KOG4211:100%****]

Danio rerio@ENSDARP00000069459[RRM2][KOG4211]Volvox carteri@jgi_Volca1_117772[RRM1][KOG1365]

Caenorhabditis elegans@Y73B6BL_33[RRM1][KOG4211]Physcomitrella patens@jgi_Phypa1_1_162342[RRM3][KOG1365]

Ciona savignyi@ENSCSAVP00000001587[RRM5][KOG4307]Thalassiosira pseudonana@jgi_Thaps3_5686[RRM2][KOG4211]

Arabidopsis thaliana@NP_188725[RRM2][hnRNP][KOG1365]Plasmodium falciparum_3D7@XP_001347519[RRM1][KOG1365]

Cryptosporidium parvum_Iowa_II@XP_627232[RRM1][put-sr][KOG0105]Cyanidioschyzon merolae@gnl_CMER_CMO334C[RRM2][KOG0126]Trypanosomatidae@XP_827554[2][RRM1:50%][.RRM2:50%][put-sr:50%]

Phaeodactylum tricornutum@jgi_Phatr2_46145[RRM2]Coelomata@ENSDARP00000093407[32][RRM2:88%***][.RRM1:12%*][KOG0108:12%*][.KOG3001:6%][.KOG0123:6%][.KOG0126:6%]

Apis mellifera@XP_394565[RRM2][KOG0147]Volvox carteri@jgi_Volca1_118759[RRM2]

Ostreococcus@jgi_Ostta4_30189[2][RRM1:50%][.RRM2:50%][put-sr:50%]Magnoliophyta@30054_m000807[2][RRM2:100%][KOG1267:50%]

Caenorhabditis elegans@F11A10_7[RRM2][KOG0131]Dictyostelium discoideum_AX4@XP_635997[RRM2]

Theileria parva_strain_Muguga@XP_766096[RRM1]Ascomycota@XP_505055[6][RRM1:83%*][.RRM2:17%]

Drosophila melanogaster@CG12288-PA[RRM2]Culicidae@AGAP003171-PA[3][RRM2:100%*][KOG0148:33%]Phytophthora@jgi_Physo1_1_157186[2][RRM1:100%][KOG0147:100%]

Strongylocentrotus purpuratus@XP_001198098[2][RRM1:100%][put-sr:100%][KOG0147:100%]Ostreococcus@jgi_Ost9901_3_42846[2][RRM1:100%][put-sr:50%][KOG0147:100%]

Volvox carteri@jgi_Volca1_84128[2][RRM1:100%][put-sr:50%][KOG0147:100%]Cryptosporidium parvum_Iowa_II@XP_628665[RRM1][KOG0147]Plasmodium falciparum_3D7@XP_001349956[RRM1][KOG0147]

Dictyostelium discoideum_AX4@XP_638966[RRM1][KOG0147]Eukaryota@ENSMLUP00000011758[47][RRM1:100%***][put-sr:91%***][UMH:64%***][.CAPER:15%*][KOG0147:100%***]

Yarrowia lipolytica@XP_504318[RRM1][KOG0147]Ascomycota@NP_594422[4][RRM1:100%*][put-sr:100%*][KOG0147:100%*]

Trypanosomatidae@XP_001467105[2][RRM1:100%][KOG4209:100%]Trypanosomatidae@XP_847474[2][RRM1:100%]

Saccharomycetaceae@XP_453677[2][RRM1:100%][KOG4209:100%]

75 - CAPER

UMH

80 - hnRNP

85 - SRrp

72 - RBM

Fig. S6

87

72

85 89

83

80

75

86

67

90

63

90

69

Ciona intestinalis@ENSCINP00000019833[3][RRM2:100%*][KOG0128:100%*]Culicidae@AAEL011963-PA[3][RRM2:100%*][KOG0128:100%*]

Strongylocentrotus purpuratus@XP_781643[RRM2][KOG0128]Tribolium castaneum@XP_972538[RRM2][KOG0128]Apocrita@XP_001602582[2][RRM2:100%][KOG0128:100%]

Euteleostomi@ENSOCUP00000014007[29][RRM2:97%***][SART3:69%**][KOG0128:100%***]Apis mellifera@XP_623573[RRM1][KOG0113]

Saccharomycetaceae@XP_001385249[2][RRM1:100%][KOG0113:100%]Saccharomycetales@NP_984033[3][RRM1:100%*][KOG0113:100%*]

Kluyveromyces lactis@XP_452557[RRM1][KOG0113]Yarrowia lipolytica@XP_503802[RRM1][KOG0113]

Embryophyta@29657_m000467[4][RRM1:100%*][put-sr:50%][snRNP:25%][KOG0113:100%*]Ciona@ENSCSAVP00000001345[2][RRM1:100%][KOG0113:100%]

Deuterostomia@XP_001178221[30][RRM1:100%***][put-sr:63%**][snRNP:70%***][KOG0113:100%***]Tribolium castaneum@XP_966565[RRM1][KOG0113]

Phytophthora@jgi_Phyra1_1_44765[2][RRM1:100%][put-sr:50%][KOG0113:100%]Coelomata@AAEL011340-PB[2][RRM1:100%][put-sr:50%][KOG0113:100%]

Rattus norvegicus@ENSRNOP00000048879[RRM1][snRNP][KOG0113]Felis catus@ENSFCAP00000006212[RRM1][put-sr][KOG0113]


Aspergillus fumigatus_Af293@XP_753306[RRM1][KOG0113]Aureococcus anophagefferens@jgi_Auran1_34517[2][RRM1:100%][put-sr:50%][KOG0113:100%]

Cryptosporidium parvum_Iowa_II@XP_627471[RRM1][KOG0113]Ostreococcus@jgi_Ostta4_11066[2][RRM1:100%][KOG0113:100%]

Eukaryota@jgi_Physo1_1_143842[43][RRM1:100%***][put-sr:47%**][snRNP:14%*][KOG0113:100%***]Ciona intestinalis@ENSCINP00000019832[3][RRM1:100%*][KOG0128:100%*]

Tribolium castaneum@XP_972538[RRM1][KOG0128]Culicidae@AAEL011961-PA[3][RRM1:100%*][KOG0128:100%*]

Apocrita@XP_001602582[2][RRM1:100%][KOG0128:100%]Strongylocentrotus purpuratus@XP_781643[RRM1][KOG0128]

Euteleostomi@ENSSTOP00000002132[31][RRM1:100%***][SART3:68%***][KOG0128:100%***]Ostreococcus tauri@jgi_Ostta4_32569[RRM2]

Aureococcus anophagefferens@jgi_Auran1_64341[RRM2][KOG0108]Phaeodactylum tricornutum@jgi_Phatr2_49387[RRM1]

Ostreococcus lucimarinus@jgi_Ost9901_3_92667[RRM1]Aureococcus anophagefferens@jgi_Auran1_9434[RRM1]

Ostreococcus@jgi_Ostta4_33150[2][RRM2:100%][KOG0108:50%]Embryophyta@28180_m000395[6][RRM2:100%*][KOG0124:50%*][.KOG4205:33%][.KOG4211:17%]

Phytophthora@jgi_Physo1_1_141766[2][RRM2:100%][KOG0148:100%]Magnoliophyta@NP_001053909[5][RRM1:100%*][nucleolin:40%][KOG0123:40%][.KOG4210:40%][.KOG1015:20%]Chlamydomonadales@jgi_Volca1_54847[2][RRM1:100%][KOG0108:100%]

stramenopiles@jgi_Auran1_17857[4][RRM1:50%][.RRM2:50%][KOG0108:50%][.KOG4205:50%]Aedes aegypti@AAEL012119-PA[RRM1]

Kluyveromyces lactis@XP_454447[RRM3][KOG0128]Viridiplantae@jgi_Chlre3_99594[25][RRM1:100%***][KOG0123:8%]

Ostreococcus@jgi_Ost9901_3_7913[3][RRM1:100%*][KOG0131:33%]Trypanosoma brucei_TREU927@XP_829593[RRM1]

Neurospora crassa_OR74A@XP_960450[RRM1]Magnoliophyta@15974_m000013_AZM5_17589[3][RRM2:67%][.RRM1:33%]

Plasmodium falciparum_3D7@XP_966051[RRM2]Ostreococcus lucimarinus@jgi_Ost9901_3_28918[RRM1]


Pichia stipitis_CBS_6054@XP_001384763[RRM1][KOG0123]Saccharomyces cerevisiae@YMR268C[RRM1][KOG0128]

Trypanosomatidae@XP_843959[2][RRM3:100%]Apocrita@XP_001602363[2][RRM1:100%][KOG1832:50%]

Drosophila melanogaster@CG3594-PA[RRM1][KOG0110]Culicidae@AAEL001997-PA[2][RRM1:100%]

Schizosaccharomyces pombe_972h-@NP_596033[RRM1]Neurospora crassa_OR74A@XP_964518[RRM1]

Sordariomycetes@XP_389032[2][RRM1:100%]Cryptococcus neoformans_var._neoformans_JEC21@XP_570477[RRM1]

Phytophthora@jgi_Physo1_1_136292[2][RRM1:100%]Phaeodactylum tricornutum@jgi_Phatr2_32836[RRM1]

Yarrowia lipolytica@XP_499736[RRM2][KOG4205]Schizosaccharomyces pombe_972h-@NP_594970[RRM2][KOG4210]Saccharomycetales@NP_982813[6][RRM2:100%*][KOG4210:100%*]

Aspergillus fumigatus_Af293@XP_755020[RRM2]Culicidae@AAEL004075-PA[3][RRM5:67%][.RRM1:33%][KOG0110:100%*]Ostreococcus@jgi_Ost9901_3_710[2][RRM4:100%][KOG0110:100%]

Magnoliophyta@NP_193696[2][RRM3:100%][KOG0110:100%]Phytophthora sojae@jgi_Physo1_1_129427[RRM4][KOG0110]

Apocrita@XP_001605134[2][RRM5:100%][KOG0110:100%]Euteleostomi@ENSGALP00000013474[20][RRM5:85%**][.RRM4:5%][.RRM3:5%][.RRM2:5%][put-sr:10%][KOG0110:100%**]


Cryptosporidium parvum_Iowa_II@XP_627799[RRM4][KOG0110]Cryptococcus neoformans_var._neoformans_JEC21@XP_569873[RRM4][KOG0110]

Ascomycota@XP_001386803[10][RRM4:90%**][.RRM2:10%][KOG0110:100%**]Saccharomycetaceae@XP_458658[2][RRM1:100%][KOG0921:100%]Phytophthora@jgi_Physo1_1_132702[3][RRM1:100%*][KOG0127:100%*]

Plasmodium falciparum_3D7@XP_001352080[RRM2]Ashbya gossypii_ATCC_10895@NP_984845[RRM3][KOG0123]

Kluyveromyces lactis@XP_451368[RRM3][KOG0123]Saccharomyces cerevisiae@YHR015W[RRM3][KOG0123]

Candida glabrata_CBS138@XP_447635[RRM3][KOG0123]Saccharomyces cerevisiae@YFR023W[RRM3][KOG0123]

Saccharomycetales@NP_986417[7][RRM1:100%*][KOG0127:100%*]Basidiomycota@XP_568669[3][RRM1:100%*][KOG0127:100%*]

Schizosaccharomyces pombe_972h-@NP_596114[RRM1][KOG0127]Euteleostomi@ENSOANP00000001262[28][RRM1:100%***][RBM:46%**][KOG0127:100%***]

Sordariomycetes@XP_382687[2][RRM1:100%][KOG0127:100%]Aspergillus fumigatus_Af293@XP_752199[RRM1][KOG0127]


Ciona@ENSCINP00000018772[3][RRM1:100%*][KOG0127:100%*]Chlamydomonadales@jgi_Chlre3_186870[2][RRM1:100%][KOG0127:100%]

Dictyostelium discoideum_AX4@XP_646584[RRM1][KOG0127]Physcomitrella patens@jgi_Phypa1_1_201182[RRM1][KOG0127]


Physcomitrella patens@jgi_Phypa1_1_167900[RRM2][KOG1015]Arabidopsis thaliana@NP_188491[RRM2][nucleolin][KOG4210]

Magnoliophyta@29675_m000389[3][RRM2:100%*][KOG0123:67%][.KOG1015:33%]Dikarya@NP_596771[2][RRM1:100%][KOG0108:50%]

Pichia stipitis_CBS_6054@XP_001384763[RRM3][KOG0123]Cryptosporidium parvum_Iowa_II@XP_001388131[RRM2][KOG1015]

Dictyostelium discoideum_AX4@XP_643642[RRM2][KOG0148]Euteleostomi@GSTENP00013801001[29][RRM1:100%***][LA:59%**][KOG1855:100%***]

Euteleostomi@ENSORLP00000006283[2][RRM1:100%][LA:50%][KOG1855:100%]Apocrita@XP_001600355[2][RRM1:100%][KOG1855:100%]

Tribolium castaneum@XP_974730[RRM1][KOG1855]Ciona@ENSCSAVP00000005375[4][RRM2:75%*][.RRM1:25%][KOG0116:75%*][.KOG2141:25%]

Physcomitrella patens@jgi_Phypa1_1_167900[3][RRM1:100%*][KOG0123:33%][.KOG4210:33%][.KOG1015:33%]Euteleostomi@ENSMODP00000021210[32][RRM2:97%***][nucleolin:59%**][KOG0123:100%***]

Ciona@ENSCINP00000008105[4][RRM1:100%*][KOG0116:50%][.KOG2141:25%]Euteleostomi@GSTENP00022906001[41][RRM3:83%***][.RRM2:10%*][.RRM1:7%*][nucleolin:54%***][KOG0123:93%***]

Tetraodontidae@GSTENP00014994001[2][RRM1:50%][.RRM3:50%][KOG0123:50%]

81 - La

70 - RBM

59

73 - SART3

36 - snRNP

37 - SART3

39

Fig. S6

88

7557

62

88

60

56

56

66

60

70

52

73

100

Cryptococcus neoformans var neoformans JEC21@XP 567374[RRM1][KOG0307]Chlamydomonas reinhardtii@jgi_Chlre3_152680[RRM1][KOG4660]

Embryophyta@30128_m008555[15][RRM1:100%**][KOG4660:100%**]Phytophthora ramorum@jgi_Phyra1_1_77702[RRM1][KOG0154]

Trypanosoma brucei_TREU927@XP_845376[RRM3][KOG0148]Volvox carteri@jgi_Volca1_120369[RRM1][put-sr][KOG0147]Schizosaccharomyces pombe_972h-@NP_596424[RRM2][KOG4206]

Pezizomycotina@XP_753458[2][RRM2:100%][put-sr:50%][KOG4206:100%]Plasmodium falciparum_3D7@XP_001349796[RRM2][KOG4206]

Saccharomyces cerevisiae@YBR119W[RRM1]Cryptococcus neoformans_var._neoformans_JEC21@XP_568533[RRM2][KOG4206]

Eukaryota@ENSGACP00000013006[79][RRM2:96%****][snRNP:30%***][KOG4206:100%****]Theileria parva_strain_Muguga@XP_764943[RRM2][KOG4206]

Cryptosporidium parvum_Iowa_II@XP_628165[RRM2][KOG4212]Saccharomycetales@XP_462132[6][RRM1:100%*][KOG0533:100%*]

Cryptococcus neoformans_var._neoformans_JEC21@XP_572037[RRM1][KOG0533]Sordariomycetes@XP_956471[2][RRM1:100%][KOG0533:100%]

Ustilago maydis_521@XP_760032[RRM1][KOG0533]Schizosaccharomyces pombe_972h-@NP_595715[RRM1][KOG0533]

Cyanidioschyzon merolae@gnl_CMER_CMH135C[RRM1]Phytophthora@jgi_Phyra1_1_97175[2][RRM1:100%][put-sr:50%][KOG0533:100%]

Euteleostomi@ENSTBEP00000009485[3][RRM1:100%*][PDIP:33%][KOG0533:33%]Endopterygota@CG6961-PA[7][RRM1:100%*][KOG0533:29%]

Eukaryota@GSTENP00007343001[69][RRM1:100%****][FCAFPA:10%*][KOG0533:99%****]Ostreococcus tauri@jgi_Ostta4_36431[RRM1][KOG0533]


Yarrowia lipolytica@XP_505140[RRM1][KOG0533]Pezizomycotina@XP_958422[3][RRM1:100%*][put-sr:33%][KOG0533:100%*]

Ustilago maydis_521@XP_757147[RRM1][KOG0533]Theileria parva_strain_Muguga@XP_764636[RRM1]

Plasmodium falciparum_3D7@XP_966143[RRM1][KOG0533]Ostreococcus lucimarinus@jgi_Ost9901_3_27365[RRM3][KOG0123]

Chlamydomonadales@jgi_Volca1_103054[2][RRM3:50%][.RRM2:50%][KOG0055:50%]Trypanosomatidae@XP_001465100[2][RRM2:100%][KOG4212:100%]Saccharomycetales@XP_446962[5][RRM1:100%*][put-sr:60%*][KOG0127:60%*][.KOG0123:40%]

Saccharomycetaceae@XP_462023[2][RRM1:100%][put-sr:100%][KOG0123:100%]Aureococcus anophagefferens@jgi_Auran1_6342[RRM2][KOG0123]

Coelomata@ENSMLUP00000006206[100][RRM2:88%****][.RRM1:12%**][put-sr:5%*][hnRNP:28%***][KOG4212:98%****]Caenorhabditis elegans@C25A1_4_2[2][RRM2:100%][put-sr:100%][KOG4212:100%]

Basidiomycota@XP_758699[7][RRM1:71%*][.RRM2:29%][put-sr:14%][KOG4212:100%*]Plasmodium falciparum_3D7@XP_001347353[RRM2][KOG4212]

Schizosaccharomyces pombe_972h-@NP_594207[RRM2][KOG4212]Pezizomycotina@XP_751108[2][RRM2:100%][put-sr:100%][KOG4212:100%]

Cryptococcus neoformans_var._neoformans_JEC21@XP_568231[RRM2][put-sr][KOG0147]Trypanosomatidae@XP_001465100[2][RRM1:100%][KOG4212:100%]

Yarrowia lipolytica@XP_503927[RRM3][put-sr][KOG4212]Dikarya@XP_568231[5][RRM3:100%*][put-sr:80%*][KOG4212:80%*][.KOG0147:20%]

Saccharomycetales@XP_888678[3][RRM3:67%][.RRM2:33%][put-sr:67%][KOG0123:67%][.KOG4212:33%]Saccharomycetales@YNL004W[4][RRM3:100%*][put-sr:50%][KOG0123:50%][.KOG0127:50%]

Kluyveromyces lactis@XP_453283[RRM2][KOG0123]Saccharomycetales@XP_001386572[3][RRM2:67%][.RRM1:33%][put-sr:67%][KOG0123:67%][.KOG4212:33%]

Cryptococcus neoformans_var._neoformans_JEC21@XP_572539[4][RRM2:100%*][KOG4212:100%*]Candida glabrata_CBS138@XP_446962[RRM2][put-sr][KOG0127]

Saccharomycetales@XP_445179[2][RRM2:100%][put-sr:100%][KOG0123:100%]Saccharomycetaceae@XP_453283[2][RRM1:50%][.RRM2:50%][KOG0123:50%][.KOG0127:50%]

Saccharomyces cerevisiae@YNL004W[RRM2][KOG0127]Cyanidioschyzon merolae@gnl_CMER_CMM078C[RRM2][KOG4212]

Chlamydomonadales@jgi_Volca1_78979[2][RRM1:100%][KOG3070:100%]Volvox carteri@jgi_Volca1_109965[RRM2][KOG4212]


Thalassiosira pseudonana@jgi_Thaps3_37126[RRM2][KOG0123]Ostreococcus@jgi_Ost9901_3_27365[2][RRM1:100%][KOG0123:50%]

Ostreococcus lucimarinus@jgi_Ost9901_3_34965[RRM2][KOG4212]Strongylocentrotus purpuratus@XP_786244[2][RRM3:100%][put-sr:100%][KOG4212:100%]

Endopterygota@CG9373-PA[4][RRM3:100%*][KOG4212:100%*]Chordata@ENSOGAP00000002890[91][RRM3:80%****][.RRM2:13%**][.RRM1:7%*][hnRNP:37%***][KOG4212:100%****]

Volvox carteri@jgi_Volca1_103054[RRM2][KOG0055]Bacillariophyta@jgi_Phatr2_7426[2][RRM1:100%]

Chlamydomonadales@jgi_Chlre3_184854[2][RRM1:100%][KOG0055:50%]Eukaryota@jgi_Volca1_109965[18][RRM1:78%**][.RRM2:22%*][put-sr:22%*][KOG4212:61%**][.KOG0123:39%*]

Ostreococcus lucimarinus@jgi_Ost9901_3_34965[RRM1][KOG4212]Cryptococcus neoformans_var._neoformans_JEC21@XP_568231[RRM1][put-sr][KOG0147]

Strongylocentrotus purpuratus@XP_001187716[4][RRM1:100%*][put-sr:100%*][KOG4212:50%][.KOG4661:50%]Coelomata@ENSOGAP00000009767[86][RRM1:100%****][hnRNP:34%***][KOG4212:100%****]Trypanosoma brucei_TREU927@XP_823301[RRM1][KOG0921]

Bilateria@XP_967263[73][RRM2:78%****][.RRM1:22%**][put-sr:79%****][SR:75%****][KOG0105:100%****]Plasmodium falciparum_3D7@XP_001347501[RRM2][put-sr][KOG0105]

Theileria parva_strain_Muguga@XP_766386[RRM2][put-sr][KOG0105]Phytophthora ramorum@jgi_Phyra1_1_84100[RRM2][KOG0105]

Phytophthora@jgi_Physo1_1_136493[2][RRM2:100%][put-sr:100%][KOG0105:100%]Fungi/Metazoa_group@AGAP004592-PA[123][RRM2:81%****][.RRM1:18%***][put-sr:100%****][SR:60%****][KOG0105:50%****][.KOG0106:46%****]

Theileria parva_strain_Muguga@XP_766728[RRM2][KOG0124]Plasmodium falciparum_3D7@XP_001347332[RRM2][put-sr][KOG0105]

Phaeodactylum tricornutum@jgi_Phatr2_33658[RRM1]Thalassiosira pseudonana@jgi_Thaps3_263845[RRM1][KOG0108]

Aureococcus anophagefferens@jgi_Auran1_17171[RRM1][KOG0108]Anopheles gambiae@AGAP000921-PA[3][RRM1:100%*]

Dictyostelium discoideum_AX4@XP_641688[RRM1][KOG0117]Leishmania infantum_JPCM5@XP_001464648[RRM1][KOG0113]

Arabidopsis thaliana@NP_175125[7][RRM1:43%*][.RRM2:29%][.RRM4:14%][.RRM3:14%][PABP:29%][KOG0123:100%*]Cyanidioschyzon merolae@gnl_CMER_CMT598C[RRM1][KOG0148]

Ciona intestinalis@ENSCINP00000004384[RRM2][KOG0148]Strongylocentrotus purpuratus@XP_001183631[2][RRM2:100%][KOG0148:100%]

Physcomitrella patens@jgi_Phypa1_1_170658[RRM1]Phaeodactylum tricornutum@jgi_Phatr2_13402[RRM1][KOG0226]

Thalassiosira pseudonana@jgi_Thaps3_18991[RRM1][KOG0226]Cryptococcus neoformans_var._neoformans_JEC21@XP_571861[RRM1][KOG0226]

Eukaryota@XP_964958[72][RRM1:100%****][KOG0226:100%****]Nasonia vitripennis@XP_001603091[RRM1][KOG0226]

Eukaryota@IMGA_AC144483_30_2[123][RRM2:83%****][.RRM1:17%***][TIATIAR:58%****][.oligoU:6%*][KOG0148:99%****]Eukaryota@ENSETEP00000015606[204][RRM3:85%*****][.RRM2:11%***][PABP:66%****][KOG0123:100%*****]

Ustilago maydis_521@XP_757329[RRM2][KOG0145]Yarrowia lipolytica@XP_501542[RRM2][KOG0131]

Ciona@ENSCSAVP00000020066[4][RRM1:50%][.RRM2:50%][KOG0131:50%]Saccharomycetales@XP_460477[6][RRM1:67%*][.RRM2:33%][KOG0148:67%*][.KOG3598:17%][.KOG0145:17%]

Saccharomycetales@XP_455748[4][RRM2:100%*][KOG0148:75%*][.KOG0145:25%]Eukaryota@ENSMUSP00000030730[72][RRM2:85%****][.RRM1:15%**][oligoU:10%*][KOG0148:58%***][.KOG0123:25%**][.KOG0131:14%**]

Debaryomyces hansenii_CBS767@XP_461354[RRM2][KOG0148]Pichia stipitis_CBS_6054@XP_001386002[RRM2][KOG0148]

Endopterygota@AAEL011988-PA[5][RRM2:100%*][KOG0144:80%*][.KOG0145:20%]Dictyostelium discoideum_AX4@XP_635179[RRM1][KOG0148]

Aureococcus anophagefferens@jgi_Auran1_28594[RRM2][KOG0148]Ustilago maydis_521@XP_758439[RRM3][KOG0123]

Cryptosporidium parvum_Iowa_II@XP_627799[RRM2][KOG0110]Phytophthora sojae@jgi_Physo1_1_132702[RRM4][KOG0127]

Phytophthora ramorum@jgi_Phyra1_1_79608[2][RRM4:100%][KOG0127:100%]Dictyostelium discoideum_AX4@XP_629950[RRM1][KOG0128]

Ciona intestinalis@ENSCINP00000019833[3][RRM2:100%*][KOG0128:100%*]

>>> RRM2 ofdual-RRM

SR proteins

77 - TIA TIAR

OligoU66 - PaBP

29 - dual-RRM

SR proteins

30 - hnRNP

PDIP

FCA FPA

41 - snRNP

4245

Fig. S6

89

76

67 80

79

81

64

50

50 58

89

99

57

Endopterygota@AGAP002256-PA[4][RRM1:100%*][KOG4454:75%*][ KOG0131:25%]Caenorhabditis elegans@Y37D8A_21_1[2][RRM1:100%][KOG4454:100%]


Eukaryota@NP_001064759[59][RRM1:100%****][snRNP:8%*][KOG0131:100%****]Saccharomycetaceae@XP_001385635[2][RRM1:100%][KOG0131:100%]

Dictyostelium discoideum_AX4@XP_647248[RRM1][KOG0131]Ashbya gossypii_ATCC_10895@NP_982888[RRM1][KOG0131]

Saccharomyces cerevisiae@YOR319W[RRM1][KOG0131]Candida glabrata_CBS138@XP_447678[RRM1][KOG0131]

Cyanidioschyzon merolae@gnl_CMER_CML202C[RRM1][put-sr]Eukaryota@8925_m000027_AZM5_1178[67][RRM1:100%****][put-sr:84%****][SR:61%***][KOG4207:61%***][.KOG4368:24%**]

Neurospora crassa_OR74A@XP_965346[RRM1][KOG0110]Gammaproteobacteria@YP_113294[2][RRM1:100%][PROK:100%]

Yarrowia lipolytica@XP_500351[RRM2][KOG0123]Encephalitozoon cuniculi_GB-M1@NP_586226[RRM3][put-sr][KOG0123]

Aureococcus anophagefferens@jgi_Auran1_9375[2][RRM1:100%][KOG0122:100%]Aureococcus anophagefferens@jgi_Auran1_17018[RRM1][KOG0111]

Aureococcus anophagefferens@jgi_Auran1_9018[RRM1]Thalassiosira pseudonana@jgi_Thaps3_20266[RRM1][KOG4207]Bacillariophyta@jgi_Thaps3_20223[2][RRM1:100%][KOG0108:100%]

Cryptosporidium parvum_Iowa_II@XP_626081[RRM1][KOG0122]Chlamydomonadales@jgi_Chlre3_184151[2][RRM1:100%][KOG0921:50%][.KOG0116:50%]

Phaeodactylum tricornutum@jgi_Phatr2_8270[RRM1][KOG4207]Phaeodactylum tricornutum@jgi_Phatr2_49481[RRM1][KOG1337]

Aureococcus anophagefferens@jgi_Auran1_17889[RRM1][KOG4207]Theileria parva_strain_Muguga@XP_765374[RRM2]


Euteleostomi@ENSORLP00000016244[7][RRM1:100%*][KOG1080:57%*]Leishmania infantum_JPCM5@XP_001468615[RRM1]

Yarrowia lipolytica@XP_503515[RRM1][KOG0122]Saccharomycetaceae@XP_001388004[2][RRM1:100%][KOG0122:100%]Saccharomycetales@XP_446998[3][RRM1:100%*][KOG0122:100%*]

Eukaryota@NP_187747[49][RRM1:100%***][KOG0122:98%***]Medicago truncatula@IMGA_AC144431_18_2[RRM1][KOG0122]

Cryptococcus neoformans_var._neoformans_JEC21@XP_567824[RRM1][KOG0122]Cyanidioschyzon merolae@gnl_CMER_CMH159C[RRM1][KOG0122]

Caenorhabditis elegans@F22B5_2[RRM1][KOG0122]Dictyostelium discoideum_AX4@XP_641693[RRM1][KOG0122]

Apicomplexa@XP_001388056[3][RRM1:100%*][KOG0122:100%*]Bacillariophyta@jgi_Thaps3_19374[2][RRM1:100%][KOG0121:100%]

Cryptosporidium parvum_Iowa_II@XP_627536[RRM1][KOG0121]Encephalitozoon cuniculi_GB-M1@NP_597585[RRM1][KOG0121]

Eukaryota@ENSMODP00000034858[66][RRM1:100%****][KOG0121:100%****]Trypanosomatidae@XP_001466901[2][RRM1:100%][KOG0121:100%]


Thalassiosira pseudonana@jgi_Thaps3_33709[RRM1][KOG0111]Schizosaccharomyces pombe_972h-@NP_595090[RRM1]

Kluyveromyces lactis@XP_453971[RRM1]Saccharomycetales@YHL034C[2][RRM1:100%]

Drosophila melanogaster@CG2050-PA[RRM2]Pichia stipitis_CBS_6054@XP_001387063[RRM1]

Encephalitozoon cuniculi_GB-M1@NP_597583[RRM1][KOG4205]Encephalitozoon cuniculi_GB-M1@NP_597583[RRM2][KOG4205]

Ostreococcus lucimarinus@jgi_Ost9901_3_8174[RRM1][KOG4207]Tribolium castaneum@XP_970765[RRM2][KOG0127]

Ostreococcus@jgi_Ostta4_7793[2][RRM1:100%][KOG0108:100%]Aureococcus anophagefferens@jgi_Auran1_17068[RRM1][KOG4207]

Murinae@ENSMUSP00000078984[3][RRM1:100%*][KOG4207:100%*]Cryptosporidium parvum_Iowa_II@XP_628282[2][RRM1:100%][put-sr:100%][KOG0111:50%][.KOG4207:50%]

Plasmodium falciparum_3D7@XP_001347950[RRM1][KOG4207]Plasmodium falciparum_3D7@XP_001351591[RRM1]

Chlamydomonadales@jgi_Volca1_121229[2][RRM1:100%][put-sr:100%][KOG0415:50%]Phytophthora@jgi_Physo1_1_136528[2][RRM1:100%][put-sr:50%][KOG3208:50%]

Viridiplantae@NP_001046448[23][RRM1:100%***][put-sr:91%***][SR:35%**][KOG4207:13%*][.KOG0127:13%*][.KOG0110:9%]Chordata@ENSETEP00000001114[45][RRM1:100%***][put-sr:96%***][SRrp:82%***][KOG0111:29%**][.KOG0415:13%*]

Phytophthora sojae@jgi_Physo1_1_138511[RRM1][put-sr]Bacillariophyta@jgi_Thaps3_23196[2][RRM1:100%][KOG4207:50%]

Strongylocentrotus purpuratus@XP_001178467[2][RRM1:100%][put-sr:100%]Endopterygota@CG5655-PA[5][RRM1:100%*][put-sr:100%*][KOG0107:80%*][.KOG0921:20%]

Eukaryota@ENSGALP00000022397[157][RRM1:100%*****][put-sr:75%****][SR:59%****][KOG0107:66%****]Strongylocentrotus purpuratus@XP_001180596[2][RRM1:100%][put-sr:100%]

Embryophyta@NP_194280[13][RRM1:100%**][put-sr:77%**][SR:62%**][KOG0106:100%**]Ostreococcus lucimarinus@jgi_Ost9901_3_8794[RRM1][KOG0105]

Plasmodium falciparum_3D7@XP_001351730[RRM1][put-sr][KOG0105]Phytophthora@jgi_Physo1_1_138982[2][RRM1:100%][KOG0105:100%]

Theileria parva_strain_Muguga@XP_766386[RRM1][put-sr][KOG0105]Eukaryota@ENSTBEP00000007356[92][RRM1:100%****][put-sr:82%****][SR:65%****][KOG0105:100%****]

Caenorhabditis elegans@T28D9_2a[3][RRM1:100%*][put-sr:100%*][SR:100%*][KOG0106:100%*]Ciona intestinalis@ENSCINP00000016525[RRM1][put-sr][KOG0106]

Aedes aegypti@AAEL012621-PA[RRM1][put-sr][KOG0105]Cavia porcellus@ENSCPOP00000010577[RRM1][put-sr][SR][KOG0106]

Eukaryota@ENSOANP00000021053[127][RRM1:100%****][put-sr:91%****][SR:61%****][KOG0106:55%****][.KOG0105:37%***]Cryptococcus neoformans_var._neoformans_JEC21@XP_567562[RRM1][KOG0106]


Phytophthora@jgi_Physo1_1_132702[3][RRM3:100%*][KOG0127:100%*]Embryophyta@28611_m000102[4][RRM2:100%*][put-sr:75%*][KOG0154:100%*]

Embryophyta@jgi_Phypa1_1_161416[4][RRM1:100%*][put-sr:75%*][KOG0154:75%*][.KOG0147:25%]Dictyostelium discoideum_AX4@XP_646990[RRM1][put-sr][KOG0147]

Spermophilus tridecemlineatus@ENSSTOP00000006011[RRM1][put-sr]Eutheria@ENSMLUP00000005283[2][RRM1:100%][put-sr:100%]

Basidiomycota@XP_757472[3][RRM1:100%*][put-sr:33%][KOG0122:33%]Caenorhabditis elegans@C18D11_4_1[2][RRM1:100%][put-sr:100%][KOG0921:100%]

Encephalitozoon cuniculi_GB-M1@NP_585779[RRM1]Dictyostelium discoideum_AX4@XP_642304[RRM1][KOG0415]

Coelomata@AGAP006798-PA[81][RRM1:100%****][put-sr:99%****][KOG0122:26%***][.KOG0125:25%**][.KOG0147:14%**][.KOG0108:9%*]Aedes aegypti@AAEL004293-PA[RRM1][put-sr]

Drosophila melanogaster@CG10128-PC[6][RRM1:100%*][put-sr:100%*]Phytophthora@jgi_Physo1_1_140019[2][RRM1:100%][KOG0116:100%]

Dictyostelium discoideum_AX4@XP_628876[RRM1]Phytophthora@jgi_Phyra1_1_74707[2][RRM3:100%][KOG0110:100%]

Volvox carteri@jgi_Volca1_63158[RRM2][KOG0110]Eukaryota@NP_001053839[55][RRM6:42%***][.RRM5:35%**][.RRM4:11%*][.RRM3:9%*][KOG0110:100%****]


Encephalitozoon cuniculi_GB-M1@NP_597181[RRM3][KOG0110]Cyanidioschyzon merolae@gnl_CMER_CMO246C[RRM5][KOG0110]

Embryophyta@IMGA_AC141435_12_2[17][RRM2:76%**][.RRM1:24%*][KOG4660:100%**]Myotis lucifugus@ENSMLUP00000003020[RRM3][PTBP][KOG1190]

Tetrapoda@ENSXETP00000004736[17][RRM2:59%**][.RRM1:41%*][PTBP:94%**][KOG1190:100%**]Encephalitozoon cuniculi_GB-M1@NP_584580[RRM1][KOG0114]Eukaryota@jgi_Phatr2_8132[54][RRM1:100%***][KOG0114:100%***]

Debaryomyces hansenii_CBS767@XP_458197[RRM1][KOG0114]Schizosaccharomyces pombe_972h-@NP_594609[RRM1][KOG4660]

Dictyostelium discoideum_AX4@XP_645848[RRM1][put-sr]Dictyostelium discoideum_AX4@XP_647083[RRM1]

Cryptococcus neoformans_var._neoformans_JEC21@XP_567374[RRM1][KOG0307]

>>> RRM1 ofSR proteins

44

43

60

16 - dual RRM

SR proteins

17 - single-RRM Zn-K

SR proteins

18

23 - SRrp

22 - single RRM

SR proteins

46

47

22 - single RRM

SR proteinsPROK

24

65

25

Fungal SR (SpSrp2)

Fig. S6

90

0.20

51

51

75

61

66

70

51

63

62

90 99

88

Gammaproteobacteria@YP_561253[27][RRM1:100%***][PROK:100%***][KOG0108:96%***]Geobacter uraniumreducens_Rf4@YP_001230384[RRM1][PROK][KOG0108]

Chlamydomonas reinhardtii@jgi_Chlre3_145376[RRM2]Alkalilimnicola ehrlichei_MLHE-1@YP_741458[RRM1][PROK]

Methanomicrobiales@YP_503016[5][RRM1:100%*][PROK:100%*][KOG0108:40%][.KOG0125:20%][.KOG0116:20%]Treponema pallidum_subsp._pallidum_str._Nichols@NP_218796[RRM1][PROK][KOG0149]

Dictyostelium discoideum_AX4@XP_638767[RRM1][KOG0123]Campylobacter@YP_001467322[2][RRM1:100%][PROK:100%][KOG0148:100%]

Candidatus Protochlamydia_amoebophila_UWE25@YP_007892[RRM1][PROK][KOG0149]Syntrophobacter fumaroxidans_MPOB@YP_845575[RRM1][PROK]

Synechococcus@YP_473618[2][RRM1:100%][PROK:100%][KOG0108:100%]Leptospira@YP_000459[4][RRM1:100%*][PROK:100%*][KOG0108:100%*]


Nitrosococcus oceani_ATCC_19707@YP_344746[RRM1][PROK][KOG0148]Bacteroidales@YP_213478[13][RRM1:100%**][PROK:100%**][KOG0108:69%**][.KOG0125:31%*]

Bacteroides@YP_001298723[3][RRM1:100%*][PROK:100%*][KOG0108:100%*]Bacteroidales@YP_001302325[2][RRM1:100%][PROK:100%][KOG0123:50%][.KOG0122:50%]

Syntrophobacter fumaroxidans_MPOB@YP_844222[RRM1][PROK][KOG0108]Ostreococcus tauri@jgi_Ostta4_19468[RRM1][KOG0127]

Ostreococcus@jgi_Ost9901_3_12693[2][RRM2:100%][KOG0127:100%]cellular_organisms@YP_001113853[137][RRM1:100%****][PROK:99%****][KOG0108:58%****][.KOG0116:14%**][.KOG0921:7%**][.KOG0149:7%**][.KOG0111:6%**]

Carboxydothermus hydrogenoformans_Z-2901@YP_359251[RRM1][PROK][KOG0108]Pezizomycotina@XP_962933[3][RRM2:100%*][KOG0127:100%*]

Schizosaccharomyces pombe_972h-@NP_596114[RRM2][KOG0127]Yarrowia lipolytica@XP_499726[RRM2][KOG0127]

Saccharomycetales@XP_459044[4][RRM2:100%*][KOG0127:100%*]Magnoliophyta@NP_001062760[4][RRM1:100%*][KOG0124:50%][.KOG0131:50%]

Ustilago maydis_521@XP_756401[RRM1]Embryophyta@jgi_Phypa1_1_134646[11][RRM1:100%**][cpRNP:9%][KOG0123:45%*][.KOG0127:36%*][.KOG2029:9%]

Magnoliophyta@NP_001058927[3][RRM1:100%*][cpRNP:33%][KOG0131:67%]Magnoliophyta@10511_m000028_AZM5_5258[15][RRM1:100%**][cpRNP:33%*][KOG0127:53%**][.KOG0131:27%*][.KOG0145:13%][.KOG0108:7%]Aureococcus anophagefferens@jgi_Auran1_8994[RRM1][KOG0149]

Magnoliophyta@29333_m001057[3][RRM2:67%][.RRM1:33%][cpRNP:33%][KOG0131:67%][.KOG0148:33%]Magnoliophyta@NP_566958[6][RRM2:67%*][.RRM1:33%][KOG0123:33%][.KOG0124:33%][.KOG0131:33%]

Magnoliophyta@IMGA_AC119413_25_2[4][RRM2:100%*][cpRNP:25%][KOG0127:100%*]Poaceae@19213_m000022_AZM5_85721[2][RRM1:50%][.RRM2:50%][KOG0127:50%]

Ricinus communis@29908_m006094[RRM2][KOG0110]Arabidopsis thaliana@NP_192643[2][RRM2:100%][KOG0110:100%]

Magnoliophyta@NP_001048500[5][RRM2:100%*][cpRNP:20%][KOG0123:100%*]rosids@NP_171616[3][RRM2:100%*][cpRNP:67%][KOG0148:67%][.KOG0110:33%]

Oryza sativa_japonica_cultivar-group@NP_001060859[RRM2][KOG0110]Ostreococcus tauri@jgi_Ostta4_24260[RRM1]

Magnoliophyta@NP_189032[4][RRM1:100%*][put-sr:100%*][KOG0670:100%*]Trypanosomatidae@XP_827855[2][RRM1:100%]


Phytophthora@jgi_Phyra1_1_75647[2][RRM1:100%]Neurospora crassa_OR74A@XP_958552[RRM3][KOG0128]

Cyanobacteria@YP_476186[8][RRM1:100%**][PROK:100%**][KOG0108:38%*][.KOG0122:12%]Cyanobacteria@NP_898344[17][RRM1:100%**][PROK:100%**][KOG0108:65%**]Synechococcus_elongatus@YP_399809[2][RRM1:100%][PROK:100%][KOG0108:100%]

Phaeodactylum tricornutum@jgi_Phatr2_16633[RRM1][KOG0125]Magnoliophyta@NP_001060859[5][RRM1:100%*][cpRNP:40%][KOG0110:40%][.KOG0148:40%]

Pelobacter carbinolicus_DSM_2380@YP_357907[RRM1][PROK][KOG0145]Desulfuromonadales@NP_952377[4][RRM1:100%*][PROK:100%*][KOG0108:50%][.KOG0145:25%]

Oryza sativa_japonica_cultivar-group@NP_001053710[RRM1][KOG0127]rosids@30054_m000821[3][RRM1:100%*][cpRNP:33%][KOG0127:100%*]Magnoliophyta@NP_001062073[4][RRM1:100%*][KOG0110:75%*][.KOG0127:25%]

Trypanosoma brucei_TREU927@XP_829716[RRM1]Clupeocephala@ENSORLP00000002364[10][RRM2:100%**][KOG0109:100%**]

Endopterygota@CG7903-PA[5][RRM1:100%*][KOG0109:80%*]Tribolium castaneum@XP_971700[RRM1]

Aedes aegypti@AAEL006876-PA[RRM1][KOG2193]Strongylocentrotus purpuratus@XP_001180991[4][RRM1:100%*]

Xenopus tropicalis@ENSXETP00000056096[RRM1][KOG0109]Mammalia@ENSTBEP00000003150[16][RRM1:100%**][RBM:94%**][KOG0109:100%**]Clupeocephala@ENSGACP00000025151[11][RRM1:100%**][KOG0109:100%**]

Ciona intestinalis@ENSCINP00000023722[RRM1][KOG0109]Ciona intestinalis@ENSCINP00000017840[RRM1][KOG0109]

Euteleostomi@ENSDNOP00000012760[63][RRM2:94%****][.RRM1:6%*][LARK:65%***][.RBM:21%**][KOG0109:97%****]Strongylocentrotus purpuratus@XP_792521[4][RRM1:100%*][put-sr:100%*][KOG0109:100%*]

Coelomata@ENSXETP00000008271[74][RRM1:100%****][LARK:61%***][KOG0109:97%****]Ciona intestinalis@ENSCINP00000017840[RRM2][KOG0109]

Ciona@ENSCSAVP00000017501[2][RRM1:50%][.RRM2:50%][KOG0109:50%]Danio rerio@ENSDARP00000065401[RRM2][KOG0109]

Endopterygota@CG8597-PE[8][RRM2:100%**][LARK:62%*][KOG0109:100%**]Percomorpha@ENSGACP00000007987[5][RRM1:100%*][IGF2BP:80%*][KOG2193:100%*]

Chlamydomonadales@jgi_Volca1_90315[3][RRM2:67%][.RRM3:33%][KOG0123:67%]Neurospora crassa_OR74A@XP_965346[RRM2][KOG0110]

Aspergillus fumigatus_Af293@XP_747328[RRM2][KOG0110]Phytophthora ramorum@jgi_Phyra1_1_76171[2][RRM1:100%][KOG0111:100%]

Phaeodactylum tricornutum@jgi_Phatr2_11308[RRM1][KOG0111]Thalassiosira pseudonana@jgi_Thaps3_31121[RRM1][KOG0111]

Cryptococcus neoformans_var._neoformans_JEC21@XP_566572[RRM1][KOG0111]Schizosaccharomyces pombe_972h-@NP_595190[RRM1][KOG0111]

Pezizomycotina@XP_755630[3][RRM1:100%*][KOG0111:100%*]Theileria parva_strain_Muguga@XP_765867[RRM1][KOG0111]Plasmodium falciparum_3D7@XP_001349948[RRM1][KOG0111]

Eukaryota@ENSGALP00000021793[59][RRM1:100%****][cyclophilin:59%***][KOG0111:98%****]Otolemur garnettii@ENSOGAP00000003225[RRM1][KOG0111]Eutheria@ENSEEUP00000009324[3][RRM1:100%*][cyclophilin:100%*][KOG0111:100%*]

Magnoliophyta@NP_001055607[4][RRM1:100%*][put-sr:25%][KOG0131:100%*]Deuterostomia@ENSXETP00000012868[47][RRM1:100%***][KOG4454:60%***][.KOG0131:40%**]

Drosophila melanogaster@CG11454-PA[RRM1][KOG4454]Endopterygota@AGAP002256-PA[4][RRM1:100%*][KOG4454:75%*][.KOG0131:25%] 47

19 - cyclophilin

51 - LARK

50 - LARK

48 - IGF2BP

49

52

88 - prokaryotic RRMS

prok-3

prok-2

prok-1

Fig. S6

91

76

88

91

69

79

52

62

56

96

91

91

65 50

92

Leishmania infantum JPCM5@XP 001466041[RRM4][KOG0123]Drosophila melanogaster@CG4612-PA[RRM2][KOG0123]

Pezizomycotina@XP_750167[2][RRM4:100%][KOG0123:100%]Eukaryota@ENSDNOP00000002400[249][RRM4:82%*****][.RRM3:11%***][.RRM2:6%**][PABP:54%****][KOG0123:100%*****]

Arabidopsis thaliana@NP_188259[RRM4][PABP][KOG0123]Aedes aegypti@AAEL007013-PA[RRM1][KOG0123]

Ciona@ENSCINP00000018772[3][RRM1:100%*][KOG0127:100%*]Trypanosoma brucei_TREU927@XP_827237[RRM3][KOG0123]

Yarrowia lipolytica@XP_500351[RRM3][KOG0123]Trypanosoma brucei_TREU927@XP_827358[RRM3][KOG0123]

Leishmania infantum_JPCM5@XP_001469222[RRM3][KOG0123]Felis catus@ENSFCAP00000004622[RRM3][PABP][KOG0123]

Caenorhabditis elegans@Y106G6H_2a_4[7][RRM3:71%*][.RRM2:29%][KOG0123:100%*]Caenorhabditis elegans@F18H3_3b[5][RRM3:100%*][KOG0123:100%*]

Dikarya@XP_960425[12][RRM3:100%**][PABP:17%][KOG0123:100%**]Phytophthora@jgi_Physo1_1_108322[2][RRM3:100%][KOG0123:100%]


Chlamydomonadales@jgi_Volca1_82578[2][RRM3:100%][PABP:100%][KOG0123:100%]Strongylocentrotus purpuratus@XP_001177782[4][RRM3:50%][.RRM2:50%][KOG0123:100%*]

Dictyostelium discoideum_AX4@XP_629007[RRM3][KOG0123]Yarrowia lipolytica@XP_501289[RRM3][KOG0123]

Encephalitozoon cuniculi_GB-M1@NP_586226[RRM3][put-sr][KOG0123]Volvox carteri@jgi_Volca1_36996[RRM1][KOG0116]

Ostreococcus@jgi_Ost9901_3_34381[2][RRM1:100%][KOG0145:100%]Culicidae@AAEL001131-PA[2][RRM1:100%][KOG0113:100%]

Anopheles gambiae@AGAP000921-PA[3][RRM1:100%*]Viridiplantae@29631_m001006[3][RRM1:100%*][put-sr:33%][KOG0108:67%][.KOG2253:33%]

Euteleostomi@ENSGACP00000016390[7][RRM1:100%*][put-sr:86%*][RBM:14%][KOG2253:100%*]Ciona@ENSCSAVP00000015853[4][RRM2:100%*][KOG0145:100%*]

Dictyostelium discoideum_AX4@XP_629639[RRM2][KOG0145]Diptera@AGAP003899-PA[15][RRM2:100%**][KOG0145:100%**]Bilateria@CG3151-PE[218][RRM2:92%*****][.RRM1:7%**][ELAV:84%*****][KOG0145:100%*****]

Coelomata@ENSORLP00000004891[62][RRM2:94%****][.RRM1:6%*][RBMS:79%***][KOG0145:100%****]Ustilago maydis_521@XP_759141[RRM2][KOG0145]

Trypanosomatidae@XP_001468777[2][RRM2:100%][KOG0144:100%]Dictyostelium discoideum_AX4@XP_644081[RRM2][KOG0123]Trypanosomatidae@XP_847495[2][RRM1:100%][KOG0110:50%][.KOG0127:50%]

Trypanosoma brucei_TREU927@XP_843985[3][RRM1:100%*][put-sr:33%][KOG0110:100%*]Leishmania infantum_JPCM5@XP_001466665[RRM1][KOG0110]


Leishmania infantum_JPCM5@XP_001464836[RRM1][KOG0145]Leishmania infantum_JPCM5@XP_001464835[2][RRM1:100%][KOG0145:100%]

Ciona@ENSCINP00000023191[4][RRM3:75%*][.RRM1:25%][KOG0145:100%*]Coelomata@ENSTBEP00000015452[229][RRM3:88%*****][.RRM2:9%**][ELAV:82%*****][KOG0145:100%*****]


Encephalitozoon cuniculi_GB-M1@NP_584552[RRM1][KOG0123]Theileria parva_strain_Muguga@XP_766466[RRM3][KOG0123]

Plasmodium falciparum_3D7@XP_001350640[RRM3][KOG0123]Pezizomycotina@XP_387225[3][RRM1:67%][.RRM2:33%][put-sr:100%*][KOG0120:100%*]

Yarrowia lipolytica@XP_503754[RRM1][KOG0120]Schizosaccharomyces pombe_972h-@NP_595396[RRM1][put-sr][KOG0120]

Plasmodium falciparum_3D7@XP_001348830[RRM2][put-sr][KOG0120]Chlamydomonadales@jgi_Volca1_48801[2][RRM1:100%][KOG0120:100%]

Eukaryota@jgi_Volca1_82970[75][RRM2:91%****][.RRM1:9%*][put-sr:80%****][snRNP:53%***][KOG0120:100%****]Phaeodactylum tricornutum@jgi_Phatr2_11145[RRM2][KOG0120]



Bilateria@ENSORLP00000021434[219][RRM1:100%*****][ELAV:79%*****][KOG0145:100%*****]Dictyostelium discoideum_AX4@XP_629639[RRM1][KOG0145]


Diptera@AAEL011150-PA[15][RRM1:100%**][KOG0145:100%**]Drosophila melanogaster@CG5213-PA[RRM1][KOG0145]

Trypanosomatidae@XP_828145[5][RRM1:100%*][KOG0145:100%*]Trypanosoma brucei_TREU927@XP_845996[RRM1][KOG0122]




Trypanosomatidae@XP_847111[2][RRM1:100%]Leishmania infantum_JPCM5@XP_001465764[RRM1]


Leishmania infantum_JPCM5@XP_001463160[RRM2][put-sr]Oryza sativa_japonica_cultivar-group@NP_001054296[RRM5][KOG0123]

Volvox carteri@jgi_Volca1_84128[RRM2][KOG0147]Oryza sativa_japonica_cultivar-group@NP_001054296[RRM4][KOG0123]

Embryophyta@jgi_Phypa1_1_189930[7][RRM1:100%*][KOG0119:86%*][.KOG0307:14%]Oryza sativa_japonica_cultivar-group@NP_001054296[RRM6][KOG0123]


Oryza sativa_japonica_cultivar-group@NP_001054296[RRM2][KOG0123]Bilateria@ENSORLP00000004891[130][RRM1:100%****][RBMS:72%****][KOG0145:99%****]

Leishmania infantum_JPCM5@XP_001467067[2][RRM1:100%][KOG0144:100%]Dictyostelium discoideum_AX4@XP_638767[RRM2][KOG0123]

Eukaryota@ENSOANP00000006980[251][RRM3:67%*****][.RRM2:24%****][.RRM1:10%***][Bruno:50%****][KOG0144:55%****][.KOG0146:45%****]Aconoidasida@XP_001349292[3][RRM2:100%*][KOG0146:67%][.KOG0144:33%]

Plasmodium falciparum_3D7@XP_001350320[RRM3][KOG0123]Plasmodium falciparum_3D7@XP_001350320[RRM2][KOG0123]

Theileria parva_strain_Muguga@XP_766017[RRM3][KOG0144]Cryptosporidium parvum_Iowa_II@XP_001388078[RRM3][put-sr][KOG0144]

Volvox carteri@jgi_Volca1_106063[RRM2]Dictyostelium discoideum_AX4@XP_636266[RRM3][KOG3598]

9 - bruno

10 - ELAV

64 - snRNP

12 - ELAV

11 - ELAV

RBMS

5 - PABP

6 - PABP

Fig. S7

92

91

51

51

99

78

83

61

59

93

87

70 79

100

52

85

50

56

Phytophthora ramorum@jgi Phyra1 1 77702[RRM1][KOG0154]Embryophyta@28611_m000102[4][RRM2:100%*][put-sr:75%*][KOG0154:100%*]

Chlamydomonas reinhardtii@jgi_Chlre3_145376[RRM2]Saccharomycetaceae@XP_451236[2][RRM1:100%][KOG0144:100%]

Saccharomyces cerevisiae@YGR250C[RRM1][KOG0108]Nasonia vitripennis@XP_001604889[RRM2][KOG0144]

Dictyostelium discoideum_AX4@XP_636266[RRM1][KOG3598]Endopterygota@CG1316-PA[5][RRM1:100%*][KOG0144:80%*][.KOG0148:20%]

Euteleostomi@ENSDNOP00000001522[23][RRM1:100%***][RBM:61%**][KOG0144:87%**][.KOG0145:13%*]Strongylocentrotus purpuratus@XP_001199679[4][RRM1:100%*][KOG0145:50%]

Arabidopsis thaliana@NP_974808[2][RRM1:100%][KOG0123:50%][.KOG0148:50%]Magnoliophyta@NP_181287[9][RRM1:100%**][oligoU:22%][KOG0148:56%*][.KOG0127:22%][.KOG0145:11%][.KOG0113:11%]

Arabidopsis thaliana@NP_173298[RRM1][GRSRBP][KOG0149]rosids@29154_m000213[5][RRM1:100%*][oligoU:40%][KOG0122:40%][.KOG0113:20%][.KOG0148:20%]

Magnoliophyta@NP_001052753[3][RRM1:100%*][oligoU:33%][KOG0108:33%][.KOG0149:33%][.KOG0127:33%]Magnoliophyta@9946_m000021_AZM5_3995[2][RRM1:100%][KOG0111:50%][.KOG0113:50%]Magnoliophyta@29930_m000611[5][RRM1:100%*][KOG0113:100%*]

Medicago truncatula@IMGA_AC122162_7_2[RRM1][KOG0149]Ricinus communis@30055_m001598[RRM1][KOG0149]

Arabidopsis thaliana@NP_565646[RRM1][KOG0149]Tribolium castaneum@XP_967803[2][RRM1:100%][KOG0117:100%]

Rattus norvegicus@ENSRNOP00000053644[RRM1][KOG0117]Eutheria@ENSCPOP00000011171[3][RRM1:100%*][hnRNP:67%][KOG0117:100%*]Bilateria@ENSGALP00000025475[210][RRM1:100%*****][hnRNP:33%****][KOG0117:100%*****]

Eutheria@ENSBTAP00000025092[6][RRM1:100%*][KOG0117:100%*]Gasterosteus aculeatus@ENSGACP00000025947[RRM1][KOG0117]

Anopheles gambiae@AGAP002326-PA[RRM1]Aedes aegypti@AAEL015050-PA[2][RRM1:100%][KOG0117:100%]

Embryophyta@29727_m000492[13][RRM3:92%**][.RRM2:8%][oligoU:46%*][KOG0148:100%**]Saccharomycetales@YNL016W[6][RRM3:100%*][put-sr:33%][KOG0148:83%*][.KOG0123:17%]

Dikarya@XP_570577[4][RRM3:100%*][KOG0148:100%*]Embryophyta@NP_001067623[8][RRM1:100%**][KOG0117:100%**]

rosids@NP_001030849[6][RRM1:100%*][KOG0117:100%*]Oryza sativa_japonica_cultivar-group@NP_001066102[RRM1][KOG0117]

Caenorhabditis elegans@C07A4_1[RRM2][KOG0148]Coelomata@CG4787-PA[102][RRM3:74%****][.RRM2:16%**][.RRM1:11%**][TIATIAR:75%****][KOG0148:100%****]

Caenorhabditis elegans@Y46G5A_13[10][RRM2:80%**][.RRM3:20%][KOG0148:100%**]Aconoidasida@XP_766017[2][RRM2:100%][KOG0144:100%]

Plasmodium falciparum_3D7@XP_001348269[RRM2][KOG0144]Cryptosporidium parvum_Iowa_II@XP_001388078[RRM2][put-sr][KOG0144]

Chlamydomonadales@jgi_Chlre3_99329[2][RRM1:50%][.RRM2:50%][KOG0144:100%]Trypanosoma brucei_TREU927@XP_845376[RRM3][KOG0148]

Thalassiosira pseudonana@jgi_Thaps3_261541[RRM2][KOG0144]Phytophthora@jgi_Physo1_1_140019[2][RRM1:100%][KOG0116:100%]

Chlamydomonas reinhardtii@jgi_Chlre3_174860[RRM2][KOG1240]Dictyostelium discoideum_AX4@XP_646268[RRM2][KOG0146]

Phytophthora sojae@jgi_Physo1_1_139371[RRM2][KOG4205]Cryptosporidium parvum_Iowa_II@XP_628265[RRM2][KOG0144]


Phytophthora@jgi_Physo1_1_133760[2][RRM2:100%][KOG0144:100%]Embryophyta@jgi_Phypa1_1_115029[9][RRM2:100%**][KOG0144:100%**]Bilateria@AGAP009477-PA[250][RRM2:73%*****][.RRM1:27%****][Bruno:59%****][KOG0144:56%****][.KOG0146:44%****]


Dictyostelium discoideum_AX4@XP_635247[RRM1][KOG0144]Poaceae@11320_m000014_AZM5_6848[3][RRM1:100%*][KOG0144:100%*]

Physcomitrella patens@jgi_Phypa1_1_107590[2][RRM1:100%][KOG0144:100%]Cryptosporidium parvum_Iowa_II@XP_628265[RRM1][KOG0144]


Takifugu rubripes@SINFRUP00000134535[RRM1][KOG0123]Trypanosomatidae@XP_845656[2][RRM1:100%][KOG0131:50%]

Trypanosomatidae@XP_001468238[3][RRM1:100%*][KOG0144:100%*]Leishmania infantum_JPCM5@XP_001468236[RRM1]

Trypanosomatidae@XP_827838[2][RRM1:100%][KOG0144:100%]Embryophyta@30076_m004622[9][RRM1:100%**][FCAFPA:22%][KOG0144:100%**]

Medicago truncatula@IMGA_AC155099_2_2[2][RRM1:100%][KOG0144:100%]Arabidopsis thaliana@NP_850472[RRM1][FCAFPA][KOG0144]

Chlamydomonadales@jgi_Volca1_72841[2][RRM3:50%][.RRM2:50%][KOG0144:100%]Chlamydomonadales@jgi_Volca1_118581[3][RRM2:67%][.RRM4:33%][KOG0144:67%][.KOG1240:33%]

Volvox carteri@jgi_Volca1_88093[RRM4][KOG1240]Chlamydomonadales@jgi_Volca1_88093[2][RRM1:100%][KOG1240:100%]

Cryptosporidium parvum_Iowa_II@XP_001388078[RRM1][put-sr][KOG0144]Theileria parva_strain_Muguga@XP_766017[RRM1][KOG0144]

Plasmodium falciparum_3D7@XP_001350299[RRM1][KOG0144]Phytophthora@jgi_Phyra1_1_82644[2][RRM1:100%][KOG0144:100%]

Coelomata@XP_782270[24][RRM1:100%***][Bruno:42%**][KOG0144:100%***]Bilateria@ENSXETP00000031370[81][RRM1:100%****][Bruno:42%***][KOG0146:84%****][.KOG0144:16%**]


Echinops telfairi@ENSETEP00000008100[RRM3][PABP][KOG0123]Trypanosomatidae@XP_827358[2][RRM2:100%][KOG0123:100%]

Saccharomycetales@NP_984279[4][RRM1:100%*][KOG0921:75%*][.KOG0106:25%]Trypanosomatidae@XP_001469326[2][RRM4:100%][KOG0123:100%]

Trypanosomatidae@XP_001469222[2][RRM4:100%][KOG0123:100%]Ricinus communis@30146_m003481[RRM3][KOG0123]


Arabidopsis thaliana@NP_195978[RRM1][KOG0123]Ustilago maydis_521@XP_759458[RRM2][KOG0123]

Cryptococcus neoformans_var._neoformans_JEC21@XP_569319[RRM1][KOG0123]Saccharomycetaceae@XP_001385635[2][RRM2:100%][KOG0131:100%]

Yarrowia lipolytica@XP_503979[RRM2][KOG0131]Eukaryota@jgi_Physo1_1_108557[316][RRM2:91%*****][.RRM1:9%***][PABP:46%****][KOG0123:79%*****][.KOG0131:21%****]

Cryptosporidium parvum_Iowa_II@XP_627780[RRM2][KOG0131]Schizosaccharomyces pombe_972h-@NP_001018242[RRM3][KOG0123]

Schizosaccharomyces pombe_972h-@NP_593427[RRM2][KOG0123]Leishmania infantum_JPCM5@XP_001466041[RRM2][KOG0123]

Encephalitozoon cuniculi_GB-M1@NP_586226[RRM2][put-sr][KOG0123]Arabidopsis thaliana@NP_174676[RRM1][PABP][KOG0123]

Oryza sativa_japonica_cultivar-group@NP_001049727[RRM2][KOG0123]rosids@30146_m003481[2][RRM2:100%][PABP:50%][KOG0123:100%]

rosids@30078_m002213[3][RRM2:100%*][PABP:33%][KOG0123:100%*]Cryptosporidium parvum_Iowa_II@XP_626158[RRM1][KOG0144]

Dikarya@NP_596771[2][RRM1:100%][KOG0108:50%]Dictyostelium discoideum_AX4@XP_646990[RRM1][put-sr][KOG0147]

Caenorhabditis elegans@T23F6_4_1[2][RRM1:100%][KOG0110:100%]Euteleostomi@GSTENP00029551001[21][RRM1:100%***][put-sr:10%][KOG0110:100%***]

Culicidae@AGAP005249-PA[2][RRM1:100%][KOG0110:100%]Apocrita@XP_624611[2][RRM1:100%][KOG0110:100%]

Drosophila melanogaster@CG3335-PA[RRM1][KOG0110]Schizosaccharomyces pombe_972h-@NP_595599[RRM1][KOG0110]

Arabidopsis thaliana@NP_196191[RRM1][KOG0110]Viridiplantae@jgi_Phypa1_1_207810[3][RRM1:100%*][KOG0110:100%*]

Dictyostelium discoideum_AX4@XP_638463[RRM1][KOG0110]Cyanidioschyzon merolae@gnl_CMER_CMO246C[RRM1][KOG0110]Saccharomycetaceae@XP_001386803[2][RRM1:100%][KOG0110:100%]

Ustilago maydis_521@XP_758493[RRM1][KOG0110]Leishmania infantum_JPCM5@XP_001466041[RRM4][KOG0123] 15

1

4 - PABP

p54nrb

PSP1

PSF

7 - Bruno

FCA FPA

8 - bruno

FCA FPA

2 - hnRNP


Fig. S7

93

68 51

81

69 95

91

54

55

77

60

55

73 94

68

80

62

86

Strongylocentrotus purpuratus@XP 001185821[2][RRM1:100%][KOG0670:100%]Pichia stipitis_CBS_6054@XP_001384462[RRM2]

Debaryomyces hansenii_CBS767@XP_460517[RRM2][KOG0117]Saccharomycetales@XP_445844[3][RRM2:100%*][KOG0123:33%]Kluyveromyces lactis@XP_455897[RRM2][KOG0123]

Euteleostomi@ENSOANP00000024755[113][RRM1:100%****][hnRNP:36%***][.RALYL:15%**]Apocrita@XP_623710[2][RRM1:100%]

Physcomitrella patens@jgi_Phypa1_1_204078[RRM1][KOG0116]Magnoliophyta@NP_001052571[5][RRM1:100%*][KOG0116:100%*]Arabidopsis thaliana@NP_189151[RRM1][NTF][KOG0116]

Tribolium castaneum@XP_969873[RRM1]Anopheles gambiae@AGAP007689-PA[RRM1]

Aedes aegypti@AAEL010101-PA[RRM1]Ustilago maydis_521@XP_757329[RRM1][KOG0145]

Trypanosoma brucei_TREU927@XP_829593[RRM1]Cryptococcus neoformans_var._neoformans_JEC21@XP_570577[RRM1][KOG0148]

Embryophyta@NP_188026[13][RRM1:100%**][oligoU:38%*][KOG0148:100%**]Bilateria@ENSSARP00000011721[82][RRM1:100%****][TIATIAR:80%****][KOG0148:100%****]

Saccharomycetales@XP_454345[4][RRM1:100%*][KOG0148:75%*][.KOG0123:25%]Sordariomycetes@XP_385593[2][RRM1:100%][KOG0148:100%]

Saccharomycetaceae@XP_001383142[2][RRM1:100%][put-sr:100%][KOG0148:100%]Yarrowia lipolytica@XP_501542[RRM1][KOG0131]

Chordata@ENSETEP00000010530[36][RRM1:50%**][.RRM2:50%**][put-sr:100%***][SRrp:75%***][KOG4676:100%***]Viridiplantae@jgi_Chlre3_99594[25][RRM1:100%***][KOG0123:8%]

Ostreococcus lucimarinus@jgi_Ost9901_3_28918[RRM1]Magnoliophyta@15974_m000013_AZM5_17589[3][RRM2:67%][.RRM1:33%]

Plasmodium falciparum_3D7@XP_966051[RRM2]Neurospora crassa_OR74A@XP_960450[RRM1]

Volvox carteri@jgi_Volca1_107013[RRM3][KOG0117]Cryptosporidium parvum_Iowa_II@XP_001388334[RRM3][KOG0123]

Dictyostelium discoideum_AX4@XP_635179[RRM2][KOG0148]Embryophyta@jgi_Phypa1_1_140180[4][RRM3:100%*][KOG0117:100%*]

Trypanosoma brucei_TREU927@XP_844190[RRM1][KOG0144]Schizosaccharomyces pombe_972h-@NP_588373[RRM1]

Dictyostelium discoideum_AX4@XP_644288[RRM2][KOG3598]Schizosaccharomyces pombe_972h-@NP_595389[RRM1][KOG4574]

Yarrowia lipolytica@XP_500252[RRM1][KOG4574]Neurospora crassa_OR74A@XP_962915[RRM1][KOG4574]

Cryptococcus neoformans_var._neoformans_JEC21@XP_570411[RRM2][KOG4574]Clupeocephala@ENSORLP00000009616[3][RRM1:100%*][KOG0548:100%*]

Strongylocentrotus purpuratus@XP_001188888[2][RRM1:100%][KOG0548:100%]Gasterosteus aculeatus@ENSGACP00000006521[RRM1][KOG0548]

Danio rerio@ENSDARP00000075089[2][RRM1:100%][KOG0548:100%]Dictyostelium discoideum_AX4@XP_629218[RRM1][KOG0151]

Dictyostelium discoideum_AX4@XP_629218[RRM2][KOG0151]Volvox carteri@jgi_Volca1_88720[RRM3]


Physcomitrella patens@jgi_Phypa1_1_176266[RRM1][KOG1924]Oryza sativa_japonica_cultivar-group@NP_001063671[RRM2][KOG0123]rosids@NP_001078046[5][RRM2:100%*][FCAFPA:80%*][KOG0117:80%*][.KOG0123:20%]

Physcomitrella patens@jgi_Phypa1_1_161310[RRM2][KOG3598]Physcomitrella patens@jgi_Phypa1_1_137240[2][RRM1:100%][KOG3598:50%]

Ricinus communis@30005_m001243[RRM1]Oryza sativa_japonica_cultivar-group@NP_001062811[RRM1][KOG1190]

Ricinus communis@29577_m000447[RRM1][KOG0123]Arabidopsis thaliana@NP_181869[4][RRM1:100%*][FCAFPA:100%*][KOG0117:100%*]

Encephalitozoon cuniculi_GB-M1@NP_586226[RRM1][put-sr][KOG0123]Dictyostelium discoideum_AX4@XP_645848[RRM2][put-sr]

Strongylocentrotus purpuratus@XP_798256[2][RRM1:100%][KOG2277:100%]Oryzias latipes@ENSORLP00000005442[2][RRM1:100%][KOG2277:100%]

Xenopus tropicalis@ENSXETP00000012439[RRM1][KOG2277]Oryctolagus cuniculus@ENSOCUP00000014792[RRM1][KOG2277]

Phytophthora@jgi_Physo1_1_138982[2][RRM1:100%][KOG0105:100%]Theileria parva_strain_Muguga@XP_766400[RRM2][put-sr][KOG4205]

Cyanidioschyzon merolae@gnl_CMER_CMT598C[RRM1][KOG0148]Theileria parva_strain_Muguga@XP_766728[RRM1][KOG0124]

Yarrowia lipolytica@XP_500797[RRM1][put-sr]Ustilago maydis_521@XP_758616[RRM1]

Schizosaccharomyces pombe_972h-@NP_596398[RRM1][put-sr][SR]Apis mellifera@XP_393878[RRM1][put-sr][KOG2193]

Ascomycota@YDL224C[8][RRM1:88%*][.RRM2:12%][KOG3598:12%][.KOG1457:12%]Ricinus communis@28452_m000049[RRM1][KOG1457]

Medicago truncatula@IMGA_CU012061_4_1[RRM1]Dictyostelium discoideum_AX4@XP_645848[RRM1][put-sr]

Caenorhabditis elegans@T11G6_8_1[2][RRM1:100%][KOG0153:100%]Coelomata@XP_975014[28][RRM1:100%***][RBM:86%***][KOG0153:100%***]

Ciona@ENSCSAVP00000015574[2][RRM1:100%][KOG0153:100%]Ostreococcus@jgi_Ost9901_3_41266[2][RRM1:100%][KOG0153:100%]

Embryophyta@jgi_Phypa1_1_185655[7][RRM1:100%*][KOG0153:100%*]Dictyostelium discoideum_AX4@XP_643642[RRM1][KOG0148]

Schizosaccharomyces pombe_972h-@NP_593427[RRM1][KOG0123]Kluyveromyces lactis@XP_454447[RRM3][KOG0128]

Apis mellifera@XP_394565[RRM1][KOG0147]Saccharomycetales@XP_454821[4][RRM1:100%*][KOG3598:50%][.KOG1984:25%]

Cryptosporidium parvum_Iowa_II@XP_626331[RRM1][KOG0146]Theileria parva_strain_Muguga@XP_766386[RRM1][put-sr][KOG0105]

Plasmodium falciparum_3D7@XP_001347876[RRM1][KOG0105]Neurospora crassa_OR74A@XP_958552[RRM1][KOG0128]

Saccharomyces cerevisiae@YMR268C[RRM1][KOG0128]Pichia stipitis_CBS_6054@XP_001384763[RRM1][KOG0123]

Cyanidioschyzon merolae@gnl_CMER_CMO009C[RRM2]Coelomata@ENSMMUP00000010529[37][RRM3:54%**][.RRM2:41%**][.RRM1:5%][put-sr:92%***][KOG0112:84%***][.KOG3598:8%*]

Strongylocentrotus purpuratus@XP_001184502[2][RRM2:100%][put-sr:100%][KOG1144:100%]Coelomata@XP_974651[54][RRM2:83%***][.RRM1:17%**][put-sr:87%***][RBM:37%**][KOG0112:100%***]

Nasonia vitripennis@XP_001604488[RRM1]Cryptosporidium parvum_Iowa_II@XP_627232[RRM1][put-sr][KOG0105]

Saccharomyces cerevisiae@YLL046C[RRM1]Plasmodium falciparum_3D7@XP_001347332[RRM1][put-sr][KOG0105]

Dictyostelium discoideum_AX4@XP_638672[RRM1][put-sr][KOG0147]Strongylocentrotus purpuratus@XP_001185906[2][RRM1:100%][KOG0107:100%]

Dictyostelium discoideum_AX4@XP_001134500[RRM1][put-sr][KOG0147]Eukaryota@ENSTBEP00000007356[92][RRM1:100%****][put-sr:82%****][SR:65%****][KOG0105:100%****]Embryophyta@NP_194280[13][RRM1:100%**][put-sr:77%**][SR:62%**][KOG0106:100%**]

Plasmodium falciparum_3D7@XP_001351730[RRM1][put-sr][KOG0105]Ostreococcus lucimarinus@jgi_Ost9901_3_8794[RRM1][KOG0105]

Caenorhabditis elegans@T28D9_2a[3][RRM1:100%*][put-sr:100%*][SR:100%*][KOG0106:100%*]Ciona intestinalis@ENSCINP00000016525[RRM1][put-sr][KOG0106]

Cavia porcellus@ENSCPOP00000010577[RRM1][put-sr][SR][KOG0106]Aedes aegypti@AAEL012621-PA[RRM1][put-sr][KOG0105]

Eukaryota@ENSOANP00000021053[127][RRM1:100%****][put-sr:91%****][SR:61%****][KOG0106:55%****][.KOG0105:37%***]Cryptococcus neoformans_var._neoformans_JEC21@XP_567562[RRM1][KOG0106]



Physcomitrella patens@jgi_Phypa1_1_161310[RRM3][KOG3598]Cryptosporidium parvum_Iowa_II@XP_626081[RRM1][KOG0122]

Embryophyta@jgi_Phypa1_1_161416[4][RRM1:100%*][put-sr:75%*][KOG0154:75%*][.KOG0147:25%]Phytophthora ramorum@jgi_Phyra1_1_77702[RRM1][KOG0154]

16 - dual-RRM

SR proteins

5553 - RBM

54

14 - RBM

34

85 - SRrp

76 - TIA TIAR

OligoU

86 - hnRNP

RALYL

Fungal SR (SpSrp1)

Fungal SR (SpSrp2)

Fig. S7

94

59

97

68

99

70

93

87

74

94

82

75

70 84

58

99

51

63

Ricinus communis@28976 m000161[RRM1][KOG4205]Ricinus communis@30170_m013671[RRM1][KOG4205]

Arabidopsis thaliana@NP_176143[RRM1][KOG4205]Chlamydomonadales@jgi_Volca1_107445[2][RRM1:100%][KOG4205:100%]

Cyanidioschyzon merolae@gnl_CMER_CMR392C[RRM1][KOG4205]Takifugu rubripes@SINFRUP00000163373[RRM1][KOG0149]

Takifugu rubripes@SINFRUP00000145256[RRM1][KOG0149]Thalassiosira pseudonana@jgi_Thaps3_25203[2][RRM1:100%][KOG4205:100%]

Phaeodactylum tricornutum@jgi_Phatr2_41450[RRM1][KOG4205]Ciona intestinalis@ENSCINP00000029053[RRM1][KOG4205]

Ciona intestinalis@ENSCINP00000006182[RRM1][KOG4205]Cryptosporidium parvum_Iowa_II@XP_626025[RRM1][KOG4205]

Chlamydomonadales@jgi_Chlre3_181880[2][RRM2:100%][KOG4205:100%]Drosophila melanogaster@CG9654-PA[RRM1][KOG4205]

Cryptosporidium parvum_Iowa_II@XP_001388284[RRM1][KOG4205]Bacillariophyta@jgi_Phatr2_21039[2][RRM1:100%][KOG4205:100%]

Phytophthora ramorum@jgi_Phyra1_1_73884[RRM2][KOG4205]Aureococcus anophagefferens@jgi_Auran1_9576[RRM1][KOG0149]

Eukaryota@ENSMODP00000031317[289][RRM1:100%*****][hnRNP:28%****][.Musashi:13%***][.Dazap:9%***][KOG4205:99%*****]Bilateria@ENSRNOP00000022054[326][RRM1:100%*****][hnRNP:54%*****][KOG4205:100%*****]



Viridiplantae@NP_851001[17][RRM2:100%**][put-sr:12%][KOG4205:94%**][.KOG1833:6%]Cryptococcus neoformans_var._neoformans_JEC21@XP_566745[2][RRM1:100%]

Endopterygota@AAEL008257-PA[8][RRM2:100%**][KOG4205:100%**]Ciona@ENSCSAVP00000001921[3][RRM2:100%*][Musashi:67%][KOG4205:100%*]

Cryptococcus neoformans_var._neoformans_JEC21@XP_568675[RRM2][KOG4205]Caenorhabditis elegans@Y73B6BL_6b_3[10][RRM1:100%**][KOG4205:100%**]

Chlamydomonadales@jgi_Volca1_107445[2][RRM2:100%][KOG4205:100%]Ostreococcus lucimarinus@jgi_Ost9901_3_24530[RRM1][KOG4205]

Oryza sativa_japonica_cultivar-group@NP_001067093[RRM1][KOG4177]Ricinus communis@28976_m000161[RRM2][KOG4205]

Plasmodium falciparum_3D7@XP_001351452[RRM1][KOG4205]Saccharomycetales@XP_449511[7][RRM2:100%*][KOG4205:100%*]

Apis mellifera@XP_623573[RRM1][KOG0113]Ascomycota@XP_961230[5][RRM2:100%*][put-sr:20%][KOG4205:100%*]

Ustilago maydis_521@XP_758567[RRM2][KOG4205]Strongylocentrotus purpuratus@NP_999784[3][RRM1:100%*][KOG4205:100%*]

Dictyostelium discoideum_AX4@XP_629598[RRM2][KOG4205]Physcomitrella patens@jgi_Phypa1_1_19696[RRM1][KOG4205]


Eukaryota@AGAP006656-PA[121][RRM2:88%****][.RRM1:12%**][Musashi:36%***][.Dazap:21%***][.hnRNP:10%**][KOG4205:100%****]Cryptosporidium parvum_Iowa_II@XP_626025[RRM2][KOG4205]

Strongylocentrotus purpuratus@NP_999784[3][RRM2:100%*][KOG4205:100%*]Strongylocentrotus purpuratus@XP_001183095[2][RRM2:100%][KOG4205:100%]

Strongylocentrotus purpuratus@XP_001176409[2][RRM2:100%][KOG4205:100%]Sorex araneus@ENSSARP00000008097[RRM2][hnRNP][KOG4205]


Caenorhabditis elegans@F42A6_7a_1[8][RRM2:100%**][KOG4205:100%**]Coelomata@CG6354-PB[373][RRM2:95%*****][hnRNP:53%*****][KOG4205:100%*****]

Drosophila melanogaster@CG9654-PA[RRM2][KOG4205]Ciona@ENSCSAVP00000016637[3][RRM2:100%*][KOG4205:100%*]Ciona@ENSCINP00000028810[2][RRM2:100%][KOG4205:100%]Euteleostomi@ENSDARP00000005968[129][RRM2:95%****][.RRM1:5%*][hnRNP:57%****][KOG4205:100%****]

Endopterygota@XP_001121454[19][RRM2:100%**][KOG4205:100%**]Physcomitrella patens@jgi_Phypa1_1_120016[RRM2][KOG4205]

Caenorhabditis elegans@Y73B6BL_6a_3[10][RRM2:100%**][KOG4205:100%**]Plasmodium falciparum_3D7@XP_001347758[RRM1][KOG0149]

Plasmodium falciparum_3D7@XP_001347758[RRM2][KOG0149]Strongylocentrotus purpuratus@XP_789716[2][RRM2:100%][KOG4205:100%]


Encephalitozoon cuniculi_GB-M1@NP_597487[RRM1][KOG4205]Embryophyta@IMGA_AC144431_42_2[6][RRM3:100%*][put-sr:17%][KOG4205:100%*]


Theileria parva_strain_Muguga@XP_766722[RRM1][KOG0144]Ciona intestinalis@ENSCINP00000027768[RRM1][KOG0548]

Dictyostelium discoideum_AX4@XP_643007[RRM1]Dictyostelium discoideum_AX4@XP_641568[RRM2][KOG3598]

Aedes aegypti@AAEL010890-PA[RRM1][put-sr][KOG0132]Plasmodium falciparum_3D7@XP_001349292[RRM1][KOG0146]


Thalassiosira pseudonana@jgi_Thaps3_2206[RRM1]Dictyostelium discoideum_AX4@XP_638966[RRM2][KOG0147]

Phaeodactylum tricornutum@jgi_Phatr2_38474[RRM1]Ustilago maydis_521@XP_760296[RRM1]

Cryptococcus neoformans_var._neoformans_JEC21@XP_572996[RRM1]Ricinus communis@30169_m006629[RRM1][KOG0123]

Euteleostomi@ENSOANP00000013028[22][RRM1:100%***]Endopterygota@XP_967886[3][RRM1:100%*]

Drosophila melanogaster@CG14414-PB[RRM1]Zea mays@11279_m000026_AZM5_6772[RRM1][put-sr][KOG0117]

Oryza sativa_japonica_cultivar-group@NP_001067112[RRM2][put-sr][KOG0117]Chlamydomonadales@jgi_Volca1_107765[2][RRM1:100%][KOG0145:100%]

Embryophyta@jgi_Phypa1_1_217831[15][RRM3:93%**][.RRM1:7%][KOG0117:100%**]Ustilago maydis_521@XP_756401[RRM1]

Bilateria@ENSLAFP00000012959[197][RRM3:93%*****][.RRM2:5%**][hnRNP:36%****][KOG0117:100%*****]Strongylocentrotus purpuratus@XP_793277[2][RRM3:100%][KOG0117:100%]

Plasmodium falciparum_3D7@XP_966276[RRM2]Encephalitozoon cuniculi_GB-M1@NP_597181[RRM1][KOG0110]

Xenopus tropicalis@ENSXETP00000056096[RRM1][KOG0109]Mammalia@ENSTBEP00000003150[16][RRM1:100%**][RBM:94%**][KOG0109:100%**]

Clupeocephala@ENSGACP00000025151[11][RRM1:100%**][KOG0109:100%**]Endopterygota@CG7903-PA[5][RRM1:100%*][KOG0109:80%*]

Tribolium castaneum@XP_971700[RRM1]Clupeocephala@ENSORLP00000002364[10][RRM2:100%**][KOG0109:100%**]

Euteleostomi@ENSDNOP00000012760[63][RRM2:94%****][.RRM1:6%*][LARK:65%***][.RBM:21%**][KOG0109:97%****]Coelomata@ENSXETP00000008271[74][RRM1:100%****][LARK:61%***][KOG0109:97%****]

Strongylocentrotus purpuratus@XP_792521[4][RRM1:100%*][put-sr:100%*][KOG0109:100%*]Ciona intestinalis@ENSCINP00000023722[RRM1][KOG0109]


Endopterygota@CG8597-PE[8][RRM2:100%**][LARK:62%*][KOG0109:100%**]Danio rerio@ENSDARP00000065401[RRM2][KOG0109]

Drosophila melanogaster@CG3312-PA[2][RRM1:100%][KOG0128:100%]Ustilago maydis_521@XP_758439[RRM3][KOG0123]

Ashbya gossypii_ATCC_10895@NP_984845[RRM2][KOG0123]Dictyostelium discoideum_AX4@XP_645138[RRM1]

Dictyostelium discoideum_AX4@XP_638767[RRM1][KOG0123]Aedes aegypti@AAEL012119-PA[RRM1]

Encephalitozoon cuniculi_GB-M1@NP_584552[RRM3][KOG0123]Dictyostelium discoideum_AX4@XP_641373[RRM1][put-sr]

Saccharomycetales@XP_455897[3][RRM1:100%*][KOG0123:67%]Strongylocentrotus purpuratus@XP_001185821[2][RRM1:100%][KOG0670:100%]

51 - LARK

50 - LARK

63 - hnRNP

52

35 - G3BP

RBM

30K RRM

hnRNP

Musashi

Dazap

TARDBP

OligoU

Fig. S7

95

64

79

95

51

64

68 64

96

59

77

77

71

Chlamydomonadales@jgi Volca1 107658[2][RRM1:100%][KOG4205:50%][ KOG0474:50%]Ciona intestinalis@ENSCINP00000024280[RRM1][KOG0113]

Aureococcus anophagefferens@jgi_Auran1_9018[RRM1]Strongylocentrotus purpuratus@XP_786044[2][RRM1:100%][KOG0117:100%]Aureococcus anophagefferens@jgi_Auran1_17889[RRM1][KOG4207]

Ustilago maydis_521@XP_761797[RRM2][put-sr][KOG3257]Euteleostomi@ENSGALP00000012472[36][RRM4:89%***][.RRM2:8%*][nucleolin:56%**][KOG0123:100%***]


Basidiomycota@XP_566835[2][RRM1:100%][KOG0148:100%]Schizosaccharomyces pombe_972h-@NP_593531[RRM1][nucleolin][KOG0147]

Saccharomycetales@XP_456900[6][RRM1:100%*][nucleolin:17%][KOG0148:50%*][.KOG0131:33%][.KOG4210:17%]Yarrowia lipolytica@XP_505375[RRM1][KOG0148]

Ostreococcus tauri@jgi_Ostta4_31833[RRM2][KOG0148]Eukaryota@YHR086W[51][RRM3:76%***][.RRM2:20%**][oligoU:10%*][KOG0148:90%***]

Schizosaccharomyces pombe_972h-@NP_594243[RRM3][KOG0148]Phytophthora@jgi_Phyra1_1_50314[2][RRM3:100%][KOG0148:100%]

Aureococcus anophagefferens@jgi_Auran1_28594[RRM3][KOG0148]Aspergillus fumigatus_Af293@XP_754657[RRM1]

Cryptococcus neoformans_var._neoformans_JEC21@XP_566835[RRM2][KOG0148]Ustilago maydis_521@XP_762340[RRM2][KOG0148]Pezizomycotina@XP_754840[2][RRM2:100%][KOG0127:50%][.KOG0148:50%]Saccharomycetales@XP_456900[7][RRM2:100%*][nucleolin:14%][KOG0148:57%*][.KOG0131:29%][.KOG4210:14%]

Schizosaccharomyces pombe_972h-@NP_593531[RRM2][nucleolin][KOG0147]rosids@NP_568388[3][RRM1:100%*][KOG0125:33%][.KOG0148:33%]

Physcomitrella patens@jgi_Phypa1_1_151460[4][RRM1:100%*][KOG0108:75%*][.KOG0149:25%]Strongylocentrotus purpuratus@XP_793862[2][RRM2:100%][KOG0144:100%]

Aureococcus anophagefferens@jgi_Auran1_8994[RRM1][KOG0149]Phytophthora@jgi_Physo1_1_134615[2][RRM1:100%]

Aureococcus anophagefferens@jgi_Auran1_66158[RRM2][put-sr][KOG0149]Oryza sativa_japonica_cultivar-group@NP_001045556[RRM1][KOG0108]

Magnoliophyta@NP_566958[6][RRM2:67%*][.RRM1:33%][KOG0123:33%][.KOG0124:33%][.KOG0131:33%]Yarrowia lipolytica@XP_505724[RRM1][KOG4198]


Ostreococcus@jgi_Ost9901_3_710[2][RRM4:100%][KOG0110:100%]Magnoliophyta@NP_193696[2][RRM3:100%][KOG0110:100%]

Apocrita@XP_001605134[2][RRM5:100%][KOG0110:100%]Phytophthora sojae@jgi_Physo1_1_129427[RRM4][KOG0110]

Euteleostomi@ENSGALP00000013474[20][RRM5:85%**][.RRM4:5%][.RRM3:5%][.RRM2:5%][put-sr:10%][KOG0110:100%**]Thalassiosira pseudonana@jgi_Thaps3_268689[RRM4][KOG0110]

Phaeodactylum tricornutum@jgi_Phatr2_20740[RRM4][KOG0110]Cryptosporidium parvum_Iowa_II@XP_627799[RRM4][KOG0110]

Ascomycota@XP_001386803[10][RRM4:90%**][.RRM2:10%][KOG0110:100%**]Cryptococcus neoformans_var._neoformans_JEC21@XP_569873[RRM4][KOG0110]

Aureococcus anophagefferens@jgi_Auran1_9354[RRM1]Aureococcus anophagefferens@jgi_Auran1_60739[RRM1][put-sr][KOG1860]


Arabidopsis thaliana@NP_179762[RRM1][oligoU]Thalassiosira pseudonana@jgi_Thaps3_20887[RRM1]

Phaeodactylum tricornutum@jgi_Phatr2_44468[RRM1]Magnoliophyta@NP_001059075[6][RRM1:100%*][put-sr:17%][GRSRBP:50%*][KOG0108:50%*][.KOG0148:33%][.KOG0111:17%]

Eukaryota@jgi_Phypa1_1_37849[169][RRM1:100%*****][put-sr:5%**][GRSRBP:33%****][.hnRNP:18%***][.RBMY:15%***][KOG0108:23%***][.KOG0111:23%***][.KOG0149:18%***][.KOG0117:11%**][.KOG0116:9%**]Phaeodactylum tricornutum@jgi_Phatr2_49481[RRM1][KOG1337]

Dictyostelium discoideum_AX4@XP_629578[RRM1][KOG0122]Ciona@ENSCINP00000012771[9][RRM1:100%**][put-sr:11%][KOG4205:100%**]

Neurospora crassa_OR74A@XP_965346[RRM1][KOG0110]Eukaryota@XP_391240[27][RRM2:67%**][.RRM1:33%**][cpRNP:19%*][KOG0127:48%**][.KOG0108:22%*][.KOG0131:15%*][.KOG0149:7%][.KOG0145:7%]

Phaeodactylum tricornutum@jgi_Phatr2_8270[RRM1][KOG4207]Bacillariophyta@jgi_Thaps3_20223[2][RRM1:100%][KOG0108:100%]Thalassiosira pseudonana@jgi_Thaps3_20266[RRM1][KOG4207]

Chlamydomonadales@jgi_Chlre3_184151[2][RRM1:100%][KOG0921:50%][.KOG0116:50%]Ostreococcus@jgi_Ost9901_3_12693[2][RRM2:100%][KOG0127:100%]

Aureococcus anophagefferens@jgi_Auran1_9375[2][RRM1:100%][KOG0122:100%]Aureococcus anophagefferens@jgi_Auran1_17018[RRM1][KOG0111]

Phaeodactylum tricornutum@jgi_Phatr2_33658[RRM1]Aureococcus anophagefferens@jgi_Auran1_31715[RRM1][KOG0149]

Phytophthora@jgi_Phyra1_1_84416[2][RRM1:100%][KOG0148:100%]Embryophyta@jgi_Phypa1_1_156290[6][RRM1:100%*][put-sr:17%][KOG4205:100%*]

Phaeodactylum tricornutum@jgi_Phatr2_21039[RRM2][KOG4205]Dictyostelium discoideum_AX4@XP_643856[3][RRM1:100%*][KOG0149:100%*]

Caenorhabditis elegans@C50B8_1[RRM1]Diptera@AAEL008317-PA[3][RRM1:100%*][KOG0149:100%*]Diptera@AAEL006645-PA[2][RRM1:100%][KOG0149:100%]

Euteleostomi@ENSSTOP00000002923[18][RRM1:100%**][KOG4205:11%]Strongylocentrotus purpuratus@XP_001188704[2][RRM1:100%][KOG0149:100%]



Cryptosporidium parvum_Iowa_II@XP_628599[RRM2][KOG4205]Dictyostelium discoideum_AX4@XP_641688[RRM1][KOG0117]Volvox carteri@jgi_Volca1_116517[RRM2][KOG1984]

Coelomata@ENSTBEP00000005385[105][RRM2:86%****][.RRM1:14%**][P54nrb:30%***][.PSP1:24%***][.PSF:21%***][KOG0115:100%****]Dictyostelium discoideum_AX4@XP_646802[RRM2][KOG0145]

Arabidopsis thaliana@NP_187353[RRM1][30kRRM][KOG0149]Eukaryota@NP_001058102[93][RRM1:100%****][RBM:52%***][.30kRRM:13%**][KOG0149:96%****]

Arabidopsis thaliana@NP_200183[2][RRM1:100%][oligoU:100%][KOG0149:100%]Phytophthora sojae@jgi_Physo1_1_139371[RRM1][KOG4205]

Physcomitrella patens@jgi_Phypa1_1_96043[RRM1]Oryza sativa_japonica_cultivar-group@NP_001054022[RRM1][KOG4205]


Cyanidioschyzon merolae@gnl_CMER_CMR392C[RRM2][KOG4205]Ostreococcus tauri@jgi_Ostta4_33731[RRM2]

Ostreococcus tauri@jgi_Ostta4_33731[RRM1]Dictyostelium discoideum_AX4@XP_643377[RRM1][KOG3598]

Caenorhabditis elegans@F56D1_7[RRM1]Coelomata@AAEL001684-PA[39][RRM1:100%***][KOG0125:21%**]

Euteleostomi@ENSEEUP00000005436[64][RRM1:95%****]Takifugu rubripes@SINFRUP00000155469[RRM1]

Tupaia belangeri@ENSTBEP00000015084[RRM1]Spermophilus tridecemlineatus@ENSSTOP00000003171[RRM1]

Oryza sativa_japonica_cultivar-group@NP_001058805[RRM1][KOG4205]Zea mays@14684_m000016_AZM5_14964[RRM1][KOG4205]

Oryza sativa_japonica_cultivar-group@NP_001051402[RRM1][KOG0149]Ciona@ENSCINP00000009845[4][RRM1:100%*][KOG0116:100%*]

Deuterostomia@ENSMODP00000011218[78][RRM1:100%****][G3BP:82%****][KOG0116:100%****]Tribolium castaneum@XP_975463[RRM1][KOG0116]

Apis mellifera@XP_623996[RRM1][KOG0116]Chlamydomonadales@jgi_Chlre3_105806[2][RRM1:100%][KOG4205:100%]


Endopterygota@CG16901-PC[19][RRM1:100%**][KOG4205:100%**]Oryctolagus cuniculus@ENSOCUP00000001170[RRM1][hnRNP][KOG4205]

Myotis lucifugus@ENSMLUP00000003070[RRM1][hnRNP][KOG4205]Theileria parva_strain_Muguga@XP_766400[RRM1][put-sr][KOG4205]

Plasmodium falciparum_3D7@XP_001351452[RRM2][KOG4205]Ricinus communis@28976_m000161[RRM1][KOG4205]

58 - GRSRBP

hnRNP

RBMY

59

78 - OligoU

associated to node 4 in RaxML and merge-RaxML

Fig. S7

96

51

71

54

53

85

57 57

78 67

57

52

87 50

91

93

65 51

73

73

75

Aspergillus fumigatus Af293@XP 750045[RRM1]Cryptococcus neoformans_var._neoformans_JEC21@XP_569809[RRM1][KOG0130]

Plasmodium falciparum_3D7@XP_001348230[RRM1][KOG0130]Yarrowia lipolytica@XP_503462[RRM1][put-sr][KOG0130]

Ustilago maydis_521@XP_760711[RRM1][put-sr][KOG0687]Eukaryota@jgi_Thaps3_18841[52][RRM1:100%***][put-sr:56%***][RBM:42%***][KOG0130:100%***]

Phaeodactylum tricornutum@jgi_Phatr2_20716[RRM1][KOG0130]Murinae@ENSMUSP00000078984[3][RRM1:100%*][KOG4207:100%*]

Dictyostelium discoideum_AX4@XP_628876[RRM1]Plasmodium falciparum_3D7@XP_001352080[RRM2]

Caenorhabditis elegans@Y55F3AM_3c_1[3][RRM2:100%*][put-sr:33%][UMH:100%*][KOG0147:100%*]Thalassiosira pseudonana@jgi_Thaps3_33709[RRM1][KOG0111]

Schizosaccharomyces pombe_972h-@NP_595090[RRM1]Bacillariophyta@jgi_Thaps3_19374[2][RRM1:100%][KOG0121:100%]



Encephalitozoon cuniculi_GB-M1@NP_597585[RRM1][KOG0121]Cryptosporidium parvum_Iowa_II@XP_627536[RRM1][KOG0121]

Yarrowia lipolytica@XP_500351[RRM1][KOG0123]Endopterygota@CG5655-PA[5][RRM1:100%*][put-sr:100%*][KOG0107:80%*][.KOG0921:20%]

Strongylocentrotus purpuratus@XP_001178467[2][RRM1:100%][put-sr:100%]Eukaryota@ENSGALP00000022397[157][RRM1:100%*****][put-sr:75%****][SR:59%****][KOG0107:66%****]

Strongylocentrotus purpuratus@XP_001180596[2][RRM1:100%][put-sr:100%]Pezizomycotina@XP_961985[2][RRM1:100%][KOG0116:50%]

Aureococcus anophagefferens@jgi_Auran1_69134[RRM1][put-sr]Tetraodontidae@GSTENP00014994001[2][RRM1:50%][.RRM3:50%][KOG0123:50%]

Euteleostomi@GSTENP00022906001[41][RRM3:83%***][.RRM2:10%*][.RRM1:7%*][nucleolin:54%***][KOG0123:93%***]Neurospora crassa_OR74A@XP_964541[RRM1]

Aspergillus fumigatus_Af293@XP_748929[RRM1]Phytophthora@jgi_Physo1_1_136528[2][RRM1:100%][put-sr:50%][KOG3208:50%]

Aureococcus anophagefferens@jgi_Auran1_17068[RRM1][KOG4207]Cryptosporidium parvum_Iowa_II@XP_628282[2][RRM1:100%][put-sr:100%][KOG0111:50%][.KOG4207:50%]

Plasmodium falciparum_3D7@XP_001351591[RRM1]Plasmodium falciparum_3D7@XP_001347950[RRM1][KOG4207]

Chordata@ENSETEP00000001114[45][RRM1:100%***][put-sr:96%***][SRrp:82%***][KOG0111:29%**][.KOG0415:13%*]Viridiplantae@NP_001046448[23][RRM1:100%***][put-sr:91%***][SR:35%**][KOG4207:13%*][.KOG0127:13%*][.KOG0110:9%]Chlamydomonadales@jgi_Volca1_121229[2][RRM1:100%][put-sr:100%][KOG0415:50%]

Bacillariophyta@jgi_Thaps3_23196[2][RRM1:100%][KOG4207:50%]Phytophthora sojae@jgi_Physo1_1_138511[RRM1][put-sr]

Eukaryota@8925_m000027_AZM5_1178[67][RRM1:100%****][put-sr:84%****][SR:61%***][KOG4207:61%***][.KOG4368:24%**]Cyanidioschyzon merolae@gnl_CMER_CML202C[RRM1][put-sr]

Gammaproteobacteria@YP_113294[2][RRM1:100%][PROK:100%]Magnoliophyta@NP_001060859[5][RRM1:100%*][cpRNP:40%][KOG0110:40%][.KOG0148:40%]

Phaeodactylum tricornutum@jgi_Phatr2_16633[RRM1][KOG0125]Tribolium castaneum@XP_970765[RRM2][KOG0127]

Ostreococcus lucimarinus@jgi_Ost9901_3_8174[RRM1][KOG4207]Dictyostelium discoideum_AX4@XP_647083[RRM1]


Chlamydomonas reinhardtii@jgi_Chlre3_152680[RRM1][KOG4660]Drosophila melanogaster@CG5213-PA[RRM2][KOG0145]

Deuterostomia@ENSDNOP00000008593[94][RRM1:100%****][P54nrb:28%***][.PSP1:21%**][.PSF:18%**][KOG0115:99%****]Endopterygota@CG10328-PA[9][RRM1:100%**][P54nrb:33%*][KOG0115:100%**]

Caenorhabditis elegans@F25B5_7d[2][RRM1:100%][KOG0115:100%]Legionella_pneumophila@YP_001249669[3][RRM1:100%*][PROK:100%*][put-sr:100%*][KOG0149:100%*]

Ostreococcus lucimarinus@jgi_Ost9901_3_7602[RRM1][KOG0145]Coxiella_burnetii@YP_001424629[2][RRM1:100%][PROK:100%][KOG0108:100%]

Embryophyta@jgi_Phypa1_1_44443[2][RRM2:100%][KOG0149:100%]Embryophyta@29900_m001607[13][RRM2:100%**][oligoU:38%*][KOG4205:77%**][.KOG0149:23%*]

Aspergillus fumigatus_Af293@XP_747328[RRM1][KOG0110]Ostreococcus lucimarinus@jgi_Ost9901_3_27365[RRM2][KOG0123]


Phytophthora@jgi_Physo1_1_140403[2][RRM1:100%][put-sr:100%][KOG0127:100%]Volvox carteri@jgi_Volca1_72841[RRM1][KOG0144]

Eukaryota@NP_001063859[35][RRM1:100%***][ZCRB1:69%***][KOG0108:40%**][.KOG0122:9%*][.KOG0117:6%][.KOG0107:6%]Phytophthora ramorum@jgi_Phyra1_1_94226[RRM1][put-sr][KOG0941]

Aedes aegypti@AAEL006197-PA[RRM1][KOG0108]Yarrowia lipolytica@XP_500351[RRM2][KOG0123]

Cryptococcus neoformans_var._neoformans_JEC21@XP_571608[RRM1][put-sr][KOG0151]Eukaryota@jgi_Volca1_104604[49][RRM1:100%***][put-sr:78%***][KOG0151:100%***]

Plasmodium falciparum_3D7@XP_001348201[RRM1][KOG0151]Cyanidioschyzon merolae@gnl_CMER_CMS187C[RRM1][KOG0123]

Chlamydomonas reinhardtii@jgi_Chlre3_194261[RRM1][KOG0123]Embryophyta@NP_001063403[14][RRM1:100%**][KOG0148:100%**]Endopterygota@XP_974444[2][RRM1:100%][KOG0144:100%]

Clupeocephala@ENSORLP00000016619[5][RRM1:100%*][KOG0131:60%*][.KOG0123:40%]Trypanosomatidae@XP_001469326[2][RRM1:100%][KOG0123:100%]

Eukaryota@ENSXETP00000023927[236][RRM1:100%*****][PABP:55%****][KOG0123:100%*****]Tetraodon nigroviridis@GSTENP00024897001[RRM1][PABP][KOG0123]Trypanosomatidae@XP_001469222[2][RRM1:100%][KOG0123:100%]

Leishmania infantum_JPCM5@XP_001466041[RRM1][KOG0123]Saccharomycetaceae@YFR023W[4][RRM1:100%*][KOG0123:100%*]

Candida glabrata_CBS138@XP_447635[RRM1][KOG0123]Danio rerio@ENSDARP00000091192[14][RRM1:100%**][put-sr:100%**][KOG0123:100%**]

rosids@30078_m002213[3][RRM1:100%*][PABP:33%][KOG0123:100%*]Oryza sativa_japonica_cultivar-group@NP_001049727[RRM1][KOG0123]Ricinus communis@30146_m003481[RRM1][KOG0123]

Arabidopsis thaliana@NP_188259[RRM1][PABP][KOG0123]Ciona intestinalis@ENSCINP00000004384[RRM2][KOG0148]

Strongylocentrotus purpuratus@XP_001183631[2][RRM2:100%][KOG0148:100%]Physcomitrella patens@jgi_Phypa1_1_170658[RRM1]


Cryptococcus neoformans_var._neoformans_JEC21@XP_571861[RRM1][KOG0226]Eukaryota@XP_964958[72][RRM1:100%****][KOG0226:100%****]Nasonia vitripennis@XP_001603091[RRM1][KOG0226]

Yarrowia lipolytica@XP_501542[RRM2][KOG0131]Eukaryota@IMGA_AC144483_30_2[123][RRM2:83%****][.RRM1:17%***][TIATIAR:58%****][.oligoU:6%*][KOG0148:99%****]

Ustilago maydis_521@XP_757329[RRM2][KOG0145]Endopterygota@AAEL011988-PA[5][RRM2:100%*][KOG0144:80%*][.KOG0145:20%]

Dictyostelium discoideum_AX4@XP_635179[RRM1][KOG0148]Aureococcus anophagefferens@jgi_Auran1_28594[RRM2][KOG0148]

Pichia stipitis_CBS_6054@XP_001386002[RRM2][KOG0148]Debaryomyces hansenii_CBS767@XP_461354[RRM2][KOG0148]Ciona@ENSCSAVP00000020066[4][RRM1:50%][.RRM2:50%][KOG0131:50%]

Saccharomycetales@XP_460477[6][RRM1:67%*][.RRM2:33%][KOG0148:67%*][.KOG3598:17%][.KOG0145:17%]Saccharomycetales@XP_455748[4][RRM2:100%*][KOG0148:75%*][.KOG0145:25%]

Eukaryota@ENSMUSP00000030730[72][RRM2:85%****][.RRM1:15%**][oligoU:10%*][KOG0148:58%***][.KOG0123:25%**][.KOG0131:14%**]Pezizomycotina@XP_961985[2][RRM2:100%][KOG0116:50%]

Schizosaccharomyces pombe_972h-@NP_595090[RRM2]Phytophthora@jgi_Phyra1_1_75647[2][RRM1:100%]

Ciona intestinalis@ENSCINP00000008726[RRM1][put-sr][KOG2193]Candida glabrata_CBS138@XP_445637[RRM1]

Ashbya gossypii_ATCC_10895@NP_983970[RRM1]Eukaryota@ENSETEP00000015606[204][RRM3:85%*****][.RRM2:11%***][PABP:66%****][KOG0123:100%*****]

Oryza sativa_japonica_cultivar-group@NP_001054954[2][RRM1:100%][KOG0108:100%]Chlamydomonadales@jgi_Volca1_107658[2][RRM1:100%][KOG4205:50%][.KOG0474:50%]

77 - TIA TIAR

OligoU

66 - PABP

3 - PABP

13

57 - ZCRB1

33 - p54nrb

PSP1

PSF42

22 - single-RRM

SR proteins

23 - SRrp

15

17 - single-RRM

Zn-K SR proteins

24

20 - RBM

Fig. S7

97

58

98 82

95

77

77 89

93

57

65

98

66

66

84 59

59

61

96

88

50

Neurospora crassa OR74A@XP 965014[RRM2][KOG0110]Phaeodactylum tricornutum@jgi_Phatr2_20740[RRM2][KOG0110]

Cryptococcus neoformans_var._neoformans_JEC21@XP_569873[RRM2][KOG0110]Caenorhabditis elegans@T23F6_4_1[2][RRM3:100%][KOG0110:100%]

Eukaryota@IMGA_AC183923_6_1[34][RRM3:74%***][.RRM1:15%*][.RRM2:12%*][put-sr:6%][KOG0110:100%***]Oryza sativa_japonica_cultivar-group@NP_001053839[RRM1][KOG0110]

Aspergillus fumigatus_Af293@XP_750233[RRM2][KOG0110]Saccharomycetales@NP_984131[7][RRM2:100%*][KOG0110:100%*]

Schizosaccharomyces pombe_972h-@NP_595599[RRM2][KOG0110]Euteleostomi@GSTENP00013801001[29][RRM1:100%***][LA:59%**][KOG1855:100%***]

Euteleostomi@ENSORLP00000006283[2][RRM1:100%][LA:50%][KOG1855:100%]Apocrita@XP_001600355[2][RRM1:100%][KOG1855:100%]

Tribolium castaneum@XP_974730[RRM1][KOG1855]Ciona@ENSCSAVP00000005375[4][RRM2:75%*][.RRM1:25%][KOG0116:75%*][.KOG2141:25%]

Physcomitrella patens@jgi_Phypa1_1_167900[3][RRM1:100%*][KOG0123:33%][.KOG4210:33%][.KOG1015:33%]Deuterostomia@ENSXETP00000012868[47][RRM1:100%***][KOG4454:60%***][.KOG0131:40%**]

Endopterygota@AGAP002256-PA[4][RRM1:100%*][KOG4454:75%*][.KOG0131:25%]Drosophila melanogaster@CG11454-PA[RRM1][KOG4454]

Magnoliophyta@NP_001055607[4][RRM1:100%*][put-sr:25%][KOG0131:100%*]Caenorhabditis elegans@Y37D8A_21_1[2][RRM1:100%][KOG4454:100%]




Saccharomyces cerevisiae@YOR319W[RRM1][KOG0131]Candida glabrata_CBS138@XP_447678[RRM1][KOG0131]

Leishmania infantum_JPCM5@XP_001468615[RRM1]Dictyostelium discoideum_AX4@XP_641693[RRM1][KOG0122]

Yarrowia lipolytica@XP_503515[RRM1][KOG0122]Saccharomycetales@XP_446998[3][RRM1:100%*][KOG0122:100%*]

Saccharomycetaceae@XP_001388004[2][RRM1:100%][KOG0122:100%]Caenorhabditis elegans@F22B5_2[RRM1][KOG0122]

Cryptococcus neoformans_var._neoformans_JEC21@XP_567824[RRM1][KOG0122]Eukaryota@NP_187747[49][RRM1:100%***][KOG0122:98%***]

Medicago truncatula@IMGA_AC144431_18_2[RRM1][KOG0122]Apicomplexa@XP_001388056[3][RRM1:100%*][KOG0122:100%*]

Cyanidioschyzon merolae@gnl_CMER_CMH159C[RRM1][KOG0122]Encephalitozoon cuniculi_GB-M1@NP_584580[RRM1][KOG0114]

Eukaryota@jgi_Phatr2_8132[54][RRM1:100%***][KOG0114:100%***]Schizosaccharomyces pombe_972h-@NP_594609[RRM1][KOG4660]

Debaryomyces hansenii_CBS767@XP_458197[RRM1][KOG0114]Theria@ENSMODP00000002817[2][RRM1:100%]

Amniota@ENSMODP00000004174[11][RRM4:55%*][.RRM3:36%*][.RRM2:9%][put-sr:100%**][KOG0112:100%**]Tribolium castaneum@XP_969008[RRM2][KOG0331]

Theileria parva_strain_Muguga@XP_764943[RRM1][KOG4206]Coelomata@ENSORLP00000008206[18][RRM1:100%**][snRNP:83%**][KOG4206:100%**]

Sordariomycetes@XP_962704[2][RRM1:100%][put-sr:50%][KOG4206:100%]Pichia stipitis_CBS_6054@XP_001382592[RRM1][KOG4206]Saccharomyces cerevisiae@YBR119W[RRM1]

Plasmodium falciparum_3D7@XP_001349796[RRM2][KOG4206]Pezizomycotina@XP_753458[2][RRM2:100%][put-sr:50%][KOG4206:100%]

Schizosaccharomyces pombe_972h-@NP_596424[RRM2][KOG4206]Cryptococcus neoformans_var._neoformans_JEC21@XP_568533[RRM2][KOG4206]

Eukaryota@ENSGACP00000013006[79][RRM2:96%****][snRNP:30%***][KOG4206:100%****]Theileria parva_strain_Muguga@XP_764943[RRM2][KOG4206]

Embryophyta@IMGA_AC141435_12_2[17][RRM2:76%**][.RRM1:24%*][KOG4660:100%**]Drosophila melanogaster@CG2050-PA[RRM3]

Ciona@ENSCSAVP00000017501[2][RRM1:50%][.RRM2:50%][KOG0109:50%]Myotis lucifugus@ENSMLUP00000003020[RRM3][PTBP][KOG1190]

Phytophthora@jgi_Phyra1_1_74707[2][RRM3:100%][KOG0110:100%]Volvox carteri@jgi_Volca1_63158[RRM2][KOG0110]

Tetrapoda@ENSXETP00000004736[17][RRM2:59%**][.RRM1:41%*][PTBP:94%**][KOG1190:100%**]Saccharomyces cerevisiae@YMR302C[RRM1]

Leishmania infantum_JPCM5@XP_001466413[RRM3][put-sr][KOG0147]Trypanosoma brucei_TREU927@XP_951655[RRM3][put-sr][KOG0109]

Trypanosoma brucei_TREU927@XP_951655[RRM2][put-sr][KOG0109]Embryophyta@jgi_Phypa1_1_201182[6][RRM2:100%*][KOG0127:100%*]

Ostreococcus@jgi_Ost9901_3_26255[2][RRM2:100%][KOG0127:100%]Chlamydomonas reinhardtii@jgi_Chlre3_186870[RRM2][KOG0127]

Schizosaccharomyces pombe_972h-@NP_596114[RRM2][KOG0127]Pezizomycotina@XP_962933[3][RRM2:100%*][KOG0127:100%*]

Saccharomycetales@XP_459044[4][RRM2:100%*][KOG0127:100%*]Yarrowia lipolytica@XP_499726[RRM2][KOG0127]

Chordata@ENSOGAP00000005376[31][RRM2:90%***][.RRM3:6%][RBM:39%**][KOG0127:100%***]Tribolium castaneum@XP_974350[RRM1][KOG0127]


Nasonia vitripennis@XP_001605703[RRM1][KOG0127]Drosophila melanogaster@CG4806-PA[RRM1][KOG0127]

Aedes aegypti@AAEL008572-PA[RRM1][KOG0127]Magnoliophyta@NP_001062073[4][RRM1:100%*][KOG0110:75%*][.KOG0127:25%]

Trypanosoma brucei_TREU927@XP_829716[RRM1]Aedes aegypti@AAEL010888-PA[RRM2]

Encephalitozoon cuniculi_GB-M1@NP_586099[RRM2][KOG0131]Cyanidioschyzon merolae@gnl_CMER_CMG025C[RRM1][KOG1080]

Saccharomyces cerevisiae@YOR319W[RRM2][KOG0131]Euteleostomi@ENSORLP00000016244[7][RRM1:100%*][KOG1080:57%*]

Aedes aegypti@AAEL010807-PA[RRM1][put-sr][KOG1080]Sordariomycetes@XP_001522188[3][RRM1:100%*][put-sr:67%]

Schizosaccharomyces pombe_972h-@NP_596549[RRM1][put-sr]Cryptococcus neoformans_var._neoformans_JEC21@XP_569824[RRM1][put-sr]

Coelomata@ENSMUSP00000057332[45][RRM1:100%***][put-sr:100%***][RNPS1:64%***][KOG4209:87%***]Caenorhabditis elegans@K02F3_11_2[2][RRM1:100%][put-sr:100%][KOG4209:100%]


Phytophthora@jgi_Physo1_1_138873[2][RRM1:100%][put-sr:100%][KOG1611:50%]Plasmodium falciparum_3D7@XP_001348607[RRM1]

Trypanosomatidae@XP_843959[2][RRM3:100%]Aedes aegypti@AAEL010887-PA[RRM6][put-sr][KOG1984]

Plasmodium falciparum_3D7@XP_001347479[RRM1]Debaryomyces hansenii_CBS767@XP_460681[RRM3][KOG0128]


Encephalitozoon cuniculi_GB-M1@NP_585779[RRM1]Mammalia@ENSETEP00000003776[19][RRM1:100%**][LA:95%**][KOG4213:100%**]

Aedes aegypti@AAEL006876-PA[RRM1][KOG2193]Plasmodium falciparum_3D7@XP_001352162[RRM1]Plasmodium falciparum_3D7@XP_001351468[RRM1]

Saccharomycetales@XP_462132[6][RRM1:100%*][KOG0533:100%*]Sordariomycetes@XP_956471[2][RRM1:100%][KOG0533:100%]


Cryptococcus neoformans_var._neoformans_JEC21@XP_572037[RRM1][KOG0533]Dictyostelium discoideum_AX4@XP_642758[RRM1]Ostreococcus@jgi_Ostta4_7793[2][RRM1:100%][KOG0108:100%]

Aureococcus anophagefferens@jgi_Auran1_71372[2][RRM3:50%][.RRM2:50%][put-sr:100%][KOG1178:100%]Ostreococcus lucimarinus@jgi_Ost9901_3_32831[RRM1]

Aspergillus fumigatus_Af293@XP_750045[RRM1]

84 - La

26 - SR45

27 - RNPS1 28

71 - RBM

41 - snRNP

40 - snRNP

45

43

44

65

46

47

49

81 - La

3233 - p54nrb

PSP1

PSf

Fungal SpRnps1

Fig. S7

98

60

51

97

69

91

95

81

71 53

92 93

99

92

69

63

96

Ustilago maydis 521@XP 756311[RRM2][put sr][KOG0147]Bilateria@Y47G6A_20a[64][RRM1:100%****][UMH:73%***][KOG0124:100%****]

Dictyostelium discoideum_AX4@XP_638262[RRM1][put-sr][KOG0670]Phytophthora ramorum@jgi_Phyra1_1_81440[2][RRM1:100%][KOG0124:100%]

Cryptosporidium parvum_Iowa_II@XP_628096[RRM1][put-sr][KOG0124]Eukaryota@ENSFCAP00000006163[84][RRM2:88%****][.RRM1:12%**][put-sr:86%****][UMH:39%***][.CAPER:8%*][KOG0147:100%****]

Bacillariophyta@jgi_Phatr2_20857[2][RRM2:100%][put-sr:100%][KOG0147:100%]Dictyostelium discoideum_AX4@XP_638262[RRM2][put-sr][KOG0670]

Cryptosporidium parvum_Iowa_II@XP_628096[RRM2][put-sr][KOG0124]Phytophthora@jgi_Phyra1_1_84640[3][RRM2:67%][.RRM1:33%][KOG0124:67%][.KOG0120:33%]

Bilateria@ENSCSAVP00000007991[62][RRM2:95%****][.RRM1:5%*][UMH:74%***][KOG0124:100%****]Phaeodactylum tricornutum@jgi_Phatr2_44442[RRM2][KOG4211]


Aureococcus anophagefferens@jgi_Auran1_8214[RRM1]Volvox carteri@jgi_Volca1_120369[RRM1][put-sr][KOG0147]

Euteleostomi@ENSMODP00000021210[32][RRM2:97%***][nucleolin:59%**][KOG0123:100%***]Ciona@ENSCINP00000008105[4][RRM1:100%*][KOG0116:50%][.KOG2141:25%]

Magnoliophyta@30131_m007093[6][RRM3:83%*][.RRM2:17%][KOG0127:100%*]Physcomitrella patens@jgi_Phypa1_1_201182[RRM3][KOG0127]

Dictyostelium discoideum_AX4@XP_646584[RRM3][KOG0127]Ostreococcus@jgi_Ostta4_19569[2][RRM3:100%][KOG0127:100%]

Chlamydomonadales@jgi_Volca1_87629[2][RRM3:100%][KOG0127:100%]Caenorhabditis elegans@B0035_12_2[2][RRM2:100%][KOG0128:100%]Ciona intestinalis@ENSCINP00000018774[2][RRM3:100%][KOG0127:100%]

Euteleostomi@ENSGACP00000016696[19][RRM3:79%**][.RRM4:11%][.RRM1:11%][RBM:58%**][KOG0127:100%**]Oryzias latipes@ENSORLP00000012079[RRM3][KOG0127]

Caenorhabditis elegans@R05H10_2[RRM2][KOG0127]Endopterygota@XP_001605703[3][RRM2:67%][.RRM3:33%][KOG0127:100%*]


Aedes aegypti@AAEL008572-PA[RRM2][KOG0127]Leishmania infantum_JPCM5@XP_001464648[RRM1][KOG0113]

Coxiella_burnetii@YP_001424503[2][RRM1:100%][PROK:100%][KOG0113:100%]Cryptosporidium parvum_Iowa_II@XP_627799[RRM2][KOG0110]

Chlamydomonas reinhardtii@jgi_Chlre3_120019[RRM2][KOG0106]Chlamydomonas reinhardtii@jgi_Chlre3_80366[RRM2][KOG0106]

Embryophyta@29742_m001371[15][RRM2:80%**][.RRM1:20%*][put-sr:87%**][SR:67%**][KOG0106:100%**]Bacillariophyta@jgi_Phatr2_47737[2][RRM1:100%][put-sr:50%]

Cryptosporidium parvum_Iowa_II@XP_628165[RRM2][KOG4212]Dictyostelium discoideum_AX4@XP_639372[RRM1][KOG0670]

Embryophyta@NP_001062111[8][RRM1:100%**][put-sr:62%*][KOG4849:38%*][.KOG4246:12%][.KOG0113:12%][.KOG4676:12%]Ostreococcus lucimarinus@jgi_Ost9901_3_26750[RRM1]

Dictyostelium discoideum_AX4@XP_629950[RRM1][KOG0128]Ciona intestinalis@ENSCINP00000019833[3][RRM2:100%*][KOG0128:100%*]

Culicidae@AAEL011963-PA[3][RRM2:100%*][KOG0128:100%*]Strongylocentrotus purpuratus@XP_781643[RRM2][KOG0128]

Tribolium castaneum@XP_972538[RRM2][KOG0128]Euteleostomi@ENSOCUP00000014007[29][RRM2:97%***][SART3:69%**][KOG0128:100%***]

Apocrita@XP_001602582[2][RRM2:100%][KOG0128:100%]Eukaryota@jgi_Ostta4_3181[66][RRM1:100%****][put-sr:47%***][cyclophilin:32%***][KOG0415:97%****]

Debaryomyces hansenii_CBS767@XP_459815[RRM1][KOG0415]Yarrowia lipolytica@XP_503802[RRM1][KOG0113]


Phytophthora@jgi_Phyra1_1_44765[2][RRM1:100%][put-sr:50%][KOG0113:100%]Embryophyta@29657_m000467[4][RRM1:100%*][put-sr:50%][snRNP:25%][KOG0113:100%*]

Tribolium castaneum@XP_966565[RRM1][KOG0113]Deuterostomia@XP_001178221[30][RRM1:100%***][put-sr:63%**][snRNP:70%***][KOG0113:100%***]

Ciona@ENSCSAVP00000001345[2][RRM1:100%][KOG0113:100%]Schizosaccharomyces pombe_972h-@NP_593779[RRM1][KOG0113]


Coelomata@AAEL011340-PB[2][RRM1:100%][put-sr:50%][KOG0113:100%]Rattus norvegicus@ENSRNOP00000048879[RRM1][snRNP][KOG0113]

Felis catus@ENSFCAP00000006212[RRM1][put-sr][KOG0113]Ostreococcus@jgi_Ostta4_11066[2][RRM1:100%][KOG0113:100%]Eukaryota@jgi_Physo1_1_143842[43][RRM1:100%***][put-sr:47%**][snRNP:14%*][KOG0113:100%***]

Cryptosporidium parvum_Iowa_II@XP_627471[RRM1][KOG0113]Aureococcus anophagefferens@jgi_Auran1_34517[2][RRM1:100%][put-sr:50%][KOG0113:100%]

Culicidae@AAEL004075-PA[3][RRM5:67%][.RRM1:33%][KOG0110:100%*]Dictyostelium discoideum_AX4@XP_646584[RRM2][KOG0127]

Phytophthora sojae@jgi_Physo1_1_132702[RRM4][KOG0127]Phytophthora ramorum@jgi_Phyra1_1_79608[2][RRM4:100%][KOG0127:100%]

Strongylocentrotus purpuratus@XP_783689[2][RRM2:100%][KOG0127:100%]Saccharomycetales@XP_001385462[7][RRM3:100%*][KOG0127:100%*]


Basidiomycota@XP_756663[3][RRM4:67%][.RRM3:33%][KOG0127:100%*]Schizosaccharomyces pombe_972h-@NP_596114[RRM3][KOG0127]

Phaeodactylum tricornutum@jgi_Phatr2_8457[RRM1][KOG0122]Ciona savignyi@ENSCSAVP00000001587[RRM5][KOG4307]

Caenorhabditis elegans@Y73B6BL_33[RRM1][KOG4211]Physcomitrella patens@jgi_Phypa1_1_162342[RRM3][KOG1365]

Thalassiosira pseudonana@jgi_Thaps3_5686[RRM2][KOG4211]Arabidopsis thaliana@NP_188725[RRM2][hnRNP][KOG1365]

Volvox carteri@jgi_Volca1_117772[RRM1][KOG1365]Plasmodium falciparum_3D7@XP_001347519[RRM1][KOG1365]

Coelomata@ENSCINP00000003632[126][RRM2:70%****][.RRM1:30%***][hnRNP:37%***][.GRSRBP:15%**][KOG4211:100%****]Danio rerio@ENSDARP00000069459[RRM2][KOG4211]

Oryzias latipes@ENSORLP00000025180[RRM2][put-sr][KOG4307]Caenorhabditis elegans@W02D3_11b[2][RRM1:100%][KOG4211:100%]

Phytophthora@jgi_Physo1_1_132702[3][RRM3:100%*][KOG0127:100%*]Caenorhabditis elegans@C18D11_4_1[2][RRM1:100%][put-sr:100%][KOG0921:100%]

Coelomata@AGAP006798-PA[81][RRM1:100%****][put-sr:99%****][KOG0122:26%***][.KOG0125:25%**][.KOG0147:14%**][.KOG0108:9%*]Basidiomycota@XP_757472[3][RRM1:100%*][put-sr:33%][KOG0122:33%]

Dictyostelium discoideum_AX4@XP_642304[RRM1][KOG0415]Aedes aegypti@AAEL004293-PA[RRM1][put-sr]

Drosophila melanogaster@CG10128-PC[6][RRM1:100%*][put-sr:100%*]Eutheria@ENSMLUP00000005283[2][RRM1:100%][put-sr:100%]

Spermophilus tridecemlineatus@ENSSTOP00000006011[RRM1][put-sr]Saccharomycetales@NP_986417[7][RRM1:100%*][KOG0127:100%*]

Schizosaccharomyces pombe_972h-@NP_596114[RRM1][KOG0127]Basidiomycota@XP_568669[3][RRM1:100%*][KOG0127:100%*]Sordariomycetes@XP_382687[2][RRM1:100%][KOG0127:100%]

Aspergillus fumigatus_Af293@XP_752199[RRM1][KOG0127]Euteleostomi@ENSOANP00000001262[28][RRM1:100%***][RBM:46%**][KOG0127:100%***]

Dictyostelium discoideum_AX4@XP_646584[RRM1][KOG0127]Chlamydomonadales@jgi_Chlre3_186870[2][RRM1:100%][KOG0127:100%]


Saccharomycetaceae@XP_458658[2][RRM1:100%][KOG0921:100%]Phytophthora@jgi_Physo1_1_132702[3][RRM1:100%*][KOG0127:100%*]

Cyanidioschyzon merolae@gnl_CMER_CMO246C[RRM2][KOG0110]Thalassiosira pseudonana@jgi_Thaps3_268689[RRM2][KOG0110]

eurosids_I@IMGA_CT963106_6_1[2][RRM1:100%][KOG0117:50%]Arabidopsis thaliana@NP_567594[RRM1][KOG0117]

Phytophthora@jgi_Physo1_1_129427[2][RRM2:100%][KOG0110:100%]Neurospora crassa_OR74A@XP_965014[RRM2][KOG0110] PSf

31

70 - RBM

80 - hnRNP

39

38 - Cyclophilin

37 - SART3

36 - snRNP



72 - RBM

67 - UMH

Fig. S7

99

74

80

63

83

52

88

55

86

97

69

73

70

57

66 70

75

58

73

84 98

Schizosaccharomyces pombe 972h @NP 594970[RRM2][KOG4210]Saccharomycetales@NP_982813[6][RRM2:100%*][KOG4210:100%*]

Aspergillus fumigatus_Af293@XP_755020[RRM2]Schizosaccharomyces pombe_972h-@NP_596033[RRM1]

Apocrita@XP_001602363[2][RRM1:100%][KOG1832:50%]Culicidae@AAEL001997-PA[2][RRM1:100%]

Drosophila melanogaster@CG3594-PA[RRM1][KOG0110]Sordariomycetes@XP_389032[2][RRM1:100%]

Neurospora crassa_OR74A@XP_964518[RRM1]Cryptococcus neoformans_var._neoformans_JEC21@XP_570477[RRM1]


Neurospora crassa_OR74A@XP_965346[RRM2][KOG0110]Aspergillus fumigatus_Af293@XP_747328[RRM2][KOG0110]

Ustilago maydis_521@XP_762237[RRM1]Schizosaccharomyces pombe_972h-@NP_595728[RRM1]

Sordariomycetes@XP_956776[2][RRM1:100%][put-sr:50%]Aspergillus fumigatus_Af293@XP_755976[RRM1]Coelomata@XP_001182806[39][RRM1:100%***][KOG0108:13%*][.KOG0116:8%*][.KOG0921:5%]

Yarrowia lipolytica@XP_504609[RRM1]Pichia stipitis_CBS_6054@XP_001384729[RRM1]

Phytophthora@jgi_Phyra1_1_83430[2][RRM1:100%]Ciona@ENSCSAVP00000001842[2][RRM1:100%]

Euteleostomi@ENSSARP00000000775[28][RRM1:100%***][eIF4B:54%**]Drosophila melanogaster@CG10837-PA[3][RRM1:100%*]

Anopheles gambiae@AGAP000525-PA[RRM1]Cryptococcus neoformans_var._neoformans_JEC21@XP_569209[RRM2][KOG0144]

Theileria parva_strain_Muguga@XP_765374[RRM1]Cryptosporidium parvum_Iowa_II@XP_001388131[RRM1][KOG1015]

Embryophyta@28180_m000395[3][RRM1:100%*][KOG0124:100%*]Arabidopsis thaliana@NP_191094[RRM1][KOG4205]

Phaeodactylum tricornutum@jgi_Phatr2_49387[RRM1]Ostreococcus lucimarinus@jgi_Ost9901_3_92667[RRM1]

Aureococcus anophagefferens@jgi_Auran1_9434[RRM1]Magnoliophyta@NP_001053909[5][RRM1:100%*][nucleolin:40%][KOG0123:40%][.KOG4210:40%][.KOG1015:20%]

Ostreococcus@jgi_Ostta4_33150[2][RRM2:100%][KOG0108:50%]Phytophthora@jgi_Physo1_1_141766[2][RRM2:100%][KOG0148:100%]

Embryophyta@28180_m000395[6][RRM2:100%*][KOG0124:50%*][.KOG4205:33%][.KOG4211:17%]stramenopiles@jgi_Auran1_17857[4][RRM1:50%][.RRM2:50%][KOG0108:50%][.KOG4205:50%]

Ostreococcus tauri@jgi_Ostta4_32569[RRM2]Aureococcus anophagefferens@jgi_Auran1_64341[RRM2][KOG0108]Ostreococcus@jgi_Ost9901_3_7913[3][RRM1:100%*][KOG0131:33%]Leishmania infantum_JPCM5@XP_001466413[RRM2][put-sr][KOG0147]

Physcomitrella patens@jgi_Phypa1_1_93324[RRM1]Ostreococcus tauri@jgi_Ostta4_10328[RRM1][KOG2476]

Arabidopsis thaliana@NP_175125[7][RRM1:43%*][.RRM2:29%][.RRM4:14%][.RRM3:14%][PABP:29%][KOG0123:100%*]Ostreococcus tauri@jgi_Ostta4_34258[RRM2]

Phytophthora@jgi_Phyra1_1_77488[2][RRM1:100%][KOG4205:100%]Phytophthora sojae@jgi_Physo1_1_139998[RRM1]


Magnoliophyta@29675_m000389[3][RRM2:100%*][KOG0123:67%][.KOG1015:33%]Arabidopsis thaliana@NP_188491[RRM2][nucleolin][KOG4210]Phytophthora@jgi_Phyra1_1_76845[2][RRM1:100%][KOG0123:100%]

Phaeodactylum tricornutum@jgi_Phatr2_44442[RRM1][KOG4211]Dictyostelium discoideum_AX4@XP_643642[RRM2][KOG0148]

Cryptosporidium parvum_Iowa_II@XP_001388131[RRM2][KOG1015]Yarrowia lipolytica@XP_504884[RRM3][KOG0123]

Thalassiosira pseudonana@jgi_Thaps3_24369[RRM1]Plasmodium falciparum_3D7@XP_966051[RRM1]

Encephalitozoon cuniculi_GB-M1@XP_965888[RRM1][KOG4209]Theileria parva_strain_Muguga@XP_765374[RRM2]

Pichia stipitis_CBS_6054@XP_001384763[RRM3][KOG0123]Phaeodactylum tricornutum@jgi_Phatr2_44395[RRM1]Poaceae@8373_m000321_c0161G04[2][RRM1:100%][KOG4205:50%][.KOG4211:50%]

Volvox carteri@jgi_Volca1_90315[RRM1]Apocrita@XP_001602582[2][RRM1:100%][KOG0128:100%]Strongylocentrotus purpuratus@XP_001180991[4][RRM1:100%*]


Physcomitrella patens@jgi_Phypa1_1_135986[RRM1][KOG0128]Cyanidioschyzon merolae@gnl_CMER_CMO334C[RRM2][KOG0126]

Ascomycota@XP_505055[6][RRM1:83%*][.RRM2:17%]Culicidae@AGAP003171-PA[3][RRM2:100%*][KOG0148:33%]

Drosophila melanogaster@CG12288-PA[RRM2]Trypanosomatidae@XP_827554[2][RRM1:50%][.RRM2:50%][put-sr:50%]

Apis mellifera@XP_394565[RRM2][KOG0147]Coelomata@ENSDARP00000093407[32][RRM2:88%***][.RRM1:12%*][KOG0108:12%*][.KOG3001:6%][.KOG0123:6%][.KOG0126:6%]

Phaeodactylum tricornutum@jgi_Phatr2_46145[RRM2]Dictyostelium discoideum_AX4@XP_635997[RRM2]

Caenorhabditis elegans@F11A10_7[RRM2][KOG0131]Magnoliophyta@30054_m000807[2][RRM2:100%][KOG1267:50%]Ostreococcus@jgi_Ostta4_30189[2][RRM1:50%][.RRM2:50%][put-sr:50%]

Volvox carteri@jgi_Volca1_118759[RRM2]Trypanosomatidae@XP_847474[2][RRM1:100%]

Trypanosomatidae@XP_001467105[2][RRM1:100%][KOG4209:100%]Saccharomycetaceae@XP_453677[2][RRM1:100%][KOG4209:100%]

Saccharomyces cerevisiae@YIR001C[RRM1][PABP][KOG4209]Candida glabrata_CBS138@XP_447800[RRM1][KOG4209]

Eukaryota@ENSCSAVP00000003369[89][RRM1:100%****][put-sr:17%**][PABP:26%***][KOG4209:100%****]Dictyostelium discoideum_AX4@XP_642788[RRM1][KOG4209]

Caenorhabditis elegans@T08B6_5[RRM1][KOG4209]Caenorhabditis elegans@EEED8_12[2][RRM1:100%][KOG4209:100%]

Ciona@ENSCSAVP00000010162[2][RRM1:100%][KOG4209:100%]Magnoliophyta@IMGA_AC160842_25_1[6][RRM1:100%*][KOG3702:83%*][.KOG4209:17%]

Physcomitrella patens@jgi_Phypa1_1_167236[RRM1][KOG4209]Volvox carteri@jgi_Volca1_103724[RRM1][put-sr][KOG0591]

Arabidopsis thaliana@NP_180012[RRM1]Phaeodactylum tricornutum@jgi_Phatr2_10122[RRM1][KOG0153]

Schizosaccharomyces pombe_972h-@NP_595190[RRM1][KOG0111]Ornithorhynchus anatinus@ENSOANP00000022523[3][RRM1:67%][.RRM2:33%][KOG2248:100%*]

Cryptococcus neoformans_var._neoformans_JEC21@XP_566572[RRM1][KOG0111]Euteleostomi@ENSMODP00000018834[25][RRM1:100%***][put-sr:64%**][KOG0147:48%**][.KOG0132:12%*]

Tribolium castaneum@XP_971953[RRM1]Strongylocentrotus purpuratus@XP_001185731[2][RRM1:100%]

Pezizomycotina@XP_755630[3][RRM1:100%*][KOG0111:100%*]Phytophthora ramorum@jgi_Phyra1_1_76171[2][RRM1:100%][KOG0111:100%]



Eukaryota@ENSGALP00000021793[59][RRM1:100%****][cyclophilin:59%***][KOG0111:98%****]Eutheria@ENSEEUP00000009324[3][RRM1:100%*][cyclophilin:100%*][KOG0111:100%*]Otolemur garnettii@ENSOGAP00000003225[RRM1][KOG0111]Phytophthora@jgi_Phyra1_1_94266[2][RRM2:100%][KOG0147:100%]

Ascomycota@XP_385341[4][RRM2:100%*][put-sr:100%*][KOG0147:100%*]Plasmodium falciparum_3D7@XP_001349956[RRM2][KOG0147]

Cryptococcus neoformans_var._neoformans_JEC21@XP_571060[RRM2][KOG0147]Yarrowia lipolytica@XP_504318[RRM2][KOG0147]

Ustilago maydis_521@XP_756311[RRM2][put-sr][KOG0147]

19 - Cyclophilin

83 - PABP

74

87 - eIF-4B

Fig. S7

100

61

65

64

93

86

54

92

61

79

88 53

69

63

54 58

64

53

90

Arabidopsis thaliana@NP 192643[2][RRM2:100%][KOG0110:100%]Yarrowia lipolytica@XP_505184[RRM1]

Chlamydomonadales@jgi_Volca1_90315[3][RRM2:67%][.RRM3:33%][KOG0123:67%]Aureococcus anophagefferens@jgi_Auran1_6342[RRM2][KOG0123]

Trypanosomatidae@XP_001465100[2][RRM2:100%][KOG4212:100%]Saccharomycetales@XP_446962[5][RRM1:100%*][put-sr:60%*][KOG0127:60%*][.KOG0123:40%]

Saccharomycetaceae@XP_462023[2][RRM1:100%][put-sr:100%][KOG0123:100%]Dikarya@XP_568231[5][RRM3:100%*][put-sr:80%*][KOG4212:80%*][.KOG0147:20%]

Yarrowia lipolytica@XP_503927[RRM3][put-sr][KOG4212]Saccharomycetales@XP_888678[3][RRM3:67%][.RRM2:33%][put-sr:67%][KOG0123:67%][.KOG4212:33%]

Saccharomycetales@YNL004W[4][RRM3:100%*][put-sr:50%][KOG0123:50%][.KOG0127:50%]Kluyveromyces lactis@XP_453283[RRM2][KOG0123]


Yarrowia lipolytica@XP_505140[RRM1][KOG0533]Pezizomycotina@XP_958422[3][RRM1:100%*][put-sr:33%][KOG0533:100%*]

Ustilago maydis_521@XP_757147[RRM1][KOG0533]Eukaryota@GSTENP00007343001[69][RRM1:100%****][FCAFPA:10%*][KOG0533:99%****]

Ostreococcus tauri@jgi_Ostta4_36431[RRM1][KOG0533]Chlamydomonadales@jgi_Volca1_90392[2][RRM1:100%][KOG0533:100%]

Dictyostelium discoideum_AX4@XP_638266[RRM1][KOG0533]Phytophthora@jgi_Phyra1_1_97175[2][RRM1:100%][put-sr:50%][KOG0533:100%]

Cyanidioschyzon merolae@gnl_CMER_CMH135C[RRM1]Euteleostomi@ENSTBEP00000009485[3][RRM1:100%*][PDIP:33%][KOG0533:33%]Endopterygota@CG6961-PA[7][RRM1:100%*][KOG0533:29%]

Coelomata@ENSMLUP00000006206[100][RRM2:88%****][.RRM1:12%**][put-sr:5%*][hnRNP:28%***][KOG4212:98%****]Caenorhabditis elegans@C25A1_4_2[2][RRM2:100%][put-sr:100%][KOG4212:100%]

Ostreococcus lucimarinus@jgi_Ost9901_3_34965[RRM2][KOG4212]Eukaryota@jgi_Volca1_109965[18][RRM1:78%**][.RRM2:22%*][put-sr:22%*][KOG4212:61%**][.KOG0123:39%*]

Trypanosomatidae@XP_001465100[2][RRM1:100%][KOG4212:100%]Chlamydomonadales@jgi_Chlre3_184854[2][RRM1:100%][KOG0055:50%]

Bacillariophyta@jgi_Phatr2_7426[2][RRM1:100%]Trypanosoma brucei_TREU927@XP_823301[RRM1][KOG0921]

Phytophthora@jgi_Physo1_1_136493[2][RRM2:100%][put-sr:100%][KOG0105:100%]Phytophthora ramorum@jgi_Phyra1_1_84100[RRM2][KOG0105]

Fungi/Metazoa_group@AGAP004592-PA[123][RRM2:81%****][.RRM1:18%***][put-sr:100%****][SR:60%****][KOG0105:50%****][.KOG0106:46%****]Bilateria@XP_967263[73][RRM2:78%****][.RRM1:22%**][put-sr:79%****][SR:75%****][KOG0105:100%****]

Theileria parva_strain_Muguga@XP_766386[RRM2][put-sr][KOG0105]Plasmodium falciparum_3D7@XP_001347501[RRM2][put-sr][KOG0105]

Phytophthora@jgi_Phyra1_1_75500[2][RRM3:100%][KOG0123:100%]Thalassiosira pseudonana@jgi_Thaps3_37126[RRM2][KOG0123]

Phaeodactylum tricornutum@jgi_Phatr2_51303[RRM2][KOG4212]Chlamydomonadales@jgi_Volca1_78979[2][RRM1:100%][KOG3070:100%]

Volvox carteri@jgi_Volca1_109965[RRM2][KOG4212]Strongylocentrotus purpuratus@XP_786244[2][RRM3:100%][put-sr:100%][KOG4212:100%]

Endopterygota@CG9373-PA[4][RRM3:100%*][KOG4212:100%*]Chordata@ENSOGAP00000002890[91][RRM3:80%****][.RRM2:13%**][.RRM1:7%*][hnRNP:37%***][KOG4212:100%****]

Cyanidioschyzon merolae@gnl_CMER_CMM078C[RRM2][KOG4212]Saccharomycetales@XP_001386572[3][RRM2:67%][.RRM1:33%][put-sr:67%][KOG0123:67%][.KOG4212:33%]

Cryptococcus neoformans_var._neoformans_JEC21@XP_572539[4][RRM2:100%*][KOG4212:100%*]Saccharomycetaceae@XP_453283[2][RRM1:50%][.RRM2:50%][KOG0123:50%][.KOG0127:50%]

Saccharomyces cerevisiae@YNL004W[RRM2][KOG0127]Saccharomycetales@XP_445179[2][RRM2:100%][put-sr:100%][KOG0123:100%]

Candida glabrata_CBS138@XP_446962[RRM2][put-sr][KOG0127]Basidiomycota@XP_758699[7][RRM1:71%*][.RRM2:29%][put-sr:14%][KOG4212:100%*]

Schizosaccharomyces pombe_972h-@NP_594207[RRM2][KOG4212]Plasmodium falciparum_3D7@XP_001347353[RRM2][KOG4212]

Pezizomycotina@XP_751108[2][RRM2:100%][put-sr:100%][KOG4212:100%]Cryptococcus neoformans_var._neoformans_JEC21@XP_568231[RRM2][put-sr][KOG0147]

Theileria parva_strain_Muguga@XP_765501[RRM1][KOG0127]Kluyveromyces lactis@XP_451368[RRM3][KOG0123]

Ashbya gossypii_ATCC_10895@NP_984845[RRM3][KOG0123]Saccharomyces cerevisiae@YHR015W[RRM3][KOG0123]

Saccharomyces cerevisiae@YFR023W[RRM3][KOG0123]Candida glabrata_CBS138@XP_447635[RRM3][KOG0123]

Trypanosomatidae@XP_001463723[2][RRM1:100%][KOG0110:100%]Drosophila melanogaster@CG2050-PA[RRM2]

Encephalitozoon cuniculi_GB-M1@NP_597583[RRM1][KOG4205]Pichia stipitis_CBS_6054@XP_001387063[RRM1]

Encephalitozoon cuniculi_GB-M1@NP_597583[RRM2][KOG4205]Saccharomycetales@YHL034C[2][RRM1:100%]

Kluyveromyces lactis@XP_453971[RRM1]Percomorpha@ENSGACP00000007987[5][RRM1:100%*][IGF2BP:80%*][KOG2193:100%*]

rosids@30155_m001644[2][RRM1:100%][KOG0116:50%]Physcomitrella patens@jgi_Phypa1_1_12664[RRM1]



Dictyostelium discoideum_AX4@XP_643547[RRM1]Caenorhabditis elegans@T04A8_6[RRM1][KOG4208]


Trypanosoma brucei_TREU927@XP_845742[RRM1][KOG0126]Saccharomycetaceae@XP_459205[2][RRM1:100%][KOG0126:100%]

Eukaryota@AAEL002461-PA[78][RRM1:100%****][put-sr:29%***][KOG0126:100%****]Ustilago maydis_521@XP_760864[RRM1][KOG0126]Chlamydomonadales@jgi_Volca1_120471[2][RRM1:100%][KOG0108:100%]

Dictyostelium discoideum_AX4@XP_640243[RRM1][KOG0117]Oryza sativa_japonica_cultivar-group@NP_001064224[RRM1][KOG0117]

Ricinus communis@30072_m000974[RRM1][KOG0117]Magnoliophyta@29709_m001182[6][RRM1:100%*][put-sr:17%][KOG0117:100%*]

Physcomitrella patens@jgi_Phypa1_1_140180[3][RRM1:100%*][KOG0117:100%*]Endopterygota@XP_624681[6][RRM1:100%*][put-sr:17%][KOG0921:67%*][.KOG1548:33%]

Euteleostomi@ENSDARP00000069729[82][RRM1:100%****][KOG1995:77%****][.KOG0921:16%**][.KOG2044:5%*]Strongylocentrotus purpuratus@XP_001196853[2][RRM1:100%][KOG1995:100%]

Arabidopsis thaliana@NP_564565[RRM1][put-sr][KOG1995]Caenorhabditis elegans@R09B3_3[3][RRM1:100%*][KOG0108:100%*]

Ciona savignyi@ENSCSAVP00000008315[4][RRM1:100%*][KOG0108:100%*]Geobacter uraniumreducens_Rf4@YP_001230384[RRM1][PROK][KOG0108]

Synechococcus@YP_473618[2][RRM1:100%][PROK:100%][KOG0108:100%]Chlamydomonas reinhardtii@jgi_Chlre3_181993[RRM1]

Ustilago maydis_521@XP_758493[RRM2][KOG0110]Aureococcus anophagefferens@jgi_Auran1_1296[RRM1][KOG0110]

Oryza sativa_japonica_cultivar-group@NP_001058465[RRM1][KOG0108]Saccharomycetaceae@XP_001383390[2][RRM1:100%][KOG0108:100%]

Cryptococcus neoformans_var._neoformans_JEC21@XP_572946[RRM1][KOG0108]Bacillariophyta@jgi_Phatr2_8451[2][RRM1:100%][KOG0108:100%]

Aureococcus anophagefferens@jgi_Auran1_23269[RRM1][KOG0108]Cryptosporidium parvum_Iowa_II@XP_627975[RRM1][KOG0108]


Thalassiosira pseudonana@jgi_Thaps3_263845[RRM1][KOG0108]Aureococcus anophagefferens@jgi_Auran1_17171[RRM1][KOG0108]

Eukaryota@ENSDARP00000064611[84][RRM1:100%****][KOG0108:99%****]Ostreococcus tauri@jgi_Ostta4_31925[RRM1][KOG0117]

Encephalitozoon cuniculi_GB-M1@NP_597167[RRM1][KOG0108]Chlamydomonadales@jgi_Volca1_54847[2][RRM1:100%][KOG0108:100%]

Yarrowia lipolytica@XP_499736[RRM2][KOG4205]Schizosaccharomyces pombe_972h-@NP_594970[RRM2][KOG4210]

62

69

87 - eIF-4B

48 - IGF2BP

29 - dual-RRM

SR proteins

30 - hnRNP

PDIP

FCA FPA

Fig. S7

101

0.20

59

99

71

61 79

66

69

91 81

60

81

51

67

83

74

87 69

61

Ostreococcus tauri@jgi_Ostta4_19468[RRM1][KOG0127]cellular_organisms@YP_001113853[137][RRM1:100%****][PROK:99%****][KOG0108:58%****][.KOG0116:14%**][.KOG0921:7%**][.KOG0149:7%**][.KOG0111:6%**]

Carboxydothermus hydrogenoformans_Z-2901@YP_359251[RRM1][PROK][KOG0108]Syntrophobacter fumaroxidans_MPOB@YP_844222[RRM1][PROK][KOG0108]Campylobacter@YP_001467322[2][RRM1:100%][PROK:100%][KOG0148:100%]

Bacteroidales@YP_213478[13][RRM1:100%**][PROK:100%**][KOG0108:69%**][.KOG0125:31%*]Bacteroides@YP_001298723[3][RRM1:100%*][PROK:100%*][KOG0108:100%*]Bacteroidales@YP_001302325[2][RRM1:100%][PROK:100%][KOG0123:50%][.KOG0122:50%]

Treponema pallidum_subsp._pallidum_str._Nichols@NP_218796[RRM1][PROK][KOG0149]Methanomicrobiales@YP_503016[5][RRM1:100%*][PROK:100%*][KOG0108:40%][.KOG0125:20%][.KOG0116:20%]

Nitrosococcus oceani_ATCC_19707@YP_344746[RRM1][PROK][KOG0148]Theileria parva_strain_Muguga@XP_766728[RRM2][KOG0124]

Plasmodium falciparum_3D7@XP_001347332[RRM2][put-sr][KOG0105]Percomorpha@ENSGACP00000011877[6][RRM1:100%*][KOG0123:100%*]

Gallus gallus@ENSGALP00000012472[2][RRM1:100%][KOG0123:100%]Syntrophobacter fumaroxidans_MPOB@YP_845575[RRM1][PROK]

Candidatus Protochlamydia_amoebophila_UWE25@YP_007892[RRM1][PROK][KOG0149]Leptospira@YP_000459[4][RRM1:100%*][PROK:100%*][KOG0108:100%*]


Alkalilimnicola ehrlichei_MLHE-1@YP_741458[RRM1][PROK]Cyanobacteria@YP_476186[8][RRM1:100%**][PROK:100%**][KOG0108:38%*][.KOG0122:12%]

Synechococcus_elongatus@YP_399809[2][RRM1:100%][PROK:100%][KOG0108:100%]Cyanobacteria@NP_898344[17][RRM1:100%**][PROK:100%**][KOG0108:65%**]

Gammaproteobacteria@YP_561253[27][RRM1:100%***][PROK:100%***][KOG0108:96%***]Neurospora crassa_OR74A@XP_958552[RRM3][KOG0128]


Pezizomycotina@XP_749317[2][RRM2:100%][KOG0128:100%]Schizosaccharomyces pombe_972h-@NP_596721[RRM2][KOG0128]

Saccharomyces cerevisiae@YMR268C[RRM2][KOG0128]Debaryomyces hansenii_CBS767@XP_460681[RRM2][KOG0128]

Plasmodium falciparum_3D7@XP_001350574[RRM3][KOG0110]Eukaryota@NP_001053839[55][RRM6:42%***][.RRM5:35%**][.RRM4:11%*][.RRM3:9%*][KOG0110:100%****]


Cryptosporidium parvum_Iowa_II@XP_627799[RRM5][KOG0110]Tribolium castaneum@XP_971197[RRM1][KOG4661]Coelomata@ENSTBEP00000011040[87][RRM1:98%****][put-sr:16%**][KOG4661:100%****]

Tribolium castaneum@XP_969134[RRM1]Caenorhabditis elegans@ZC404_8_2[2][RRM1:100%][KOG0125:100%]

Bilateria@ENSORLP00000014121[125][RRM1:100%****][FOX:75%****][KOG0125:100%****]Felis catus@ENSFCAP00000007638[RRM1][KOG0125]

Phytophthora@jgi_Physo1_1_137237[2][RRM1:100%][put-sr:100%][KOG0125:50%][.KOG0148:50%]Plasmodium falciparum_3D7@XP_001347313[RRM1][KOG0127]

Embryophyta@jgi_Phypa1_1_28366[17][RRM1:100%**][put-sr:76%**][KOG0127:29%*][.KOG0125:12%][.KOG4661:6%][.KOG0147:6%]Schizosaccharomyces pombe_972h-@NP_001018280[RRM1][KOG0145]

Cryptococcus neoformans_var._neoformans_JEC21@XP_570425[RRM1][put-sr][KOG0145]Pezizomycotina@XP_960722[3][RRM1:100%*][put-sr:33%][KOG0113:33%]

Yarrowia lipolytica@XP_499712[RRM1][KOG0145]Ciona intestinalis@ENSCINP00000019832[3][RRM1:100%*][KOG0128:100%*]

Culicidae@AAEL011961-PA[3][RRM1:100%*][KOG0128:100%*]Tribolium castaneum@XP_972538[RRM1][KOG0128]

Euteleostomi@ENSSTOP00000002132[31][RRM1:100%***][SART3:68%***][KOG0128:100%***]Strongylocentrotus purpuratus@XP_781643[RRM1][KOG0128]

Ciona intestinalis@ENSCINP00000023563[RRM1][KOG0108]Coelomata@ENSOGAP00000009767[86][RRM1:100%****][hnRNP:34%***][KOG4212:100%****]

Strongylocentrotus purpuratus@XP_001187716[4][RRM1:100%*][put-sr:100%*][KOG4212:50%][.KOG4661:50%]Encephalitozoon cuniculi_GB-M1@NP_585962[RRM2][KOG0123]

Dictyostelium discoideum_AX4@XP_001134510[RRM4][KOG0123]Strongylocentrotus purpuratus@XP_001198098[2][RRM1:100%][put-sr:100%][KOG0147:100%]

Phytophthora@jgi_Physo1_1_157186[2][RRM1:100%][KOG0147:100%]Dictyostelium discoideum_AX4@XP_638966[RRM1][KOG0147]

Eukaryota@ENSMLUP00000011758[47][RRM1:100%***][put-sr:91%***][UMH:64%***][.CAPER:15%*][KOG0147:100%***]Ascomycota@NP_594422[4][RRM1:100%*][put-sr:100%*][KOG0147:100%*]

Yarrowia lipolytica@XP_504318[RRM1][KOG0147]Ostreococcus@jgi_Ost9901_3_42846[2][RRM1:100%][put-sr:50%][KOG0147:100%]

Volvox carteri@jgi_Volca1_84128[2][RRM1:100%][put-sr:50%][KOG0147:100%]Plasmodium falciparum_3D7@XP_001349956[RRM1][KOG0147]

Cryptosporidium parvum_Iowa_II@XP_628665[RRM1][KOG0147]Leptospira@YP_001385[4][RRM1:100%*][PROK:100%*]

Ustilago maydis_521@XP_761797[RRM1][put-sr][KOG3257]Ostreococcus@jgi_Ost9901_3_27365[2][RRM1:100%][KOG0123:50%]


Magnoliophyta@NP_189032[4][RRM1:100%*][put-sr:100%*][KOG0670:100%*]Ostreococcus tauri@jgi_Ostta4_24260[RRM1]

Trypanosomatidae@XP_827855[2][RRM1:100%]Aureococcus anophagefferens@jgi_Auran1_67810[RRM1][put-sr][KOG0120]

Aureococcus anophagefferens@jgi_Auran1_66158[RRM1][put-sr][KOG0149]Magnoliophyta@10511_m000028_AZM5_5258[15][RRM1:100%**][cpRNP:33%*][KOG0127:53%**][.KOG0131:27%*][.KOG0145:13%][.KOG0108:7%]

Chlamydomonadales@jgi_Volca1_103054[2][RRM3:50%][.RRM2:50%][KOG0055:50%]rosids@30054_m000821[3][RRM1:100%*][cpRNP:33%][KOG0127:100%*]

Oryza sativa_japonica_cultivar-group@NP_001053710[RRM1][KOG0127]Magnoliophyta@NP_001058927[3][RRM1:100%*][cpRNP:33%][KOG0131:67%]Magnoliophyta@NP_001062760[4][RRM1:100%*][KOG0124:50%][.KOG0131:50%]

Embryophyta@jgi_Phypa1_1_134646[11][RRM1:100%**][cpRNP:9%][KOG0123:45%*][.KOG0127:36%*][.KOG2029:9%]rosids@NP_171616[3][RRM2:100%*][cpRNP:67%][KOG0148:67%][.KOG0110:33%]

Oryza sativa_japonica_cultivar-group@NP_001060859[RRM2][KOG0110]Magnoliophyta@29333_m001057[3][RRM2:67%][.RRM1:33%][cpRNP:33%][KOG0131:67%][.KOG0148:33%]

Magnoliophyta@NP_001048500[5][RRM2:100%*][cpRNP:20%][KOG0123:100%*]Ostreococcus lucimarinus@jgi_Ost9901_3_27365[RRM3][KOG0123]

Magnoliophyta@IMGA_AC119413_25_2[4][RRM2:100%*][cpRNP:25%][KOG0127:100%*]Poaceae@19213_m000022_AZM5_85721[2][RRM1:50%][.RRM2:50%][KOG0127:50%]


75 - CAPER

UMH

73 - SART3

68 - FOX

60


Fig. S7

102

91

60

57 74

59

92

82

68

51

53

69

50

Aureococcus anophagefferens@jgi Auran1 60739[RRM1][put-sr][KOG1860]Trypanosomatidae@XP_847111[2][RRM1:100%]

Leishmania infantum_JPCM5@XP_001465764[RRM1]Trypanosoma brucei_TREU927@XP_846161[RRM2]

Trypanosoma brucei_TREU927@XP_846161[RRM1]Leishmania infantum_JPCM5@XP_001463160[RRM2][put-sr]

Ricinus communis@30146_m003481[RRM3][KOG0123]Phytophthora@jgi_Physo1_1_108322[2][RRM3:100%][KOG0123:100%]


Cryptosporidium parvum_Iowa_II@XP_001388334[RRM3][KOG0123]Theileria parva_strain_Muguga@XP_766466[RRM3][KOG0123]Plasmodium falciparum_3D7@XP_001350640[RRM3][KOG0123]

Debaryomyces hansenii_CBS767@XP_460681[RRM2][KOG0128]Saccharomyces cerevisiae@YMR268C[RRM2][KOG0128]

Schizosaccharomyces pombe_972h-@NP_596721[RRM2][KOG0128]Pezizomycotina@XP_749317[2][RRM2:100%][KOG0128:100%]

Strongylocentrotus purpuratus@XP_786044[2][RRM1:100%][KOG0117:100%]Embryophyta@jgi_Phypa1_1_140180[4][RRM3:100%*][KOG0117:100%*]

Trypanosoma brucei_TREU927@XP_844190[RRM1][KOG0144]Dictyostelium discoideum_AX4@XP_635793[RRM1][KOG0145]


Dictyostelium discoideum_AX4@XP_646802[RRM1][KOG0145]Bilateria@ENSORLP00000021434[219][RRM1:100%*****][ELAV:79%*****][KOG0145:100%*****]Diptera@AAEL011150-PA[15][RRM1:100%**][KOG0145:100%**]

Drosophila melanogaster@CG5213-PA[RRM1][KOG0145]Trypanosomatidae@XP_828145[5][RRM1:100%*][KOG0145:100%*]

Trypanosoma brucei_TREU927@XP_845996[RRM1][KOG0122]Trypanosomatidae@XP_843886[2][RRM1:100%][KOG0145:100%]



Coelomata@ENSTBEP00000015452[229][RRM3:88%*****][.RRM2:9%**][ELAV:82%*****][KOG0145:100%*****]Ciona@ENSCINP00000023191[4][RRM3:75%*][.RRM1:25%][KOG0145:100%*]

Plasmodium falciparum_3D7@XP_001350320[RRM3][KOG0123]Aconoidasida@XP_001349292[3][RRM2:100%*][KOG0146:67%][.KOG0144:33%]

Cryptosporidium parvum_Iowa_II@XP_626331[RRM1][KOG0146]Bilateria@ENSORLP00000004891[130][RRM1:100%****][RBMS:72%****][KOG0145:99%****]

Eukaryota@ENSOANP00000006980[251][RRM3:67%*****][.RRM2:24%****][.RRM1:10%***][Bruno:50%****][KOG0144:55%****][.KOG0146:45%****]Cryptosporidium parvum_Iowa_II@XP_001388078[RRM3][put-sr][KOG0144]


Yarrowia lipolytica@XP_500351[RRM1][KOG0123]Tetraodon nigroviridis@GSTENP00024897001[RRM1][PABP][KOG0123]

Eukaryota@ENSXETP00000023927[236][RRM1:100%*****][PABP:55%****][KOG0123:100%*****]Trypanosomatidae@XP_001469222[2][RRM1:100%][KOG0123:100%]Leishmania infantum_JPCM5@XP_001466041[RRM1][KOG0123]

Trypanosomatidae@XP_001469326[2][RRM1:100%][KOG0123:100%]Saccharomycetaceae@YFR023W[4][RRM1:100%*][KOG0123:100%*]

Candida glabrata_CBS138@XP_447635[RRM1][KOG0123]Oryza sativa_japonica_cultivar-group@NP_001049727[RRM1][KOG0123]

Danio rerio@ENSDARP00000091192[14][RRM1:100%**][put-sr:100%**][KOG0123:100%**]rosids@30078_m002213[3][RRM1:100%*][PABP:33%][KOG0123:100%*]


Encephalitozoon cuniculi_GB-M1@NP_584552[RRM3][KOG0123]Myotis lucifugus@ENSMLUP00000003020[RRM3][PTBP][KOG1190]Embryophyta@IMGA_AC141435_12_2[17][RRM2:76%**][.RRM1:24%*][KOG4660:100%**]

Tetrapoda@ENSXETP00000004736[17][RRM2:59%**][.RRM1:41%*][PTBP:94%**][KOG1190:100%**]Drosophila melanogaster@CG2050-PA[RRM3]

Theria@ENSMODP00000002817[2][RRM1:100%]Theileria parva_strain_Muguga@XP_764943[RRM1][KOG4206]

Pichia stipitis_CBS_6054@XP_001382592[RRM1][KOG4206]Coelomata@ENSORLP00000008206[18][RRM1:100%**][snRNP:83%**][KOG4206:100%**]

Sordariomycetes@XP_962704[2][RRM1:100%][put-sr:50%][KOG4206:100%]Ciona intestinalis@ENSCINP00000027768[RRM1][KOG0548]


Plasmodium falciparum_3D7@XP_001348072[RRM1][KOG0144]Clupeocephala@ENSORLP00000009616[3][RRM1:100%*][KOG0548:100%*]

Strongylocentrotus purpuratus@XP_001188888[2][RRM1:100%][KOG0548:100%]Dictyostelium discoideum_AX4@XP_645138[RRM1]

Danio rerio@ENSDARP00000075089[2][RRM1:100%][KOG0548:100%]Gasterosteus aculeatus@ENSGACP00000006521[RRM1][KOG0548]




Schizosaccharomyces pombe_972h-@NP_588373[RRM1]Physcomitrella patens@jgi_Phypa1_1_176266[RRM1][KOG1924]

Oryza sativa_japonica_cultivar-group@NP_001063671[RRM2][KOG0123]rosids@NP_001078046[5][RRM2:100%*][FCAFPA:80%*][KOG0117:80%*][.KOG0123:20%]


Dictyostelium discoideum_AX4@XP_629218[RRM1][KOG0151]Aedes aegypti@AAEL010888-PA[RRM2]

Saccharomyces cerevisiae@YMR302C[RRM1]Physcomitrella patens@jgi_Phypa1_1_161310[RRM3][KOG3598]Volvox carteri@jgi_Volca1_88720[RRM3]

Chlamydomonas reinhardtii@jgi_Chlre3_148816[RRM2][KOG3598]Physcomitrella patens@jgi_Phypa1_1_137240[2][RRM1:100%][KOG3598:50%]

Arabidopsis thaliana@NP_181869[4][RRM1:100%*][FCAFPA:100%*][KOG0117:100%*]Ricinus communis@29577_m000447[RRM1][KOG0123]

Ricinus communis@30005_m001243[RRM1]Oryza sativa_japonica_cultivar-group@NP_001062811[RRM1][KOG1190]

40 - snRNP

43

3 - PABP

9 - Bruno

12 - ELAV

10 - ELAV

Fig. S8

103

98

56 76

81

77

97

51

61 58

85

73

60 59

64

80

51

83

Chlamydomonadales@jgi Volca1 118581[3][RRM2:67%][.RRM4:33%][KOG0144:67%][.KOG1240:33%]Volvox carteri@jgi_Volca1_88093[RRM4][KOG1240]


Medicago truncatula@IMGA_AC155099_2_2[2][RRM1:100%][KOG0144:100%]Saccharomycetaceae@XP_451236[2][RRM1:100%][KOG0144:100%]

Saccharomyces cerevisiae@YGR250C[RRM1][KOG0108]Eutheria@ENSBTAP00000025092[6][RRM1:100%*][KOG0117:100%*]

Gasterosteus aculeatus@ENSGACP00000025947[RRM1][KOG0117]Aedes aegypti@AAEL015050-PA[2][RRM1:100%][KOG0117:100%]

Anopheles gambiae@AGAP002326-PA[RRM1]Tribolium castaneum@XP_967803[2][RRM1:100%][KOG0117:100%]

Rattus norvegicus@ENSRNOP00000053644[RRM1][KOG0117]Eutheria@ENSCPOP00000011171[3][RRM1:100%*][hnRNP:67%][KOG0117:100%*]Bilateria@ENSGALP00000025475[210][RRM1:100%*****][hnRNP:33%****][KOG0117:100%*****]

Dictyostelium discoideum_AX4@XP_646268[RRM2][KOG0146]Chlamydomonadales@jgi_Volca1_88093[2][RRM1:100%][KOG1240:100%]

Theileria parva_strain_Muguga@XP_766017[RRM1][KOG0144]Cryptosporidium parvum_Iowa_II@XP_001388078[RRM1][put-sr][KOG0144]


Phytophthora@jgi_Phyra1_1_82644[2][RRM1:100%][KOG0144:100%]Coelomata@XP_782270[24][RRM1:100%***][Bruno:42%**][KOG0144:100%***]

Bilateria@ENSXETP00000031370[81][RRM1:100%****][Bruno:42%***][KOG0146:84%****][.KOG0144:16%**]Thalassiosira pseudonana@jgi_Thaps3_261541[RRM1][KOG0144]

Phaeodactylum tricornutum@jgi_Phatr2_42828[RRM1][KOG0144]Plasmodium falciparum_3D7@XP_001348607[RRM1]

Chlamydomonadales@jgi_Volca1_107765[2][RRM1:100%][KOG0145:100%]Saccharomycetales@NP_984279[4][RRM1:100%*][KOG0921:75%*][.KOG0106:25%]

Drosophila melanogaster@CG3312-PA[2][RRM1:100%][KOG0128:100%]Drosophila melanogaster@CG5213-PA[RRM2][KOG0145]

Dictyostelium discoideum_AX4@XP_645848[RRM1][put-sr]Dictyostelium discoideum_AX4@XP_647083[RRM1]


Chlamydomonas reinhardtii@jgi_Chlre3_152680[RRM1][KOG4660]Embryophyta@28611_m000102[4][RRM2:100%*][put-sr:75%*][KOG0154:100%*]

Chlamydomonas reinhardtii@jgi_Chlre3_145376[RRM2]Phytophthora ramorum@jgi_Phyra1_1_77702[RRM1][KOG0154]

Volvox carteri@jgi_Volca1_120369[RRM1][put-sr][KOG0147]Schizosaccharomyces pombe_972h-@NP_596424[RRM2][KOG4206]

Pezizomycotina@XP_753458[2][RRM2:100%][put-sr:50%][KOG4206:100%]Saccharomyces cerevisiae@YBR119W[RRM1]


Eukaryota@ENSGACP00000013006[79][RRM2:96%****][snRNP:30%***][KOG4206:100%****]Cryptococcus neoformans_var._neoformans_JEC21@XP_568533[RRM2][KOG4206]

Cyanidioschyzon merolae@gnl_CMER_CMS187C[RRM1][KOG0123]Dictyostelium discoideum_AX4@XP_644081[RRM2][KOG0123]

Trypanosomatidae@XP_001468777[2][RRM2:100%][KOG0144:100%]Culicidae@AAEL001131-PA[2][RRM1:100%][KOG0113:100%]


Aureococcus anophagefferens@jgi_Auran1_31715[RRM1][KOG0149]Volvox carteri@jgi_Volca1_84128[RRM2][KOG0147]


Embryophyta@jgi_Phypa1_1_189930[7][RRM1:100%*][KOG0119:86%*][.KOG0307:14%]Oryza sativa_japonica_cultivar-group@NP_001054296[RRM6][KOG0123]


Oryza sativa_japonica_cultivar-group@NP_001054296[RRM3][KOG0123]Phytophthora ramorum@jgi_Phyra1_1_94226[RRM1][put-sr][KOG0941]

Eukaryota@NP_001063859[35][RRM1:100%***][ZCRB1:69%***][KOG0108:40%**][.KOG0122:9%*][.KOG0117:6%][.KOG0107:6%]Aedes aegypti@AAEL006197-PA[RRM1][KOG0108]

Chlamydomonas reinhardtii@jgi_Chlre3_120019[RRM2][KOG0106]Chlamydomonas reinhardtii@jgi_Chlre3_80366[RRM2][KOG0106]

Embryophyta@29742_m001371[15][RRM2:80%**][.RRM1:20%*][put-sr:87%**][SR:67%**][KOG0106:100%**]Bacillariophyta@jgi_Phatr2_47737[2][RRM1:100%][put-sr:50%]

Cyanidioschyzon merolae@gnl_CMER_CMO009C[RRM2]Thalassiosira pseudonana@jgi_Thaps3_2206[RRM1]

Phaeodactylum tricornutum@jgi_Phatr2_38474[RRM1]Ricinus communis@30169_m006629[RRM1][KOG0123]

Cyanidioschyzon merolae@gnl_CMER_CMG025C[RRM1][KOG1080]Ustilago maydis_521@XP_760296[RRM1]

Cryptococcus neoformans_var._neoformans_JEC21@XP_572996[RRM1]Euteleostomi@ENSOANP00000013028[22][RRM1:100%***]

Endopterygota@XP_967886[3][RRM1:100%*]Drosophila melanogaster@CG14414-PB[RRM1]

Phaeodactylum tricornutum@jgi_Phatr2_10122[RRM1][KOG0153]Leishmania infantum_JPCM5@XP_001466666[RRM1][KOG0145]Leishmania infantum_JPCM5@XP_001464835[2][RRM1:100%][KOG0145:100%]

Leishmania infantum_JPCM5@XP_001464836[RRM1][KOG0145]Trypanosoma brucei_TREU927@XP_843985[3][RRM1:100%*][put-sr:33%][KOG0110:100%*]


Trypanosomatidae@XP_847495[2][RRM1:100%][KOG0110:50%][.KOG0127:50%]Nasonia vitripennis@XP_001604889[RRM2][KOG0144]

Dictyostelium discoideum_AX4@XP_636266[RRM1][KOG3598]Strongylocentrotus purpuratus@XP_001199679[4][RRM1:100%*][KOG0145:50%]

Euteleostomi@ENSDNOP00000001522[23][RRM1:100%***][RBM:61%**][KOG0144:87%**][.KOG0145:13%*]Endopterygota@CG1316-PA[5][RRM1:100%*][KOG0144:80%*][.KOG0148:20%]

Encephalitozoon cuniculi_GB-M1@NP_584552[RRM1][KOG0123]Dictyostelium discoideum_AX4@XP_641568[RRM3][KOG3598]

Schizosaccharomyces pombe_972h-@NP_595190[RRM1][KOG0111]Chlamydomonas reinhardtii@jgi_Chlre3_194261[RRM1][KOG0123]

Embryophyta@NP_001063403[14][RRM1:100%**][KOG0148:100%**]Clupeocephala@ENSORLP00000016619[5][RRM1:100%*][KOG0131:60%*][.KOG0123:40%]Endopterygota@XP_974444[2][RRM1:100%][KOG0144:100%]

Cryptosporidium parvum_Iowa_II@XP_627780[RRM2][KOG0131]Saccharomyces cerevisiae@YOR319W[RRM2][KOG0131]

Eukaryota@jgi_Physo1_1_108557[316][RRM2:91%*****][.RRM1:9%***][PABP:46%****][KOG0123:79%*****][.KOG0131:21%****]Yarrowia lipolytica@XP_503979[RRM2][KOG0131]

Saccharomycetaceae@XP_001385635[2][RRM2:100%][KOG0131:100%]Plasmodium falciparum_3D7@XP_001348201[RRM1][KOG0151]

Eukaryota@jgi_Volca1_104604[49][RRM1:100%***][put-sr:78%***][KOG0151:100%***]Cryptococcus neoformans_var._neoformans_JEC21@XP_571608[RRM1][put-sr][KOG0151]

Saccharomycetales@XP_454345[4][RRM1:100%*][KOG0148:75%*][.KOG0123:25%]Sordariomycetes@XP_385593[2][RRM1:100%][KOG0148:100%]

Saccharomycetaceae@XP_001383142[2][RRM1:100%][put-sr:100%][KOG0148:100%]Yarrowia lipolytica@XP_501542[RRM1][KOG0131]

Cryptococcus neoformans_var._neoformans_JEC21@XP_570577[RRM1][KOG0148]Ustilago maydis_521@XP_757329[RRM1][KOG0145]

Embryophyta@NP_188026[13][RRM1:100%**][oligoU:38%*][KOG0148:100%**]Bilateria@ENSSARP00000011721[82][RRM1:100%****][TIATIAR:80%****][KOG0148:100%****]



Aureococcus anophagefferens@jgi_Auran1_60739[RRM1][put sr][KOG1860]

76 - TIA TIAR

OligoU

13

4 - PABP

PSP1

PSF

p54rnb missing

green plant-specific


- 56

57 - ZCRB1

41 - snRNP

42

2 - hnRNP

7 - Bruno

FCA FPA


Fig. S8

104

64

61 50

65

89

80

75

68

52

81

73

98

Oryza sativa japonica cultivar-group@NP 001067112[RRM2][put-sr][KOG0117]Saccharomycetales@XP_454821[4][RRM1:100%*][KOG3598:50%][.KOG1984:25%]

Coelomata@XP_974651[54][RRM2:83%***][.RRM1:17%**][put-sr:87%***][RBM:37%**][KOG0112:100%***]Strongylocentrotus purpuratus@XP_001184502[2][RRM2:100%][put-sr:100%][KOG1144:100%]

Coelomata@ENSMMUP00000010529[37][RRM3:54%**][.RRM2:41%**][.RRM1:5%][put-sr:92%***][KOG0112:84%***][.KOG3598:8%*]Ciona intestinalis@ENSCINP00000004384[RRM2][KOG0148]

Dictyostelium discoideum_AX4@XP_641688[RRM1][KOG0117]Strongylocentrotus purpuratus@XP_001183631[2][RRM2:100%][KOG0148:100%]

Physcomitrella patens@jgi_Phypa1_1_170658[RRM1]Phaeodactylum tricornutum@jgi_Phatr2_13402[RRM1][KOG0226]

Thalassiosira pseudonana@jgi_Thaps3_18991[RRM1][KOG0226]Cryptococcus neoformans_var._neoformans_JEC21@XP_571861[RRM1][KOG0226]

Nasonia vitripennis@XP_001603091[RRM1][KOG0226]Eukaryota@XP_964958[72][RRM1:100%****][KOG0226:100%****]

Yarrowia lipolytica@XP_501542[RRM2][KOG0131]Eukaryota@IMGA_AC144483_30_2[123][RRM2:83%****][.RRM1:17%***][TIATIAR:58%****][.oligoU:6%*][KOG0148:99%****]

Ustilago maydis_521@XP_757329[RRM2][KOG0145]Dictyostelium discoideum_AX4@XP_635179[RRM1][KOG0148]

Saccharomycetales@XP_460477[6][RRM1:67%*][.RRM2:33%][KOG0148:67%*][.KOG3598:17%][.KOG0145:17%]Eukaryota@ENSMUSP00000030730[72][RRM2:85%****][.RRM1:15%**][oligoU:10%*][KOG0148:58%***][.KOG0123:25%**][.KOG0131:14%**]

Saccharomycetales@XP_455748[4][RRM2:100%*][KOG0148:75%*][.KOG0145:25%]Pichia stipitis_CBS_6054@XP_001386002[RRM2][KOG0148]

Debaryomyces hansenii_CBS767@XP_461354[RRM2][KOG0148]Aureococcus anophagefferens@jgi_Auran1_28594[RRM2][KOG0148]Endopterygota@AAEL011988-PA[5][RRM2:100%*][KOG0144:80%*][.KOG0145:20%]

Ciona@ENSCSAVP00000020066[4][RRM1:50%][.RRM2:50%][KOG0131:50%]Strongylocentrotus purpuratus@XP_793862[2][RRM2:100%][KOG0144:100%]

Volvox carteri@jgi_Volca1_116517[RRM2][KOG1984]Dictyostelium discoideum_AX4@XP_646802[RRM2][KOG0145]

Coelomata@ENSTBEP00000005385[105][RRM2:86%****][.RRM1:14%**][P54nrb:30%***][.PSP1:24%***][.PSF:21%***][KOG0115:100%****]Trypanosomatidae@XP_001469326[2][RRM4:100%][KOG0123:100%]


Cryptococcus neoformans_var._neoformans_JEC21@XP_569319[RRM1][KOG0123]Ustilago maydis_521@XP_759458[RRM2][KOG0123]


rosids@30078_m002213[3][RRM3:100%*][PABP:33%][KOG0123:100%*]Arabidopsis thaliana@NP_195978[RRM1][KOG0123]

Schizosaccharomyces pombe_972h-@NP_593427[RRM2][KOG0123]Schizosaccharomyces pombe_972h-@NP_001018242[RRM3][KOG0123]

Ashbya gossypii_ATCC_10895@NP_984845[RRM2][KOG0123]Leishmania infantum_JPCM5@XP_001466041[RRM2][KOG0123]

Encephalitozoon cuniculi_GB-M1@NP_586226[RRM2][put-sr][KOG0123]Arabidopsis thaliana@NP_174676[RRM1][PABP][KOG0123]


rosids@30146_m003481[2][RRM2:100%][PABP:50%][KOG0123:100%]Yarrowia lipolytica@XP_500351[RRM3][KOG0123]

Aedes aegypti@AAEL007013-PA[RRM1][KOG0123]Pezizomycotina@XP_750167[2][RRM4:100%][KOG0123:100%]

Eukaryota@ENSDNOP00000002400[249][RRM4:82%*****][.RRM3:11%***][.RRM2:6%**][PABP:54%****][KOG0123:100%*****]Arabidopsis thaliana@NP_188259[RRM4][PABP][KOG0123]

Leishmania infantum_JPCM5@XP_001466041[RRM4][KOG0123]Drosophila melanogaster@CG4612-PA[RRM2][KOG0123]

Dictyostelium discoideum_AX4@XP_629007[RRM3][KOG0123]Anopheles gambiae@AGAP000921-PA[3][RRM1:100%*]

Eukaryota@ENSETEP00000015606[204][RRM3:85%*****][.RRM2:11%***][PABP:66%****][KOG0123:100%*****]Trypanosoma brucei_TREU927@XP_827358[RRM3][KOG0123]

Leishmania infantum_JPCM5@XP_001469222[RRM3][KOG0123]Felis catus@ENSFCAP00000004622[RRM3][PABP][KOG0123]

Encephalitozoon cuniculi_GB-M1@NP_586099[RRM2][KOG0131]Caenorhabditis elegans@Y106G6H_2a_4[7][RRM3:71%*][.RRM2:29%][KOG0123:100%*]

Caenorhabditis elegans@F18H3_3b[5][RRM3:100%*][KOG0123:100%*]Trypanosoma brucei_TREU927@XP_827237[RRM3][KOG0123]

Dikarya@XP_960425[12][RRM3:100%**][PABP:17%][KOG0123:100%**]Yarrowia lipolytica@XP_501289[RRM3][KOG0123]

Echinops telfairi@ENSETEP00000008100[RRM3][PABP][KOG0123]Chlamydomonadales@jgi_Volca1_82578[2][RRM3:100%][PABP:100%][KOG0123:100%]

Strongylocentrotus purpuratus@XP_001177782[4][RRM3:50%][.RRM2:50%][KOG0123:100%*]Neurospora crassa_OR74A@XP_958552[RRM3][KOG0128]

Trypanosoma brucei_TREU927@XP_845376[RRM3][KOG0148]Diptera@AGAP003899-PA[15][RRM2:100%**][KOG0145:100%**]Bilateria@CG3151-PE[218][RRM2:92%*****][.RRM1:7%**][ELAV:84%*****][KOG0145:100%*****]

Ciona@ENSCSAVP00000015853[4][RRM2:100%*][KOG0145:100%*]Coelomata@ENSORLP00000004891[62][RRM2:94%****][.RRM1:6%*][RBMS:79%***][KOG0145:100%****]

Ustilago maydis_521@XP_759141[RRM2][KOG0145]Embryophyta@29727_m000492[13][RRM3:92%**][.RRM2:8%][oligoU:46%*][KOG0148:100%**]Dikarya@XP_570577[4][RRM3:100%*][KOG0148:100%*]

Saccharomycetales@YNL016W[6][RRM3:100%*][put-sr:33%][KOG0148:83%*][.KOG0123:17%]Coelomata@CG4787-PA[102][RRM3:74%****][.RRM2:16%**][.RRM1:11%**][TIATIAR:75%****][KOG0148:100%****]

Caenorhabditis elegans@Y46G5A_13[10][RRM2:80%**][.RRM3:20%][KOG0148:100%**]Caenorhabditis elegans@C07A4_1[RRM2][KOG0148]

Embryophyta@NP_001067623[8][RRM1:100%**][KOG0117:100%**]Oryza sativa_japonica_cultivar-group@NP_001066102[RRM1][KOG0117]

rosids@NP_001030849[6][RRM1:100%*][KOG0117:100%*]Ornithorhynchus anatinus@ENSOANP00000022523[3][RRM1:67%][.RRM2:33%][KOG2248:100%*]

Physcomitrella patens@jgi_Phypa1_1_140180[3][RRM1:100%*][KOG0117:100%*]Magnoliophyta@29709_m001182[6][RRM1:100%*][put-sr:17%][KOG0117:100%*]

Ricinus communis@30072_m000974[RRM1][KOG0117]Oryza sativa_japonica_cultivar-group@NP_001064224[RRM1][KOG0117]

Dictyostelium discoideum_AX4@XP_641568[RRM2][KOG3598]Caenorhabditis elegans@F25B5_7d[2][RRM1:100%][KOG0115:100%]Deuterostomia@ENSDNOP00000008593[94][RRM1:100%****][P54nrb:28%***][.PSP1:21%**][.PSF:18%**][KOG0115:99%****]

Endopterygota@CG10328-PA[9][RRM1:100%**][P54nrb:33%*][KOG0115:100%**]Thalassiosira pseudonana@jgi_Thaps3_261541[RRM2][KOG0144]

Aconoidasida@XP_766017[2][RRM2:100%][KOG0144:100%]Cryptosporidium parvum_Iowa_II@XP_001388078[RRM2][put-sr][KOG0144]

Plasmodium falciparum_3D7@XP_001348269[RRM2][KOG0144]Arabidopsis thaliana@NP_850472[RRM2][FCAFPA][KOG0144]

Embryophyta@29889_m003323[11][RRM2:100%**][FCAFPA:18%][KOG0144:100%**]Dictyostelium discoideum_AX4@XP_635247[RRM2][KOG0144]Bilateria@AGAP009477-PA[250][RRM2:73%*****][.RRM1:27%****][Bruno:59%****][KOG0144:56%****][.KOG0146:44%****]

Embryophyta@jgi_Phypa1_1_115029[9][RRM2:100%**][KOG0144:100%**]Phytophthora@jgi_Physo1_1_133760[2][RRM2:100%][KOG0144:100%]


Chlamydomonadales@jgi_Chlre3_99329[2][RRM1:50%][.RRM2:50%][KOG0144:100%]Volvox carteri@jgi_Volca1_72841[RRM1][KOG0144]


Poaceae@11320_m000014_AZM5_6848[3][RRM1:100%*][KOG0144:100%*]Physcomitrella patens@jgi_Phypa1_1_107590[2][RRM1:100%][KOG0144:100%]Trypanosomatidae@XP_845656[2][RRM1:100%][KOG0131:50%]

Trypanosomatidae@XP_001468238[3][RRM1:100%*][KOG0144:100%*]Leishmania infantum_JPCM5@XP_001468236[RRM1]

Chlamydomonadales@jgi_Volca1_72841[2][RRM3:50%][.RRM2:50%][KOG0144:100%]Trypanosomatidae@XP_827838[2][RRM1:100%][KOG0144:100%]

Cryptosporidium parvum_Iowa_II@XP_628265[RRM2][KOG0144]Chlamydomonadales@jgi_Volca1_118581[3][RRM2:67%][.RRM4:33%][KOG0144:67%][.KOG1240:33%]

8 - Bruno

FCA FPA

Part of 33 - p54nrb

62

79 - TIA TIAR

OligoU11 - ELAV

RBMS

5 - PABP

6 - PABP

66 - PaBP

Part of 4 -

p54rnb

77 - TIA TIAR

OligoU

53 - RBM

5455

Fig. S8

105

60

71 71

82

79

50

80 58

70

69

55 50

53

71

93

Deuterostomia@ENSMODP00000011218[78][RRM1:100%****][G3BP:82%****][KOG0116:100%****]Tribolium castaneum@XP_975463[RRM1][KOG0116]

Apis mellifera@XP_623996[RRM1][KOG0116]Neurospora crassa_OR74A@XP_958552[RRM1][KOG0128]

Leishmania infantum_JPCM5@XP_001466413[RRM3][put-sr][KOG0147]Xenopus tropicalis@ENSXETP00000012439[RRM1][KOG2277]

Strongylocentrotus purpuratus@XP_798256[2][RRM1:100%][KOG2277:100%]Oryzias latipes@ENSORLP00000005442[2][RRM1:100%][KOG2277:100%]

Oryctolagus cuniculus@ENSOCUP00000014792[RRM1][KOG2277]Strongylocentrotus purpuratus@XP_001178467[2][RRM1:100%][put-sr:100%]Endopterygota@CG5655-PA[5][RRM1:100%*][put-sr:100%*][KOG0107:80%*][.KOG0921:20%]

Strongylocentrotus purpuratus@XP_001180596[2][RRM1:100%][put-sr:100%]Eukaryota@ENSGALP00000022397[157][RRM1:100%*****][put-sr:75%****][SR:59%****][KOG0107:66%****]

Theileria parva_strain_Muguga@XP_766728[RRM1][KOG0124]Dictyostelium discoideum_AX4@XP_001134500[RRM1][put-sr][KOG0147]

Strongylocentrotus purpuratus@XP_001185906[2][RRM1:100%][KOG0107:100%]Dictyostelium discoideum_AX4@XP_638672[RRM1][put-sr][KOG0147]

Phytophthora@jgi_Physo1_1_140403[2][RRM1:100%][put-sr:100%][KOG0127:100%]Dictyostelium discoideum_AX4@XP_628876[RRM1]

Yarrowia lipolytica@XP_500797[RRM1][put-sr]Schizosaccharomyces pombe_972h-@NP_596398[RRM1][put-sr][SR]

Ustilago maydis_521@XP_758616[RRM1]Plasmodium falciparum_3D7@XP_001351730[RRM1][put-sr][KOG0105]

Ostreococcus lucimarinus@jgi_Ost9901_3_8794[RRM1][KOG0105]Embryophyta@NP_194280[13][RRM1:100%**][put-sr:77%**][SR:62%**][KOG0106:100%**]

Ascomycota@YDL224C[8][RRM1:88%*][.RRM2:12%][KOG3598:12%][.KOG1457:12%]Ricinus communis@28452_m000049[RRM1][KOG1457]

Medicago truncatula@IMGA_CU012061_4_1[RRM1]Phytophthora@jgi_Physo1_1_138982[2][RRM1:100%][KOG0105:100%]

Eukaryota@ENSTBEP00000007356[92][RRM1:100%****][put-sr:82%****][SR:65%****][KOG0105:100%****]Theileria parva_strain_Muguga@XP_766386[RRM1][put-sr][KOG0105]

Plasmodium falciparum_3D7@XP_001347876[RRM1][KOG0105]Aedes aegypti@AAEL012621-PA[RRM1][put-sr][KOG0105]

Caenorhabditis elegans@T28D9_2a[3][RRM1:100%*][put-sr:100%*][SR:100%*][KOG0106:100%*]Cavia porcellus@ENSCPOP00000010577[RRM1][put-sr][SR][KOG0106]

Ciona intestinalis@ENSCINP00000016525[RRM1][put-sr][KOG0106]Eukaryota@ENSOANP00000021053[127][RRM1:100%****][put-sr:91%****][SR:61%****][KOG0106:55%****][.KOG0105:37%***]

Cryptococcus neoformans_var._neoformans_JEC21@XP_567562[RRM1][KOG0106]Schizosaccharomyces pombe_972h-@NP_594570[RRM1][put-sr][KOG0106]

Neurospora crassa_OR74A@XP_960334[RRM1][put-sr][KOG0105]Coxiella_burnetii@YP_001424503[2][RRM1:100%][PROK:100%][KOG0113:100%]

Aedes aegypti@AAEL010887-PA[RRM6][put-sr][KOG1984]Trypanosomatidae@XP_843959[2][RRM3:100%]

Aspergillus fumigatus_Af293@XP_747328[RRM1][KOG0110]Coxiella_burnetii@YP_001424629[2][RRM1:100%][PROK:100%][KOG0108:100%]

Embryophyta@29900_m001607[13][RRM2:100%**][oligoU:38%*][KOG4205:77%**][.KOG0149:23%*]Embryophyta@jgi_Phypa1_1_44443[2][RRM2:100%][KOG0149:100%]

Legionella_pneumophila@YP_001249669[3][RRM1:100%*][PROK:100%*][put-sr:100%*][KOG0149:100%*]Ostreococcus lucimarinus@jgi_Ost9901_3_7602[RRM1][KOG0145]

Dictyostelium discoideum_AX4@XP_643007[RRM1]eurosids_I@IMGA_CT963106_6_1[2][RRM1:100%][KOG0117:50%]

Arabidopsis thaliana@NP_567594[RRM1][KOG0117]Plasmodium falciparum_3D7@XP_966276[RRM2]

Bilateria@ENSLAFP00000012959[197][RRM3:93%*****][.RRM2:5%**][hnRNP:36%****][KOG0117:100%*****]Strongylocentrotus purpuratus@XP_793277[2][RRM3:100%][KOG0117:100%]

Thalassiosira pseudonana@jgi_Thaps3_263845[RRM1][KOG0108]Phaeodactylum tricornutum@jgi_Phatr2_33658[RRM1]

Dictyostelium discoideum_AX4@XP_638262[RRM1][put-sr][KOG0670]Bilateria@Y47G6A_20a[64][RRM1:100%****][UMH:73%***][KOG0124:100%****]

Phytophthora ramorum@jgi_Phyra1_1_81440[2][RRM1:100%][KOG0124:100%]Cryptosporidium parvum_Iowa_II@XP_628096[RRM1][put-sr][KOG0124]

Dictyostelium discoideum_AX4@XP_638262[RRM2][put-sr][KOG0670]Bilateria@ENSCSAVP00000007991[62][RRM2:95%****][.RRM1:5%*][UMH:74%***][KOG0124:100%****]

Phytophthora@jgi_Phyra1_1_84640[3][RRM2:67%][.RRM1:33%][KOG0124:67%][.KOG0120:33%]Cryptosporidium parvum_Iowa_II@XP_628096[RRM2][put-sr][KOG0124]

Plasmodium falciparum_3D7@XP_001349956[RRM2][KOG0147]Phytophthora@jgi_Phyra1_1_94266[2][RRM2:100%][KOG0147:100%]

Dictyostelium discoideum_AX4@XP_638966[RRM2][KOG0147]Eukaryota@ENSFCAP00000006163[84][RRM2:88%****][.RRM1:12%**][put-sr:86%****][UMH:39%***][.CAPER:8%*][KOG0147:100%****]

Bacillariophyta@jgi_Phatr2_20857[2][RRM2:100%][put-sr:100%][KOG0147:100%]Caenorhabditis elegans@Y55F3AM_3c_1[3][RRM2:100%*][put-sr:33%][UMH:100%*][KOG0147:100%*]

Plasmodium falciparum_3D7@XP_001352080[RRM2]Ascomycota@XP_385341[4][RRM2:100%*][put-sr:100%*][KOG0147:100%*]


Yarrowia lipolytica@XP_504318[RRM2][KOG0147]Dictyostelium discoideum_AX4@XP_636266[RRM3][KOG3598]

Volvox carteri@jgi_Volca1_106063[RRM2]Trypanosoma brucei_TREU927@XP_845742[RRM1][KOG0126]

Saccharomycetaceae@XP_459205[2][RRM1:100%][KOG0126:100%]Eukaryota@AAEL002461-PA[78][RRM1:100%****][put-sr:29%***][KOG0126:100%****]Ustilago maydis_521@XP_760864[RRM1][KOG0126]


Dictyostelium discoideum_AX4@XP_643547[RRM1]Phaeodactylum tricornutum@jgi_Phatr2_45356[RRM1][KOG4208]

Thalassiosira pseudonana@jgi_Thaps3_18198[RRM1][KOG4208]Caenorhabditis elegans@T04A8_6[RRM1][KOG4208]


Dictyostelium discoideum_AX4@XP_640243[RRM1][KOG0117]Encephalitozoon cuniculi_GB-M1@NP_585962[RRM2][KOG0123]


Caenorhabditis elegans@T11G6_8_1[2][RRM1:100%][KOG0153:100%]Coelomata@XP_975014[28][RRM1:100%***][RBM:86%***][KOG0153:100%***]

Ciona@ENSCSAVP00000015574[2][RRM1:100%][KOG0153:100%]Embryophyta@jgi_Phypa1_1_185655[7][RRM1:100%*][KOG0153:100%*]

Ostreococcus@jgi_Ost9901_3_41266[2][RRM1:100%][KOG0153:100%]Dictyostelium discoideum_AX4@XP_635179[RRM2][KOG0148]

Ostreococcus tauri@jgi_Ostta4_31833[RRM2][KOG0148]Schizosaccharomyces pombe_972h-@NP_594243[RRM3][KOG0148]

Eukaryota@YHR086W[51][RRM3:76%***][.RRM2:20%**][oligoU:10%*][KOG0148:90%***]Aureococcus anophagefferens@jgi_Auran1_28594[RRM3][KOG0148]

Phytophthora@jgi_Phyra1_1_50314[2][RRM3:100%][KOG0148:100%]Pichia stipitis_CBS_6054@XP_001384462[RRM2]

Debaryomyces hansenii_CBS767@XP_460517[RRM2][KOG0117]Saccharomycetales@XP_445844[3][RRM2:100%*][KOG0123:33%]

Kluyveromyces lactis@XP_455897[RRM2][KOG0123]Tribolium castaneum@XP_969873[RRM1]

Strongylocentrotus purpuratus@XP_001185821[2][RRM1:100%][KOG0670:100%]Apocrita@XP_623710[2][RRM1:100%]

Euteleostomi@ENSOANP00000024755[113][RRM1:100%****][hnRNP:36%***][.RALYL:15%**]Aedes aegypti@AAEL010890-PA[RRM1][put-sr][KOG0132]

Volvox carteri@jgi_Volca1_107013[RRM3][KOG0117]Saccharomyces cerevisiae@YLL046C[RRM1]

Plasmodium falciparum_3D7@XP_001347332[RRM1][put-sr][KOG0105]Apis mellifera@XP_394565[RRM1][KOG0147]

Zea mays@11279_m000026_AZM5_6772[RRM1][put-sr][KOG0117]Oryza sativa_japonica_cultivar group@NP_001067112[RRM2][put sr][KOG0117]

86 - hnRNP/RALYL

78 - OligoU

14 - RBM

82

69

67 - UMH

Part of 63 - hnRNP

31

16 - dual RRM

SR proteins

17 - single-RRM Zn-K

SR proteins

18

34

Part of 35 - Rasputin

Fungal SR (SpSrp1)

Fungal SR (SpSrp2)

Fig. S8

106

84

71 91

76

97

51

56

70

85 75

53

64

66

91

61

62

Coelomata@XP 001182806[39][RRM1:100%***][KOG0108:13%*][.KOG0116:8%*][.KOG0921:5%]Euteleostomi@ENSSARP00000000775[28][RRM1:100%***][eIF4B:54%**]Ciona@ENSCSAVP00000001842[2][RRM1:100%]

Anopheles gambiae@AGAP000525-PA[RRM1]Drosophila melanogaster@CG10837-PA[3][RRM1:100%*]

Ostreococcus@jgi_Ostta4_33150[2][RRM2:100%][KOG0108:50%]Embryophyta@28180_m000395[6][RRM2:100%*][KOG0124:50%*][.KOG4205:33%][.KOG4211:17%]

Phytophthora@jgi_Physo1_1_141766[2][RRM2:100%][KOG0148:100%]Ostreococcus tauri@jgi_Ostta4_32569[RRM2]

Aureococcus anophagefferens@jgi_Auran1_64341[RRM2][KOG0108]Phaeodactylum tricornutum@jgi_Phatr2_44442[RRM2][KOG4211]

Physcomitrella patens@jgi_Phypa1_1_204078[RRM1][KOG0116]Magnoliophyta@NP_001052571[5][RRM1:100%*][KOG0116:100%*]

Arabidopsis thaliana@NP_189151[RRM1][NTF][KOG0116]Physcomitrella patens@jgi_Phypa1_1_96043[RRM1]

Caenorhabditis elegans@B0035_12_2[2][RRM2:100%][KOG0128:100%]Physcomitrella patens@jgi_Phypa1_1_201182[RRM3][KOG0127]

Magnoliophyta@30131_m007093[6][RRM3:83%*][.RRM2:17%][KOG0127:100%*]Ostreococcus@jgi_Ostta4_19569[2][RRM3:100%][KOG0127:100%]


Theileria parva_strain_Muguga@XP_765501[RRM2][KOG0127]Ciona intestinalis@ENSCINP00000018774[2][RRM3:100%][KOG0127:100%]

Caenorhabditis elegans@R05H10_2[RRM2][KOG0127]Oryzias latipes@ENSORLP00000012079[RRM3][KOG0127]

Euteleostomi@ENSGACP00000016696[19][RRM3:79%**][.RRM4:11%][.RRM1:11%][RBM:58%**][KOG0127:100%**]Strongylocentrotus purpuratus@XP_783689[2][RRM2:100%][KOG0127:100%]Endopterygota@XP_001605703[3][RRM2:67%][.RRM3:33%][KOG0127:100%*]


Aedes aegypti@AAEL008572-PA[RRM2][KOG0127]Phytophthora sojae@jgi_Physo1_1_132702[RRM4][KOG0127]

Phytophthora ramorum@jgi_Phyra1_1_79608[2][RRM4:100%][KOG0127:100%]Saccharomycetales@XP_001385462[7][RRM3:100%*][KOG0127:100%*]

Basidiomycota@XP_756663[3][RRM4:67%][.RRM3:33%][KOG0127:100%*]Schizosaccharomyces pombe_972h-@NP_596114[RRM3][KOG0127]

Aspergillus fumigatus_Af293@XP_752199[RRM3][KOG0127]Sordariomycetes@XP_962933[2][RRM3:100%][KOG0127:100%]


Aureococcus anophagefferens@jgi_Auran1_8214[RRM1]Pichia stipitis_CBS_6054@XP_001384763[RRM3][KOG0123]Dictyostelium discoideum_AX4@XP_643642[RRM2][KOG0148]

Cryptosporidium parvum_Iowa_II@XP_001388131[RRM2][KOG1015]Euteleostomi@ENSORLP00000006283[2][RRM1:100%][LA:50%][KOG1855:100%]

Euteleostomi@GSTENP00013801001[29][RRM1:100%***][LA:59%**][KOG1855:100%***]Tribolium castaneum@XP_974730[RRM1][KOG1855]

Apocrita@XP_001600355[2][RRM1:100%][KOG1855:100%]Takifugu rubripes@SINFRUP00000134535[RRM1][KOG0123]

Aspergillus fumigatus_Af293@XP_750045[RRM1]Ostreococcus lucimarinus@jgi_Ost9901_3_32831[RRM1]

Leishmania infantum_JPCM5@XP_001468615[RRM1]Embryophyta@jgi_Phypa1_1_217831[15][RRM3:93%**][.RRM1:7%][KOG0117:100%**]

Plasmodium falciparum_3D7@XP_001347479[RRM1]Debaryomyces hansenii_CBS767@XP_460681[RRM3][KOG0128]


Nasonia vitripennis@XP_001604488[RRM1]Phytophthora@jgi_Physo1_1_140019[2][RRM1:100%][KOG0116:100%]


Eukaryota@NP_001053839[55][RRM6:42%***][.RRM5:35%**][.RRM4:11%*][.RRM3:9%*][KOG0110:100%****]Plasmodium falciparum_3D7@XP_001350574[RRM3][KOG0110]Cryptosporidium parvum_Iowa_II@XP_627799[RRM5][KOG0110]


Embryophyta@jgi_Phypa1_1_201182[6][RRM2:100%*][KOG0127:100%*]Chlamydomonas reinhardtii@jgi_Chlre3_186870[RRM2][KOG0127]

Ostreococcus@jgi_Ost9901_3_26255[2][RRM2:100%][KOG0127:100%]Dictyostelium discoideum_AX4@XP_646584[RRM2][KOG0127]

Schizosaccharomyces pombe_972h-@NP_596114[RRM2][KOG0127]Pezizomycotina@XP_962933[3][RRM2:100%*][KOG0127:100%*]Saccharomycetales@XP_459044[4][RRM2:100%*][KOG0127:100%*]

Yarrowia lipolytica@XP_499726[RRM2][KOG0127]Chordata@ENSOGAP00000005376[31][RRM2:90%***][.RRM3:6%][RBM:39%**][KOG0127:100%***]

Drosophila melanogaster@CG4806-PA[RRM1][KOG0127]Aedes aegypti@AAEL008572-PA[RRM1][KOG0127]

Nasonia vitripennis@XP_001605703[RRM1][KOG0127]Tribolium castaneum@XP_974350[RRM1][KOG0127]


Plasmodium falciparum_3D7@XP_001348230[RRM1][KOG0130]Yarrowia lipolytica@XP_503462[RRM1][put-sr][KOG0130]

Ustilago maydis_521@XP_760711[RRM1][put-sr][KOG0687]Cryptococcus neoformans_var._neoformans_JEC21@XP_569809[RRM1][KOG0130]

Phaeodactylum tricornutum@jgi_Phatr2_20716[RRM1][KOG0130]Eukaryota@jgi_Thaps3_18841[52][RRM1:100%***][put-sr:56%***][RBM:42%***][KOG0130:100%***]

Sordariomycetes@XP_001522188[3][RRM1:100%*][put-sr:67%]Cryptococcus neoformans_var._neoformans_JEC21@XP_569824[RRM1][put-sr]

Schizosaccharomyces pombe_972h-@NP_596549[RRM1][put-sr]Coelomata@ENSMUSP00000057332[45][RRM1:100%***][put-sr:100%***][RNPS1:64%***][KOG4209:87%***]

Caenorhabditis elegans@K02F3_11_2[2][RRM1:100%][put-sr:100%][KOG4209:100%]Dictyostelium discoideum_AX4@XP_636445[RRM1][put-sr]

Viridiplantae@jgi_Phypa1_1_105411[8][RRM1:100%**][put-sr:100%**][SR:25%][KOG0117:12%][.KOG0462:12%]Phytophthora@jgi_Physo1_1_138873[2][RRM1:100%][put-sr:100%][KOG1611:50%]

Pezizomycotina@XP_958422[3][RRM1:100%*][put-sr:33%][KOG0533:100%*]Ustilago maydis_521@XP_757147[RRM1][KOG0533]

Plasmodium falciparum_3D7@XP_966143[RRM1][KOG0533]Theileria parva_strain_Muguga@XP_764636[RRM1]

Yarrowia lipolytica@XP_505140[RRM1][KOG0533]Eukaryota@GSTENP00007343001[69][RRM1:100%****][FCAFPA:10%*][KOG0533:99%****]

Ostreococcus tauri@jgi_Ostta4_36431[RRM1][KOG0533]Dictyostelium discoideum_AX4@XP_638266[RRM1][KOG0533]

Chlamydomonadales@jgi_Volca1_90392[2][RRM1:100%][KOG0533:100%]Phytophthora@jgi_Phyra1_1_97175[2][RRM1:100%][put-sr:50%][KOG0533:100%]

Cyanidioschyzon merolae@gnl_CMER_CMH135C[RRM1]Euteleostomi@ENSTBEP00000009485[3][RRM1:100%*][PDIP:33%][KOG0533:33%]

Endopterygota@CG6961-PA[7][RRM1:100%*][KOG0533:29%]Saccharomycetales@XP_462132[6][RRM1:100%*][KOG0533:100%*]




Dictyostelium discoideum_AX4@XP_642758[RRM1]Cyanidioschyzon merolae@gnl_CMER_CMT598C[RRM1][KOG0148]

Leptospira@YP_001385[4][RRM1:100%*][PROK:100%*]Ciona@ENSCINP00000009845[4][RRM1:100%*][KOG0116:100%*]

Deuterostomia@ENSMODP00000011218[78][RRM1:100% ][G3BP:82% ][KOG0116:100% ] p

Part of 30 - PDIP

FCA FPA

26 - SR45

27 - RNPS128

20 - RBM

71 - RBM

60

Part of 63 - hnRNP

81 - La

72 - RBM

87 - eIF-4B

Fungal SpRnps1

Fig. S8

107

75

54

75

65

80

72

66

77

63

Viridiplantae@jgi Phypa1 1 207810[3][RRM1:100%*][KOG0110:100%*]Dictyostelium discoideum_AX4@XP_638463[RRM1][KOG0110]

Cyanidioschyzon merolae@gnl_CMER_CMO246C[RRM1][KOG0110]Ustilago maydis_521@XP_758493[RRM1][KOG0110]

Saccharomycetaceae@XP_001386803[2][RRM1:100%][KOG0110:100%]Aspergillus fumigatus_Af293@XP_748929[RRM1]

Neurospora crassa_OR74A@XP_964541[RRM1]Theileria parva_strain_Muguga@XP_766096[RRM1]

Chlamydomonadales@jgi_Volca1_54847[2][RRM1:100%][KOG0108:100%]Physcomitrella patens@jgi_Phypa1_1_167900[3][RRM1:100%*][KOG0123:33%][.KOG4210:33%][.KOG1015:33%]

Ostreococcus tauri@jgi_Ostta4_10328[RRM1][KOG2476]Arabidopsis thaliana@NP_175125[7][RRM1:43%*][.RRM2:29%][.RRM4:14%][.RRM3:14%][PABP:29%][KOG0123:100%*]

Magnoliophyta@NP_001053909[5][RRM1:100%*][nucleolin:40%][KOG0123:40%][.KOG4210:40%][.KOG1015:20%]stramenopiles@jgi_Auran1_17857[4][RRM1:50%][.RRM2:50%][KOG0108:50%][.KOG4205:50%]

Phaeodactylum tricornutum@jgi_Phatr2_49387[RRM1]Aureococcus anophagefferens@jgi_Auran1_9434[RRM1]

Ostreococcus lucimarinus@jgi_Ost9901_3_92667[RRM1]Cryptococcus neoformans_var._neoformans_JEC21@XP_569209[RRM2][KOG0144]Thalassiosira pseudonana@jgi_Thaps3_24369[RRM1]


Phaeodactylum tricornutum@jgi_Phatr2_44395[RRM1]Poaceae@8373_m000321_c0161G04[2][RRM1:100%][KOG4205:50%][.KOG4211:50%]

Volvox carteri@jgi_Volca1_90315[RRM1]Mammalia@ENSETEP00000003776[19][RRM1:100%**][LA:95%**][KOG4213:100%**]

Embryophyta@28180_m000395[3][RRM1:100%*][KOG0124:100%*]Arabidopsis thaliana@NP_191094[RRM1][KOG4205]

Aureococcus anophagefferens@jgi_Auran1_71372[2][RRM3:50%][.RRM2:50%][put-sr:100%][KOG1178:100%]Phytophthora@jgi_Phyra1_1_77488[2][RRM1:100%][KOG4205:100%]

Phytophthora sojae@jgi_Physo1_1_139998[RRM1]Caenorhabditis elegans@W02D3_11b[2][RRM1:100%][KOG4211:100%]

Coelomata@ENSCINP00000003632[126][RRM2:70%****][.RRM1:30%***][hnRNP:37%***][.GRSRBP:15%**][KOG4211:100%****]Danio rerio@ENSDARP00000069459[RRM2][KOG4211]

Volvox carteri@jgi_Volca1_117772[RRM1][KOG1365]Caenorhabditis elegans@Y73B6BL_33[RRM1][KOG4211]

Physcomitrella patens@jgi_Phypa1_1_162342[RRM3][KOG1365]Ciona savignyi@ENSCSAVP00000001587[RRM5][KOG4307]

Oryzias latipes@ENSORLP00000025180[RRM2][put-sr][KOG4307]Plasmodium falciparum_3D7@XP_001347519[RRM1][KOG1365]

Arabidopsis thaliana@NP_188725[RRM2][hnRNP][KOG1365]Thalassiosira pseudonana@jgi_Thaps3_5686[RRM2][KOG4211]

Saccharomycetales@NP_982813[6][RRM2:100%*][KOG4210:100%*]Aspergillus fumigatus_Af293@XP_755020[RRM2]


Caenorhabditis elegans@R09B3_3[3][RRM1:100%*][KOG0108:100%*]Phytophthora@jgi_Phyra1_1_83430[2][RRM1:100%]

Cryptococcus neoformans_var._neoformans_JEC21@XP_566745[2][RRM1:100%]Pichia stipitis_CBS_6054@XP_001384729[RRM1]

Yarrowia lipolytica@XP_504609[RRM1]Neurospora crassa_OR74A@XP_965346[RRM2][KOG0110]

Aspergillus fumigatus_Af293@XP_747328[RRM2][KOG0110]Euteleostomi@GSTENP00022906001[41][RRM3:83%***][.RRM2:10%*][.RRM1:7%*][nucleolin:54%***][KOG0123:93%***]

Tetraodontidae@GSTENP00014994001[2][RRM1:50%][.RRM3:50%][KOG0123:50%]Euteleostomi@ENSMODP00000021210[32][RRM2:97%***][nucleolin:59%**][KOG0123:100%***]

Ciona@ENSCINP00000008105[4][RRM1:100%*][KOG0116:50%][.KOG2141:25%]Pezizomycotina@XP_754840[2][RRM2:100%][KOG0127:50%][.KOG0148:50%]

Aspergillus fumigatus_Af293@XP_754657[RRM1]Cryptococcus neoformans_var._neoformans_JEC21@XP_566835[RRM2][KOG0148]

Ustilago maydis_521@XP_762340[RRM2][KOG0148]Schizosaccharomyces pombe_972h-@NP_593531[RRM2][nucleolin][KOG0147]Saccharomycetales@XP_456900[7][RRM2:100%*][nucleolin:14%][KOG0148:57%*][.KOG0131:29%][.KOG4210:14%]

Drosophila melanogaster@CG12288-PA[RRM2]Culicidae@AGAP003171-PA[3][RRM2:100%*][KOG0148:33%]

Chlamydomonadales@jgi_Volca1_120471[2][RRM1:100%][KOG0108:100%]Ciona intestinalis@ENSCINP00000024280[RRM1][KOG0113]

Cyanidioschyzon merolae@gnl_CMER_CMO334C[RRM2][KOG0126]Ascomycota@XP_505055[6][RRM1:83%*][.RRM2:17%]

Trypanosomatidae@XP_827554[2][RRM1:50%][.RRM2:50%][put-sr:50%]Phaeodactylum tricornutum@jgi_Phatr2_46145[RRM2]

Apis mellifera@XP_394565[RRM2][KOG0147]Coelomata@ENSDARP00000093407[32][RRM2:88%***][.RRM1:12%*][KOG0108:12%*][.KOG3001:6%][.KOG0123:6%][.KOG0126:6%]

Volvox carteri@jgi_Volca1_118759[RRM2]Ostreococcus@jgi_Ostta4_30189[2][RRM1:50%][.RRM2:50%][put-sr:50%]

Magnoliophyta@30054_m000807[2][RRM2:100%][KOG1267:50%]Dictyostelium discoideum_AX4@XP_635997[RRM2]

Caenorhabditis elegans@F11A10_7[RRM2][KOG0131]Ciona@ENSCSAVP00000005375[4][RRM2:75%*][.RRM1:25%][KOG0116:75%*][.KOG2141:25%]

Encephalitozoon cuniculi_GB-M1@NP_597583[RRM1][KOG4205]Physcomitrella patens@jgi_Phypa1_1_188347[RRM2][KOG0123]

Physcomitrella patens@jgi_Phypa1_1_167900[RRM2][KOG1015]Magnoliophyta@29675_m000389[3][RRM2:100%*][KOG0123:67%][.KOG1015:33%]

Arabidopsis thaliana@NP_188491[RRM2][nucleolin][KOG4210]Dictyostelium discoideum_AX4@XP_638966[RRM1][KOG0147]

Phytophthora@jgi_Physo1_1_157186[2][RRM1:100%][KOG0147:100%]Strongylocentrotus purpuratus@XP_001198098[2][RRM1:100%][put-sr:100%][KOG0147:100%]Eukaryota@ENSMLUP00000011758[47][RRM1:100%***][put-sr:91%***][UMH:64%***][.CAPER:15%*][KOG0147:100%***]

Ascomycota@NP_594422[4][RRM1:100%*][put-sr:100%*][KOG0147:100%*]Yarrowia lipolytica@XP_504318[RRM1][KOG0147]

Ostreococcus@jgi_Ost9901_3_42846[2][RRM1:100%][put-sr:50%][KOG0147:100%]Volvox carteri@jgi_Volca1_84128[2][RRM1:100%][put-sr:50%][KOG0147:100%]


Chlamydomonadales@jgi_Volca1_90315[3][RRM2:67%][.RRM3:33%][KOG0123:67%]Chordata@ENSETEP00000010530[36][RRM1:50%**][.RRM2:50%**][put-sr:100%***][SRrp:75%***][KOG4676:100%***]

Magnoliophyta@15974_m000013_AZM5_17589[3][RRM2:67%][.RRM1:33%]Caenorhabditis elegans@T08B6_5[RRM1][KOG4209]

Caenorhabditis elegans@EEED8_12[2][RRM1:100%][KOG4209:100%]Eukaryota@ENSCSAVP00000003369[89][RRM1:100%****][put-sr:17%**][PABP:26%***][KOG4209:100%****]

Dictyostelium discoideum_AX4@XP_642788[RRM1][KOG4209]Ciona@ENSCSAVP00000010162[2][RRM1:100%][KOG4209:100%]

Magnoliophyta@IMGA_AC160842_25_1[6][RRM1:100%*][KOG3702:83%*][.KOG4209:17%]Physcomitrella patens@jgi_Phypa1_1_167236[RRM1][KOG4209]

Arabidopsis thaliana@NP_180012[RRM1]Volvox carteri@jgi_Volca1_103724[RRM1][put-sr][KOG0591]

Aedes aegypti@AAEL012119-PA[RRM1]Apocrita@XP_001602582[2][RRM1:100%][KOG0128:100%]

Euteleostomi@ENSSTOP00000002132[31][RRM1:100%***][SART3:68%***][KOG0128:100%***]Strongylocentrotus purpuratus@XP_781643[RRM1][KOG0128]

Ciona intestinalis@ENSCINP00000019832[3][RRM1:100%*][KOG0128:100%*]Tribolium castaneum@XP_972538[RRM1][KOG0128]Culicidae@AAEL011961-PA[3][RRM1:100%*][KOG0128:100%*]

Schizosaccharomyces pombe_972h-@NP_595728[RRM1]Ostreococcus@jgi_Ost9901_3_31221[2][RRM1:100%][KOG0128:100%]

Magnoliophyta@29609_m000574[4][RRM1:100%*][KOG0128:100%*]Physcomitrella patens@jgi_Phypa1_1_135986[RRM1][KOG0128]

Ustilago maydis_521@XP_762237[RRM1]Aspergillus fumigatus_Af293@XP_755976[RRM1]

Sordariomycetes@XP_956776[2][RRM1:100%][put-sr:50%]Coelomata@XP_001182806[39][RRM1:100% ][KOG0108:13% ][.KOG0116:8% ][.KOG0921:5%]

73 - SART3

74

83 - PABP

75 - CAPER

UMH

85 - SRrp

80 - hnRNP

84 - La

Fig. S8

108

81 94

93

77

52 68

99

57

94

94

67

54

62

62

57

Pezizomycotina@XP 755630[3][RRM1:100%*][KOG0111:100%*]Cryptococcus neoformans_var._neoformans_JEC21@XP_566572[RRM1][KOG0111]


Eukaryota@ENSGALP00000021793[59][RRM1:100%****][cyclophilin:59%***][KOG0111:98%****]Eutheria@ENSEEUP00000009324[3][RRM1:100%*][cyclophilin:100%*][KOG0111:100%*]Otolemur garnettii@ENSOGAP00000003225[RRM1][KOG0111]Deuterostomia@ENSXETP00000012868[47][RRM1:100%***][KOG4454:60%***][.KOG0131:40%**]

Endopterygota@AGAP002256-PA[4][RRM1:100%*][KOG4454:75%*][.KOG0131:25%]Drosophila melanogaster@CG11454-PA[RRM1][KOG4454]

Magnoliophyta@NP_001055607[4][RRM1:100%*][put-sr:25%][KOG0131:100%*]Caenorhabditis elegans@Y37D8A_21_1[2][RRM1:100%][KOG4454:100%]




Candida glabrata_CBS138@XP_447678[RRM1][KOG0131]Saccharomyces cerevisiae@YOR319W[RRM1][KOG0131]

Percomorpha@ENSGACP00000007987[5][RRM1:100%*][IGF2BP:80%*][KOG2193:100%*]Strongylocentrotus purpuratus@XP_001180991[4][RRM1:100%*]


Physcomitrella patens@jgi_Phypa1_1_93324[RRM1]Trypanosomatidae@XP_847474[2][RRM1:100%]Trypanosomatidae@XP_001467105[2][RRM1:100%][KOG4209:100%]

Saccharomycetaceae@XP_453677[2][RRM1:100%][KOG4209:100%]Saccharomyces cerevisiae@YIR001C[RRM1][PABP][KOG4209]

Candida glabrata_CBS138@XP_447800[RRM1][KOG4209]Embryophyta@jgi_Phypa1_1_161416[4][RRM1:100%*][put-sr:75%*][KOG0154:75%*][.KOG0147:25%]

Encephalitozoon cuniculi_GB-M1@NP_586226[RRM1][put-sr][KOG0123]Dictyostelium discoideum_AX4@XP_645848[RRM2][put-sr]

Arabidopsis thaliana@NP_974808[2][RRM1:100%][KOG0123:50%][.KOG0148:50%]Ustilago maydis_521@XP_758439[RRM3][KOG0123]

Caenorhabditis elegans@F56D1_7[RRM1]Takifugu rubripes@SINFRUP00000155469[RRM1]

Coelomata@AAEL001684-PA[39][RRM1:100%***][KOG0125:21%**]Euteleostomi@ENSEEUP00000005436[64][RRM1:95%****]

Tupaia belangeri@ENSTBEP00000015084[RRM1]Spermophilus tridecemlineatus@ENSSTOP00000003171[RRM1]

Amniota@ENSMODP00000004174[11][RRM4:55%*][.RRM3:36%*][.RRM2:9%][put-sr:100%**][KOG0112:100%**]Dictyostelium discoideum_AX4@XP_646990[RRM1][put-sr][KOG0147]

Theileria parva_strain_Muguga@XP_766400[RRM2][put-sr][KOG4205]Strongylocentrotus purpuratus@XP_001185731[2][RRM1:100%]

Tribolium castaneum@XP_971953[RRM1]Euteleostomi@ENSMODP00000018834[25][RRM1:100%***][put-sr:64%**][KOG0147:48%**][.KOG0132:12%*]

Eutheria@ENSMLUP00000005283[2][RRM1:100%][put-sr:100%]Spermophilus tridecemlineatus@ENSSTOP00000006011[RRM1][put-sr]

Dictyostelium discoideum_AX4@XP_642304[RRM1][KOG0415]Aedes aegypti@AAEL004293-PA[RRM1][put-sr]

Coelomata@AGAP006798-PA[81][RRM1:100%****][put-sr:99%****][KOG0122:26%***][.KOG0125:25%**][.KOG0147:14%**][.KOG0108:9%*]Drosophila melanogaster@CG10128-PC[6][RRM1:100%*][put-sr:100%*]Basidiomycota@XP_757472[3][RRM1:100%*][put-sr:33%][KOG0122:33%]Caenorhabditis elegans@C18D11_4_1[2][RRM1:100%][put-sr:100%][KOG0921:100%]

Encephalitozoon cuniculi_GB-M1@NP_585779[RRM1]Saccharomycetaceae@XP_458658[2][RRM1:100%][KOG0921:100%]

Physcomitrella patens@jgi_Phypa1_1_12664[RRM1]rosids@30155_m001644[2][RRM1:100%][KOG0116:50%]

Euteleostomi@ENSDARP00000069729[82][RRM1:100%****][KOG1995:77%****][.KOG0921:16%**][.KOG2044:5%*]Endopterygota@XP_624681[6][RRM1:100%*][put-sr:17%][KOG0921:67%*][.KOG1548:33%]

Strongylocentrotus purpuratus@XP_001196853[2][RRM1:100%][KOG1995:100%]Arabidopsis thaliana@NP_564565[RRM1][put-sr][KOG1995]

Cryptosporidium parvum_Iowa_II@XP_001388131[RRM1][KOG1015]Theileria parva_strain_Muguga@XP_765374[RRM1]

Dictyostelium discoideum_AX4@XP_643642[RRM1][KOG0148]Ostreococcus tauri@jgi_Ostta4_34258[RRM2]

Saccharomycetaceae@XP_001383390[2][RRM1:100%][KOG0108:100%]Oryza sativa_japonica_cultivar-group@NP_001058465[RRM1][KOG0108]

Cryptococcus neoformans_var._neoformans_JEC21@XP_572946[RRM1][KOG0108]Aureococcus anophagefferens@jgi_Auran1_23269[RRM1][KOG0108]

Bacillariophyta@jgi_Phatr2_8451[2][RRM1:100%][KOG0108:100%]Kluyveromyces lactis@XP_453283[RRM2][KOG0123]

Dikarya@NP_596771[2][RRM1:100%][KOG0108:50%]Tribolium castaneum@XP_969008[RRM2][KOG0331]


Aureococcus anophagefferens@jgi_Auran1_17171[RRM1][KOG0108]Eukaryota@ENSDARP00000064611[84][RRM1:100%****][KOG0108:99%****]

Encephalitozoon cuniculi_GB-M1@NP_597167[RRM1][KOG0108]Ostreococcus tauri@jgi_Ostta4_31925[RRM1][KOG0117]

Viridiplantae@29631_m001006[3][RRM1:100%*][put-sr:33%][KOG0108:67%][.KOG2253:33%]Euteleostomi@ENSGACP00000016390[7][RRM1:100%*][put-sr:86%*][RBM:14%][KOG2253:100%*]

Schizosaccharomyces pombe_972h-@NP_595396[RRM1][put-sr][KOG0120]Chlamydomonadales@jgi_Volca1_48801[2][RRM1:100%][KOG0120:100%]

Plasmodium falciparum_3D7@XP_001348830[RRM2][put-sr][KOG0120]Phaeodactylum tricornutum@jgi_Phatr2_11145[RRM2][KOG0120]

Eukaryota@jgi_Volca1_82970[75][RRM2:91%****][.RRM1:9%*][put-sr:80%****][snRNP:53%***][KOG0120:100%****]Pezizomycotina@XP_387225[3][RRM1:67%][.RRM2:33%][put-sr:100%*][KOG0120:100%*]

Yarrowia lipolytica@XP_503754[RRM1][KOG0120]Trypanosoma brucei_TREU927@XP_829593[RRM1]

Ostreococcus@jgi_Ost9901_3_7913[3][RRM1:100%*][KOG0131:33%]Viridiplantae@jgi_Chlre3_99594[25][RRM1:100%***][KOG0123:8%]

Ostreococcus tauri@jgi_Ostta4_24260[RRM1]Magnoliophyta@NP_189032[4][RRM1:100%*][put-sr:100%*][KOG0670:100%*]


Trypanosomatidae@XP_827855[2][RRM1:100%]Kluyveromyces lactis@XP_454447[RRM3][KOG0128]

Saccharomyces cerevisiae@YMR268C[RRM1][KOG0128]Cryptosporidium parvum_Iowa_II@XP_627232[RRM1][put-sr][KOG0105]

Plasmodium falciparum_3D7@XP_966051[RRM2]Ostreococcus lucimarinus@jgi_Ost9901_3_28918[RRM1]


Neurospora crassa_OR74A@XP_960450[RRM1]Pichia stipitis_CBS_6054@XP_001384763[RRM1][KOG0123]

Trypanosoma brucei_TREU927@XP_951655[RRM3][put-sr][KOG0109]Leishmania infantum_JPCM5@XP_001466413[RRM2][put-sr][KOG0147]

Trypanosoma brucei_TREU927@XP_951655[RRM2][put-sr][KOG0109]Trypanosomatidae@XP_827358[2][RRM2:100%][KOG0123:100%]

Encephalitozoon cuniculi_GB-M1@NP_597181[RRM1][KOG0110]Schizosaccharomyces pombe_972h-@NP_595599[RRM1][KOG0110]

Drosophila melanogaster@CG3335-PA[RRM1][KOG0110]Apocrita@XP_624611[2][RRM1:100%][KOG0110:100%]

Caenorhabditis elegans@T23F6_4_1[2][RRM1:100%][KOG0110:100%]Culicidae@AGAP005249-PA[2][RRM1:100%][KOG0110:100%]

Euteleostomi@GSTENP00029551001[21][RRM1:100%***][put-sr:10%][KOG0110:100%***]Arabidopsis thaliana@NP_196191[RRM1][KOG0110]

Viridiplantae@jgi_Phypa1_1_207810[3][RRM1:100% ][KOG0110:100% ]

1

64 - snRNP

61

46

47

48 - IGF2BP

19 - cyclophilin

49

Fig. S8

109

91

61

91

64

85

97

81

79

72

61

73

87

90 81

79 50

64

Phytophthora sojae@jgi Physo1 1 138511[RRM1][put-sr]Kluyveromyces lactis@XP_451368[RRM3][KOG0123]

Ashbya gossypii_ATCC_10895@NP_984845[RRM3][KOG0123]Saccharomyces cerevisiae@YHR015W[RRM3][KOG0123]

Saccharomyces cerevisiae@YFR023W[RRM3][KOG0123]Candida glabrata_CBS138@XP_447635[RRM3][KOG0123]

Neurospora crassa_OR74A@XP_965346[RRM1][KOG0110]Phytophthora@jgi_Physo1_1_132702[3][RRM3:100%*][KOG0127:100%*]

Cyanidioschyzon merolae@gnl_CMER_CMO246C[RRM2][KOG0110]Anopheles gambiae@AGAP007689-PA[RRM1]

Aedes aegypti@AAEL010101-PA[RRM1]Saccharomycetales@NP_986417[7][RRM1:100%*][KOG0127:100%*]

Schizosaccharomyces pombe_972h-@NP_596114[RRM1][KOG0127]Basidiomycota@XP_568669[3][RRM1:100%*][KOG0127:100%*]

Euteleostomi@ENSOANP00000001262[28][RRM1:100%***][RBM:46%**][KOG0127:100%***]Sordariomycetes@XP_382687[2][RRM1:100%][KOG0127:100%]

Aspergillus fumigatus_Af293@XP_752199[RRM1][KOG0127]Phytophthora@jgi_Physo1_1_132702[3][RRM1:100%*][KOG0127:100%*]


Ciona@ENSCINP00000018772[3][RRM1:100%*][KOG0127:100%*]Magnoliophyta@NP_565513[6][RRM1:100%*][KOG0127:100%*]

Physcomitrella patens@jgi_Phypa1_1_201182[RRM1][KOG0127]Chlamydomonadales@jgi_Chlre3_186870[2][RRM1:100%][KOG0127:100%]

Dictyostelium discoideum_AX4@XP_646584[RRM1][KOG0127]Saccharomycetaceae@XP_001388004[2][RRM1:100%][KOG0122:100%]

Saccharomycetales@XP_446998[3][RRM1:100%*][KOG0122:100%*]Dictyostelium discoideum_AX4@XP_641693[RRM1][KOG0122]

Yarrowia lipolytica@XP_503515[RRM1][KOG0122]Cryptococcus neoformans_var._neoformans_JEC21@XP_567824[RRM1][KOG0122]Cyanidioschyzon merolae@gnl_CMER_CMH159C[RRM1][KOG0122]

Caenorhabditis elegans@F22B5_2[RRM1][KOG0122]Apicomplexa@XP_001388056[3][RRM1:100%*][KOG0122:100%*]

Eukaryota@NP_187747[49][RRM1:100%***][KOG0122:98%***]Medicago truncatula@IMGA_AC144431_18_2[RRM1][KOG0122]

Phaeodactylum tricornutum@jgi_Phatr2_8457[RRM1][KOG0122]Cryptosporidium parvum_Iowa_II@XP_626158[RRM1][KOG0144]

Volvox carteri@jgi_Volca1_63158[RRM2][KOG0110]Phytophthora@jgi_Phyra1_1_74707[2][RRM3:100%][KOG0110:100%]

Oryza sativa_japonica_cultivar-group@NP_001053839[RRM1][KOG0110]Trypanosomatidae@XP_001463723[2][RRM1:100%][KOG0110:100%]

Phytophthora@jgi_Physo1_1_129427[2][RRM2:100%][KOG0110:100%]Cyanidioschyzon merolae@gnl_CMER_CML202C[RRM1][put-sr]Theileria parva_strain_Muguga@XP_765501[RRM1][KOG0127]

Thalassiosira pseudonana@jgi_Thaps3_268689[RRM2][KOG0110]Encephalitozoon cuniculi_GB-M1@NP_584580[RRM1][KOG0114]Eukaryota@jgi_Phatr2_8132[54][RRM1:100%***][KOG0114:100%***]

Debaryomyces hansenii_CBS767@XP_458197[RRM1][KOG0114]Schizosaccharomyces pombe_972h-@NP_594609[RRM1][KOG4660]

Eukaryota@IMGA_AC183923_6_1[34][RRM3:74%***][.RRM1:15%*][.RRM2:12%*][put-sr:6%][KOG0110:100%***]Ustilago maydis_521@XP_758493[RRM2][KOG0110]

Aureococcus anophagefferens@jgi_Auran1_1296[RRM1][KOG0110]Phaeodactylum tricornutum@jgi_Phatr2_20740[RRM2][KOG0110]

Neurospora crassa_OR74A@XP_965014[RRM2][KOG0110]Cryptococcus neoformans_var._neoformans_JEC21@XP_569873[RRM2][KOG0110]Caenorhabditis elegans@T23F6_4_1[2][RRM3:100%][KOG0110:100%]


Saccharomycetales@NP_984131[7][RRM2:100%*][KOG0110:100%*]Dictyostelium discoideum_AX4@XP_639372[RRM1][KOG0670]Ostreococcus lucimarinus@jgi_Ost9901_3_26750[RRM1]

Embryophyta@NP_001062111[8][RRM1:100%**][put-sr:62%*][KOG4849:38%*][.KOG4246:12%][.KOG0113:12%][.KOG4676:12%]Saccharomycetales@XP_455897[3][RRM1:100%*][KOG0123:67%]

Cryptosporidium parvum_Iowa_II@XP_627799[RRM2][KOG0110]Dictyostelium discoideum_AX4@XP_629950[RRM1][KOG0128]

Ciona intestinalis@ENSCINP00000019833[3][RRM2:100%*][KOG0128:100%*]Culicidae@AAEL011963-PA[3][RRM2:100%*][KOG0128:100%*]

Strongylocentrotus purpuratus@XP_781643[RRM2][KOG0128]Tribolium castaneum@XP_972538[RRM2][KOG0128]Euteleostomi@ENSOCUP00000014007[29][RRM2:97%***][SART3:69%**][KOG0128:100%***]

Apocrita@XP_001602582[2][RRM2:100%][KOG0128:100%]Drosophila melanogaster@CG2050-PA[RRM2]

Apocrita@XP_001602363[2][RRM1:100%][KOG1832:50%]Culicidae@AAEL001997-PA[2][RRM1:100%]

Drosophila melanogaster@CG3594-PA[RRM1][KOG0110]Schizosaccharomyces pombe_972h-@NP_596033[RRM1]Cryptococcus neoformans_var._neoformans_JEC21@XP_570477[RRM1]


Neurospora crassa_OR74A@XP_964518[RRM1]Sordariomycetes@XP_389032[2][RRM1:100%]

Culicidae@AAEL004075-PA[3][RRM5:67%][.RRM1:33%][KOG0110:100%*]Ostreococcus@jgi_Ost9901_3_710[2][RRM4:100%][KOG0110:100%]

Magnoliophyta@NP_193696[2][RRM3:100%][KOG0110:100%]Thalassiosira pseudonana@jgi_Thaps3_268689[RRM4][KOG0110]

Phaeodactylum tricornutum@jgi_Phatr2_20740[RRM4][KOG0110]Euteleostomi@ENSGALP00000013474[20][RRM5:85%**][.RRM4:5%][.RRM3:5%][.RRM2:5%][put-sr:10%][KOG0110:100%**]

Phytophthora sojae@jgi_Physo1_1_129427[RRM4][KOG0110]Apocrita@XP_001605134[2][RRM5:100%][KOG0110:100%]

Cryptococcus neoformans_var._neoformans_JEC21@XP_569873[RRM4][KOG0110]Cryptosporidium parvum_Iowa_II@XP_627799[RRM4][KOG0110]Ascomycota@XP_001386803[10][RRM4:90%**][.RRM2:10%][KOG0110:100%**]


Yarrowia lipolytica@XP_503802[RRM1][KOG0113]Leishmania infantum_JPCM5@XP_001464648[RRM1][KOG0113]

Apis mellifera@XP_623573[RRM1][KOG0113]Dictyostelium discoideum_AX4@XP_641373[RRM1][put-sr]

Debaryomyces hansenii_CBS767@XP_459815[RRM1][KOG0415]Eukaryota@jgi_Ostta4_3181[66][RRM1:100%****][put-sr:47%***][cyclophilin:32%***][KOG0415:97%****]

Embryophyta@29657_m000467[4][RRM1:100%*][put-sr:50%][snRNP:25%][KOG0113:100%*]Tribolium castaneum@XP_966565[RRM1][KOG0113]

Deuterostomia@XP_001178221[30][RRM1:100%***][put-sr:63%**][snRNP:70%***][KOG0113:100%***]Ciona@ENSCSAVP00000001345[2][RRM1:100%][KOG0113:100%]

Phytophthora@jgi_Phyra1_1_44765[2][RRM1:100%][put-sr:50%][KOG0113:100%]Coelomata@AAEL011340-PB[2][RRM1:100%][put-sr:50%][KOG0113:100%]

Rattus norvegicus@ENSRNOP00000048879[RRM1][snRNP][KOG0113]Felis catus@ENSFCAP00000006212[RRM1][put-sr][KOG0113]


Aspergillus fumigatus_Af293@XP_753306[RRM1][KOG0113]Eukaryota@jgi_Physo1_1_143842[43][RRM1:100%***][put-sr:47%**][snRNP:14%*][KOG0113:100%***]

Ostreococcus@jgi_Ostta4_11066[2][RRM1:100%][KOG0113:100%]Aureococcus anophagefferens@jgi_Auran1_34517[2][RRM1:100%][put-sr:50%][KOG0113:100%]

Cryptosporidium parvum_Iowa_II@XP_627471[RRM1][KOG0113]Phytophthora ramorum@jgi_Phyra1_1_76171[2][RRM1:100%][KOG0111:100%]

Thalassiosira pseudonana@jgi_Thaps3_31121[RRM1][KOG0111]Phaeodactylum tricornutum@jgi_Phatr2_11308[RRM1][KOG0111]Pezizomycotina@XP_755630[3][RRM1:100% ][KOG0111:100% ]

38 - Cyclophilin

36 - snRNP

37 - SART3

39

59

Part of 32

Part of 32

44

65

70 - RBM

22 - single RRM

SR proteins

Fig. S8

110

50

69

59

87 78

69

67

77

52

53 63

Thalassiosira pseudonana@jgi Thaps3 37126[RRM2][KOG0123]Phytophthora@jgi_Phyra1_1_75500[2][RRM3:100%][KOG0123:100%]

Cyanidioschyzon merolae@gnl_CMER_CMM078C[RRM2][KOG4212]Trypanosomatidae@XP_001465100[2][RRM2:100%][KOG4212:100%]

Saccharomycetales@XP_446962[5][RRM1:100%*][put-sr:60%*][KOG0127:60%*][.KOG0123:40%]Saccharomycetaceae@XP_462023[2][RRM1:100%][put-sr:100%][KOG0123:100%]

Saccharomycetaceae@XP_453283[2][RRM1:50%][.RRM2:50%][KOG0123:50%][.KOG0127:50%]Saccharomyces cerevisiae@YNL004W[RRM2][KOG0127]

Saccharomycetales@XP_445179[2][RRM2:100%][put-sr:100%][KOG0123:100%]Candida glabrata_CBS138@XP_446962[RRM2][put-sr][KOG0127]

Cryptococcus neoformans_var._neoformans_JEC21@XP_572539[4][RRM2:100%*][KOG4212:100%*]Basidiomycota@XP_758699[7][RRM1:71%*][.RRM2:29%][put-sr:14%][KOG4212:100%*]Saccharomycetales@XP_001386572[3][RRM2:67%][.RRM1:33%][put-sr:67%][KOG0123:67%][.KOG4212:33%]

Chlamydomonadales@jgi_Volca1_103054[2][RRM3:50%][.RRM2:50%][KOG0055:50%]Coelomata@ENSMLUP00000006206[100][RRM2:88%****][.RRM1:12%**][put-sr:5%*][hnRNP:28%***][KOG4212:98%****]

Caenorhabditis elegans@C25A1_4_2[2][RRM2:100%][put-sr:100%][KOG4212:100%]Schizosaccharomyces pombe_972h-@NP_594207[RRM2][KOG4212]

Plasmodium falciparum_3D7@XP_001347353[RRM2][KOG4212]Pezizomycotina@XP_751108[2][RRM2:100%][put-sr:100%][KOG4212:100%]

Trypanosomatidae@XP_001465100[2][RRM1:100%][KOG4212:100%]Cryptococcus neoformans_var._neoformans_JEC21@XP_568231[RRM2][put-sr][KOG0147]

Saccharomycetales@YNL004W[4][RRM3:100%*][put-sr:50%][KOG0123:50%][.KOG0127:50%]Saccharomycetales@XP_888678[3][RRM3:67%][.RRM2:33%][put-sr:67%][KOG0123:67%][.KOG4212:33%]

Dikarya@XP_568231[5][RRM3:100%*][put-sr:80%*][KOG4212:80%*][.KOG0147:20%]Yarrowia lipolytica@XP_503927[RRM3][put-sr][KOG4212]

Yarrowia lipolytica@XP_505724[RRM1][KOG4198]Caenorhabditis elegans@ZC404_8_2[2][RRM1:100%][KOG0125:100%]

Felis catus@ENSFCAP00000007638[RRM1][KOG0125]Bilateria@ENSORLP00000014121[125][RRM1:100%****][FOX:75%****][KOG0125:100%****]Gammaproteobacteria@YP_113294[2][RRM1:100%][PROK:100%]

Aureococcus anophagefferens@jgi_Auran1_9354[RRM1]Dictyostelium discoideum_AX4@XP_629578[RRM1][KOG0122]

Cryptosporidium parvum_Iowa_II@XP_626081[RRM1][KOG0122]Coelomata@ENSTBEP00000011040[87][RRM1:98%****][put-sr:16%**][KOG4661:100%****]

Tribolium castaneum@XP_969134[RRM1]Tribolium castaneum@XP_971197[RRM1][KOG4661]

Embryophyta@jgi_Phypa1_1_28366[17][RRM1:100%**][put-sr:76%**][KOG0127:29%*][.KOG0125:12%][.KOG4661:6%][.KOG0147:6%]Phytophthora@jgi_Physo1_1_137237[2][RRM1:100%][put-sr:100%][KOG0125:50%][.KOG0148:50%]

Plasmodium falciparum_3D7@XP_001347313[RRM1][KOG0127]Cryptococcus neoformans_var._neoformans_JEC21@XP_570425[RRM1][put-sr][KOG0145]

Yarrowia lipolytica@XP_499712[RRM1][KOG0145]Pezizomycotina@XP_960722[3][RRM1:100%*][put-sr:33%][KOG0113:33%]Schizosaccharomyces pombe_972h-@NP_001018280[RRM1][KOG0145]

Chlamydomonas reinhardtii@jgi_Chlre3_152139[RRM1][KOG0117]Phaeodactylum tricornutum@jgi_Phatr2_16633[RRM1][KOG0125]


Oryza sativa_japonica_cultivar-group@NP_001053710[RRM1][KOG0127]rosids@30054_m000821[3][RRM1:100%*][cpRNP:33%][KOG0127:100%*]

Magnoliophyta@NP_001062760[4][RRM1:100%*][KOG0124:50%][.KOG0131:50%]Ustilago maydis_521@XP_756401[RRM1]

Magnoliophyta@NP_001058927[3][RRM1:100%*][cpRNP:33%][KOG0131:67%]Embryophyta@jgi_Phypa1_1_134646[11][RRM1:100%**][cpRNP:9%][KOG0123:45%*][.KOG0127:36%*][.KOG2029:9%]

Magnoliophyta@10511_m000028_AZM5_5258[15][RRM1:100%**][cpRNP:33%*][KOG0127:53%**][.KOG0131:27%*][.KOG0145:13%][.KOG0108:7%]Magnoliophyta@NP_001060859[5][RRM1:100%*][cpRNP:40%][KOG0110:40%][.KOG0148:40%]

Magnoliophyta@NP_001062073[4][RRM1:100%*][KOG0110:75%*][.KOG0127:25%]Trypanosoma brucei_TREU927@XP_829716[RRM1]

Clupeocephala@ENSORLP00000002364[10][RRM2:100%**][KOG0109:100%**]Endopterygota@CG7903-PA[5][RRM1:100%*][KOG0109:80%*]

Tribolium castaneum@XP_971700[RRM1]Aedes aegypti@AAEL006876-PA[RRM1][KOG2193]

Euteleostomi@ENSDNOP00000012760[63][RRM2:94%****][.RRM1:6%*][LARK:65%***][.RBM:21%**][KOG0109:97%****]Strongylocentrotus purpuratus@XP_792521[4][RRM1:100%*][put-sr:100%*][KOG0109:100%*]

Coelomata@ENSXETP00000008271[74][RRM1:100%****][LARK:61%***][KOG0109:97%****]Ciona intestinalis@ENSCINP00000017840[RRM1][KOG0109]


Ciona@ENSCSAVP00000017501[2][RRM1:50%][.RRM2:50%][KOG0109:50%]Endopterygota@CG8597-PE[8][RRM2:100%**][LARK:62%*][KOG0109:100%**]

Danio rerio@ENSDARP00000065401[RRM2][KOG0109]Eukaryota@8925_m000027_AZM5_1178[67][RRM1:100%****][put-sr:84%****][SR:61%***][KOG4207:61%***][.KOG4368:24%**]Thalassiosira pseudonana@jgi_Thaps3_20266[RRM1][KOG4207]

Bacillariophyta@jgi_Thaps3_20223[2][RRM1:100%][KOG0108:100%]Chlamydomonadales@jgi_Chlre3_184151[2][RRM1:100%][KOG0921:50%][.KOG0116:50%]

Phaeodactylum tricornutum@jgi_Phatr2_8270[RRM1][KOG4207]Phaeodactylum tricornutum@jgi_Phatr2_49481[RRM1][KOG1337]



Euteleostomi@ENSORLP00000016244[7][RRM1:100%*][KOG1080:57%*]Pezizomycotina@XP_961985[2][RRM1:100%][KOG0116:50%]

Aureococcus anophagefferens@jgi_Auran1_69134[RRM1][put-sr]Pichia stipitis_CBS_6054@XP_001387063[RRM1]

Ashbya gossypii_ATCC_10895@NP_983970[RRM1]Candida glabrata_CBS138@XP_445637[RRM1]

Ciona intestinalis@ENSCINP00000008726[RRM1][put-sr][KOG2193]Apis mellifera@XP_393878[RRM1][put-sr][KOG2193]

Encephalitozoon cuniculi_GB-M1@NP_586226[RRM3][put-sr][KOG0123]Synechococcus@YP_473618[2][RRM1:100%][PROK:100%][KOG0108:100%]Ostreococcus@jgi_Ostta4_7793[2][RRM1:100%][KOG0108:100%]

Ciona savignyi@ENSCSAVP00000008315[4][RRM1:100%*][KOG0108:100%*]Aureococcus anophagefferens@jgi_Auran1_9018[RRM1]

Aureococcus anophagefferens@jgi_Auran1_9375[2][RRM1:100%][KOG0122:100%]Aureococcus anophagefferens@jgi_Auran1_17018[RRM1][KOG0111]Thalassiosira pseudonana@jgi_Thaps3_33709[RRM1][KOG0111]

Schizosaccharomyces pombe_972h-@NP_595090[RRM1]Saccharomycetales@YHL034C[2][RRM1:100%]

Kluyveromyces lactis@XP_453971[RRM1]Chlamydomonadales@jgi_Volca1_107658[2][RRM1:100%][KOG4205:50%][.KOG0474:50%]

Murinae@ENSMUSP00000078984[3][RRM1:100%*][KOG4207:100%*]Ostreococcus lucimarinus@jgi_Ost9901_3_8174[RRM1][KOG4207]

Tribolium castaneum@XP_970765[RRM2][KOG0127]Bacillariophyta@jgi_Thaps3_19374[2][RRM1:100%][KOG0121:100%]

Cryptosporidium parvum_Iowa_II@XP_627536[RRM1][KOG0121]Encephalitozoon cuniculi_GB-M1@NP_597585[RRM1][KOG0121]



Aureococcus anophagefferens@jgi_Auran1_17068[RRM1][KOG4207]Cryptosporidium parvum_Iowa_II@XP_628282[2][RRM1:100%][put-sr:100%][KOG0111:50%][.KOG4207:50%]


Chordata@ENSETEP00000001114[45][RRM1:100%***][put-sr:96%***][SRrp:82%***][KOG0111:29%**][.KOG0415:13%*]Phytophthora@jgi_Physo1_1_136528[2][RRM1:100%][put-sr:50%][KOG3208:50%]

Chlamydomonadales@jgi_Volca1_121229[2][RRM1:100%][put-sr:100%][KOG0415:50%]Viridiplantae@NP_001046448[23][RRM1:100%***][put-sr:91%***][SR:35%**][KOG4207:13%*][.KOG0127:13%*][.KOG0110:9%]

Bacillariophyta@jgi_Thaps3_23196[2][RRM1:100%][KOG4207:50%]Phytophthora sojae@jgi_Physo1_1_138511[RRM1][put sr]

23 - SRrp

24

22 - single RRM

SR proteins

25

51 - LARK

68 - FOX

29 - dual-RRM

SR proteins

Part of 30

- hnRNP

Fig. S8

111

62

93

73

63

52

85

76

89

74

81 61

60

73

64

54

Magnoliophyta@NP 001042672[10][RRM1:100%**][oligoU:50%*][KOG4205:80%**][.KOG0149:20%]Arabidopsis thaliana@NP_850021[4][RRM1:100%*][oligoU:100%*][KOG0149:75%*][.KOG2186:25%]




Bilateria@ENSRNOP00000022054[326][RRM1:100%*****][hnRNP:54%*****][KOG4205:100%*****]Eukaryota@ENSMODP00000031317[289][RRM1:100%*****][hnRNP:28%****][.Musashi:13%***][.Dazap:9%***][KOG4205:99%*****]

Endopterygota@CG16901-PC[19][RRM1:100%**][KOG4205:100%**]Myotis lucifugus@ENSMLUP00000003070[RRM1][hnRNP][KOG4205]

Oryctolagus cuniculus@ENSOCUP00000001170[RRM1][hnRNP][KOG4205]Bacillariophyta@jgi_Phatr2_21039[2][RRM1:100%][KOG4205:100%]

Dictyostelium discoideum_AX4@XP_643377[RRM1][KOG3598]Plasmodium falciparum_3D7@XP_001351452[RRM2][KOG4205]

Theileria parva_strain_Muguga@XP_766400[RRM1][put-sr][KOG4205]Cryptosporidium parvum_Iowa_II@XP_626025[RRM1][KOG4205]

Strongylocentrotus purpuratus@NP_999784[3][RRM1:100%*][KOG4205:100%*]Chlamydomonadales@jgi_Chlre3_181880[2][RRM2:100%][KOG4205:100%]

Drosophila melanogaster@CG9654-PA[RRM1][KOG4205]Cryptosporidium parvum_Iowa_II@XP_001388284[RRM1][KOG4205]

Phytophthora ramorum@jgi_Phyra1_1_73884[RRM2][KOG4205]Ascomycota@XP_961230[5][RRM2:100%*][put-sr:20%][KOG4205:100%*]

Saccharomycetales@XP_449511[7][RRM2:100%*][KOG4205:100%*]Ricinus communis@28976_m000161[RRM2][KOG4205]

Thalassiosira pseudonana@jgi_Thaps3_25203[2][RRM1:100%][KOG4205:100%]Phaeodactylum tricornutum@jgi_Phatr2_41450[RRM1][KOG4205]

Dictyostelium discoideum_AX4@XP_629598[RRM2][KOG4205]Ostreococcus lucimarinus@jgi_Ost9901_3_24530[RRM1][KOG4205]

Ustilago maydis_521@XP_758567[RRM2][KOG4205]Chlamydomonadales@jgi_Volca1_107445[2][RRM2:100%][KOG4205:100%]

Physcomitrella patens@jgi_Phypa1_1_19696[RRM1][KOG4205]Caenorhabditis elegans@Y73B6BL_6b_3[10][RRM1:100%**][KOG4205:100%**]

Phaeodactylum tricornutum@jgi_Phatr2_21039[RRM2][KOG4205]Oryza sativa_japonica_cultivar-group@NP_001067093[RRM1][KOG4177]

Cryptococcus neoformans_var._neoformans_JEC21@XP_568675[RRM2][KOG4205]Endopterygota@AAEL008257-PA[8][RRM2:100%**][KOG4205:100%**]

Viridiplantae@NP_851001[17][RRM2:100%**][put-sr:12%][KOG4205:94%**][.KOG1833:6%]Strongylocentrotus purpuratus@XP_001176409[2][RRM2:100%][KOG4205:100%]

Strongylocentrotus purpuratus@XP_001183095[2][RRM2:100%][KOG4205:100%]Caenorhabditis elegans@F42A6_7a_1[8][RRM2:100%**][KOG4205:100%**]

Coelomata@CG6354-PB[373][RRM2:95%*****][hnRNP:53%*****][KOG4205:100%*****]Drosophila melanogaster@CG9654-PA[RRM2][KOG4205]

Sorex araneus@ENSSARP00000008097[RRM2][hnRNP][KOG4205]Ciona@ENSCINP00000008394[8][RRM2:100%**][KOG4205:100%**]Ciona intestinalis@ENSCINP00000012771[RRM2][put-sr][KOG4205]

Strongylocentrotus purpuratus@NP_999784[3][RRM2:100%*][KOG4205:100%*]Plasmodium falciparum_3D7@XP_001351452[RRM1][KOG4205]

Eukaryota@AGAP006656-PA[121][RRM2:88%****][.RRM1:12%**][Musashi:36%***][.Dazap:21%***][.hnRNP:10%**][KOG4205:100%****]Cryptosporidium parvum_Iowa_II@XP_626025[RRM2][KOG4205]


Ciona@ENSCSAVP00000001921[3][RRM2:100%*][Musashi:67%][KOG4205:100%*]Ciona@ENSCINP00000028810[2][RRM2:100%][KOG4205:100%]

Ciona@ENSCSAVP00000016637[3][RRM2:100%*][KOG4205:100%*]Euteleostomi@ENSDARP00000005968[129][RRM2:95%****][.RRM1:5%*][hnRNP:57%****][KOG4205:100%****]

Endopterygota@XP_001121454[19][RRM2:100%**][KOG4205:100%**]Caenorhabditis elegans@Y73B6BL_6a_3[10][RRM2:100%**][KOG4205:100%**]

Physcomitrella patens@jgi_Phypa1_1_120016[RRM2][KOG4205]Plasmodium falciparum_3D7@XP_001347758[RRM2][KOG0149]

Plasmodium falciparum_3D7@XP_001347758[RRM1][KOG0149]Encephalitozoon cuniculi_GB-M1@NP_597583[RRM2][KOG4205]


Chlamydomonadales@jgi_Volca1_43575[2][RRM3:100%][KOG4205:100%]Encephalitozoon cuniculi_GB-M1@NP_597487[RRM1][KOG4205]

Embryophyta@IMGA_AC144431_42_2[6][RRM3:100%*][put-sr:17%][KOG4205:100%*]Strongylocentrotus purpuratus@XP_789716[2][RRM2:100%][KOG4205:100%]

Strongylocentrotus purpuratus@XP_780859[2][RRM2:100%][KOG4205:100%]Volvox carteri@jgi_Volca1_36996[RRM1][KOG0116]

Tribolium castaneum@XP_970765[RRM1][KOG0127]Ciona intestinalis@ENSCINP00000023563[RRM1][KOG0108]Ostreococcus lucimarinus@jgi_Ost9901_3_27365[RRM3][KOG0123]


Magnoliophyta@29333_m001057[3][RRM2:67%][.RRM1:33%][cpRNP:33%][KOG0131:67%][.KOG0148:33%]Magnoliophyta@IMGA_AC119413_25_2[4][RRM2:100%*][cpRNP:25%][KOG0127:100%*]

Poaceae@19213_m000022_AZM5_85721[2][RRM1:50%][.RRM2:50%][KOG0127:50%]Arabidopsis thaliana@NP_192643[2][RRM2:100%][KOG0110:100%]

Ricinus communis@29908_m006094[RRM2][KOG0110]Magnoliophyta@NP_001048500[5][RRM2:100%*][cpRNP:20%][KOG0123:100%*]

rosids@NP_171616[3][RRM2:100%*][cpRNP:67%][KOG0148:67%][.KOG0110:33%]Oryza sativa_japonica_cultivar-group@NP_001060859[RRM2][KOG0110]

Diptera@AAEL006645-PA[2][RRM1:100%][KOG0149:100%]Diptera@AAEL008317-PA[3][RRM1:100%*][KOG0149:100%*]

Dictyostelium discoideum_AX4@XP_643856[3][RRM1:100%*][KOG0149:100%*]Strongylocentrotus purpuratus@XP_001188704[2][RRM1:100%][KOG0149:100%]

Euteleostomi@ENSSTOP00000002923[18][RRM1:100%**][KOG4205:11%]Caenorhabditis elegans@C50B8_1[RRM1]

Ustilago maydis_521@XP_761797[RRM1][put-sr][KOG3257]Yarrowia lipolytica@XP_505184[RRM1]

Ostreococcus@jgi_Ost9901_3_27365[2][RRM1:100%][KOG0123:50%]Ostreococcus lucimarinus@jgi_Ost9901_3_34965[RRM2][KOG4212]

Cryptosporidium parvum_Iowa_II@XP_628165[RRM2][KOG4212]Eukaryota@jgi_Volca1_109965[18][RRM1:78%**][.RRM2:22%*][put-sr:22%*][KOG4212:61%**][.KOG0123:39%*]


Ostreococcus lucimarinus@jgi_Ost9901_3_34965[RRM1][KOG4212]Volvox carteri@jgi_Volca1_103054[RRM2][KOG0055]Chlamydomonadales@jgi_Chlre3_184854[2][RRM1:100%][KOG0055:50%]

Bacillariophyta@jgi_Phatr2_7426[2][RRM1:100%]Strongylocentrotus purpuratus@XP_786244[2][RRM3:100%][put-sr:100%][KOG4212:100%]

Chordata@ENSOGAP00000002890[91][RRM3:80%****][.RRM2:13%**][.RRM1:7%*][hnRNP:37%***][KOG4212:100%****]Endopterygota@CG9373-PA[4][RRM3:100%*][KOG4212:100%*]

Strongylocentrotus purpuratus@XP_001187716[4][RRM1:100%*][put-sr:100%*][KOG4212:50%][.KOG4661:50%]Coelomata@ENSOGAP00000009767[86][RRM1:100%****][hnRNP:34%***][KOG4212:100%****]

Trypanosoma brucei_TREU927@XP_823301[RRM1][KOG0921]Theileria parva_strain_Muguga@XP_766728[RRM2][KOG0124]

Plasmodium falciparum_3D7@XP_001347332[RRM2][put-sr][KOG0105]Phytophthora ramorum@jgi_Phyra1_1_84100[RRM2][KOG0105]

Phytophthora@jgi_Physo1_1_136493[2][RRM2:100%][put-sr:100%][KOG0105:100%]Fungi/Metazoa_group@AGAP004592-PA[123][RRM2:81%****][.RRM1:18%***][put-sr:100%****][SR:60%****][KOG0105:50%****][.KOG0106:46%****]

Theileria parva_strain_Muguga@XP_766386[RRM2][put-sr][KOG0105]Bilateria@XP_967263[73][RRM2:78%****][.RRM1:22%**][put-sr:79%****][SR:75%****][KOG0105:100%****]Plasmodium falciparum_3D7@XP_001347501[RRM2][put-sr][KOG0105]

Volvox carteri@jgi_Volca1_109965[RRM2][KOG4212]Chlamydomonadales@jgi_Volca1_78979[2][RRM1:100%][KOG3070:100%]

Phaeodactylum tricornutum@jgi_Phatr2_51303[RRM2][KOG4212]Thalassiosira pseudonana@jgi_Thaps3_37126[RRM2][KOG0123] SR proteins

35 - G3BP

RBM

30K-RRM

hnRNP

Musashi

Dazap

TARDBP

OligoU

Fig. S8

112

0.20

69

57

65

76

76

91

62 66

Campylobacter@YP_001467322[2][RRM1:100%][PROK:100%][KOG0148:100%]Dictyostelium discoideum_AX4@XP_638767[RRM1][KOG0123]

cellular_organisms@YP_001113853[137][RRM1:100%****][PROK:99%****][KOG0108:58%****][.KOG0116:14%**][.KOG0921:7%**][.KOG0149:7%**][.KOG0111:6%**]Carboxydothermus hydrogenoformans_Z-2901@YP_359251[RRM1][PROK][KOG0108]

Methanomicrobiales@YP_503016[5][RRM1:100%*][PROK:100%*][KOG0108:40%][.KOG0125:20%][.KOG0116:20%]Treponema pallidum_subsp._pallidum_str._Nichols@NP_218796[RRM1][PROK][KOG0149]

Chlamydomonas reinhardtii@jgi_Chlre3_174860[RRM2][KOG1240]Gammaproteobacteria@YP_561253[27][RRM1:100%***][PROK:100%***][KOG0108:96%***]

Geobacter uraniumreducens_Rf4@YP_001230384[RRM1][PROK][KOG0108]Alkalilimnicola ehrlichei_MLHE-1@YP_741458[RRM1][PROK]

Schizosaccharomyces pombe_972h-@NP_593427[RRM1][KOG0123]Chlamydomonas reinhardtii@jgi_Chlre3_181993[RRM1]

Clupeocephala@ENSGACP00000025151[11][RRM1:100%**][KOG0109:100%**]Xenopus tropicalis@ENSXETP00000056096[RRM1][KOG0109]Mammalia@ENSTBEP00000003150[16][RRM1:100%**][RBM:94%**][KOG0109:100%**]

Syntrophobacter fumaroxidans_MPOB@YP_844222[RRM1][PROK][KOG0108]Ostreococcus@jgi_Ost9901_3_12693[2][RRM2:100%][KOG0127:100%]

Ostreococcus tauri@jgi_Ostta4_19468[RRM1][KOG0127]Bacteroidales@YP_001302325[2][RRM1:100%][PROK:100%][KOG0123:50%][.KOG0122:50%]Bacteroidales@YP_213478[13][RRM1:100%**][PROK:100%**][KOG0108:69%**][.KOG0125:31%*]Bacteroides@YP_001298723[3][RRM1:100%*][PROK:100%*][KOG0108:100%*]

Nitrosococcus oceani_ATCC_19707@YP_344746[RRM1][PROK][KOG0148]Syntrophobacter fumaroxidans_MPOB@YP_845575[RRM1][PROK]

Candidatus Protochlamydia_amoebophila_UWE25@YP_007892[RRM1][PROK][KOG0149]Leptospira@YP_000459[4][RRM1:100%*][PROK:100%*][KOG0108:100%*]


Ustilago maydis_521@XP_761797[RRM2][put-sr][KOG3257]Schizosaccharomyces pombe_972h-@NP_593531[RRM1][nucleolin][KOG0147]Yarrowia lipolytica@XP_505375[RRM1][KOG0148]

Saccharomycetales@XP_456900[6][RRM1:100%*][nucleolin:17%][KOG0148:50%*][.KOG0131:33%][.KOG4210:17%]Basidiomycota@XP_566835[2][RRM1:100%][KOG0148:100%]

Neurospora crassa_OR74A@XP_963862[RRM1][KOG0127]Aspergillus fumigatus_Af293@XP_754840[RRM1][KOG0148]

Phytophthora@jgi_Phyra1_1_75647[2][RRM1:100%]Magnoliophyta@NP_566958[6][RRM2:67%*][.RRM1:33%][KOG0123:33%][.KOG0124:33%][.KOG0131:33%]

Ostreococcus@jgi_Ost9901_3_34381[2][RRM1:100%][KOG0145:100%]Cyanobacteria@YP_476186[8][RRM1:100%**][PROK:100%**][KOG0108:38%*][.KOG0122:12%]

Cyanobacteria@NP_898344[17][RRM1:100%**][PROK:100%**][KOG0108:65%**]Synechococcus_elongatus@YP_399809[2][RRM1:100%][PROK:100%][KOG0108:100%]

Leishmania infantum_JPCM5@XP_001467067[2][RRM1:100%][KOG0144:100%]Dictyostelium discoideum_AX4@XP_638767[RRM2][KOG0123]

Pezizomycotina@XP_961985[2][RRM2:100%][KOG0116:50%]Schizosaccharomyces pombe_972h-@NP_595090[RRM2]

Eukaryota@XP_391240[27][RRM2:67%**][.RRM1:33%**][cpRNP:19%*][KOG0127:48%**][.KOG0108:22%*][.KOG0131:15%*][.KOG0149:7%][.KOG0145:7%]Oryza sativa_japonica_cultivar-group@NP_001045556[RRM1][KOG0108]

Magnoliophyta@NP_181287[9][RRM1:100%**][oligoU:22%][KOG0148:56%*][.KOG0127:22%][.KOG0145:11%][.KOG0113:11%]Magnoliophyta@29930_m000611[5][RRM1:100%*][KOG0113:100%*]

Magnoliophyta@9946_m000021_AZM5_3995[2][RRM1:100%][KOG0111:50%][.KOG0113:50%]rosids@29154_m000213[5][RRM1:100%*][oligoU:40%][KOG0122:40%][.KOG0113:20%][.KOG0148:20%]

Magnoliophyta@NP_001052753[3][RRM1:100%*][oligoU:33%][KOG0108:33%][.KOG0149:33%][.KOG0127:33%]Medicago truncatula@IMGA_AC122162_7_2[RRM1][KOG0149]Ricinus communis@30055_m001598[RRM1][KOG0149]

Arabidopsis thaliana@NP_565646[RRM1][KOG0149]Eukaryota@jgi_Phypa1_1_37849[169][RRM1:100%*****][put-sr:5%**][GRSRBP:33%****][.hnRNP:18%***][.RBMY:15%***][KOG0108:23%***][.KOG0111:23%***][.KOG0149:18%***][.KOG0117:11%**][.KOG0116:9%**]

Euteleostomi@ENSGALP00000012472[36][RRM4:89%***][.RRM2:8%*][nucleolin:56%**][KOG0123:100%***]Yarrowia lipolytica@XP_500351[RRM2][KOG0123]

Arabidopsis thaliana@NP_173298[RRM1][GRSRBP][KOG0149]Magnoliophyta@NP_001059075[6][RRM1:100%*][put-sr:17%][GRSRBP:50%*][KOG0108:50%*][.KOG0148:33%][.KOG0111:17%]

Physcomitrella patens@jgi_Phypa1_1_151460[4][RRM1:100%*][KOG0108:75%*][.KOG0149:25%]rosids@NP_568388[3][RRM1:100%*][KOG0125:33%][.KOG0148:33%]

Oryza sativa_japonica_cultivar-group@NP_001054954[2][RRM1:100%][KOG0108:100%]Phytophthora@jgi_Phyra1_1_84416[2][RRM1:100%][KOG0148:100%]

Arabidopsis thaliana@NP_179762[RRM1][oligoU]Phytophthora@jgi_Physo1_1_134615[2][RRM1:100%]

Aureococcus anophagefferens@jgi_Auran1_66158[RRM2][put-sr][KOG0149]Ciona@ENSCINP00000012771[9][RRM1:100%**][put-sr:11%][KOG4205:100%**]

Ricinus communis@28976_m000161[RRM1][KOG4205]Ricinus communis@30170_m013671[RRM1][KOG4205]

Arabidopsis thaliana@NP_176143[RRM1][KOG4205]Zea mays@14684_m000016_AZM5_14964[RRM1][KOG4205]


Aureococcus anophagefferens@jgi_Auran1_9576[RRM1][KOG0149]Cyanidioschyzon merolae@gnl_CMER_CMR392C[RRM1][KOG4205]

Chlamydomonadales@jgi_Volca1_107445[2][RRM1:100%][KOG4205:100%]Embryophyta@jgi_Phypa1_1_156290[6][RRM1:100%*][put-sr:17%][KOG4205:100%*]

Chlamydomonadales@jgi_Chlre3_105806[2][RRM1:100%][KOG4205:100%]Strongylocentrotus purpuratus@XP_789716[2][RRM1:100%][KOG4205:100%]

Coelomata@SINFRUP00000146060[58][RRM1:100%****][TARDBP:72%***][KOG4205:98%****]Ostreococcus tauri@jgi_Ostta4_33731[RRM1]

Ostreococcus tauri@jgi_Ostta4_33731[RRM2]Cyanidioschyzon merolae@gnl_CMER_CMR392C[RRM2][KOG4205]



Cryptosporidium parvum_Iowa_II@XP_628599[RRM2][KOG4205]Takifugu rubripes@SINFRUP00000163373[RRM1][KOG0149]

Takifugu rubripes@SINFRUP00000145256[RRM1][KOG0149]Arabidopsis thaliana@NP_187353[RRM1][30kRRM][KOG0149]

Arabidopsis thaliana@NP_200183[2][RRM1:100%][oligoU:100%][KOG0149:100%]Eukaryota@NP_001058102[93][RRM1:100%****][RBM:52%***][.30kRRM:13%**][KOG0149:96%****]

Phytophthora sojae@jgi_Physo1_1_139371[RRM2][KOG4205]Phytophthora sojae@jgi_Physo1_1_139371[RRM1][KOG4205]

Oryza sativa_japonica_cultivar-group@NP_001054022[RRM1][KOG4205]Magnoliophyta@NP_001042672[10][RRM1:100% ][oligoU:50% ][KOG4205:80% ][.KOG0149:20%]

58 - GSRBP

hnRNP

RBMY

50 - LARK


Fig. S8

113

56

80

60

83

74

72

73

55

Diptera@PRO AAEL008317 PA[8][RRM1:100%**][KOG0149:100%**]Basidiomycota@PRO_XP_568669[11][RRM1:100%**][KOG0127:100%**]

Euteleostomi@PRO_ENSOANP00000001262[52][RRM1:100%***][RBM:54%***][KOG0127:100%***]Pezizomycotina@REF_XP_661934[24][RRM1:100%***][put-sr:12%*][KOG0127:100%***]

Saccharomycetales@REF_XP_710417[26][RRM1:100%***][KOG0127:100%***]Schizosaccharomyces_pombe@PRO_NP_596114[3][RRM1:100%*][KOG0127:100%*]

Phytophthora@PRO_jgi_Physo1_1_132702[3][RRM1:100%*][KOG0127:100%*]Chlamydomonadales@PRO_jgi_Chlre3_186870[2][RRM1:100%][KOG0127:100%]

Nematostella vectensis@REF_XP_001631286[RRM1][KOG0127]Dictyostelium discoideum_AX4@PRO_XP_646584[3][RRM1:100%*][KOG0127:100%*]

Physcomitrella patens@PRO_jgi_Phypa1_1_201182[RRM1][KOG0127]Magnoliophyta@PRO_NP_565513[12][RRM1:100%**][KOG0127:100%**]

Ciona@PRO_ENSCINP00000018772[3][RRM1:100%*][KOG0127:100%*]Ostreococcus_lucimarinus@PRO_jgi_Ost9901_3_26255[2][RRM1:100%][KOG0127:100%]

Ostreococcus tauri@PRO_jgi_Ostta4_19569[RRM1][KOG0127]Trichomonas vaginalis_G3@REF_XP_001319505[RRM2]

Strongylocentrotus purpuratus@PRO_XP_001198098[4][RRM1:100%*][put-sr:100%*][KOG0147:100%*]Dictyostelium discoideum_AX4@SMA_Q54QQ7_DICDI[3][RRM1:100%*][KOG0147:100%*]Phytophthora@PRO_jgi_Physo1_1_157186[2][RRM1:100%][KOG0147:100%]Eukaryota@REF_NP_060577[180][RRM1:100%*****][put-sr:93%*****][UMH:38%****][.CAPER:22%***][KOG0147:100%*****]

Yarrowia lipolytica@PRO_XP_504318[3][RRM1:100%*][KOG0147:100%*]Ostreococcus@PRO_jgi_Ost9901_3_42846[3][RRM1:100%*][put-sr:67%][KOG0147:100%*]

Volvox carteri@PRO_jgi_Volca1_84128[2][RRM1:100%][put-sr:50%][KOG0147:100%]Apicomplexa@REF_XP_666635[20][RRM1:100%**][put-sr:25%*][KOG0147:100%**]

Cyanidioschyzon merolae@PRO_gnl_CMER_CMT598C[RRM1][KOG0148]Saccharomycetales@REF_XP_001524014[3][RRM1:100%*]

Yarrowia lipolytica@SMA_Q6C0L4_YARLI[RRM1][put-sr]Saccharomycetales@PRO_XP_454821[11][RRM1:100%**][KOG3598:45%*][.KOG1984:27%*]

Trichocomaceae@REF_XP_001270976[2][RRM1:100%][put-sr:100%][KOG0107:50%]Giardia lamblia_ATCC_50803@REF_XP_001708899[2][RRM1:100%][KOG0131:100%]Saccharomycetales@REF_XP_001525882[11][RRM1:100%**][KOG0131:100%**]

Trypanosoma@SMA_Q4DAT0_TRYCR[2][RRM1:100%][KOG0131:100%]Cryptosporidium@PRO_XP_627780[4][RRM1:100%*][KOG0131:100%*]

Danio rerio@REF_XP_694258[RRM1][KOG4454]Eumetazoa@REF_NP_001084686[104][RRM1:100%****][KOG4454:62%****][.KOG0131:38%***]

Sophophora@PRO_CG11454-PA[5][RRM1:100%*][KOG4454:100%*]Endopterygota@SMA_ENSANGP00000021860[12][RRM1:100%**][KOG4454:58%*][.KOG0131:42%*]

Dictyostelium discoideum_AX4@PRO_XP_647248[3][RRM1:100%*][KOG0131:100%*]Bigelowiella natans@SMA_Q3LWM7_CHLS6[RRM1][KOG0131]

Caenorhabditis@REF_XP_001664456[6][RRM1:100%*][KOG4454:100%*]Entamoeba histolytica_HM-1_IMSS@REF_XP_655332[2][RRM1:100%][KOG0131:100%]

Magnoliophyta@SMA_Q75HQ8_ORYSA[12][RRM1:100%**][put-sr:8%][KOG0131:92%**][.KOG2288:8%]Tetraodon nigroviridis@SMA_Q4SJ30_TETNG[RRM1][KOG0131]

Eukaryota@PRO_NP_001064759[182][RRM1:100%*****][snRNP:5%**][KOG0131:100%*****]Kluyveromyces lactis@SMA_Q6CT95_KLULA[RRM1][KOG0131]

Saccharomycetales@SMA_Q75E82_ASHGO[6][RRM1:100%*][KOG0131:100%*]Saccharomycetaceae@SMA_HSH49_YEAST[4][RRM1:100%*][KOG0131:100%*]

Phytophthora@PRO_jgi_Physo1_1_132702[3][RRM3:100%*][KOG0127:100%*]Schizosaccharomyces_pombe@PRO_NP_001018280[3][RRM1:100%*][KOG0145:100%*]

Arabidopsis thaliana@PRO_NP_974808[5][RRM1:100%*][KOG0123:60%*][.KOG0148:40%]Ustilago maydis_521@PRO_XP_758439[3][RRM3:67%][.RRM2:33%][KOG0123:100%*]

Oryza sativa_japonica_cultivar-group@SMA_Q5F1W8_ORYSA[2][RRM1:100%][put-sr:100%][KOG0147:100%]Chlamydomonas reinhardtii@PRO_jgi_Chlre3_152139[RRM1][KOG0117]

Basidiomycota@PRO_XP_757472[13][RRM1:100%**][put-sr:23%*][KOG0122:38%*]Anopheles gambiae_str._PEST@SMA_Q7QFZ7_ANOGA[RRM2][KOG0145]

Caenorhabditis@PRO_C18D11_4_1[6][RRM1:100%*][put-sr:100%*][KOG0921:67%*][.KOG0122:33%]Encephalitozoon_cuniculi@PRO_NP_585779[3][RRM1:100%*]

Dictyostelium discoideum_AX4@PRO_XP_642304[3][RRM1:100%*][KOG0415:100%*]Anopheles_gambiae@SMA_ENSANGP00000010299[2][RRM1:100%][put-sr:100%]

Aedes aegypti@PRO_AAEL004293-PA[2][RRM1:100%][put-sr:100%]Schistosoma japonicum@SMA_Q5D9L3_SCHJA[RRM1][put-sr]

Pan troglodytes@REF_XP_001157764[RRM1][put-sr]Eutheria@PRO_ENSMLUP00000005283[2][RRM1:100%][put-sr:100%]Spermophilus tridecemlineatus@PRO_ENSSTOP00000006011[RRM1][put-sr]

Entamoeba histolytica_HM-1_IMSS@REF_XP_655465[2][RRM1:100%][put-sr:100%][KOG0145:100%]Ustilago maydis_521@SMA_Q4PBP3_USTMA[RRM1][put-sr]Cryptococcus_neoformans_var._neoformans@SMA_Q55TK9_CRYNE

Yarrowia lipolytica@PRO_XP_499712[3][RRM1:100%*][KOG0145:100%*]Pezizomycotina@PRO_XP_960722[24][RRM1:100%***][put-sr:38%**][KOG0116:17%*][.KOG0113:12%*]

Embryophyta@PRO_jgi_Phypa1_1_28366[34][RRM1:100%***][put-sr:82%***][KOG0127:26%**][.KOG4661:6%][.KOG0125:6%]Tribolium castaneum@PRO_XP_969134[3][RRM1:100%*]

Tribolium castaneum@PRO_XP_971197[3][RRM1:100%*][KOG4661:100%*]Eumetazoa@PRO_ENSTBEP00000011040[221][RRM1:98%*****][put-sr:11%***][KOG4661:100%*****]

Caenorhabditis briggsae@SMA_Q61WJ8_CAEBR[RRM1][put-sr]Dictyostelium discoideum_AX4@SMA_Q54CU2_DICDI[3][RRM1:100%*][KOG0122:100%*]

Pan troglodytes@SMA_UPI0000493D8A[RRM1][KOG0125]Caenorhabditis@PRO_ZC404_8_2[6][RRM1:100%*][KOG0125:100%*]

Eumetazoa@SMA_ENSPTRP00000024635[311][RRM1:100%*****][FOX:80%*****][KOG0125:100%*****]Felis catus@PRO_ENSFCAP00000007638[RRM1][KOG0125]

Phytophthora@PRO_jgi_Physo1_1_137237[2][RRM1:100%][put-sr:100%][KOG0125:50%][.KOG0148:50%]Plasmodium@PRO_XP_001347313[6][RRM1:100%*][KOG0127:100%*]

Entamoeba histolytica_HM-1_IMSS@REF_XP_650669[2][RRM2:100%][KOG0145:100%]Paramecium tetraurelia@REF_XP_001457311[RRM1][put-sr][KOG4207]

Tetrahymena thermophila_SB210@REF_XP_001021930[2][RRM1:100%][put-sr:100%]Tetrahymena thermophila_SB210@SMA_Q23YX0_TETTH[2][RRM2:100%][put-sr:100%]

68 - FOX

46

47

46

49

75 - CAPER

UMH

70 - RBM

Fig. S9

114

62

74

94

53

87

68

93

76

55

65

76

78

Arabidopsis thaliana@SMA Q9FFR1 ARATH[29][RRM1:38%**][ RRM2:34%**][ RRM4:14%*][ RRM3:14%*][PABP:28%**][KOG0123:100%***]Arabidopsis thaliana@SMA_Q9M300_ARATH[RRM1][KOG2159]

Sclerotiniaceae@REF_XP_001593549[2][RRM3:50%][.RRM2:50%][KOG0128:100%]Magnaporthe grisea_70-15@REF_XP_362282[2][RRM3:50%][.RRM2:50%][KOG0123:100%]

Ophiostoma ulmi@SMA_Q01491_OPHUL[RRM3][KOG0128]Sordariales@PRO_XP_958552[5][RRM3:100%*][KOG0128:60%*][.KOG0117:40%]

Trichomonas vaginalis_G3@REF_XP_001326638[RRM1]Caenorhabditis@REF_XP_001670277[6][RRM2:100%*][KOG0128:100%*]

Physcomitrella patens@PRO_jgi_Phypa1_1_201182[RRM3][KOG0127]Magnoliophyta@PRO_NP_001051595[12][RRM3:92%**][.RRM2:8%][KOG0127:100%**]

Dictyostelium discoideum_AX4@PRO_XP_646584[3][RRM3:100%*][KOG0127:100%*]Chlamydomonadales@PRO_jgi_Volca1_87629[2][RRM3:100%][KOG0127:100%]

Ostreococcus@PRO_jgi_Ostta4_19569[3][RRM3:100%*][KOG0127:100%*]Nematostella vectensis@REF_XP_001631286[RRM3][KOG0127]

Ciona intestinalis@PRO_ENSCINP00000018774[2][RRM3:100%][KOG0127:100%]Caenorhabditis@PRO_R05H10_2[4][RRM2:100%*][KOG0127:100%*]

Euteleostomi@PRO_ENSGACP00000016696[46][RRM3:80%***][.RRM1:11%*][.RRM4:9%*][RBM:65%***][KOG0127:100%***]Saccharomycetales@REF_XP_001642245[26][RRM3:96%***][KOG0127:100%***]Pezizomycotina@SMA_Q2H6T1_CHAGB[23][RRM3:100%***][put-sr:13%*][KOG0127:100%***]

Basidiomycota@SMA_Q4PH97_USTMA[11][RRM4:55%*][.RRM3:45%*][KOG0127:100%**]Schizosaccharomyces_pombe@SMA_O74400_SCHPO[3][RRM3:100%*][KOG0127:100%*]

Strongylocentrotus purpuratus@SMA_UPI0000584CE1[5][RRM2:80%*][.RRM1:20%][KOG0127:100%*]Endopterygota@PRO_XP_001605703[8][RRM2:75%*][.RRM3:25%][KOG0127:100%**]

Sophophora@SMA_Q293A7_DROPS[5][RRM2:100%*][KOG0127:100%*]Culicidae@SMA_ENSANGP00000021189[3][RRM2:67%][.RRM1:33%][KOG0127:100%*]

Schizosaccharomyces_pombe@PRO_NP_596518[3][RRM1:100%*][KOG0116:100%*]Filobasidiella_neoformans@PRO_XP_572946[5][RRM1:100%*][KOG0108:100%*]

Poaceae@PRO_NP_001058465[4][RRM1:100%*][KOG0108:100%*]Aureococcus anophagefferens@PRO_jgi_Auran1_23269[RRM1][KOG0108]

Bacillariophyta@PRO_jgi_Phatr2_8451[2][RRM1:100%][KOG0108:100%]Plasmodium@REF_XP_001608355[10][RRM1:100%**][KOG0108:100%**]Cryptosporidium_parvum@PRO_XP_627975[3][RRM1:100%*][KOG0108:100%*]

Pan troglodytes@SMA_ENSPTRP00000041315[RRM1][KOG0108]Eukaryota@PRO_ENSDARP00000064611[234][RRM1:100%*****][KOG0108:98%*****]

Ostreococcus tauri@PRO_jgi_Ostta4_31925[RRM1][KOG0117]Microsporidia@SMA_Q6E6D6_ANTLO[4][RRM1:100%*][KOG0108:100%*]

Viridiplantae@SMA_O80743_ARATH[5][RRM1:100%*][put-sr:20%][KOG2253:60%*][.KOG0108:40%]Cryptosporidium@SMA_Q5CGW1_CRYHO[2][RRM1:100%]Bilateria@SMA_Q22859_CAEEL[44][RRM1:100%***][put-sr:80%***][RBM:70%***][KOG2253:98%***]

Paramecium tetraurelia@REF_XP_001425767[RRM1][KOG2253]Cryptosporidium@PRO_XP_628165[4][RRM2:100%*][KOG4212:100%*]

Yarrowia lipolytica@SMA_Q6C133_YARLI[RRM1]Trichomonas vaginalis_G3@REF_XP_001315389[RRM1]

Dikarya@PRO_NP_596771[7][RRM1:100%*][KOG0108:57%*]Trichomonas vaginalis_G3@REF_XP_001300735[2][RRM1:100%]

Pezizomycotina@REF_XP_001242919[19][RRM1:100%**][put-sr:26%*][KOG0533:89%**][.KOG0122:5%][.KOG0517:5%]Dictyostelium discoideum_AX4@PRO_XP_638266[3][RRM1:100%*][KOG0533:100%*]

Yarrowia lipolytica@PRO_XP_505140[3][RRM1:100%*][KOG0533:100%*]Ustilago maydis_521@PRO_XP_757147[3][RRM1:100%*][KOG0533:100%*]

Theileria@PRO_XP_764636[5][RRM1:100%*][KOG0533:40%]Plasmodium@PRO_XP_966143[6][RRM1:100%*][KOG0533:50%*]

Chlamydomonadales@PRO_jgi_Volca1_90392[2][RRM1:100%][KOG0533:100%]Schizosaccharomyces pombe@SMA_YBLC_SCHPO[RRM1][KOG0533]

Eukaryota@PRO_GSTENP00007343001[207][RRM1:99%*****][FCAFPA:9%**][KOG0533:99%*****]Ostreococcus tauri@PRO_jgi_Ostta4_36431[RRM1][KOG0533]

Drosophila melanogaster@SMA_Q9VK76_DROME[RRM1][KOG0533]Phytophthora@PRO_jgi_Phyra1_1_97175[2][RRM1:100%][put-sr:50%][KOG0533:100%]

Cyanidioschyzon merolae@PRO_gnl_CMER_CMH135C[RRM1]Euteleostomi@PRO_ENSTBEP00000009485[20][RRM1:100%**][PDIP:75%**][KOG0533:60%**]

Strongylocentrotus purpuratus@SMA_UPI000058710F[RRM1]Endopterygota@PRO_CG6961-PA[19][RRM1:100%**][KOG0533:26%*]

Ustilago maydis_521@SMA_Q4P7M8_USTMA[3][RRM1:100%*][KOG0533:100%*]Filobasidiella_neoformans@PRO_XP_572037[4][RRM1:100%*][KOG0533:100%*]

Schizosaccharomyces_pombe@PRO_NP_595715[3][RRM1:100%*][KOG0533:100%*]Sordariomycetes@REF_XP_370171[11][RRM1:100%**][KOG0533:100%**]

Eurotiomycetidae@REF_XP_001259289[6][RRM1:100%*][KOG0533:100%*]Saccharomycetales@PRO_XP_462132[14][RRM1:100%**][KOG0533:100%**]

Leishmania@REF_XP_001682242[5][RRM1:100%*][KOG0113:100%*]Trypanosoma@SMA_Q4D8I9_TRYCR[2][RRM1:100%][KOG0113:100%]

Trichomonas vaginalis_G3@REF_XP_001319130[RRM1]Trichomonas vaginalis_G3@REF_XP_001330225[RRM1]

Phytophthora ramorum@PRO_jgi_Phyra1_1_94226[RRM1][put-sr][KOG0941]Eukaryota@PRO_NP_001063859[81][RRM1:100%****][ZCRB1:69%****][KOG0108:52%***][.KOG0122:10%**][.KOG0117:9%*]

Culicidae@SMA_ENSANGP00000028861[4][RRM1:100%*][KOG0108:50%][.KOG0117:50%]Chlamydomonas reinhardtii@PRO_jgi_Chlre3_120019[RRM2][KOG0106]

Chlamydomonas reinhardtii@PRO_jgi_Chlre3_80366[RRM2][KOG0106]Embryophyta@PRO_29742_m001371[30][RRM2:87%***][.RRM1:13%*][put-sr:93%***][SR:77%***][KOG0106:100%***]

Bacillariophyta@PRO_jgi_Phatr2_47737[2][RRM1:100%][put-sr:50%]Cyanidioschyzon merolae@PRO_gnl_CMER_CMO009C[RRM2]

Dictyostelium discoideum_AX4@PRO_XP_628876[3][RRM1:100%*]Bacillariophyta@PRO_jgi_Thaps3_19374[2][RRM1:100%][KOG0121:100%]

Entamoeba histolytica_HM-1_IMSS@REF_XP_652915[2][RRM1:100%][KOG0121:100%]Trichomonas vaginalis_G3@REF_XP_001315386[RRM1][KOG0121]

Encephalitozoon_cuniculi@PRO_NP_597585[3][RRM1:100%*][KOG0121:100%*]Cryptosporidium@REF_XP_666381[5][RRM1:100%*][KOG0121:100%*]

Paramecium tetraurelia@REF_XP_001451996[2][RRM1:100%][KOG0121:100%]Eukaryota@SMA_UPI00004950A8[177][RRM1:100%*****][KOG0121:100%*****]

Chaetomium globosum_CBS_148.51@SMA_Q2H8U9_CHAGB[RRM1][KOG0121]Tetrahymena thermophila_SB210@SMA_Q22J29_TETTH[2][RRM1:100%][KOG0121:100%]Plasmodium@REF_XP_001615036[8][RRM1:100%**][KOG0121:100%**]

Piroplasmida@SMA_Q8IS02_BABBO[7][RRM1:100%*][KOG0121:100%*]Piroplasmida@REF_XP_953469[5][RRM1:100%*][KOG0117:40%]

Caenorhabditis@PRO_R09B3_3[15][RRM1:100%**][KOG0108:100%**]Brugia malayi@SMA_P90699_BRUMA[RRM1][KOG0108]

Entamoeba histolytica_HM-1_IMSS@REF_XP_648980[3][RRM1:100%*][KOG0123:100%*]Entamoeba histolytica_HM-1_IMSS@REF_XP_654358[3][RRM2:100%*][KOG0123:100%*]

Trichomonas vaginalis_G3@REF_XP_001297747[RRM2][KOG0123]Trichomonas vaginalis_G3@REF_XP_001294506[RRM2][KOG0123]Dikarya@SMA_Q5KLL0_CRYNE[8][RRM2:100%**][KOG0117:38%*]

Nematostella vectensis@REF_XP_001632599[RRM1][KOG0127]Caenorhabditis@REF_XP_001679781[6][RRM1:100%*]

Nematostella vectensis@REF_XP_001635220[RRM1]Trichomonas vaginalis_G3@REF_XP_001305703[RRM3][KOG0123]

Trichomonas vaginalis_G3@REF_XP_001319505[RRM1]Plasmodium@REF_XP_676651[9][RRM1:100%**][KOG0144:100%**]Cryptosporidium@PRO_XP_628599[5][RRM1:100%*][KOG4205:100%*]

Nematostella vectensis@REF_XP_001637248[RRM1]Coelomata@PRO_AAEL001684-PA[87][RRM1:100%****][KOG0125:26%***]Euteleostomi@PRO_ENSEEUP00000005436[162][RRM1:92%*****][.RRM2:6%**]

Takifugu rubripes@PRO_SINFRUP00000155469[2][RRM1:100%]Spermophilus tridecemlineatus@PRO_ENSSTOP00000003171[RRM1]Tupaia belangeri@PRO_ENSTBEP00000015084[RRM1]

Tetrahymena thermophila_SB210@REF_XP_001026299[2][RRM1:100%]Paramecium tetraurelia@REF_XP_001428916[RRM1]

Dictyostelium_discoideum@SMA_Q86I71_DICDI[9][RRM1:100%**][KOG0149:100%**]Nematostella vectensis@REF_XP_001628811[RRM1][KOG0149]Euteleostomi@PRO_ENSSTOP00000002923[42][RRM1:100%***][KOG4205:14%*]

Strongylocentrotus purpuratus@PRO_XP_001188704[4][RRM1:100%*][KOG0149:100%*]Diptera@SMA_Q7PX54_ANOGA[8][RRM1:100%**][KOG0149:100%**]

Diptera@PRO_AAEL008317-PA[8][RRM1:100%**][KOG0149:100%**]

24



57 - ZCRB1

part of 30 - hnRNP

PDIP

FCA FPA

72 - RBM

Fig. S9

115

80

59

92

50

53

60 71

62

Anopheles gambiae@PRO AGAP000525 PA[4][RRM1:100%*]Drosophila melanogaster@PRO_CG10837-PA[7][RRM1:100%*]

Entamoeba histolytica_HM-1_IMSS@SMA_Q50YJ3_ENTHI[RRM1]Entamoeba histolytica_HM-1_IMSS@REF_XP_657381[2][RRM1:100%]

Paramecium tetraurelia@REF_XP_001435565[2][RRM2:100%][KOG0123:50%][.KOG0147:50%]Chlamydomonadales@PRO_jgi_Volca1_54847[2][RRM1:100%][KOG0108:100%]

Tetrahymena_thermophila@REF_XP_001019282[5][RRM2:60%*][.RRM3:40%][KOG4205:60%*][.KOG0123:40%]Physcomitrella patens@PRO_jgi_Phypa1_1_167900[3][RRM1:100%*][KOG0123:33%][.KOG4210:33%][.KOG1015:33%]

Ostreococcus tauri@PRO_jgi_Ostta4_10328[RRM1][KOG2476]Magnoliophyta@SMA_Q41042_PEA[16][RRM1:100%**][nucleolin:38%*][KOG0123:44%*][.KOG4210:38%*][.KOG1015:12%][.KOG0148:6%]

Entamoeba histolytica_HM-1_IMSS@REF_XP_655048[2][RRM1:100%][put-sr:100%][KOG0123:100%]Phaeodactylum tricornutum@PRO_jgi_Phatr2_49387[RRM1]

Aureococcus anophagefferens@PRO_jgi_Auran1_9434[RRM1]Ostreococcus_lucimarinus@PRO_jgi_Ost9901_3_92667[2][RRM1:100%]

Embryophyta@PRO_28180_m000395[12][RRM2:100%**][KOG4205:50%*][.KOG0124:42%*][.KOG4211:8%]Phytophthora@PRO_jgi_Physo1_1_141766[2][RRM2:100%][KOG0148:100%]

stramenopiles@PRO_jgi_Auran1_17857[4][RRM1:50%][.RRM2:50%][KOG0108:50%][.KOG4205:50%]Aureococcus anophagefferens@PRO_jgi_Auran1_64341[RRM2][KOG0108]

Ostreococcus tauri@PRO_jgi_Ostta4_32569[RRM2]Strongylocentrotus purpuratus@PRO_XP_001180991[8][RRM1:100%**]

Nematostella vectensis@REF_XP_001630508[RRM1][KOG1015]Ostreococcus@PRO_jgi_Ost9901_3_31221[3][RRM1:100%*][KOG0128:100%*]

Magnoliophyta@PRO_29609_m000574[10][RRM1:100%**][KOG0128:100%**]Physcomitrella patens@PRO_jgi_Phypa1_1_135986[RRM1][KOG0128]Ascomycota@PRO_NP_595728[23][RRM1:100%***][put-sr:13%*]

Ustilago maydis_521@PRO_XP_762237[3][RRM1:100%*]Schistosoma japonicum@SMA_Q5D9X4_SCHJA[RRM1]

Ostreococcus@PRO_jgi_Ostta4_33150[3][RRM2:100%*][KOG0108:33%]Trichomonas vaginalis_G3@REF_XP_001317333[RRM2]

Nematostella vectensis@REF_XP_001636038[RRM2][KOG1874]Chordata@PRO_ENSETEP00000010530[72][RRM1:64%***][.RRM2:36%***][put-sr:97%****][SRrp:72%***][KOG4676:100%****]

Caenorhabditis@SMA_RSP7_CAEEL[2][RRM1:100%][put-sr:100%][SR:100%][KOG4676:100%]Culicidae@PRO_AAEL011961-PA[7][RRM1:100%*][KOG0128:100%*]

Tetrahymena thermophila_SB210@REF_XP_001015927[2][RRM2:100%][KOG0128:100%]Apocrita@PRO_XP_001602582[7][RRM1:100%*][KOG0128:100%*]

Caenorhabditis@SMA_Q17430_CAEEL[2][RRM1:100%][KOG0128:100%]Ciona intestinalis@PRO_ENSCINP00000019832[3][RRM1:100%*][KOG0128:100%*]

Nematostella vectensis@REF_XP_001629405[RRM1][KOG0128]Tribolium castaneum@PRO_XP_972538[2][RRM1:100%][KOG0128:100%]

Euteleostomi@PRO_ENSSTOP00000002132[65][RRM1:100%****][SART3:74%***][KOG0128:100%****]Strongylocentrotus purpuratus@PRO_XP_781643[3][RRM1:100%*][KOG0128:100%*]

Strongylocentrotus purpuratus@REF_XP_001198948[RRM1]Cyanidioschyzon merolae@PRO_gnl_CMER_CMO334C[RRM2][KOG0126]

Caenorhabditis@PRO_F11A10_7[5][RRM2:100%*][KOG0131:60%*]Magnoliophyta@PRO_30054_m000807[5][RRM2:100%*][KOG1267:20%]Ostreococcus@PRO_jgi_Ostta4_30189[3][RRM1:67%][.RRM2:33%][put-sr:67%]

Volvox carteri@PRO_jgi_Volca1_118759[RRM2]Filobasidiella neoformans@SMA_Q5KL47_CRYNE[RRM1]

Dictyostelium discoideum_AX4@SMA_Q54GS2_DICDI[3][RRM2:100%*]Trypanosomatidae@PRO_XP_827554[12][RRM2:83%**][.RRM1:17%][put-sr:33%*][KOG0108:33%*]

Apis mellifera@PRO_XP_394565[3][RRM2:100%*][KOG0147:100%*]Eumetazoa@REF_XP_001630180[62][RRM2:87%***][.RRM1:13%**][KOG0108:16%**][.KOG0126:6%*][.KOG3001:5%*][.KOG0123:5%*]

Phaeodactylum tricornutum@PRO_jgi_Phatr2_46145[RRM2]Strongylocentrotus purpuratus@SMA_UPI0000587A00[RRM2][KOG0147]

Tetrahymena thermophila_SB210@REF_XP_001031760[2][RRM2:100%]Paramecium tetraurelia@REF_XP_001427059[RRM2]

Ascomycota@PRO_XP_505055[21][RRM1:86%**][.RRM2:14%*]Drosophila melanogaster@PRO_CG12288-PA[3][RRM2:100%*]

Trypanosomatidae@REF_XP_001566882[11][RRM1:100%**][KOG4209:100%**]Tetrahymena thermophila_SB210@REF_XP_001018896[2][RRM1:100%][KOG4209:100%]

Paramecium tetraurelia@REF_XP_001433584[2][RRM1:100%][KOG4209:100%]Aedes aegypti@PRO_AAEL012119-PA[2][RRM1:100%]

Ciona intestinalis@SMA_ENSCINP00000024280[2][RRM1:100%][KOG0113:100%]Tetrahymena thermophila_SB210@SMA_Q23GR5_TETTH[RRM3][KOG0128]

Saccharomycetaceae@PRO_XP_453677[6][RRM1:100%*][KOG4209:100%*]Saccharomyces cerevisiae@PRO_YIR001C[3][RRM1:100%*][PABP:100%*][KOG4209:100%*]

Candida_glabrata@PRO_XP_447800[3][RRM1:100%*][KOG4209:100%*]Vanderwaltozyma polyspora_DSM_70294@REF_XP_001643854[RRM1][KOG4209]

Trichomonas vaginalis_G3@REF_XP_001305136[RRM1][KOG4209]Eukaryota@PRO_ENSCSAVP00000003369[259][RRM1:100%*****][put-sr:19%***][PABP:27%****][KOG4209:100%*****]

Dictyostelium_discoideum@PRO_XP_642788[4][RRM1:100%*][KOG4209:100%*]Caenorhabditis@REF_XP_001670634[10][RRM1:100%**][KOG4209:100%**]

Caenorhabditis elegans@PRO_T08B6_5[3][RRM1:100%*][KOG4209:100%*]Ciona@PRO_ENSCSAVP00000010162[3][RRM1:100%*][KOG4209:100%*]

Arabidopsis thaliana@PRO_NP_180012[3][RRM1:100%*]Volvox carteri@PRO_jgi_Volca1_103724[RRM1][put-sr][KOG0591]

Physcomitrella patens@PRO_jgi_Phypa1_1_167236[RRM1][KOG4209]Magnoliophyta@PRO_IMGA_AC160842_25_1[14][RRM1:100%**][KOG3702:79%**][.KOG4209:21%*]

Physcomitrella patens@PRO_jgi_Phypa1_1_96043[RRM1]Tetrapoda@PRO_ENSMODP00000004174[30][RRM4:40%**][.RRM3:37%**][.RRM2:23%*][put-sr:97%***][KOG0112:100%***]Leishmania@REF_XP_848168[4][RRM3:100%*][put-sr:100%*][KOG0147:75%*]

Embryophyta@PRO_28611_m000102[9][RRM2:100%**][put-sr:89%**][KOG0154:100%**]Phytophthora ramorum@PRO_jgi_Phyra1_1_77702[RRM1][KOG0154]

Embryophyta@PRO_jgi_Phypa1_1_161416[8][RRM1:100%**][put-sr:88%*][KOG0154:88%*][.KOG0147:12%]Dictyostelium discoideum_AX4@PRO_XP_646990[2][RRM1:100%][put-sr:100%][KOG0147:100%]

Tetrapoda@SMA_ENSPTRP00000025797[17][RRM1:100%**][put-sr:88%**][RBM:82%**][KOG0154:94%**]Amniota@SMA_ENSBTAP00000020421[2][RRM1:50%][.RRM2:50%][KOG0110:100%]

Plasmodium@REF_XP_678221[6][RRM1:100%*][KOG1365:100%*]Trypanosoma@REF_XP_813187[4][RRM2:100%*][KOG4211:100%*]

Caenorhabditis elegans@PRO_Y73B6BL_33[3][RRM1:100%*][KOG4211:100%*]Paramecium tetraurelia@REF_XP_001462005[RRM2][KOG4211]

Strongylocentrotus purpuratus@REF_XP_793087[2][RRM1:100%][KOG4211:100%]Coelomata@SMA_Q5E9J1_BOVIN[34][RRM3:68%***][.RRM2:18%*][.RRM1:15%*][hnRNP:32%**][KOG4211:100%***]

Ciona savignyi@PRO_ENSCSAVP00000001587[RRM5][KOG4307]Physcomitrella patens@PRO_jgi_Phypa1_1_162342[RRM3][KOG1365]

core_eudicotyledons@PRO_NP_188725[3][RRM2:67%][.RRM1:33%][hnRNP:67%][KOG1365:100%*]Thalassiosira pseudonana@PRO_jgi_Thaps3_5686[RRM2][KOG4211]

Caenorhabditis elegans@PRO_W02D3_11b[4][RRM1:100%*][KOG4211:100%*]Oryzias latipes@PRO_ENSORLP00000025180[RRM2][put-sr][KOG4307]

Tetrahymena thermophila_SB210@REF_XP_001023750[RRM2][KOG1365]Danio rerio@PRO_ENSDARP00000069459[2][RRM2:100%][KOG4211:100%]Eumetazoa@PRO_ENSCINP00000003632[278][RRM2:76%*****][.RRM1:24%****][hnRNP:41%****][.GRSRBP:17%***][KOG4211:100%*****]

Volvox carteri@PRO_jgi_Volca1_117772[RRM1][KOG1365]Caenorhabditis briggsae@SMA_Q626N2_CAEBR[RRM1][KOG1365]Xenopus@SMA_Q6GL26_XENTR[3][RRM1:100%*][KOG4211:100%*]Xenopus tropicalis@SMA_UPI000069EA05[RRM1][KOG4211]

Danio rerio@SMA_UPI0000546C4F[RRM1][KOG4211]Theileria_annulata@REF_XP_954308[2][RRM1:100%]

Theileria@SMA_Q4N143_THEPA[2][RRM1:100%][KOG0128:100%]Trypanosomatidae@SMA_Q381I4_9TRYP[2][RRM1:50%][.RRM2:50%][KOG0127:100%]

Entamoeba histolytica_HM-1_IMSS@REF_XP_650506[2][RRM1:100%]Schizosaccharomyces pombe_972h-@PRO_NP_594609[2][RRM1:100%][KOG4660:100%]

Cryptosporidium@PRO_XP_626158[5][RRM1:100%*][KOG0144:100%*]Phaeodactylum tricornutum@PRO_jgi_Phatr2_8457[RRM1][KOG0122]

Trypanosoma brucei@SMA_Q57WD0_9TRYP[RRM2][KOG0110]Ciona@PRO_ENSCSAVP00000005376[7][RRM1:100%*][KOG0116:57%*][.KOG2141:14%]Euteleostomi@PRO_ENSMODP00000021210[88][RRM2:95%****][.RRM1:5%*][nucleolin:67%****][KOG0123:99%****]

Takifugu rubripes@SMA_UPI00003645BC[RRM1]Volvox carteri@PRO_jgi_Volca1_120369[RRM1][put-sr][KOG0147]

Arabidopsis thaliana@SMA_Q9FFR1_ARATH[29][RRM1:38%**][.RRM2:34%**][.RRM4:14%*][.RRM3:14%*][PABP:28%**][KOG0123:100%***]

80 - hnRNP

61

83 - PABP

74

85 - SRrp

73 - SART3

Fig. S9

116

71

71

78

67

61

88

52

57

85

77

65

87

87

72

56

61 53

52

80

Solanum tuberosum@SMA Q2XTB3 SOLTU[2][RRM1:100%][hnRNP:100%][KOG1190:100%]Tetrahymena thermophila_SB210@REF_XP_001013166[3][RRM1:100%*][KOG0123:100%*]

Saccharomyces cerevisiae@PRO_YMR302C[2][RRM1:100%]Tetrahymena thermophila_SB210@REF_XP_001019724[2][RRM1:100%]

Plasmodium@SMA_Q6LFK1_PLAF7[2][RRM1:100%][KOG1190:100%]Trichomonas vaginalis_G3@REF_XP_001324476[RRM3][KOG0110]

Trichocomaceae@REF_XP_658025[3][RRM3:100%*][KOG0110:100%*]Phytophthora@PRO_jgi_Phyra1_1_74707[2][RRM3:100%][KOG0110:100%]

Volvox carteri@PRO_jgi_Volca1_63158[RRM2][KOG0110]Encephalitozoon_cuniculi@SMA_Q8SR30_ENCCU[3][RRM3:100%*][put-sr:100%*][KOG0123:100%*]

Guillardia theta@REF_NP_113380[2][RRM1:50%][.RRM3:50%]Phytophthora@PRO_jgi_Physo1_1_140019[2][RRM1:100%][KOG0116:100%]

Plasmodium_falciparum_3D7@SMA_Q4Z240_PLABE[3][RRM1:67%][.RRM2:33%]Cryptosporidium@PRO_XP_626331[5][RRM1:100%*][KOG0146:100%*]

Paramecium tetraurelia@REF_XP_001454919[RRM5][KOG0110]Entamoeba histolytica_HM-1_IMSS@REF_XP_655058[2][RRM4:50%][.RRM5:50%][KOG0110:100%]

Cyanidioschyzon merolae@PRO_gnl_CMER_CMO246C[RRM5][KOG0110]Giardia lamblia_ATCC_50803@SMA_Q7R479_GIALA[RRM4][KOG0110]

Tetrahymena thermophila_SB210@REF_XP_001020766[2][RRM5:100%][KOG0110:100%]Eukaryota@REF_XP_001670884[186][RRM5:44%****][.RRM6:28%***][.RRM4:12%***][.RRM3:10%**][KOG0110:100%*****]

Encephalitozoon_cuniculi@PRO_NP_597181[3][RRM3:67%][.RRM2:33%][KOG0110:100%*]Trichomonas vaginalis_G3@REF_XP_001324476[RRM4][KOG0110]

Cryptosporidium@PRO_XP_627799[5][RRM5:100%*][KOG0110:100%*]Ciona intestinalis@SMA_ENSCINP00000023563[2][RRM1:100%][KOG0108:100%]

Trypanosomatidae@PRO_XP_843959[10][RRM3:70%*][.RRM1:20%][.RRM2:10%]Plasmodium@SMA_Q4XDU8_PLACH[8][RRM1:100%**]

Trypanosoma_cruzi@REF_XP_810070[3][RRM1:100%*]Trichomonas vaginalis_G3@REF_XP_001579646[RRM1]

Dictyostelium discoideum_AX4@SMA_Q552N9_DICDI[3][RRM1:100%*][KOG0148:100%*]Cryptosporidium@PRO_XP_001388131[4][RRM1:100%*][KOG0117:50%][.KOG1015:50%]Apicomplexa@SMA_Q5PY68_TOXGO[2][RRM1:100%][KOG0116:50%][.KOG1015:50%]Theileria@REF_XP_951908[5][RRM1:100%*][KOG0117:40%]

Paramecium tetraurelia@REF_XP_001432122[2][RRM1:100%][KOG0123:50%][.KOG0147:50%]Tetrahymena_thermophila@REF_XP_001019281[7][RRM1:71%*][.RRM2:29%][KOG0123:57%*][.KOG4205:43%*]

Ostreococcus tauri@PRO_jgi_Ostta4_34258[RRM2]Phytophthora@PRO_jgi_Phyra1_1_77488[2][RRM1:100%][KOG4205:100%]

Phytophthora sojae@PRO_jgi_Physo1_1_139998[RRM1]Aureococcus anophagefferens@PRO_jgi_Auran1_71372[2][RRM3:50%][.RRM2:50%][put-sr:100%][KOG1178:100%]

Amniota@PRO_ENSETEP00000003776[37][RRM1:100%***][LA:97%***][KOG4213:100%***]Gibberella zeae@SMA_Q4ILE0_GIBZE[RRM1]

Phaeodactylum tricornutum@PRO_jgi_Phatr2_44395[RRM1]Volvox carteri@PRO_jgi_Volca1_90315[RRM1]

Poaceae@PRO_8373_m000321_c0161G04[4][RRM1:100%*][KOG4205:75%*][.KOG4211:25%]Arabidopsis thaliana@SMA_Q681R8_ARATH[3][RRM1:100%*][KOG4205:100%*]

Embryophyta@PRO_28180_m000395[5][RRM1:100%*][KOG0124:100%*]Sophophora@REF_NP_648606[4][RRM1:100%*]

Thalassiosira pseudonana@PRO_jgi_Thaps3_24369[RRM1]Tetrahymena thermophila_SB210@REF_XP_001014712[2][RRM1:100%][KOG4211:100%]

Paramecium tetraurelia@REF_XP_001425448[2][RRM1:100%][KOG4205:50%][.KOG0131:50%]Phytophthora@PRO_jgi_Phyra1_1_76845[2][RRM1:100%][KOG0123:100%]

Phaeodactylum tricornutum@PRO_jgi_Phatr2_44442[RRM1][KOG4211]Filobasidiella_neoformans@SMA_Q55YF3_CRYNE[2][RRM1:100%]

Sophophora@REF_XP_001358879[4][RRM2:100%*]Culicidae@PRO_AGAP003171-PA[8][RRM2:100%**][KOG0148:38%*]

Plasmodium@PRO_XP_966051[4][RRM2:75%*][.RRM1:25%][put-sr:50%][KOG0147:25%]Magnoliophyta@PRO_15974_m000013_AZM5_17589[12][RRM2:92%**][.RRM1:8%][KOG0123:8%]

Viridiplantae@PRO_jgi_Chlre3_99594[54][RRM1:100%***][KOG0123:6%*]Ostreococcus@PRO_jgi_Ost9901_3_7913[5][RRM1:100%*][KOG0131:20%]

Trypanosoma_brucei@PRO_XP_829593[3][RRM1:100%*]Magnoliophyta@PRO_NP_189032[9][RRM1:100%**][put-sr:100%**][KOG0670:100%**]

Ostreococcus tauri@PRO_jgi_Ostta4_24260[RRM1]Aedes aegypti@REF_XP_001655024[RRM1][put-sr][KOG1984]

Trypanosomatidae@SMA_Q388M7_9TRYP[10][RRM1:100%**]Filobasidiella_neoformans@SMA_Q55QJ2_CRYNE[2][RRM1:100%][KOG0120:100%]

Dictyostelium discoideum_AX4@REF_XP_637725[RRM1][put-sr][KOG0120]Bilateria@SMA_U2AF2_DROME[24][RRM1:100%***][put-sr:100%***][snRNP:58%**][KOG0120:100%***]

Leishmania@REF_XP_001565981[5][RRM2:80%*][.RRM1:20%][put-sr:100%*][KOG0147:80%*]Trypanosoma@PRO_XP_951655[7][RRM2:100%*][put-sr:100%*][KOG0109:100%*]

Trypanosoma_cruzi@REF_XP_817546[3][RRM3:100%*][put-sr:100%*][KOG0109:100%*]Trypanosoma_brucei@PRO_XP_951655[4][RRM3:100%*][put-sr:100%*][KOG0109:100%*]

Drosophila pseudoobscura@REF_XP_001355406[2][RRM1:100%][KOG0128:100%]Ostreococcus lucimarinus@PRO_jgi_Ost9901_3_28918[RRM1]

Giardia lamblia_ATCC_50803@REF_XP_001706513[2][RRM1:100%][KOG0110:100%]Entamoeba histolytica_HM-1_IMSS@REF_XP_654661[2][RRM1:100%]

Yarrowia lipolytica@SMA_Q6C378_YARLI[RRM2][KOG0123]Apis mellifera@SMA_UPI00003BFBCE[RRM1][put-sr][KOG2193]

Aedes aegypti@PRO_AAEL006876-PA[2][RRM1:100%][KOG2193:100%]Hydra magnipapillata@SMA_Q9GV12_HYDMA[RRM3][KOG0335]

Hydra magnipapillata@SMA_Q9GV12_HYDMA[RRM1][KOG0335]Hydra magnipapillata@SMA_Q9GV12_HYDMA[RRM2][KOG0335]

Theileria@SMA_Q4N895_THEPA[5][RRM1:100%*]Babesia bovis@REF_XP_001608797[RRM1]

Paramecium tetraurelia@REF_XP_001451287[2][RRM2:100%][KOG4205:50%][.KOG0131:50%]Tetrahymena thermophila_SB210@SMA_Q23DH4_TETTH[2][RRM2:100%][KOG4211:100%]

Plasmodium@PRO_XP_966051[2][RRM1:100%][put-sr:50%][KOG0147:50%]Encephalitozoon_cuniculi@PRO_XP_965888[3][RRM1:100%*][KOG4209:100%*]

Pezizomycotina@REF_XP_001226806[5][RRM1:100%*]Pichia stipitis_CBS_6054@PRO_XP_001384763[2][RRM1:100%][KOG0123:100%]

Ajellomyces capsulatus_NAm1@REF_XP_001536207[RRM1][KOG0128]Trichocomaceae@SMA_Q2U0H3_ASPOR[6][RRM1:100%*][KOG0128:100%*]Saccharomycetaceae@REF_XP_001643044[3][RRM1:100%*][KOG0128:100%*]

Pezizomycotina@REF_XP_001593549[7][RRM1:100%*][KOG0128:71%*][.KOG0123:14%]Paramecium tetraurelia@REF_XP_001455469[RRM1][KOG0117]

Tetrahymena thermophila_SB210@SMA_Q23GR5_TETTH[2][RRM1:100%][KOG0128:100%]Pichia stipitis_CBS_6054@PRO_XP_001384763[2][RRM3:100%][KOG0123:100%]

Guillardia theta@SMA_Q98RZ7_GUITH[2][RRM3:100%][KOG0123:100%]Phytophthora@PRO_jgi_Phyra1_1_76845[2][RRM2:100%][KOG0123:100%]

Aureococcus anophagefferens@PRO_jgi_Auran1_8214[RRM1]Thalassiosira pseudonana@PRO_jgi_Thaps3_1374[RRM2][KOG0116]

Entamoeba histolytica_HM-1_IMSS@REF_XP_654966[3][RRM1:100%*][KOG0147:67%]Phaeodactylum tricornutum@PRO_jgi_Phatr2_44442[RRM2][KOG4211]

Oryza sativa_japonica_cultivar-group@SMA_Q6ZG86_ORYSA[RRM1][KOG0116]rosids@SMA_Q2PEQ3_TRIPR[3][RRM1:100%*][NTF:33%][KOG0116:100%*]

Oryza sativa_japonica_cultivar-group@SMA_Q7Y1L6_ORYSA[RRM1][KOG0116]Embryophyta@PRO_NP_001052571[15][RRM1:100%**][NTF:27%*][KOG0116:100%**]

Schizosaccharomyces_pombe@PRO_NP_593531[3][RRM2:100%*][nucleolin:100%*][KOG0147:100%*]Dikarya@SMA_Q2U4B5_ASPOR[53][RRM2:100%***][nucleolin:6%*][KOG0148:79%***][.KOG0131:11%*][.KOG0127:6%*]

Trichocomaceae@REF_XP_001397624[8][RRM1:100%**][KOG1924:12%]Phytophthora@PRO_jgi_Phyra1_1_83430[2][RRM1:100%]

Ajellomyces capsulatus_NAm1@REF_XP_001541377[RRM1]Yarrowia lipolytica@PRO_XP_504609[2][RRM1:100%]

Eumetazoa@REF_XP_001631718[111][RRM1:100%****][KOG0108:14%**][.KOG0116:8%**][.KOG0921:5%*]Ciona@PRO_ENSCSAVP00000001842[3][RRM1:100%*]

Saccharomycetales@SMA_Q5A4L8_CANAL[5][RRM1:100%*]Encephalitozoon_cuniculi@SMA_Q8SSA1_ENCCU[3][RRM2:100%*][KOG4205:100%*]

Eumetazoa@PRO_ENSSARP00000000775[84][RRM1:100%****][eIF4B:68%****]Strongylocentrotus purpuratus@SMA_UPI0000583F6E[RRM1]

Apis mellifera@SMA_UPI0000519CF4[RRM1]Tribolium castaneum@SMA_UPI0000D5730A[RRM1][put-sr]

Anopheles_gambiae@PRO_AGAP000525-PA[4][RRM1:100%*]87 - eIF-4B

84 - La

60

Fig. S9

117

90

97

51

59

99

82

70

95

51 86

60

61

70 63

69

71

50

54

57

Candida glabrata@PRO XP 446891[3][RRM3:67%][ RRM2:33%][KOG0128:100%*]Saccharomyces cerevisiae@PRO_YMR268C[2][RRM3:100%][KOG0128:100%]

Debaryomyces_hansenii@PRO_XP_460681[3][RRM3:67%][.RRM2:33%][KOG0128:100%*]Pichia guilliermondii_ATCC_6260@REF_XP_001485760[RRM3][KOG0123]

Eremothecium gossypii@SMA_Q756X0_ASHGO[RRM2][KOG0128]Paramecium tetraurelia@REF_XP_001428031[RRM1]

Paramecium tetraurelia@REF_XP_001440032[RRM2]Tetrahymena thermophila_SB210@REF_XP_001031517[2][RRM1:100%]

Babesia bovis@REF_XP_001609703[RRM2][KOG0110]Theileria@REF_XP_764035[3][RRM2:67%][.RRM1:33%][KOG0110:100%*]

Tetrahymena thermophila_SB210@REF_XP_001024046[2][RRM1:100%][KOG0127:100%]Nasonia vitripennis@PRO_XP_001605703[2][RRM1:100%][KOG0127:100%]

Sophophora@PRO_CG4806-PA[5][RRM1:100%*][KOG0127:100%*]Aedes aegypti@PRO_AAEL008572-PA[2][RRM1:100%][KOG0127:100%]

Tribolium castaneum@PRO_XP_974350[3][RRM1:100%*][KOG0127:100%*]Apis mellifera@PRO_XP_624495[3][RRM1:100%*][KOG0127:100%*]

Nasonia vitripennis@PRO_XP_001605703[2][RRM2:100%][KOG0127:100%]Chordata@PRO_ENSOGAP00000005376[57][RRM2:91%***][.RRM3:7%*][RBM:47%***][KOG0127:100%****]

Nematostella vectensis@REF_XP_001631286[RRM2][KOG0127]Caenorhabditis@SMA_Q60SI3_CAEBR[2][RRM1:100%][KOG0127:100%]

Trichomonas vaginalis_G3@REF_XP_001330706[2][RRM2:100%][KOG0123:50%]Embryophyta@PRO_jgi_Phypa1_1_201182[12][RRM2:100%**][KOG0127:100%**]

Ostreococcus@PRO_jgi_Ost9901_3_26255[3][RRM2:100%*][KOG0127:100%*]Chlamydomonas reinhardtii@PRO_jgi_Chlre3_186870[RRM2][KOG0127]

Tetrahymena thermophila_SB210@SMA_Q234T4_TETTH[2][RRM2:100%][put-sr:100%][KOG0147:100%]Trichomonas vaginalis_G3@REF_XP_001318929[2][RRM1:100%][KOG0125:100%]

Embryophyta@PRO_jgi_Phypa1_1_217831[33][RRM3:91%***][.RRM1:9%*][KOG0117:100%***]Oryza sativa_japonica_cultivar-group@PRO_NP_001067112[2][RRM2:100%][put-sr:100%][KOG0117:100%]Poaceae@SMA_Q2QN68_ORYSA[2][RRM1:100%][put-sr:100%][KOG0117:100%]

Pezizomycotina@REF_XP_001596374[20][RRM2:100%**][put-sr:10%][KOG0116:35%*]Schizosaccharomyces_pombe@PRO_NP_595090[2][RRM2:100%]

Entamoeba histolytica_HM-1_IMSS@REF_XP_651599[3][RRM2:100%*][KOG0127:100%*]Entamoeba_histolytica@SMA_Q50XT4_ENTHI[6][RRM2:50%*][.RRM3:33%][.RRM1:17%][KOG0123:100%*]

Yarrowia lipolytica@PRO_XP_500351[3][RRM1:100%*][KOG0123:100%*]Aureococcus anophagefferens@PRO_jgi_Auran1_17889[RRM1][KOG4207]

Tribolium castaneum@PRO_XP_970765[3][RRM2:100%*][KOG0127:100%*]Yarrowia lipolytica@PRO_XP_504884[3][RRM3:100%*][KOG0123:100%*]Endopterygota@SMA_UPI0000D56681[3][RRM1:100%*][put-sr:67%][KOG1080:67%]

Euteleostomi@PRO_ENSORLP00000016244[25][RRM1:100%***][KOG1080:68%**]Nematostella vectensis@REF_XP_001636608[RRM1]

Leishmania infantum_JPCM5@PRO_XP_001468615[RRM1]Trypanosoma_cruzi@REF_XP_805765[3][RRM1:100%*][KOG0122:100%*]

Dictyostelium discoideum_AX4@PRO_XP_641693[3][RRM1:100%*][KOG0122:100%*]Yarrowia lipolytica@PRO_XP_503515[3][RRM1:100%*][KOG0122:100%*]

Cryptococcus_neoformans_var._neoformans@PRO_XP_567824_RRMSaccharomycetales@REF_XP_001525703[9][RRM1:100%**][KOG0122:100%**]Saccharomycetales@REF_XP_001646780[11][RRM1:100%**][KOG0122:100%**]

Eukaryota@SMA_Q4L1A3_WHEAT[169][RRM1:100%*****][KOG0122:99%*****]Medicago truncatula@SMA_Q1SH93_MEDTR[2][RRM1:100%][KOG0122:100%]

Schistosoma japonicum@SMA_Q5DF32_SCHJA[RRM1][KOG0122]Cyanidioschyzon merolae@PRO_gnl_CMER_CMH159C[RRM1][KOG0122]Caenorhabditis@PRO_F22B5_2[5][RRM1:100%*][KOG0122:100%*]

Nematostella vectensis@REF_XP_001627253[2][RRM1:100%][KOG0921:100%]Dictyostelium discoideum_AX4@SMA_Q54I03_DICDI[RRM1][put-sr]

Oryza_sativa@SMA_Q33B10_ORYSA[3][RRM2:100%*][KOG0117:100%*]Magnoliophyta@SMA_Q2HTD6_MEDTR[2][RRM2:100%][KOG0117:100%]

Strongylocentrotus purpuratus@REF_XP_782196[2][RRM1:100%][KOG2193:100%]Euteleostomi@PRO_ENSGACP00000007987[16][RRM1:100%**][IGF2BP:88%**][KOG2193:100%**]

Takifugu rubripes@SMA_UPI000065D15B[RRM1][KOG0117]Eumetazoa@PRO_ENSGALP00000025475[469][RRM1:100%******][hnRNP:33%*****][KOG0117:100%******]Eutheria@PRO_ENSCPOP00000011171[3][RRM1:100%*][hnRNP:67%][KOG0117:100%*]

Tribolium castaneum@PRO_XP_967803[6][RRM1:100%*][KOG0117:100%*]Apis mellifera@SMA_UPI0000514B1D[2][RRM1:100%][KOG0117:100%]

Euteleostomi@REF_XP_001086896[19][RRM1:100%**][KOG0117:100%**]Aedes aegypti@PRO_AAEL015050-PA[4][RRM1:100%*][KOG0117:100%*]

Anopheles_gambiae@PRO_AGAP002326-PA[3][RRM1:100%*]Phaeodactylum tricornutum@PRO_jgi_Phatr2_16633[RRM1][KOG0125]

Entamoeba histolytica_HM-1_IMSS@REF_XP_650669[2][RRM1:100%][KOG0145:100%]Trichomonas vaginalis_G3@REF_XP_001312349[RRM1]

Trichomonas vaginalis_G3@REF_XP_001324542[RRM1]Giardia lamblia_ATCC_50803@SMA_Q7R0N0_GIALA[RRM1]

Amniota@SMA_Q2L7G6_HUMAN[13][RRM2:85%**][.RRM1:15%][hnRNP:100%**][KOG0117:100%**]Physcomitrella patens@PRO_jgi_Phypa1_1_12664[RRM1]

Oryza_sativa@SMA_Q259U0_ORYSA[2][RRM1:100%][KOG3671:50%]rosids@PRO_30155_m001644[5][RRM1:100%*][KOG0116:20%]

Saccharomycetaceae@PRO_XP_458658[5][RRM1:100%*][KOG0921:100%*]Candida albicans_SC5314@REF_XP_715038[2][RRM1:100%][KOG0921:100%]

Lodderomyces elongisporus_NRRL_YB-4239@REF_XP_001525705[RRM1][KOG0921]Saccharomyces cerevisiae@SMA_YHH5_YEAST[3][RRM3:100%*][KOG0123:100%*]

Saccharomyces cerevisiae@PRO_YFR023W[3][RRM3:100%*][KOG0123:100%*]Candida_glabrata@PRO_XP_447635[3][RRM3:100%*][KOG0123:100%*]

Nematostella vectensis@REF_XP_001637104[RRM1]Vanderwaltozyma polyspora_DSM_70294@REF_XP_001643543[RRM3][KOG0123]

Eremothecium_gossypii@PRO_NP_984845[3][RRM3:100%*][KOG0123:100%*]Kluyveromyces lactis@PRO_XP_451368[RRM3][KOG0123]

Pezizomycotina@PRO_XP_961985[19][RRM1:100%**][put-sr:11%][KOG0116:37%*]Aureococcus anophagefferens@PRO_jgi_Auran1_69134[RRM1][put-sr]

Entamoeba histolytica_HM-1_IMSS@REF_XP_654958[3][RRM1:100%*][put-sr:100%*]Aspergillus nidulans_FGSC_A4@REF_XP_681204[2][RRM1:100%][KOG0131:100%]

Aspergillus nidulans_FGSC_A4@REF_XP_662872[2][RRM1:100%]Eurotiomycetidae@REF_XP_664326[11][RRM1:100%**][KOG0254:18%]

Sclerotiniaceae@REF_XP_001591248[2][RRM1:100%]Sordariales@PRO_XP_964541[5][RRM1:100%*]

Magnaporthe grisea_70-15@SMA_UPI000021B0CF[RRM1]Magnaporthe grisea_70-15@REF_XP_360963[2][RRM1:100%]

Paramecium tetraurelia@REF_XP_001455469[RRM3][KOG0117]Apis mellifera@PRO_XP_393878[2][RRM1:100%][put-sr:100%][KOG2193:100%]

Ciona intestinalis@PRO_ENSCINP00000008726[2][RRM1:100%][put-sr:100%][KOG2193:100%]Saccharomycetales@PRO_XP_001387063[5][RRM1:100%*]

Pichia guilliermondii_ATCC_6260@REF_XP_001486542[RRM1]Candida_glabrata@PRO_XP_445637[3][RRM1:100%*]

Saccharomyces cerevisiae@SMA_YFK2_YEAST[RRM1]Eremothecium_gossypii@PRO_NP_983970[3][RRM1:100%*]

Kluyveromyces lactis@SMA_Q6CQM2_KLULA[RRM1]Paramecium tetraurelia@REF_XP_001454919[RRM2][KOG0110]

Tetrahymena thermophila_SB210@REF_XP_001020766[2][RRM2:100%][KOG0110:100%]Tetrahymena thermophila_SB210@REF_XP_001033357[2][RRM2:100%][KOG0144:100%]

Caenorhabditis@SMA_O76366_CAEEL[3][RRM1:100%*][KOG0112:100%*]Ciona intestinalis@SMA_ENSCINP00000027547[RRM1][put-sr]

Coelomata@PRO_XP_974651[122][RRM2:68%****][.RRM1:32%***][put-sr:88%****][RBM:30%***][KOG0112:100%****]Sophophora@PRO_CG2050-PA[4][RRM3:75%*][.RRM2:25%]

Nematostella vectensis@REF_XP_001641758[RRM1][KOG0112]Nematostella vectensis@REF_XP_001632954[RRM2][KOG0112]

Strongylocentrotus purpuratus@PRO_XP_001184502[5][RRM2:80%*][.RRM1:20%][put-sr:80%*][KOG1144:80%*][.KOG0123:20%]Coelomata@PRO_ENSMMUP00000010529[79][RRM2:47%***][.RRM3:39%***][.RRM1:14%**][put-sr:92%****][KOG0112:78%****][.KOG3598:10%**]

Triturus carnifex@SMA_Q8QFS6_TRICI[RRM2][KOG0123]Anopheles gambiae_str._PEST@SMA_Q7PZY1_ANOGA[RRM1][KOG2314]

Euteleostomi@PRO_GSTENP00022906001[99][RRM3:86%****][.RRM1:9%**][.RRM2:5%*][nucleolin:62%****][KOG0123:96%****]Tetraodontidae@PRO_GSTENP00014994001[4][RRM1:50%][.RRM3:25%][.RRM2:25%][KOG0123:50%]

Solanum tuberosum@SMA_Q2XTB3_SOLTU[2][RRM1:100%][hnRNP:100%][KOG1190:100%]

55

48 - IGF2BP

2 - hnRNP

65

part of 63 - hnRNP

71 - RBM

53

+

54

Fig. S9

118

63

54

72 71

55

76

56

80

80

60

54

100

54

56

93 66

60

77 89

97

Trichomonas vaginalis G3@REF XP 001312327[RRM2][KOG0123]Trichomonas vaginalis_G3@REF_XP_001326368[RRM2][KOG0123]

Dictyostelium discoideum_AX4@SMA_Q54FZ3_DICDI[RRM1][KOG0153]Dictyostelium discoideum_AX4@PRO_XP_635179[3][RRM2:100%*][KOG0148:100%*]

Ostreococcus tauri@PRO_jgi_Ostta4_31833[RRM2][KOG0148]Candida albicans_SC5314@SMA_Q59U75_CANAL[RRM2][put-sr][KOG0148]

Aureococcus anophagefferens@PRO_jgi_Auran1_28594[RRM3][KOG0148]Phytophthora@PRO_jgi_Phyra1_1_50314[2][RRM3:100%][KOG0148:100%]

Schizosaccharomyces_pombe@PRO_NP_594243[3][RRM3:100%*][KOG0148:100%*]Eukaryota@PRO_YHR086W[145][RRM3:73%****][.RRM2:23%***][oligoU:12%**][KOG0148:91%****]

Encephalitozoon_cuniculi@PRO_NP_584552[3][RRM3:100%*][KOG0123:100%*]Dictyostelium discoideum_AX4@PRO_XP_645138[3][RRM1:100%*]

Percomorpha@SMA_Q4SDN6_TETNG[2][RRM1:100%][KOG0548:100%]Danio rerio@PRO_ENSDARP00000075089[4][RRM1:100%*][KOG0548:100%*]

Plasmodium@SMA_Q8IHX4_PLAF7[8][RRM1:100%**][KOG0144:100%**]Trichomonas vaginalis_G3@REF_XP_001307992[RRM3][KOG0123]

Trichomonas vaginalis_G3@REF_XP_001314386[2][RRM3:100%][KOG0123:100%]Trichomonas vaginalis_G3@REF_XP_001313255[RRM3][KOG0123]

Strongylocentrotus purpuratus@PRO_XP_001188888[5][RRM1:100%*][KOG0548:100%*]Clupeocephala@PRO_ENSORLP00000009616[5][RRM1:100%*][KOG0548:100%*]

Tetrahymena thermophila_SB210@REF_XP_001023234[2][RRM1:100%][KOG0153:100%]Eumetazoa@SMA_UPI0000D56CC9[76][RRM1:100%****][RBM:75%****][KOG0153:100%****]Caenorhabditis@REF_XP_001671467[6][RRM1:100%*][KOG0153:100%*]

Ciona@PRO_ENSCSAVP00000015574[4][RRM1:100%*][KOG0153:100%*]Embryophyta@PRO_jgi_Phypa1_1_185655[18][RRM1:100%**][KOG0153:100%**]

Ostreococcus@PRO_jgi_Ost9901_3_41266[3][RRM1:100%*][KOG0153:100%*]Paramecium tetraurelia@REF_XP_001451420[2][RRM1:100%][put-sr:100%]

Physcomitrella patens@PRO_jgi_Phypa1_1_137240[2][RRM1:100%][KOG3598:50%]Physcomitrella patens@PRO_jgi_Phypa1_1_161310[RRM3][KOG3598]

Arabidopsis thaliana@SMA_UPI000034F1EC[RRM2][put-sr][oligoU][KOG4206]Oryza sativa_japonica_cultivar-group@PRO_NP_001062811[3][RRM1:100%*][KOG1190:100%*]

rosids@REF_NP_193001[5][RRM1:100%*][put-sr:40%][oligoU:60%*][KOG4206:40%]Arabidopsis thaliana@SMA_O22855_ARATH[11][RRM1:100%**][FCAFPA:100%**][KOG0117:82%**]

Ricinus communis@PRO_29577_m000447[RRM1][KOG0123]Oryza sativa_japonica_cultivar-group@SMA_Q69IL3_ORYSA[RRM1][KOG0123]

Euteleostomi@SMA_UPI000061000C[15][RRM1:100%**][put-sr:100%**][KOG0112:93%**]Filobasidiella_neoformans@SMA_Q55UF0_CRYNE[2][RRM1:100%][KOG4574:100%]Pezizomycotina@SMA_Q5AW56_EMENI[10][RRM1:100%**][KOG4574:100%**]

Basidiomycota@SMA_Q55UF0_CRYNE[6][RRM2:100%*][KOG4574:100%*]Yarrowia lipolytica@PRO_XP_500252[3][RRM1:100%*][KOG4574:100%*]

Schizosaccharomyces pombe_972h-@PRO_NP_595389[2][RRM1:100%][KOG4574:100%]Trypanosoma@SMA_Q584Q1_9TRYP[3][RRM2:100%*][KOG0148:67%]

Leishmania major@SMA_Q4Q7J2_LEIMA[RRM1]Volvox carteri@PRO_jgi_Volca1_88720[RRM3]

Chlamydomonas reinhardtii@PRO_jgi_Chlre3_148816[RRM2][KOG3598]Dictyostelium discoideum_AX4@PRO_XP_629218[3][RRM2:100%*][KOG0151:100%*]

Dictyostelium discoideum_AX4@PRO_XP_629218[3][RRM1:100%*][KOG0151:100%*]Deuterostomia@SMA_PTBP1_HUMAN[23][RRM4:43%**][.RRM3:35%**][.RRM2:17%*][PTBP:83%**][KOG1190:100%***]

Physcomitrella patens@PRO_jgi_Phypa1_1_176266[RRM1][KOG1924]Oryza sativa_japonica_cultivar-group@PRO_NP_001063671[3][RRM2:100%*][KOG0123:100%*]

Physcomitrella patens@PRO_jgi_Phypa1_1_161310[RRM2][KOG3598]rosids@PRO_NP_001078046[11][RRM2:100%**][FCAFPA:91%**][KOG0117:82%**][.KOG0123:9%]

Dictyostelium discoideum_AX4@PRO_XP_644288[3][RRM1:100%*][KOG3598:100%*]Dikarya@SMA_Q4P665_USTMA[8][RRM4:100%**][KOG0117:38%*]

Schizosaccharomyces pombe@SMA_NRD1_SCHPO[RRM4]Dictyostelium discoideum_AX4@PRO_XP_644288[3][RRM2:100%*][KOG3598:100%*]

Schizosaccharomyces pombe@SMA_YCQ9_SCHPO[RRM1]Schizosaccharomyces pombe_972h-@PRO_NP_588373[2][RRM1:100%]

Entamoeba histolytica_HM-1_IMSS@REF_XP_654040[2][RRM1:50%][.RRM2:50%]Vanderwaltozyma polyspora_DSM_70294@REF_XP_001643044[RRM3][KOG0128]

Aedes aegypti@PRO_AAEL010887-PA[2][RRM6:100%][put-sr:100%][KOG1984:100%]Anopheles gambiae@SMA_ENSANGP00000026818[RRM1]

Entamoeba histolytica_HM-1_IMSS@SMA_Q517P3_ENTHI[2][RRM1:100%]Volvox carteri@PRO_jgi_Volca1_107013[RRM3][KOG0117]

Kluyveromyces lactis@PRO_XP_454447[3][RRM3:100%*][KOG0128:100%*]Xenopus laevis@SMA_Q569S7_XENLA[RRM1][KOG4205]

Tetrahymena thermophila_SB210@SMA_Q22FI2_TETTH[RRM1]Dictyostelium discoideum_AX4@SMA_Q54GS2_DICDI[RRM1]

Plasmodium@REF_XP_726028[8][RRM1:100%**]Trypanosoma_cruzi@REF_XP_803950[4][RRM1:100%*]

Apis mellifera@PRO_XP_394565[3][RRM1:100%*][KOG0147:100%*]Anopheles_gambiae@SMA_ENSANGP00000016551[2][RRM1:100%][KOG0148:50%]

Caenorhabditis@SMA_Q95QL3_CAEEL[2][RRM1:100%][KOG0131:50%]Nematostella vectensis@REF_XP_001637979[RRM1][KOG0149]

Dictyostelium discoideum_AX4@SMA_Q54D57_DICDI[RRM3][KOG0145]Paramecium tetraurelia@REF_XP_001425411[RRM1][KOG0123]

Paramecium tetraurelia@REF_XP_001459353[3][RRM1:100%*][KOG0123:100%*]Tetrahymena thermophila_SB210@REF_XP_001023043[2][RRM2:100%][KOG0144:100%]

Tetrapoda@REF_XP_001092330[39][RRM1:59%***][.RRM2:41%**][PTBP:97%***][KOG1190:100%***]Coelomata@REF_XP_424912[51][RRM2:63%***][.RRM3:31%**][.RRM1:6%*][PTBP:84%***][KOG1190:100%***]

Magnoliophyta@SMA_Q1RYN5_MEDTR[5][RRM2:80%*][.RRM1:20%][put-sr:20%][hnRNP:60%*][KOG1190:80%*][.KOG2946:20%]Coelomata@SMA_UPI0000587D6B[17][RRM3:88%**][.RRM2:12%][UMH:82%**][KOG0124:100%**]

Candida albicans_SC5314@REF_XP_718102[2][RRM1:100%][KOG1548:100%]Paramecium tetraurelia@REF_XP_001444867[RRM2]

Oryza sativa_japonica_cultivar-group@REF_NP_001053200[2][RRM1:100%][KOG1548:100%]Tribolium castaneum@PRO_XP_969008[2][RRM2:100%][KOG0331:100%]Caenorhabditis elegans@SMA_Q9BL57_CAEEL[RRM1][UMH][KOG1548]

Caenorhabditis@SMA_Q18265_CAEEL[2][RRM1:100%][KOG0921:100%]Sophophora@SMA_Q294Y2_DROPS[2][RRM1:100%][KOG1995:100%]

Coelomata@PRO_ENSDARP00000069729[324][RRM1:100%*****][KOG1995:79%*****][.KOG0921:15%***]Strongylocentrotus purpuratus@PRO_XP_001196853[5][RRM1:100%*][KOG1995:100%*]

Magnoliophyta@SMA_Q69TN3_ORYSA[5][RRM1:100%*][put-sr:60%*][KOG1995:100%*]Coxiella_burnetii@PRO_YP_001424503[7][RRM1:100%*][PROK:100%*][KOG0113:100%*]Coxiella_burnetii@SMA_Q83CD7_COXBU[6][RRM1:100%*][PROK:100%*][KOG0108:100%*]

Embryophyta@PRO_jgi_Phypa1_1_44443[2][RRM2:100%][KOG0149:100%]Embryophyta@PRO_29900_m001607[30][RRM2:100%***][oligoU:43%**][KOG4205:87%***][.KOG0149:13%*]

Oryza sativa_japonica_cultivar-group@SMA_Q2R1J0_ORYSA[RRM2][KOG0148]Dictyostelium discoideum_AX4@SMA_Q55CC1_DICDI[RRM1]

Paramecium tetraurelia@REF_XP_001454031[2][RRM1:100%][put-sr:100%]Tetrahymena thermophila_SB210@REF_XP_001030321[2][RRM1:100%]

Eukaryota@REF_XP_001541559[147][RRM1:100%****][KOG0114:100%****]Encephalitozoon_cuniculi@SMA_Q8SWE3_ENCCU[3][RRM1:100%*][KOG0114:100%*]

Trichomonas vaginalis_G3@REF_XP_001325623[RRM1][KOG0114]Saccharomycetaceae@PRO_XP_458197[4][RRM1:100%*][KOG0114:100%*]

Lodderomyces elongisporus_NRRL_YB-4239@REF_XP_001527422[RRM1][KOG0114]Candida albicans_SC5314@REF_XP_714695[2][RRM1:100%][KOG0114:100%]

Caenorhabditis@SMA_Q621Q9_CAEBR[2][RRM1:100%][KOG1947:100%]Trichomonas vaginalis_G3@REF_XP_001328261[RRM1]

Euteleostomi@SMA_ENSPTRP00000017835[12][RRM1:100%**][KOG0145:42%*][.KOG0123:33%*]Trichomonas vaginalis_G3@REF_XP_001301635[RRM2][KOG0123]

Babesia bovis@REF_XP_001609195[RRM2][put-sr][KOG0127]Theileria@SMA_Q4UFR5_THEAN[5][RRM2:100%*][KOG0127:100%*]

Tetrahymena thermophila_SB210@SMA_Q246Z1_TETTH[2][RRM2:100%][KOG0127:100%]Entamoeba histolytica_HM-1_IMSS@SMA_Q50UL9_ENTHI[4][RRM1:100%*][KOG0127:100%*]

Phytophthora ramorum@PRO_jgi_Phyra1_1_79608[2][RRM4:100%][KOG0127:100%]Phytophthora sojae@PRO_jgi_Physo1_1_132702[RRM4][KOG0127]

Theileria@REF_XP_951783[5][RRM1:100%*][KOG0127:100%*]Plasmodium@REF_XP_001614741[10][RRM2:90%**][.RRM1:10%][KOG0123:10%]

Debaryomyces hansenii@SMA_Q6BS29_DEBHA[RRM1]Candida_glabrata@PRO_XP_446891[3][RRM3:67%][.RRM2:33%][KOG0128:100%*]

44

14 - RBM

78 - OligoU

Fig. S9

119

81

63

59

67

62

53

97 65

55

63

Schizosaccharomyces pombe@PRO NP 594970[3][RRM2:100%*][KOG4210:100%*]Pezizomycotina@REF_XP_661031[11][RRM2:82%**][.RRM1:18%][put-sr:9%][KOG4210:27%*][.KOG0149:18%]

Saccharomycetales@REF_XP_719745[23][RRM2:87%**][.RRM1:13%*][KOG4210:100%***]Strongylocentrotus purpuratus@SMA_UPI0000583E2F[RRM1]

Nematostella vectensis@REF_XP_001641436[RRM1]Apocrita@PRO_XP_001602363[4][RRM1:100%*][KOG1832:50%]

Culicidae@PRO_AAEL001997-PA[6][RRM1:100%*]Sophophora@PRO_CG3594-PA[5][RRM1:100%*][KOG0110:100%*]

Cryptococcus_neoformans_var._neoformans@PRO_XP_570477_RRMPhaeodactylum tricornutum@PRO_jgi_Phatr2_32836[RRM1]

Phytophthora@PRO_jgi_Physo1_1_136292[2][RRM1:100%]Schizosaccharomyces_pombe@PRO_NP_596033[3][RRM1:100%*]

Ustilago maydis_521@SMA_Q4PGP7_USTMA[RRM1]Neurospora_crassa@PRO_XP_964518[3][RRM1:100%*]

Sordariomycetes@PRO_XP_389032[6][RRM1:100%*]Trichocomaceae@SMA_Q4WWL6_ASPFU[2][RRM1:100%]

Cryptosporidium@PRO_XP_627799[5][RRM2:100%*][KOG0110:100%*]Tetrahymena thermophila_SB210@SMA_Q22V25_TETTH[RRM1][KOG2476]

Schizosaccharomyces pombe@SMA_MSA1_SCHPO[RRM1][KOG0123]Sclerotiniaceae@REF_XP_001594190[2][RRM1:100%][put-sr:100%][KOG0123:100%]

Saccharomycetales@REF_XP_001482891[11][RRM1:100%**][KOG0123:55%*]Magnoliophyta@SMA_Q9C5A7_ARATH[7][RRM3:71%*][.RRM4:29%][KOG0110:100%*]

Paramecium tetraurelia@REF_XP_001454919[RRM4][KOG0110]Tetrahymena thermophila_SB210@REF_XP_001020766[2][RRM4:100%][KOG0110:100%]

Phaeodactylum tricornutum@PRO_jgi_Phatr2_20740[RRM4][KOG0110]Thalassiosira pseudonana@PRO_jgi_Thaps3_268689[RRM4][KOG0110]

Plasmodium vivax@REF_XP_001617268[RRM3][KOG0110]Ornithorhynchus anatinus@REF_XP_001519607[RRM2][KOG0110]

Babesia bovis@REF_XP_001609703[RRM4][KOG0110]Cryptosporidium@PRO_XP_627799[5][RRM4:100%*][KOG0110:100%*]

Dictyostelium discoideum_AX4@SMA_Q54PB2_DICDI[RRM4][KOG0110]Dikarya@REF_XP_721604[52][RRM4:88%***][.RRM3:6%*][.RRM2:6%*][KOG0110:100%***]

Filobasidiella_neoformans@PRO_XP_569873[2][RRM4:50%][.RRM3:50%][KOG0110:100%]Caenorhabditis@SMA_Q9XU67_CAEEL[3][RRM4:33%][.RRM3:33%][.RRM5:33%][KOG0110:100%*]

Ostreococcus@PRO_jgi_Ost9901_3_710[3][RRM4:100%*][KOG0110:100%*]Apocrita@PRO_XP_001605134[8][RRM4:50%*][.RRM5:50%*][KOG0110:100%**]Euteleostomi@SMA_UPI00004BE5E2[55][RRM5:64%***][.RRM4:24%**][.RRM3:5%*][.RRM2:5%*][put-sr:9%*][KOG0110:100%****]

Phytophthora sojae@PRO_jgi_Physo1_1_129427[RRM4][KOG0110]Entamoeba histolytica_HM-1_IMSS@REF_XP_655058[2][RRM4:50%][.RRM3:50%][KOG0110:100%]

Nematostella vectensis@REF_XP_001639550[RRM5][KOG0110]Strongylocentrotus purpuratus@SMA_UPI0000583F7B[RRM1][KOG0110]

Chironomus tentans@SMA_Q95ZH1_CHITE[RRM5][KOG0110]Culicidae@PRO_AAEL004075-PA[8][RRM5:75%*][.RRM1:25%][KOG0110:100%**]Drosophila melanogaster@SMA_Q9VT19_DROME[RRM3][KOG0110]

Yarrowia lipolytica@PRO_XP_503802[3][RRM1:100%*][KOG0113:100%*]Saccharomycetales@PRO_XP_001385249[10][RRM1:100%**][KOG0113:100%**]

Saccharomycetales@PRO_NP_984033[10][RRM1:100%**][put-sr:10%][KOG0113:100%**]Kluyveromyces lactis@PRO_XP_452557[3][RRM1:100%*][KOG0113:100%*]

Apis mellifera@PRO_XP_623573[3][RRM1:100%*][KOG0113:100%*]Entamoeba histolytica_HM-1_IMSS@SMA_Q51GC5_ENTHI[RRM1][KOG0144]

Entamoeba histolytica_HM-1_IMSS@SMA_Q50S61_ENTHI[2][RRM1:100%][KOG0148:50%]Entamoeba histolytica_HM-1_IMSS@REF_XP_648918[2][RRM1:100%][KOG0148:100%]

Bigelowiella natans@SMA_Q3LVZ3_CHLS6[RRM1][KOG0415]Trichomonas vaginalis_G3@REF_XP_001324009[RRM1][KOG0415]

Eukaryota@PRO_jgi_Ostta4_3181[197][RRM1:100%*****][put-sr:42%****][cyclophilin:23%***][KOG0415:97%*****]Debaryomyces_hansenii@PRO_XP_459815[3][RRM1:100%*][KOG0415:100%*]

Ciona@PRO_ENSCSAVP00000001345[3][RRM1:100%*][KOG0113:100%*]Nematostella vectensis@REF_XP_001634361[RRM1][KOG0113]Embryophyta@PRO_29657_m000467[9][RRM1:100%**][put-sr:22%][snRNP:44%*][KOG0113:100%**]

Deuterostomia@PRO_XP_001178221[66][RRM1:100%****][put-sr:62%***][snRNP:71%***][KOG0113:100%****]Tribolium castaneum@PRO_XP_966565[3][RRM1:100%*][KOG0113:100%*]

Entamoeba histolytica_HM-1_IMSS@REF_XP_656357[2][RRM1:100%][KOG0113:100%]Phytophthora@PRO_jgi_Phyra1_1_44765[2][RRM1:100%][put-sr:50%][KOG0113:100%]

Aureococcus anophagefferens@PRO_jgi_Auran1_34517[2][RRM1:100%][put-sr:50%][KOG0113:100%]Aspergillus fumigatus_Af293@PRO_XP_753306[2][RRM1:100%][KOG0113:100%]

Schizosaccharomyces_pombe@PRO_NP_593779[3][RRM1:100%*][KOG0113:100%*]Tetrahymena thermophila_SB210@REF_XP_001011681[2][RRM1:100%][KOG0113:100%]

Ostreococcus@PRO_jgi_Ostta4_11066[3][RRM1:100%*][KOG0113:100%*]Eukaryota@SMA_Q94LP1_ORYSA[146][RRM1:100%****][put-sr:38%****][snRNP:10%**][KOG0113:100%****]

Paramecium tetraurelia@REF_XP_001457841[3][RRM1:100%*][put-sr:100%*][KOG0113:100%*]Coelomata@PRO_AAEL011340-PB[3][RRM1:100%*][put-sr:33%][KOG0113:100%*]Felis catus@PRO_ENSFCAP00000006212[RRM1][put-sr][KOG0113]

Rattus norvegicus@PRO_ENSRNOP00000048879[RRM1][snRNP][KOG0113]Geobacter uraniumreducens_Rf4@SMA_Q2DJM1_9DELT[3][RRM1:100%*][PROK:100%*][KOG0108:100%*]

Beggiatoa sp._PS@REF_ZP_02002958[RRM1][PROK][KOG0145]Pedobacter sp._BAL39@REF_ZP_01882770[RRM1][PROK][KOG0108]

Leptospira@PRO_YP_000459[9][RRM1:100%**][PROK:100%**][KOG0108:100%**]Entamoeba_histolytica@REF_XP_649106[3][RRM2:67%][.RRM1:33%][KOG0123:67%][.KOG0125:33%]

Candidatus Protochlamydia_amoebophila_UWE25@SMA_Q6MCT2_PARUW_RRSyntrophobacter fumaroxidans_MPOB@PRO_YP_845575[2][RRM1:100%][PROK:100%]Schizosaccharomyces_pombe@PRO_NP_595396[3][RRM1:100%*][put-sr:100%*][KOG0120:100%*]Chlamydomonadales@PRO_jgi_Volca1_48801[2][RRM1:100%][KOG0120:100%]

Tetrahymena thermophila_SB210@REF_XP_001021657[2][RRM1:100%][put-sr:100%][KOG0120:100%]Yarrowia lipolytica@PRO_XP_503754[2][RRM1:100%][KOG0120:100%]

Tetrahymena thermophila_SB210@REF_XP_001470832[2][RRM1:50%][.RRM2:50%][put-sr:50%][KOG0120:100%]Piroplasmida@SMA_Q4N3F2_THEPA[5][RRM2:60%*][.RRM1:40%][KOG0120:100%*]

Plasmodium@PRO_XP_001348830[10][RRM2:60%*][.RRM1:40%*][put-sr:40%*][KOG0120:100%**]Eukaryota@PRO_jgi_Volca1_82970[198][RRM2:88%*****][.RRM1:12%***][put-sr:82%*****][snRNP:51%****][KOG0120:100%*****]

Phaeodactylum tricornutum@PRO_jgi_Phatr2_11145[RRM2][KOG0120]Oligohymenophorea@REF_XP_001028025[6][RRM1:100%*][KOG0120:100%*]

Dictyostelium_discoideum@PRO_XP_642758[4][RRM1:100%*]Dictyostelium discoideum_AX4@PRO_XP_641568[3][RRM3:67%][.RRM2:33%][KOG3598:100%*]

Nematostella vectensis@REF_XP_001638999[RRM3][KOG0144]Eukaryota@PRO_jgi_Volca1_104604[103][RRM1:100%****][put-sr:80%****][KOG0151:100%****]

Filobasidiella_neoformans@SMA_Q55R42_CRYNE[5][RRM1:100%*][put-sr:100%*][KOG0151:100%*]Plasmodium@REF_XP_672919[11][RRM1:100%**][KOG0151:100%**]

Pichia guilliermondii_ATCC_6260@REF_XP_001486325[RRM1][put-sr][KOG0148]Saccharomycetales@PRO_XP_454345[13][RRM1:100%**][KOG0148:77%**][.KOG0123:23%*]

Saccharomycetales@PRO_XP_001383142[8][RRM1:100%**][put-sr:100%**][KOG0148:100%**]Yarrowia lipolytica@PRO_XP_501542[3][RRM1:100%*][KOG0131:100%*]

Filobasidiella_neoformans@PRO_XP_570577[4][RRM1:100%*][KOG0148:100%*]Pezizomycotina@REF_XP_658695[19][RRM1:100%**][KOG0148:100%**]

Encephalitozoon_cuniculi@PRO_NP_584552[3][RRM1:100%*][KOG0123:100%*]Saccharomyces cerevisiae@PRO_YBR119W[RRM1]

Trichomonas vaginalis_G3@REF_XP_001328901[RRM2][KOG4206]Theileria parva_strain_Muguga@PRO_XP_764943[RRM2][KOG4206]

Tetrahymena thermophila_SB210@REF_XP_001027266[RRM2][KOG4206]Plasmodium@PRO_XP_001349796[6][RRM2:100%*][KOG4206:100%*]

Schizosaccharomyces_pombe@PRO_NP_596424[3][RRM2:100%*][KOG4206:100%*]Pezizomycotina@SMA_Q5BH71_EMENI[9][RRM2:100%**][put-sr:33%*][KOG4206:89%**][.KOG1943:11%]

Eukaryota@PRO_ENSGACP00000013006[198][RRM2:95%*****][.RRM1:5%**][snRNP:35%****][KOG4206:100%*****]Cryptococcus_neoformans_var._neoformans@PRO_XP_568533_RRM

Caenorhabditis@SMA_Q21322_CAEEL[2][RRM2:100%][KOG4206:100%]Caenorhabditis@SMA_Q61A17_CAEBR[2][RRM2:100%][KOG4206:100%]

Entamoeba histolytica_HM-1_IMSS@REF_XP_655803[2][RRM1:100%][KOG0148:100%]Trichomonas vaginalis_G3@REF_XP_001318438[RRM1]

Trichomonas vaginalis_G3@REF_XP_001317501[RRM1]Saccharomyces cerevisiae@PRO_YOR319W[2][RRM2:100%][KOG0131:100%]

Plasmodium@REF_XP_742863[2][RRM1:100%]Trichomonas vaginalis_G3@REF_XP_001312327[RRM2][KOG0123]

41 - snRNP

13

64 - snRNP

38 - cyclophilin

36 - snRNP

59

part of 39

Fig. S9

120

83 78

52

52

71

83

93

54

61

71

67

75 52

57

61

Dictyostelium discoideum AX4@PRO XP 638262[3][RRM2:100%*][put sr:100%*][KOG0670:100%*]Cryptosporidium@PRO_XP_628096[5][RRM2:100%*][put-sr:100%*][KOG0124:100%*]Eumetazoa@PRO_ENSCSAVP00000007991[136][RRM2:97%****][UMH:82%****][KOG0124:100%****]

Phytophthora@PRO_jgi_Phyra1_1_84640[3][RRM2:67%][.RRM1:33%][KOG0124:67%][.KOG0120:33%]Dictyostelium discoideum_AX4@PRO_XP_638262[3][RRM1:100%*][put-sr:100%*][KOG0670:100%*]

Eumetazoa@PRO_Y47G6A_20a[142][RRM1:100%****][UMH:81%****][KOG0124:100%****]Theileria@SMA_Q4U9D6_THEAN[4][RRM1:100%*][put-sr:100%*][KOG0124:100%*]

Cryptosporidium@PRO_XP_628096[5][RRM1:100%*][put-sr:100%*][KOG0124:100%*]Phytophthora ramorum@PRO_jgi_Phyra1_1_81440[2][RRM1:100%][KOG0124:100%]

Phytophthora@PRO_jgi_Phyra1_1_94266[2][RRM2:100%][KOG0147:100%]Cryptococcus_neoformans_var._neoformans@PRO_XP_571060_RRM

Cicer arietinum@SMA_Q9FT01_CICAR[RRM2][KOG0147]Yarrowia lipolytica@PRO_XP_504318[3][RRM2:100%*][KOG0147:100%*]

Volvox carteri@PRO_jgi_Volca1_106063[RRM2]Dictyostelium discoideum_AX4@SMA_Q54HN5_DICDI[3][RRM3:100%*][KOG3598:100%*]

Nematostella vectensis@REF_XP_001635913[RRM3][KOG0144]Arabidopsis thaliana@SMA_Q9LYN7_ARATH[RRM2][KOG4660]

Embryophyta@PRO_IMGA_AC141435_12_2[42][RRM2:79%***][.RRM1:21%**][KOG4660:100%***]Entamoeba histolytica_HM-1_IMSS@REF_XP_652879[2][RRM2:100%][KOG4660:100%]

Entamoeba histolytica_HM-1_IMSS@SMA_Q50LX7_ENTHI[2][RRM1:100%][KOG4660:100%]Entamoeba histolytica_HM-1_IMSS@REF_XP_655248[4][RRM1:50%][.RRM2:50%][KOG4660:100%*]

Coelomata@SMA_Q80VS9_MOUSE[12][RRM2:67%**][.RRM1:33%*][RBM:67%**]Amniota@PRO_ENSMODP00000002817[15][RRM1:100%**]Pezizomycotina@PRO_XP_962704[12][RRM1:100%**][put-sr:17%][KOG4206:100%**]

Debaryomyces hansenii@SMA_Q6BW78_DEBHA[RRM1][KOG4206]Pichia stipitis_CBS_6054@PRO_XP_001382592[RRM1][KOG4206]

Entamoeba histolytica_HM-1_IMSS@SMA_Q51EE9_ENTHI[RRM1][KOG4206]Candida albicans_SC5314@SMA_Q5A4F9_CANAL[RRM1][KOG4206]Schizosaccharomyces pombe@SMA_O74968_SCHPO[RRM1][KOG4206]

Theileria annulata@SMA_Q4UD23_THEAN[RRM1][KOG4206]Plasmodium falciparum_3D7@SMA_Q8IEP6_PLAF7[RRM1][KOG4206]

Ascomycota@SMA_RU2B_SCHPO[4][RRM1:100%*][KOG4206:100%*]Yarrowia lipolytica@SMA_Q6C824_YARLI[RRM1][KOG4206]

root@SMA_UPI00005145B2[100][RRM1:100%****][snRNP:54%***][KOG4206:100%****]Schistosoma japonicum@SMA_Q5DD61_SCHJA[RRM1][KOG4206]

Tetrahymena thermophila_SB210@REF_XP_001027266[2][RRM1:100%][KOG4206:100%]Plasmodium@SMA_Q7RQA6_PLAYO[4][RRM1:100%*][KOG4206:100%*]

Theileria@PRO_XP_764943[5][RRM1:100%*][KOG4206:100%*]Tetrahymena thermophila_SB210@SMA_Q22CK3_TETTH[RRM1][KOG4206]

Kluyveromyces lactis@SMA_Q6CVJ3_KLULA[RRM1][KOG4206]Saccharomyces cerevisiae@SMA_MSL1_YEAST[RRM1][KOG4206]

Nematostella vectensis@REF_XP_001624470[RRM1]Gallus gallus@PRO_ENSGALP00000012472[3][RRM1:100%*][KOG0123:100%*]

Euteleostomi@PRO_ENSGACP00000011877[11][RRM1:100%**][nucleolin:27%*][KOG0123:100%**]Trichomonas vaginalis_G3@REF_XP_001315258[RRM1][KOG0116]

Sclerotiniaceae@REF_XP_001591252[2][RRM1:100%][KOG0148:100%]Coccidioides immitis_RS@REF_XP_001244865[RRM1][KOG0110]

Trichocomaceae@REF_XP_001213939[9][RRM1:100%**][KOG0110:100%**]Trichomonas vaginalis_G3@REF_XP_001314467[2][RRM1:100%][KOG0108:100%]

Eurotiomycetidae@REF_XP_001246170[12][RRM3:100%**][KOG0128:100%**]Ostreococcus_lucimarinus@PRO_jgi_Ost9901_3_27365[2][RRM2:100%][KOG0123:100%]

Trichomonas vaginalis_G3@REF_XP_001319048[RRM1]Entamoeba histolytica_HM-1_IMSS@SMA_Q50UR4_ENTHI[3][RRM1:100%*][KOG0127:100%*]

Entamoeba histolytica_HM-1_IMSS@SMA_Q50Q51_ENTHI[2][RRM1:100%][KOG0123:100%]Trichomonas vaginalis_G3@REF_XP_001304682[RRM1]

Trichomonas vaginalis_G3@REF_XP_001319448[RRM1][KOG0148]Trichomonas vaginalis_G3@REF_XP_001329123[RRM1]

cellular_organisms@REF_XP_657084[3][RRM1:100%*][PROK:33%][KOG0148:67%][.KOG0149:33%]Entamoeba histolytica_HM-1_IMSS@REF_XP_652707[2][RRM1:100%][put-sr:100%][KOG0117:100%]

Ustilago maydis_521@PRO_XP_761797[3][RRM2:100%*][put-sr:100%*][KOG3257:100%*]Trichomonas vaginalis_G3@REF_XP_001295319[RRM1]

Nematostella vectensis@REF_XP_001630508[RRM2][KOG1015]Trichomonas_vaginalis@REF_XP_001323895[2][RRM1:100%][KOG4205:50%][.KOG0149:50%]

Trichomonas vaginalis_G3@REF_XP_001315624[RRM1][KOG0149]Trichomonas vaginalis_G3@REF_XP_001308576[RRM1]

Trichomonas vaginalis_G3@REF_XP_001327731[RRM1]Yarrowia lipolytica@SMA_Q6CG61_YARLI[3][RRM2:100%*][KOG0123:100%*]

Tetraodontidae@SMA_Q4SP55_TETNG[2][RRM3:50%][.RRM2:50%][KOG0123:50%]Euteleostomi@PRO_ENSGALP00000012472[89][RRM4:89%****][.RRM2:7%*][nucleolin:62%****][KOG0123:99%****]

Nectria haematococca@SMA_Q00880_NECHA[RRM1][KOG0148]Pezizomycotina@REF_XP_001585064[13][RRM1:100%**][KOG0148:100%**]

Sordariomycetes@REF_XP_363342[7][RRM1:100%*][KOG0148:57%*][.KOG0127:43%*]Dikarya@PRO_XP_566835[36][RRM1:100%***][nucleolin:17%*][KOG0148:69%***][.KOG0131:17%*][.KOG0147:8%*][.KOG4210:6%]

Trichomonas vaginalis_G3@REF_XP_001323074[RRM1]Dictyostelium discoideum_AX4@PRO_XP_641373[3][RRM1:100%*][put-sr:100%*]

Paramecium tetraurelia@REF_XP_001427555[4][RRM1:100%*][KOG0107:25%]Phytophthora@PRO_jgi_Physo1_1_140403[2][RRM1:100%][put-sr:100%][KOG0127:100%]

Phaeodactylum tricornutum@PRO_jgi_Phatr2_10122[RRM1][KOG0153]Paramecium tetraurelia@REF_XP_001458086[RRM1][put-sr]

Tetrahymena thermophila_SB210@SMA_Q246W1_TETTH[RRM1][put-sr]Dictyostelium discoideum_AX4@PRO_XP_639372[3][RRM1:100%*][KOG0670:100%*]

Tetrapoda@SMA_CPSF6_MOUSE[19][RRM1:100%**][put-sr:95%**][KOG4849:100%**]Ostreococcus_lucimarinus@PRO_jgi_Ost9901_3_26750[2][RRM1:100%]

Oryza sativa@SMA_Q7XJW3_ORYSA[RRM1][put-sr]Embryophyta@SMA_Q6ZBP8_ORYSA[16][RRM1:100%**][put-sr:69%**][KOG4849:31%*][.KOG4246:19%*][.KOG4676:19%*][.KOG0113:6%]

Embryophyta@SMA_Q9SX79_ARATH[45][RRM1:100%***][oligoU:16%*][KOG0148:98%***]Tetrahymena thermophila_SB210@REF_XP_001022345[RRM1][KOG0148]

Euteleostomi@REF_XP_865602[9][RRM1:100%**][KOG0131:56%*][.KOG0123:22%]Bilateria@PRO_XP_974444[8][RRM1:100%**][KOG0144:62%*][.KOG0123:25%]Schizosaccharomyces pombe@SMA_YG41_SCHPO[RRM1][KOG0148]

Aspergillus fumigatus@SMA_Q4WAR5_ASPFU[RRM1][KOG0148]rosids@PRO_NP_200794[10][RRM1:100%**][oligoU:70%*][KOG0113:30%*][.KOG0122:30%*][.KOG0148:10%]

Magnoliophyta@PRO_29930_m000611[11][RRM1:100%**][KOG0113:100%**]Magnoliophyta@PRO_9946_m000021_AZM5_3995[4][RRM1:100%*][KOG0113:75%*][.KOG0111:25%]Magnoliophyta@PRO_NP_001052753[7][RRM1:100%*][oligoU:43%*][KOG0108:43%*][.KOG0149:43%*][.KOG0127:14%]

Giardia lamblia_ATCC_50803@REF_XP_001706513[2][RRM2:100%][KOG0110:100%]Ricinus communis@PRO_30055_m001598[RRM1][KOG0149]

Arabidopsis thaliana@PRO_NP_565646[3][RRM1:100%*][KOG0149:100%*]Medicago truncatula@SMA_Q1T5G5_MEDTR[2][RRM1:100%][KOG0149:100%]

Oryza sativa_japonica_cultivar-group@PRO_NP_001045556[3][RRM1:100%*][KOG0108:67%][.KOG0113:33%]Entamoeba histolytica_HM-1_IMSS@REF_XP_651783[2][RRM1:100%][KOG0123:100%]

Paramecium tetraurelia@REF_XP_001436649[2][RRM1:100%][KOG0123:100%]Cyanidioschyzon merolae@PRO_gnl_CMER_CMG025C[RRM1][KOG1080]

Trichomonas vaginalis_G3@REF_XP_001329617[RRM1][put-sr]Plasmodium@REF_XP_001615651[10][RRM2:100%**][KOG0147:100%**]

Babesia bovis@REF_XP_001611287[RRM2][put-sr][KOG0147]Theileria@REF_XP_762815[4][RRM2:100%*][put-sr:100%*][KOG0147:100%*]

Ciona intestinalis@PRO_ENSCINP00000019833[3][RRM2:100%*][KOG0128:100%*]Eumetazoa@SMA_ENSDARP00000051594[63][RRM2:98%****][SART3:75%***][KOG0128:100%****]

Culicidae@PRO_AAEL011963-PA[8][RRM2:100%**][KOG0128:100%**]Strongylocentrotus purpuratus@SMA_UPI0000584378[3][RRM2:100%*][KOG0128:100%*]

Tribolium castaneum@PRO_XP_972538[3][RRM2:100%*][KOG0128:100%*]Apocrita@PRO_XP_001602582[5][RRM2:100%*][KOG0128:100%*]

Schistosoma japonicum@SMA_Q5DH08_SCHJA[RRM1][KOG0123]Ascomycota@SMA_Q6C1Y4_YARLI[28][RRM1:96%***][KOG1457:14%*][.KOG3598:7%]

Dictyostelium discoideum_AX4@PRO_XP_629950[3][RRM1:100%*][KOG0128:100%*]Candida albicans_SC5314@SMA_Q5A422_CANAL[RRM1]

Trichomonas vaginalis_G3@REF_XP_001312066[RRM1]Yarrowia lipolytica@PRO_XP_499736[3][RRM2:67%][.RRM1:33%][KOG4205:100%*]

Schizosaccharomyces_pombe@PRO_NP_594970[3][RRM2:100%*][KOG4210:100%*]

37 - SART3

40 - snRNP

43

67 - UMH

part of 39

Fig. S9

121

96

62

67

96

100

56

69

61

Trichomonas vaginalis G3@REF XP 001313255[RRM1][KOG0123]Trichomonas vaginalis_G3@REF_XP_001314386[2][RRM1:100%][KOG0123:100%]

Strongylocentrotus purpuratus@PRO_XP_001185731[4][RRM1:100%*]Endopterygota@SMA_NELFE_DROVI[8][RRM1:100%**]

Yarrowia lipolytica@PRO_XP_503462[3][RRM1:100%*][put-sr:100%*][KOG0130:100%*]Filobasidiella_neoformans@PRO_XP_569809[5][RRM1:100%*][KOG0130:100%*]

Phaeodactylum tricornutum@PRO_jgi_Phatr2_20716[RRM1][KOG0130]Babesia bovis@REF_XP_001611322[RRM1][KOG0130]

Eukaryota@REF_XP_001462151[152][RRM1:100%*****][put-sr:58%****][RBM:35%***][KOG0130:98%*****]Plasmodium_yoelii_yoelii@REF_XP_724364[2][RRM1:100%][KOG0130:100%]

Plasmodium@REF_XP_001616889[4][RRM1:100%*][KOG0130:100%*]Schistosoma japonicum@SMA_Q5DH48_SCHJA[RRM2][KOG4205]Trichomonas vaginalis_G3@REF_XP_001321938[3][RRM1:100%*][KOG0111:100%*]

Cryptococcus_neoformans_var._neoformans@PRO_XP_566572_RRMOrnithorhynchus anatinus@PRO_ENSOANP00000022523[3][RRM1:67%][.RRM2:33%][KOG2248:100%*]

Paramecium tetraurelia@REF_XP_001461630[2][RRM1:100%][KOG0111:100%]Schizosaccharomyces_pombe@PRO_NP_595190[3][RRM1:100%*][KOG0111:100%*]

Theileria@SMA_Q4UGS2_THEAN[5][RRM1:100%*][KOG0111:100%*]Babesia bovis@REF_XP_001610344[RRM1][KOG0111]

Entamoeba histolytica_HM-1_IMSS@REF_XP_656069[2][RRM1:100%][KOG0111:100%]Plasmodium@PRO_XP_001349948[8][RRM1:100%**][KOG0111:100%**]

Thalassiosira pseudonana@PRO_jgi_Thaps3_31121[RRM1][KOG0111]Phaeodactylum tricornutum@PRO_jgi_Phatr2_11308[RRM1][KOG0111]

Eukaryota@SMA_Q4G338_HAECO[134][RRM1:100%****][cyclophilin:66%****][KOG0111:98%****]Pezizomycotina@PRO_XP_755630[23][RRM1:100%***][KOG0111:100%***]

Apis mellifera@SMA_UPI00005132BD[RRM1][cyclophilin][KOG0111]Eutheria@PRO_ENSEEUP00000009324[3][RRM1:100%*][cyclophilin:100%*][KOG0111:100%*]Otolemur garnettii@PRO_ENSOGAP00000003225[RRM1][KOG0111]Caenorhabditis@REF_XP_001671871[8][RRM2:100%**][put-sr:62%*][UMH:100%**][KOG0147:100%**]

Euteleostomi@SMA_ENSBTAP00000008515[11][RRM2:91%**][.RRM1:9%][put-sr:82%**][RBM:9%][KOG0112:100%**]Anopheles gambiae@SMA_ENSANGP00000011942[RRM1][KOG0880]

Caenorhabditis briggsae@REF_XP_001680458[RRM1][KOG0105]Cryptosporidium_parvum@PRO_XP_627232[3][RRM1:100%*][put-sr:100%*][KOG0105:100%*]

Tetrahymena thermophila_SB210@REF_XP_001012866[2][RRM2:100%][put-sr:100%][KOG0117:100%]Tetrahymena thermophila_SB210@REF_XP_001012866[2][RRM3:100%][put-sr:100%][KOG0117:100%]

Saccharomyces cerevisiae@PRO_YLL046C[3][RRM1:100%*]Plasmodium@REF_XP_001617331[10][RRM3:100%**][KOG0123:100%**]

Theileria@SMA_Q4N775_THEPA[5][RRM3:100%*][KOG0123:100%*]Babesia bovis@REF_XP_001610750[RRM3][KOG0123]

Cryptosporidium@SMA_Q5CLX5_CRYHO[5][RRM3:100%*][KOG0123:100%*]Dictyostelium discoideum_AX4@PRO_XP_645848[3][RRM1:100%*][put-sr:100%*]

Encephalitozoon cuniculi@SMA_Q8SR30_ENCCU[RRM4][put-sr][KOG0123]Entamoeba histolytica_HM-1_IMSS@REF_XP_648918[2][RRM2:100%][KOG0148:100%]

Entamoeba histolytica_HM-1_IMSS@SMA_Q51CH0_ENTHI[RRM1][KOG0144]Entamoeba histolytica_HM-1_IMSS@SMA_Q511G4_ENTHI[RRM2][KOG0148]

Aconoidasida@REF_XP_001613785[16][RRM1:100%**][put-sr:88%**][KOG0105:100%**]Tetrahymena thermophila_SB210@REF_XP_001023381[RRM1][put-sr]

Sclerotiniaceae@REF_XP_001594190[2][RRM2:100%][put-sr:100%][KOG0123:100%]Theileria@REF_XP_953908[5][RRM1:100%*][put-sr:100%*][KOG0105:100%*]

Plasmodium@PRO_XP_001347876[4][RRM1:100%*][KOG0105:100%*]Toxoplasma gondii@SMA_Q6GYB0_TOXGO[RRM1][put-sr][KOG0105]

Eukaryota@PRO_ENSTBEP00000007356[224][RRM1:100%*****][put-sr:83%*****][SR:73%*****][KOG0105:100%*****]Eutheria@REF_XP_001160597[2][RRM1:100%][put-sr:100%][SR:100%][KOG0105:100%]

Caenorhabditis briggsae@REF_XP_001676750[2][RRM1:100%][KOG0107:100%]Theileria@REF_XP_954918[3][RRM1:100%*][put-sr:67%][KOG0107:33%]

Bigelowiella natans@SMA_Q5YES7_CHLS6[RRM1][put-sr]Yarrowia lipolytica@PRO_XP_505724[2][RRM1:100%][KOG4198:100%]

Endopterygota@PRO_CG5655-PA[19][RRM1:100%**][put-sr:89%**][KOG0107:79%**][.KOG0921:16%*]Strongylocentrotus purpuratus@PRO_XP_001178467[5][RRM1:100%*][put-sr:100%*]

Eukaryota@SMA_UPI0000D68409[351][RRM1:100%*****][put-sr:74%*****][SR:61%*****][KOG0107:69%*****]Schistosoma japonicum@SMA_Q5DD33_SCHJA[2][RRM1:100%][put-sr:50%][KOG0107:50%]

Bilateria@PRO_XP_001180596[7][RRM1:100%*][put-sr:71%*][KOG0107:14%]Phytophthora@PRO_jgi_Physo1_1_138982[2][RRM1:100%][KOG0105:100%]

Trichomonas vaginalis_G3@REF_XP_001299622[2][RRM1:100%]Eremothecium gossypii@SMA_Q756B8_ASHGO[RRM1]

Dikarya@PRO_NP_596398[10][RRM1:100%**][put-sr:70%*][SR:30%*]Yarrowia lipolytica@PRO_XP_500797[2][RRM1:100%][put-sr:100%]

Embryophyta@PRO_NP_194280[27][RRM1:100%***][put-sr:89%***][SR:74%**][KOG0106:100%***]Ostreococcus_lucimarinus@PRO_jgi_Ost9901_3_8794[2][RRM1:100%][KOG0105:100%]

Dictyostelium discoideum_AX4@PRO_XP_638672[3][RRM1:100%*][put-sr:100%*][KOG0147:100%*]Dictyostelium_discoideum@PRO_XP_001134500[4][RRM1:100%*][put-sr:100%*][KOG0147:100%*]

Strongylocentrotus purpuratus@SMA_UPI0000587C32[6][RRM1:100%*][KOG0107:83%*]Nematostella vectensis@REF_XP_001641195[RRM1][put-sr][KOG0109]

Nematostella vectensis@REF_XP_001623720[RRM1][put-sr][KOG0106]Ciona intestinalis@PRO_ENSCINP00000016525[RRM1][put-sr][KOG0106]

Caenorhabditis@REF_XP_001679560[11][RRM1:100%**][put-sr:100%**][SR:100%**][KOG0106:100%**]Cavia porcellus@PRO_ENSCPOP00000010577[RRM1][put-sr][SR][KOG0106]

Aedes aegypti@PRO_AAEL012621-PA[2][RRM1:100%][put-sr:100%][KOG0105:100%]Eukaryota@PRO_ENSOANP00000021053[343][RRM1:100%*****][put-sr:83%*****][SR:65%*****][KOG0106:57%*****][.KOG0105:36%****]

Filobasidiella_neoformans@PRO_XP_567562[4][RRM1:100%*][KOG0106:100%*]Schizosaccharomyces_pombe@PRO_NP_594570[3][RRM1:100%*][put-sr:100%*][KOG0106:100%*]

Pezizomycotina@PRO_XP_960334[15][RRM1:100%**][put-sr:87%**][KOG0105:53%**][.KOG0106:47%*]Entamoeba histolytica_HM-1_IMSS@REF_XP_656450[2][RRM1:100%]

Thalassiosira pseudonana@PRO_jgi_Thaps3_2206[RRM1]Dictyostelium discoideum_AX4@PRO_XP_638966[3][RRM2:100%*][KOG0147:100%*]

Dictyostelium discoideum_AX4@PRO_XP_643007[3][RRM1:100%*]Paramecium tetraurelia@REF_XP_001426030[RRM2][put-sr][KOG0148]

Tetrahymena thermophila_SB210@REF_XP_001024078[2][RRM1:100%]Tetrahymena thermophila_SB210@SMA_Q247H9_TETTH[2][RRM1:50%][.RRM2:50%][KOG1190:100%]Tetrahymena thermophila_SB210@SMA_Q22GW9_TETTH[RRM1][KOG1190]

Babesia bovis@REF_XP_001610592[RRM1][KOG0123]Theileria@SMA_Q4UJ52_THEAN[5][RRM1:100%*][KOG0124:100%*]

Aedes aegypti@PRO_AAEL010890-PA[2][RRM1:100%][put-sr:100%][KOG0132:100%]Trichomonas vaginalis_G3@REF_XP_001305138[RRM1]

Tetrahymena thermophila_SB210@REF_XP_001020597[2][RRM1:100%][put-sr:50%][KOG0107:50%][.KOG0109:50%]Plasmodium@SMA_Q4YSH6_PLABE[10][RRM1:100%**][put-sr:80%**][KOG0105:100%**]

Dictyostelium discoideum_AX4@PRO_XP_645848[3][RRM2:100%*][put-sr:100%*]Trichomonas vaginalis_G3@REF_XP_001312176[RRM1]

Paramecium tetraurelia@REF_XP_001450678[RRM1]Paramecium tetraurelia@REF_XP_001442708[4][RRM1:100%*][put-sr:100%*][KOG0105:25%]

Chlamydomonadales@PRO_jgi_Volca1_120471[2][RRM1:100%][KOG0108:100%]Trichomonas vaginalis_G3@REF_XP_001316284[RRM1]

Trichomonas vaginalis_G3@REF_XP_001326015[RRM1]Trichomonas vaginalis_G3@REF_XP_001317742[RRM1]Paramecium tetraurelia@REF_XP_001448078[2][RRM1:100%][KOG1029:50%]

Phytophthora@PRO_jgi_Physo1_1_138873[2][RRM1:100%][put-sr:100%][KOG1611:50%]Theileria@REF_XP_764360[2][RRM1:100%]

Plasmodium@REF_XP_001615424[7][RRM1:100%*]Viridiplantae@PRO_jgi_Phypa1_1_105411[16][RRM1:100%**][put-sr:100%**][SR:31%*][KOG0117:19%*][.KOG0462:6%]

Dictyostelium discoideum_AX4@PRO_XP_636445[3][RRM1:100%*][put-sr:100%*]Eumetazoa@PRO_ENSMUSP00000057332[133][RRM1:100%****][put-sr:97%****][RNPS1:64%****][KOG4209:86%****]Apis mellifera@SMA_UPI0000513642[RRM1][put-sr]Caenorhabditis@PRO_K02F3_11_2[6][RRM1:100%*][put-sr:100%*][KOG4209:67%*]

Schizosaccharomyces_pombe@PRO_NP_596549[4][RRM1:100%*][put-sr:100%*]Pezizomycotina@SMA_Q2PIY9_ASPOR[16][RRM1:100%**][put-sr:81%**][KOG0111:6%]Filobasidiella_neoformans@PRO_XP_569824[5][RRM1:100%*][put-sr:100%*]

Pan troglodytes@SMA_UPI0000494C3A[RRM1][put-sr][KOG0147]Eukaryota@PRO_ENSFCAP00000006163[253][RRM2:92%*****][.RRM1:8%***][put-sr:87%*****][UMH:28%****][.CAPER:19%***][KOG0147:100%*****]

Bacillariophyta@PRO_jgi_Phatr2_20857[2][RRM2:100%][put-sr:100%][KOG0147:100%]Dictyostelium discoideum_AX4@PRO_XP_638262[3][RRM2:100%*][put-sr:100%*][KOG0670:100%*]

2827 - RNPS1

26 - SR45

17 - single-RRM

Zc-K SR proteins

part of 16

- dual-RRM

SR proteins

18

21

19 - cyclophilin

20 - RBM

part of 16

- dual-RRM

SR proteins

Fungal SR (SpSrp2)

Fungal SR (SpSrp1)

Fungal SpRnps1Fig. S9

122

79

80

84

51

83

58

69

65

86

66

Dictyostelium discoideum AX4@PRO XP 644081[3][RRM3:100%*][KOG0123:100%*]Paramecium tetraurelia@REF_XP_001432601[2][RRM2:100%][KOG0146:100%]

Tetrahymena thermophila_SB210@SMA_Q22JW6_TETTH[4][RRM1:50%][.RRM3:50%][KOG0144:50%][.KOG0146:50%]Cryptosporidium@SMA_Q5CJX5_CRYHO[4][RRM3:100%*][put-sr:100%*][KOG0144:100%*]

Eukaryota@REF_XP_742626[566][RRM3:69%*****][.RRM2:20%****][.RRM1:10%****][Bruno:46%*****][KOG0144:51%*****][.KOG0146:49%*****]Tetrahymena thermophila_SB210@REF_XP_001023043[2][RRM3:100%][KOG0144:100%]

Plasmodium@PRO_XP_001350320[4][RRM2:75%*][.RRM1:25%][KOG0123:100%*]Plasmodium@PRO_XP_001350320[4][RRM3:75%*][.RRM2:25%][KOG0123:100%*]Aconoidasida@REF_XP_672316[30][RRM2:60%**][.RRM1:40%**][KOG0146:73%***][.KOG0144:17%*][.KOG0145:10%*]

Plasmodium yoelii_yoelii@SMA_Q7RL66_PLAYO[RRM2][KOG0146]Trichomonas vaginalis_G3@REF_XP_001302991[2][RRM4:100%][KOG0123:100%]Trichomonas vaginalis_G3@REF_XP_001303266[RRM4][KOG0123]

Caenorhabditis briggsae@REF_XP_001670970[RRM2][KOG0117]Trichomonas vaginalis_G3@REF_XP_001302992[11][RRM2:100%**][KOG0123:100%**]

Sordariomycetes@REF_XP_360527[6][RRM1:100%*][KOG0110:83%*][.KOG0123:17%]Saccharomycetaceae@PRO_NP_984845[4][RRM2:100%*][KOG0123:100%*]

Encephalitozoon_cuniculi@SMA_Q8SR30_ENCCU[3][RRM2:100%*][put-sr:100%*][KOG0123:100%*]Eukaryota@SMA_UPI0000494B5B[859][RRM2:95%******][.RRM1:5%***][PABP:44%*****][KOG0123:78%******][.KOG0131:22%*****]

Leishmania@PRO_XP_001466041[5][RRM2:100%*][KOG0123:100%*]Arabidopsis thaliana@SMA_Q9FX22_ARATH[4][RRM1:75%*][.RRM2:25%][PABP:100%*][KOG0123:100%*]

Schizosaccharomyces_pombe@PRO_NP_593427[3][RRM2:100%*][KOG0123:100%*]Schizosaccharomyces_pombe@SMA_PABPX_SCHPO[3][RRM3:100%*][KOG0123:100%*]

Oryza sativa_japonica_cultivar-group@PRO_NP_001049727[2][RRM2:100%][KOG0123:100%]rosids@PRO_30146_m003481[4][RRM2:100%*][PABP:75%*][KOG0123:100%*]

rosids@PRO_30078_m002213[5][RRM2:100%*][PABP:60%*][KOG0123:100%*]Trypanosomatidae@SMA_Q643Z0_CRIFA[11][RRM4:100%**][KOG0123:100%**]

Trypanosomatidae@SMA_Q4E4I9_TRYCR[11][RRM4:100%**][KOG0123:100%**]Oryza sativa_japonica_cultivar-group@PRO_NP_001049727[2][RRM3:100%][KOG0123:100%]

rosids@PRO_30078_m002213[5][RRM3:100%*][PABP:60%*][KOG0123:100%*]Arabidopsis thaliana@PRO_NP_195978[3][RRM1:100%*][KOG0123:100%*]

Ricinus communis@PRO_30146_m003481[RRM3][KOG0123]Dictyostelium discoideum_AX4@SMA_Q54D57_DICDI[3][RRM2:100%*][KOG0145:100%*]

Filobasidiella_neoformans@SMA_Q55XM4_CRYNE[5][RRM1:100%*][put-sr:40%][KOG0123:60%*][.KOG0148:40%]Ustilago maydis_521@SMA_Q4P9A2_USTMA[3][RRM2:100%*][KOG0123:100%*]

Dictyostelium_discoideum@PRO_XP_001134510[4][RRM4:100%*][KOG0123:100%*]Trichomonas vaginalis_G3@REF_XP_001324580[RRM2][KOG0131]

Yarrowia lipolytica@PRO_XP_503979[3][RRM2:100%*][KOG0131:100%*]Saccharomycetales@PRO_XP_001385635[11][RRM2:100%**][KOG0131:100%**]

Tetrahymena thermophila_SB210@REF_XP_001008485[2][RRM2:100%][KOG0131:100%]Bigelowiella natans@SMA_Q3LWM7_CHLS6[RRM2][KOG0131]

Cryptosporidium@SMA_Q5CWM4_CRYPV[4][RRM2:100%*][KOG0131:100%*]Dictyostelium discoideum_AX4@SMA_Q556F3_DICDI[3][RRM2:100%*][KOG0123:100%*]

Trypanosomatidae@PRO_XP_001468777[9][RRM2:100%**][KOG0144:100%**]Volvox carteri@PRO_jgi_Volca1_116517[RRM2][KOG1984]

Dictyostelium discoideum_AX4@PRO_XP_646802[3][RRM2:100%*][KOG0145:100%*]Eumetazoa@PRO_ENSTBEP00000005385[198][RRM2:90%*****][.RRM1:10%**][P54nrb:38%****][.PSF:22%***][.PSP1:20%***][KOG0115:100%*****]

Yarrowia lipolytica@SMA_Q6CG61_YARLI[3][RRM3:100%*][KOG0123:100%*]Bilateria@SMA_Q5U586_XENLA[4][RRM3:100%*][KOG0123:100%*]

Leishmania@PRO_XP_001466041[5][RRM4:100%*][KOG0123:100%*]Sophophora@SMA_Q28WW6_DROPS[5][RRM2:100%*][KOG0123:100%*]

Pezizomycotina@SMA_Q5B630_EMENI[15][RRM4:100%**][KOG0123:100%**]Arabidopsis thaliana@SMA_O04319_ARATH[3][RRM4:100%*][PABP:100%*][KOG0123:100%*]

Aedes aegypti@PRO_AAEL007013-PA[2][RRM1:100%][KOG0123:100%]Oryza_sativa@SMA_Q259G3_ORYSA[4][RRM3:100%*][KOG0123:100%*]

Oikopleura dioica@SMA_Q6E7B9_OIKDI[RRM4][KOG0123]Canis familiaris@SMA_UPI00005A28E0[2][RRM4:100%][PABP:100%][KOG0123:100%]Pan troglodytes@SMA_UPI0000494B5B[RRM4][KOG0123]

Trypanosomatidae@SMA_O96971_9TRYP[11][RRM3:100%**][KOG0123:100%**]Echinops telfairi@PRO_ENSETEP00000008100[RRM3][PABP][KOG0123]

Rattus norvegicus@REF_XP_001070732[RRM1][KOG0123]Eukaryota@REF_XP_001154366[1189][RRM4:46%******][.RRM3:45%******][.RRM2:6%****][PABP:61%******][KOG0123:100%*******]

Encephalitozoon cuniculi_GB-M1@PRO_NP_586099[RRM2][KOG0131]Felis catus@PRO_ENSFCAP00000004622[RRM3][PABP][KOG0123]

Trypanosomatidae@SMA_Q4E4I9_TRYCR[5][RRM3:100%*][KOG0123:100%*]Trichomonas vaginalis_G3@REF_XP_001303266[RRM3][KOG0123]

Dikarya@REF_XP_001560741[58][RRM3:100%****][PABP:10%*][KOG0123:100%****]Yarrowia lipolytica@SMA_Q6CDH3_YARLI[3][RRM3:100%*][KOG0123:100%*]

Strongylocentrotus purpuratus@REF_NP_001091917[7][RRM3:71%*][.RRM2:29%][KOG0123:100%*]Dictyostelium discoideum_AX4@SMA_Q54BM2_DICDI[3][RRM3:100%*][KOG0123:100%*]

Chlamydomonadales@PRO_jgi_Volca1_82578[3][RRM3:100%*][PABP:100%*][KOG0123:100%*]Oikopleura dioica@SMA_Q6E7B9_OIKDI[RRM3][KOG0123]

Thalassiosira pseudonana@PRO_jgi_Thaps3_13224[RRM3][KOG0123]Phytophthora@PRO_jgi_Physo1_1_108322[2][RRM3:100%][KOG0123:100%]

Phaeodactylum tricornutum@PRO_jgi_Phatr2_23959[RRM3][KOG0123]Strongylocentrotus purpuratus@SMA_UPI0000584A56[5][RRM1:100%*][KOG0117:80%*][.KOG0122:20%]

Trypanosomatidae@REF_XP_001568515[11][RRM2:100%**][KOG0123:100%**]Entamoeba histolytica_HM-1_IMSS@SMA_Q50S75_ENTHI[RRM1][KOG0123]

Entamoeba histolytica_HM-1_IMSS@REF_XP_649839[2][RRM2:100%][KOG0123:100%]Trypanosomatidae@SMA_Q4D576_TRYCR[5][RRM1:100%*][KOG0144:100%*]

Oryza sativa_japonica_cultivar-group@SMA_Q7EY44_ORYSA[RRM2][KOG0117]Embryophyta@PRO_jgi_Phypa1_1_140180[10][RRM2:50%*][.RRM3:40%*][.RRM1:10%][KOG0117:100%**]

Oryza sativa_japonica_cultivar-group@SMA_Q6ZLD1_ORYSA[RRM3][KOG0117]Entamoeba_histolytica@REF_XP_655058[3][RRM1:100%*][KOG0110:67%][.KOG0123:33%]

Schizosaccharomyces_pombe@PRO_NP_595599[2][RRM1:100%][KOG0110:100%]Plasmodium@SMA_Q4X692_PLACH[10][RRM1:90%**][.RRM2:10%]

Kluyveromyces lactis@SMA_MRD1_KLULA[RRM1][KOG0110]Saccharomycetales@SMA_MRD1_ASHGO[3][RRM1:100%*][KOG0110:100%*]

Dictyostelium discoideum_AX4@PRO_XP_638463[3][RRM1:100%*][KOG0110:100%*]Cryptosporidium@SMA_Q5CMP8_CRYHO[2][RRM1:100%][KOG0110:100%]

Trichomonas vaginalis_G3@REF_XP_001324476[RRM1][KOG0110]Trichocomaceae@SMA_MRD1_ASPFU[3][RRM1:100%*][KOG0110:100%*]

Pezizomycotina@SMA_UPI000021AFC7[6][RRM1:100%*][KOG0110:100%*]Viridiplantae@PRO_jgi_Phypa1_1_207810[5][RRM1:100%*][KOG0110:100%*]

Cyanidioschyzon merolae@PRO_gnl_CMER_CMO246C[RRM1][KOG0110]Saccharomycetales@PRO_XP_001386803[11][RRM1:100%**][KOG0110:100%**]

Ustilago_maydis@PRO_XP_758493[3][RRM1:100%*][KOG0110:100%*]Arabidopsis thaliana@PRO_NP_196191[5][RRM1:100%*][KOG0110:100%*]

Encephalitozoon_cuniculi@PRO_NP_597181[2][RRM1:100%][KOG0110:100%]Drosophila melanogaster@PRO_CG3335-PA[3][RRM1:100%*][KOG0110:100%*]

Apocrita@PRO_XP_624611[8][RRM1:100%**][KOG0110:100%**]Oligohymenophorea@REF_XP_001454919[3][RRM1:100%*][KOG0110:100%*]

Chironomus tentans@SMA_Q95ZH1_CHITE[RRM1][KOG0110]Caenorhabditis@PRO_T23F6_4_1[6][RRM1:100%*][KOG0110:100%*]

Culicidae@PRO_AGAP005249-PA[6][RRM1:100%*][KOG0110:100%*]Euteleostomi@PRO_GSTENP00029551001[53][RRM1:100%***][put-sr:9%*][KOG0110:100%***]

Rattus norvegicus@SMA_UPI0000507A4B[RRM1][KOG0110]Entamoeba histolytica_HM-1_IMSS@SMA_Q50XW2_ENTHI[RRM1][put-sr]

Entamoeba histolytica_HM-1_IMSS@REF_XP_649199[2][RRM1:100%][put-sr:100%]Bombyx mori@REF_NP_001037313[2][RRM1:100%][KOG4365:100%]

Nasonia vitripennis@PRO_XP_001604488[2][RRM1:100%]Gallus gallus@SMA_UPI0000448E6E[2][RRM1:100%][KOG4365:100%]

Encephalitozoon_cuniculi@SMA_Q8SR30_ENCCU[3][RRM1:100%*][put-sr:100%*][KOG0123:100%*]Apis mellifera@SMA_UPI0000519A16[RRM1][KOG4341]

Trichomonas vaginalis_G3@REF_XP_001300794[RRM1]Trichomonas vaginalis_G3@REF_XP_001328309[3][RRM1:100%*][KOG0123:100%*]

Trichomonas vaginalis_G3@REF_XP_001303266[RRM1][KOG0123]Trichomonas vaginalis_G3@REF_XP_001309092[RRM1][KOG0123]

Trichomonas vaginalis_G3@REF_XP_001301635[RRM1][KOG0123]Trichomonas vaginalis_G3@REF_XP_001307992[RRM1][KOG0123]

Trichomonas vaginalis_G3@REF_XP_001313255[RRM1][KOG0123]

1

5 - PABP

6 - PABP

4 - PABP

p54nrb

PSP1

PSF

includes 67 - UMH

9 - Bruno

Fig. S9

123

57

78

96

80

78

88 68

68

90

87

67 56

89

Oryza sativa japonica cultivar group@SMA Q6ZLD1 ORYSA[RRM1][KOG0117]Trichomonas vaginalis_G3@REF_XP_001300116[RRM1]

Phaeodactylum tricornutum@PRO_jgi_Phatr2_44468[RRM1]Thalassiosira pseudonana@PRO_jgi_Thaps3_20887[RRM1]

Plasmodium@PRO_XP_966276[8][RRM1:50%*][.RRM2:50%*][KOG0117:38%*][.KOG0148:12%]Tribolium castaneum@SMA_UPI0000D5702C[RRM1][put-sr]

Paramecium tetraurelia@REF_XP_001459353[4][RRM2:100%*][KOG0123:100%*]Paramecium tetraurelia@REF_XP_001425411[RRM2][KOG0123]

Nematostella vectensis@REF_XP_001628761[RRM1]Tribolium castaneum@PRO_XP_969873[3][RRM1:100%*]

Apocrita@PRO_XP_001604373[7][RRM1:100%*]Strongylocentrotus purpuratus@PRO_XP_001185821[5][RRM1:100%*][KOG0670:80%*]

Euteleostomi@SMA_UPI0000548A84[3][RRM1:100%*][put-sr:33%][KOG0670:33%]Caenorhabditis briggsae@SMA_Q61CW8_CAEBR[RRM1]

Strongylocentrotus purpuratus@REF_XP_001176395[3][RRM1:100%*]Drosophila melanogaster@REF_NP_996010[2][RRM1:100%][KOG0107:100%]

Euteleostomi@PRO_ENSOANP00000024755[315][RRM1:100%*****][hnRNP:53%*****][.RALYL:13%***]Tetrahymena thermophila_SB210@REF_XP_001022345[2][RRM1:50%][.RRM2:50%][KOG0148:50%]

Encephalitozoon_cuniculi@PRO_NP_585962[3][RRM2:100%*][KOG0123:100%*]Aureococcus anophagefferens@PRO_jgi_Auran1_67810[RRM1][put-sr][KOG0120]

Aureococcus anophagefferens@PRO_jgi_Auran1_66158[RRM1][put-sr][KOG0149]Nematostella vectensis@REF_XP_001640397[RRM1][KOG0111]Theileria@SMA_Q4N1I8_THEPA[4][RRM1:100%*][KOG0151:100%*]

rosids@PRO_NP_568388[5][RRM1:100%*][KOG0148:60%*][.KOG0125:20%]Physcomitrella patens@PRO_jgi_Phypa1_1_151460[4][RRM1:100%*][KOG0108:75%*][.KOG0149:25%]

Chlamydomonas reinhardtii@PRO_jgi_Chlre3_194261[RRM1][KOG0123]Aureococcus anophagefferens@PRO_jgi_Auran1_17171[RRM1][KOG0108]

Phaeodactylum tricornutum@PRO_jgi_Phatr2_33658[RRM1]Thalassiosira pseudonana@PRO_jgi_Thaps3_263845[RRM1][KOG0108]

Anopheles_gambiae@PRO_AGAP000921-PA[9][RRM1:100%**]Ustilago maydis_521@PRO_XP_757329[3][RRM1:100%*][KOG0145:100%*]

Entamoeba histolytica_HM-1_IMSS@REF_XP_649094[2][RRM1:100%][KOG0148:100%]Nematostella vectensis@REF_XP_001624592[RRM1][KOG0148]

Bilateria@PRO_ENSSARP00000011721[211][RRM1:100%*****][TIATIAR:80%*****][KOG0148:100%*****]Oryza_sativa@SMA_Q9XEV3_ORYSA[2][RRM1:100%][KOG0148:100%]

Embryophyta@PRO_NP_188026[30][RRM1:100%***][oligoU:43%**][KOG0148:100%***]Vanderwaltozyma polyspora_DSM_70294@REF_XP_001647444[RRM1][KOG0123]

Saccharomycetaceae@SMA_PES4_YEAST[13][RRM1:100%**][KOG0123:100%**]Candida_glabrata@PRO_XP_447635[3][RRM1:100%*][KOG0123:100%*]

rosids@PRO_30078_m002213[5][RRM1:100%*][PABP:60%*][KOG0123:100%*]Ricinus communis@PRO_30146_m003481[RRM1][KOG0123]

Arabidopsis thaliana@PRO_NP_188259[3][RRM1:100%*][PABP:100%*][KOG0123:100%*]Oryza sativa_japonica_cultivar-group@PRO_NP_001049727[2][RRM1:100%][KOG0123:100%]

Leishmania@REF_XP_001565513[5][RRM1:100%*][KOG0123:100%*]Trypanosomatidae@REF_XP_001568515[11][RRM1:100%**][KOG0123:100%**]

Danio rerio@PRO_ENSDARP00000091192[32][RRM1:100%***][put-sr:97%***][KOG0123:100%***]Tetraodon nigroviridis@PRO_GSTENP00024897001[RRM1][PABP][KOG0123]

Pan troglodytes@SMA_UPI00004927B4[RRM1][PABP][KOG0123]Eukaryota@PRO_ENSXETP00000023927[663][RRM1:100%******][PABP:56%*****][KOG0123:100%******]

Tetraodon nigroviridis@SMA_Q4RJX8_TETNG[RRM1][KOG0123]Ciona intestinalis@PRO_ENSCINP00000004384[RRM2][KOG0148]

Nematostella vectensis@REF_XP_001624592[RRM2][KOG0148]Entamoeba histolytica_HM-1_IMSS@SMA_Q50Q39_ENTHI[2][RRM2:100%][KOG0148:100%]

Dictyostelium discoideum_AX4@PRO_XP_641688[3][RRM1:100%*][KOG0117:100%*]Strongylocentrotus purpuratus@PRO_XP_001183631[5][RRM2:100%*][KOG0148:100%*]

Physcomitrella patens@PRO_jgi_Phypa1_1_170658[RRM1]Phaeodactylum tricornutum@PRO_jgi_Phatr2_13402[RRM1][KOG0226]

Thalassiosira pseudonana@PRO_jgi_Thaps3_18991[RRM1][KOG0226]Cryptococcus_neoformans_var._neoformans@PRO_XP_571861_RRM

Trichomonas vaginalis_G3@REF_XP_001324421[RRM1][KOG0226]Nasonia vitripennis@PRO_XP_001603091[2][RRM1:100%][KOG0226:100%]Eukaryota@PRO_XP_964958[208][RRM1:100%*****][KOG0226:100%*****]

Eukaryota@PRO_IMGA_AC144483_30_2[327][RRM2:85%*****][.RRM1:15%***][TIATIAR:53%*****][.oligoU:5%**][KOG0148:99%*****]Ustilago maydis_521@PRO_XP_757329[3][RRM2:100%*][KOG0145:100%*]

Yarrowia lipolytica@PRO_XP_501542[3][RRM2:100%*][KOG0131:100%*]Saccharomycetales@REF_XP_001525917[4][RRM2:75%*][.RRM1:25%][put-sr:75%*][KOG0148:100%*]

Saccharomycetaceae@PRO_XP_461354[6][RRM2:83%*][.RRM1:17%][KOG0148:100%*]Dictyostelium discoideum_AX4@PRO_XP_635179[3][RRM1:100%*][KOG0148:100%*]

Aureococcus anophagefferens@PRO_jgi_Auran1_28594[RRM2][KOG0148]Saccharomycetales@PRO_XP_448512[22][RRM1:68%**][.RRM2:32%*][KOG0148:73%**][.KOG3598:14%*][.KOG0145:14%*]

Strongylocentrotus purpuratus@PRO_XP_793862[5][RRM2:80%*][.RRM1:20%][KOG0144:80%*][.KOG0148:20%]Endopterygota@PRO_AAEL011988-PA[16][RRM2:94%**][.RRM1:6%][KOG0144:62%**][.KOG0145:31%*][.KOG0123:6%]

Schistosoma japonicum@SMA_Q5DE20_SCHJA[RRM2][KOG0123]Gallus gallus@SMA_UPI0000447A2F[RRM1]

Eukaryota@PRO_ENSMUSP00000030730[184][RRM2:86%*****][.RRM1:14%***][oligoU:12%***][KOG0148:64%****][.KOG0123:19%***][.KOG0131:11%**]Caenorhabditis@SMA_Q22318_CAEEL[2][RRM2:100%][KOG0144:100%]

Cyanidioschyzon merolae@PRO_gnl_CMER_CMS187C[RRM1][KOG0123]Trichomonas vaginalis_G3@REF_XP_001309092[RRM2][KOG0123]

Chlamydomonadales@PRO_jgi_Volca1_107765[2][RRM1:100%][KOG0145:100%]Dictyostelium discoideum_AX4@PRO_XP_629639[3][RRM1:100%*][KOG0145:100%*]

Nematostella vectensis@REF_XP_001634736[RRM1][KOG0145]Trypanosoma_cruzi@REF_XP_803891[2][RRM1:100%][put-sr:100%][KOG0145:100%]

Eumetazoa@PRO_ENSORLP00000021434[539][RRM1:100%******][ELAV:70%*****][KOG0145:100%******]Drosophila melanogaster@PRO_CG5213-PA[3][RRM1:100%*][KOG0145:100%*]

Trypanosomatidae@REF_XP_806018[11][RRM1:100%**][KOG0145:100%**]Trypanosomatidae@PRO_XP_828145[27][RRM1:100%***][KOG0145:100%***]Trypanosoma@PRO_XP_845996[6][RRM1:100%*][KOG0145:50%*][.KOG0122:50%*]

Trypanosomatidae@PRO_XP_829272[11][RRM1:100%**][KOG0122:73%**][.KOG0145:27%*]Leishmania@PRO_XP_001463468[5][RRM1:100%*]

Trypanosomatidae@SMA_Q382W9_9TRYP[11][RRM1:100%**][KOG0145:45%*]Bilateria@SMA_UPI000065CB41[270][RRM1:100%*****][RBMS:74%*****][KOG0145:99%*****]

Schizosaccharomyces pombe@SMA_O94381_SCHPO[RRM1][KOG0145]Sordariales@SMA_Q2H0P1_CHAGB[2][RRM1:100%][KOG0145:100%]Aspergillus fumigatus@SMA_Q4WM63_ASPFU[RRM1][KOG0145]

Trypanosomatidae@SMA_Q57W93_9TRYP[11][RRM1:100%**]Leishmania@REF_XP_001683407[5][RRM1:100%*]Trypanosoma@REF_XP_811157[6][RRM2:100%*][KOG0145:50%*]Trypanosoma@SMA_Q4DZG2_TRYCR[6][RRM1:100%*][KOG0145:50%*]

Leishmania@PRO_XP_001463160[4][RRM2:100%*][put-sr:100%*]Leishmania major@SMA_Q4QJ00_LEIMA[RRM1][put-sr]

Tetrahymena thermophila_SB210@REF_XP_001023873[2][RRM1:100%][KOG0108:100%]Paramecium tetraurelia@REF_XP_001435827[2][RRM1:100%][KOG4208:100%]

Dictyostelium_discoideum@PRO_XP_643547[4][RRM1:100%*]Anopheles_gambiae@PRO_AGAP006090-PA[4][RRM1:100%*][KOG4208:25%]

Phaeodactylum tricornutum@PRO_jgi_Phatr2_45356[RRM1][KOG4208]Eukaryota@PRO_CG6937-PA[195][RRM1:100%*****][KOG4208:98%*****]

Caenorhabditis@REF_XP_001665662[5][RRM1:100%*][KOG4208:100%*]Trypanosomatidae@PRO_XP_001467067[14][RRM1:100%**][KOG0144:100%**]

Leishmania major_strain_Friedlin@SMA_Q4FXR5_LEIMA[RRM1][KOG0144]Dictyostelium discoideum_AX4@SMA_Q556F3_DICDI[3][RRM1:100%*][KOG0123:100%*]

Dictyostelium discoideum_AX4@SMA_Q55BM9_DICDI[3][RRM1:100%*][KOG0145:100%*]Guillardia theta@REF_NP_113243[2][RRM2:100%][KOG0123:100%]

Dictyostelium discoideum_AX4@SMA_Q54G90_DICDI[3][RRM2:100%*][KOG0145:100%*]Dictyostelium discoideum_AX4@PRO_XP_635793[3][RRM1:100%*][KOG0145:100%*]

Trichomonas vaginalis_G3@REF_XP_001319541[RRM1][KOG0144]Trichomonas vaginalis_G3@REF_XP_001579752[2][RRM1:100%][KOG0145:100%]

Trichomonas vaginalis_G3@REF_XP_001325514[RRM1][KOG0145]Kluyveromyces lactis@SMA_Q6CXV3_KLULA[RRM2][KOG0144]

Saccharomycetales@SMA_Q6FTW8_CANGA[2][RRM3:50%][.RRM2:50%][KOG0108:50%]Dictyostelium discoideum_AX4@PRO_XP_644081[3][RRM3:100%*][KOG0123:100%*]

82

10 - ELAV

77 - TIA TIAR

OligoU

3 - PABP

76 - TIA TIAR

OligoU

86 - hnRNP

RALYL

62

Fig. S9

124

52

70 65

65

67

61

63 67

96

56 64

68

70

77

63

83

67

Coelomata@PRO CG4787 PA[243][RRM3:73%*****][ RRM2:16%***][ RRM1:12%***][TIATIAR:75%*****][KOG0148:100%*****]Caenorhabditis@PRO_Y46G5A_13[22][RRM2:55%**][.RRM3:45%**][KOG0148:100%***]

Embryophyta@SMA_Q1SGW2_MEDTR[34][RRM3:91%***][.RRM2:9%*][oligoU:47%**][KOG0148:100%***]Entamoeba histolytica_HM-1_IMSS@SMA_Q50Q39_ENTHI[2][RRM3:100%][KOG0148:100%]

Dikarya@REF_XP_001486325[48][RRM3:94%***][put-sr:19%**][KOG0148:96%***]Anopheles_gambiae@SMA_ENSANGP00000019784[2][RRM1:100%]

Anopheles gambiae_str._PEST@SMA_Q7QK15_ANOGA[RRM1]Euteleostomi@SMA_ENSDARP00000002433[17][RRM2:100%**][RBM:59%**][KOG0144:76%**][.KOG0145:18%*]

Apocrita@PRO_XP_001604889[3][RRM2:100%*][KOG0144:100%*]Dictyostelium discoideum_AX4@PRO_XP_636266[3][RRM1:100%*][KOG3598:100%*]

Endopterygota@PRO_CG1316-PA[17][RRM1:100%**][KOG0144:71%**][.KOG0148:29%*]Euteleostomi@PRO_ENSDNOP00000001522[53][RRM1:100%***][RBM:64%***][KOG0144:83%***][.KOG0145:13%*]

Strongylocentrotus purpuratus@PRO_XP_001199679[9][RRM1:100%**][KOG0145:56%*]Culicidae@PRO_AAEL001131-PA[6][RRM1:100%*][KOG0113:100%*]

Nematostella vectensis@REF_XP_001638999[RRM2][KOG0144]Ciona@PRO_ENSCSAVP00000018820[2][RRM2:100%][KOG0145:100%]

Euteleostomi@PRO_ENSXETP00000044031[104][RRM2:79%****][.RRM1:21%***][KOG0145:38%***][.KOG0123:18%**][.KOG0110:12%**]Nematostella vectensis@REF_XP_001630797[RRM2][KOG0117]

Eumetazoa@PRO_ENSLAFP00000012959[458][RRM3:90%******][.RRM2:7%***][hnRNP:36%*****][KOG0117:100%******]Aureococcus anophagefferens@PRO_jgi_Auran1_31715[RRM1][KOG0149]Volvox carteri@PRO_jgi_Volca1_84128[RRM2][KOG0147]

Oryza_sativa@SMA_Q259G3_ORYSA[4][RRM4:100%*][KOG0123:100%*]Oryza_sativa@SMA_Q259G3_ORYSA[4][RRM5:100%*][KOG0123:100%*]

Ustilago maydis_521@SMA_Q4PI09_USTMA[3][RRM1:100%*]Cryptococcus neoformans_var._neoformans_B-3501A@SMA_Q55MI2_CRYN

Embryophyta@PRO_jgi_Phypa1_1_189930[13][RRM1:100%**][KOG0119:85%**][.KOG0307:15%]Oryza_sativa@SMA_Q259G3_ORYSA[4][RRM6:100%*][KOG0123:100%*]

Oryza_sativa@SMA_Q259G3_ORYSA[4][RRM1:100%*][KOG0123:100%*]Oryza_sativa@PRO_NP_001054296[4][RRM2:100%*][KOG0123:100%*]

Drosophila melanogaster@PRO_CG5213-PA[3][RRM2:100%*][KOG0145:100%*]Anopheles gambiae_str._PEST@SMA_Q5TTX2_ANOGA[RRM1]

Caenorhabditis@REF_XP_001664781[8][RRM1:100%**][KOG0115:100%**]Ricinus communis@PRO_30169_m006629[RRM1][KOG0123]

Filobasidiella_neoformans@PRO_XP_572996[5][RRM1:100%*]Ustilago maydis_521@PRO_XP_760296[3][RRM1:100%*]

Endopterygota@REF_NP_001040210[9][RRM1:100%**]Drosophila melanogaster@PRO_CG14414-PB[3][RRM1:100%*]

Euteleostomi@PRO_ENSOANP00000013028[46][RRM1:100%***]Nematostella vectensis@REF_XP_001638014[RRM1]

Trypanosomatidae@SMA_Q57TU8_9TRYP[11][RRM1:100%**][KOG0110:45%*][.KOG0127:27%*][.KOG0145:18%][.KOG0144:9%]Leishmania@PRO_XP_001466659[5][RRM1:100%*][KOG0145:100%*]

Leishmania@SMA_Q4FXR8_LEIMA[5][RRM1:100%*][KOG0110:100%*]Trypanosoma@SMA_Q57WC9_9TRYP[15][RRM1:100%**][put-sr:20%*][KOG0110:100%**]

Leishmania@SMA_Q4FXR7_LEIMA[5][RRM1:100%*][KOG0148:60%*][.KOG0145:40%]Leishmania@REF_XP_001563945[10][RRM1:100%**][put-sr:10%][KOG0145:100%**]

Leishmania@PRO_XP_001464836[5][RRM1:100%*][KOG0145:80%*][.KOG0148:20%]Endopterygota@SMA_SXL_CHRRU[56][RRM2:100%****][KOG0145:100%****]

Trichocomaceae@SMA_Q5BFT8_EMENI[3][RRM1:67%][.RRM2:33%][KOG0145:67%]Eumetazoa@PRO_ENSORLP00000004891[177][RRM2:92%*****][.RRM1:8%**][RBMS:80%****][KOG0145:100%*****]Sordariomycetes@SMA_UPI000021B021[4][RRM2:100%*][KOG0145:100%*]

Nematostella vectensis@REF_XP_001634736[RRM2][KOG0145]Ustilago maydis_521@PRO_XP_759141[3][RRM2:100%*][KOG0145:100%*]

Bilateria@SMA_Q966S6_BRABE[470][RRM2:95%******][.RRM1:5%***][ELAV:83%*****][KOG0145:100%******]Nematostella vectensis@REF_XP_001626979[RRM2][KOG0145]

Thalassiosira pseudonana@PRO_jgi_Thaps3_261541[RRM2][KOG0144]Apicomplexa@REF_XP_678037[28][RRM2:96%***][put-sr:14%*][KOG0144:96%***]

Embryophyta@PRO_29889_m003323[28][RRM2:96%***][FCAFPA:36%**][KOG0144:100%***]Cryptosporidium_parvum@PRO_XP_628265[3][RRM2:100%*][KOG0144:100%*]

Tetrahymena thermophila_SB210@SMA_Q22JW7_TETTH[2][RRM2:100%][KOG0144:100%]Eumetazoa@SMA_ENSANGP00000005501[568][RRM2:74%******][.RRM1:26%****][Bruno:56%*****][KOG0146:53%*****][.KOG0144:47%*****]

Dictyostelium discoideum_AX4@SMA_Q54EJ3_DICDI[3][RRM2:100%*][KOG0144:100%*]Dictyostelium discoideum_AX4@SMA_Q55D63_DICDI[3][RRM2:100%*][KOG0146:100%*]

Phytophthora@PRO_jgi_Physo1_1_133760[2][RRM2:100%][KOG0144:100%]Embryophyta@PRO_jgi_Phypa1_1_115029[20][RRM2:95%**][.RRM1:5%][KOG0144:100%**]

Oryza sativa_japonica_cultivar-group@SMA_Q7XAN8_ORYSA[3][RRM2:100%*][KOG0144:100%*]Volvox carteri@PRO_jgi_Volca1_72841[RRM1][KOG0144]

Chlamydomonadales@SMA_Q6RBZ0_CHLRE[3][RRM1:67%][.RRM2:33%][KOG0144:100%*]Chlamydomonadales@PRO_jgi_Volca1_72841[3][RRM2:67%][.RRM3:33%][KOG0144:100%*]Trypanosomatidae@SMA_Q4E5H3_TRYCR[10][RRM1:100%**][KOG0144:100%**]Chlamydomonadales@PRO_jgi_Volca1_118581[3][RRM2:67%][.RRM4:33%][KOG0144:67%][.KOG1240:33%]

Volvox carteri@PRO_jgi_Volca1_88093[RRM4][KOG1240]Embryophyta@PRO_30076_m004622[20][RRM1:100%**][FCAFPA:30%*][KOG0144:100%**]

Arabidopsis thaliana@SMA_O22905_ARATH[4][RRM1:100%*][FCAFPA:100%*][KOG0144:100%*]Medicago truncatula@PRO_IMGA_AC155099_2_2[3][RRM1:100%*][KOG0144:100%*]Chlamydomonadales@PRO_jgi_Volca1_88093[2][RRM1:100%][KOG1240:100%]

Thalassiosira pseudonana@PRO_jgi_Thaps3_261541[RRM1][KOG0144]Phaeodactylum tricornutum@PRO_jgi_Phatr2_42828[RRM1][KOG0144]

Phytophthora@PRO_jgi_Phyra1_1_82644[2][RRM1:100%][KOG0144:100%]Cryptosporidium@SMA_Q5CJX5_CRYHO[4][RRM1:100%*][put-sr:100%*][KOG0144:100%*]

Aconoidasida@SMA_Q8IDB7_PLAF7[17][RRM1:100%**][KOG0144:100%**]Plasmodium_vivax@SMA_Q4Z2X6_PLABE[3][RRM1:100%*][KOG0144:100%*]

Plasmodium@REF_XP_001614930[11][RRM1:100%**][KOG0146:55%*][.KOG0145:27%*][.KOG0144:18%]Theileria@SMA_Q4N6G9_THEPA[5][RRM1:100%*][KOG0144:100%*]

Eumetazoa@SMA_UPI0000583CBC[354][RRM1:100%*****][Bruno:51%*****][KOG0146:56%*****][.KOG0144:44%*****]Tetrahymena thermophila_SB210@REF_XP_001033355[2][RRM1:100%][KOG0144:100%]

Tetrahymena thermophila_SB210@SMA_Q242R7_TETTH[RRM1][KOG0144]Trypanosomatidae@SMA_Q57U22_9TRYP[12][RRM1:100%**][KOG0144:33%*][.KOG0131:25%*]

Leishmania@PRO_XP_001468236[2][RRM1:100%]Trypanosomatidae@PRO_XP_001468238[22][RRM1:100%***][KOG0144:100%***]

Embryophyta@PRO_jgi_Phypa1_1_107590[15][RRM1:100%**][KOG0144:100%**]Cryptosporidium_parvum@SMA_Q5CYW5_CRYPV[3][RRM1:100%*][KOG0144:100%*]

Dictyostelium discoideum_AX4@PRO_XP_646268[3][RRM1:100%*][KOG0146:100%*]Rattus norvegicus@SMA_UPI000050653E[RRM1][KOG0146]

Dictyostelium discoideum_AX4@SMA_Q54EJ3_DICDI[3][RRM1:100%*][KOG0144:100%*]Trichomonas vaginalis_G3@REF_XP_001312833[RRM1]Endopterygota@SMA_UPI0000D5773E[17][RRM1:100%**][put-sr:100%**][KOG0132:100%**]

Euteleostomi@SMA_UPI0000D61501[57][RRM1:100%****][put-sr:95%***][KOG0132:100%****]Theileria@REF_XP_953895[5][RRM2:100%*][put-sr:100%*][KOG4205:100%*]

Babesia bovis@REF_XP_001610820[RRM2][KOG4205]Saccharomyces cerevisiae@PRO_YGR250C[3][RRM1:100%*][KOG0108:100%*]

Saccharomycetaceae@SMA_Q6CXV3_KLULA[7][RRM1:100%*][put-sr:14%][KOG0144:86%*][.KOG0108:14%]Paramecium tetraurelia@REF_XP_001458533[RRM1][put-sr]

Sordariomycetes@SMA_Q2KH70_MAGGR[3][RRM1:100%*][KOG0153:100%*]Euteleostomi@PRO_ENSMODP00000018834[60][RRM1:100%****][put-sr:70%***][KOG0147:47%***][.KOG0132:18%**]

Ciona intestinalis@SMA_ENSCINP00000011919[RRM1]Ciona intestinalis@PRO_ENSCINP00000027768[2][RRM1:100%][KOG0548:100%]

Dictyostelium_discoideum@PRO_XP_640243[4][RRM1:100%*][KOG0117:100%*]Cryptosporidium@SMA_Q5CI46_CRYHO[2][RRM1:100%]

Trypanosoma brucei_TREU927@PRO_XP_845742[2][RRM1:100%][KOG0126:100%]Eukaryota@PRO_ENSCINP00000014101[206][RRM1:100%*****][put-sr:35%****][KOG0126:100%*****]

Ustilago maydis_521@PRO_XP_760864[3][RRM1:100%*][KOG0126:100%*]Entamoeba histolytica_HM-1_IMSS@REF_XP_656000[2][RRM1:100%][KOG0126:100%]

Embryophyta@PRO_NP_001067623[18][RRM1:100%**][KOG0117:100%**]Oryza sativa_japonica_cultivar-group@PRO_NP_001066102[3][RRM1:100%*][KOG0117:100%*]rosids@PRO_NP_001030849[10][RRM1:100%**][KOG0117:100%**]

Oryza sativa_japonica_cultivar-group@PRO_NP_001064224[3][RRM1:100%*][KOG0117:100%*]Magnoliophyta@SMA_Q6YH14_VITVI[13][RRM1:100%**][put-sr:8%][KOG0117:100%**]

Physcomitrella patens@PRO_jgi_Phypa1_1_140180[3][RRM1:100%*][KOG0117:100%*]Ricinus communis@PRO_30072_m000974[RRM1][KOG0117]

Oryza sativa_japonica_cultivar-group@SMA_Q6ZLD1_ORYSA[RRM1][KOG0117] 62

69

7 - Bruno

FCA FPA

8 - Bruno

FCA FPA

11 - ELAV

RBMS

part of 63 - hnRNP

79 - TIA TIAR

OligoU

15

Fig. S9

125

88

58

66

53

69

88

83

64

52

88

68

Ciona@PRO ENSCSAVP00000005375[6][RRM2:83%*][ RRM1:17%][KOG0116:83%*][ KOG2141:17%]Trichomonas vaginalis_G3@REF_XP_001319495[RRM1]

Encephalitozoon_cuniculi@SMA_Q8SSA1_ENCCU[3][RRM1:100%*][KOG4205:100%*]Physcomitrella patens@PRO_jgi_Phypa1_1_167900[RRM2][KOG1015]

Physcomitrella patens@PRO_jgi_Phypa1_1_188347[RRM2][KOG0123]Magnoliophyta@SMA_Q9FVQ1_ARATH[11][RRM2:91%**][.RRM1:9%][nucleolin:18%][KOG0123:55%*][.KOG4210:18%][.KOG1015:18%][.KOG0148:9%]

Arabidopsis thaliana@PRO_NP_188491[3][RRM2:100%*][nucleolin:100%*][KOG4210:100%*]Sordariomycetes@REF_XP_001221988[7][RRM2:86%*][.RRM1:14%][KOG0110:71%*][.KOG0108:14%][.KOG0123:14%]

Pezizomycotina@REF_XP_001262069[12][RRM2:100%**][KOG0110:83%**][.KOG0148:17%]Aureococcus anophagefferens@PRO_jgi_Auran1_9375[2][RRM1:100%][KOG0122:100%]

Aureococcus anophagefferens@PRO_jgi_Auran1_17018[RRM1][KOG0111]Opitutaceae bacterium_TAV2@REF_ZP_02010994[RRM1][PROK][KOG0108]

Thalassiosira pseudonana@PRO_jgi_Thaps3_33709[RRM1][KOG0111]Eukaryota@PRO_8925_m000027_AZM5_1178[175][RRM1:100%*****][put-sr:87%*****][SR:60%****][KOG4207:60%****][.KOG4368:22%***]

Thalassiosira pseudonana@PRO_jgi_Thaps3_20266[RRM1][KOG4207]Bacillariophyta@PRO_jgi_Thaps3_20223[2][RRM1:100%][KOG0108:100%]

Phaeodactylum tricornutum@PRO_jgi_Phatr2_8270[RRM1][KOG4207]Phaeodactylum tricornutum@PRO_jgi_Phatr2_49481[RRM1][KOG1337]

Cryptosporidium@PRO_XP_626081[5][RRM1:100%*][KOG0122:100%*]Pezizomycotina@PRO_XP_962933[24][RRM2:100%***][put-sr:12%*][KOG0127:100%***]

Ascomycota@PRO_XP_499726[23][RRM2:100%***][KOG0127:100%***]Plesiocystis pacifica_SIR-1@REF_ZP_01913111[RRM1][PROK][KOG0149]

Guillardia theta@SMA_Q5K255_GUITH[RRM1][put-sr][KOG0116]Chlamydomonadales@PRO_jgi_Chlre3_184151[3][RRM1:100%*][KOG0116:67%][.KOG0921:33%]

Schizosaccharomyces_pombe@PRO_NP_595090[3][RRM1:100%*]Saccharomycetales@PRO_YHL034C[4][RRM1:100%*]

Kluyveromyces lactis@PRO_XP_453971[RRM1]Trichomonas vaginalis_G3@REF_XP_001582304[RRM1]

Entamoeba histolytica_HM-1_IMSS@REF_XP_651660[2][RRM1:100%][KOG0117:100%]Cryptosporidium@SMA_Q5CKZ4_CRYHO[2][RRM1:100%]

Dictyostelium discoideum_AX4@SMA_Q55GV1_DICDI[3][RRM1:100%*]Ustilago maydis_521@SMA_Q4PBP1_USTMA[RRM1]

Filobasidiella_neoformans@PRO_XP_567374[4][RRM1:100%*][KOG0307:100%*]Embryophyta@PRO_30128_m008555[34][RRM1:100%***][KOG4660:100%***]

Entamoeba histolytica_HM-1_IMSS@SMA_Q511G8_ENTHI[RRM1][KOG4660]Chlamydomonas reinhardtii@PRO_jgi_Chlre3_152680[RRM1][KOG4660]

Filobasidiella_neoformans@SMA_Q55HC8_CRYNE[2][RRM2:100%][KOG0127:100%]Dictyostelium discoideum_AX4@PRO_XP_646584[3][RRM2:100%*][KOG0127:100%*]

Culicidae@PRO_AAEL010888-PA[3][RRM2:100%*]Aureococcus anophagefferens@PRO_jgi_Auran1_9018[RRM1]

Ostreococcus_lucimarinus@PRO_jgi_Ost9901_3_8174[2][RRM1:100%][KOG4207:100%]Ostreococcus@PRO_jgi_Ostta4_7793[3][RRM1:100%*][KOG0108:100%*]

Aureococcus anophagefferens@PRO_jgi_Auran1_17068[RRM1][KOG4207]Apicomplexa@REF_XP_764028[35][RRM1:100%***][put-sr:54%**][KOG4207:66%***][.KOG0111:14%*]

Murinae@PRO_ENSMUSP00000078984[6][RRM1:100%*][KOG4207:100%*]Phytophthora@PRO_jgi_Physo1_1_136528[2][RRM1:100%][put-sr:50%][KOG3208:50%]

Chlamydomonadales@PRO_jgi_Volca1_121229[2][RRM1:100%][put-sr:100%][KOG0415:50%]Bacillariophyta@PRO_jgi_Thaps3_23196[2][RRM1:100%][KOG4207:50%]

Phytophthora sojae@PRO_jgi_Physo1_1_138511[RRM1][put-sr]Viridiplantae@PRO_NP_001046448[46][RRM1:100%***][put-sr:96%***][SR:54%***][KOG0127:15%*][.KOG0110:11%*][.KOG4207:9%*][.KOG0122:9%*]

Schistosoma japonicum@SMA_Q86EX2_SCHJA[RRM1][put-sr]Eumetazoa@PRO_ENSETEP00000001114[107][RRM1:100%****][put-sr:93%****][SRrp:82%****][KOG0111:33%***][.KOG0415:17%**][.KOG4207:8%**]

Ciona@SMA_Q9U5Y7_CIOIN[6][RRM1:100%*][KOG0108:100%*]Euteleostomi@PRO_ENSORLP00000006283[3][RRM1:100%*][LA:67%][KOG1855:100%*]

Euteleostomi@PRO_GSTENP00013801001[72][RRM1:100%****][LA:71%***][KOG1855:97%****]Strongylocentrotus purpuratus@SMA_UPI0000586A7E[RRM1][KOG1855]

Nematostella vectensis@REF_XP_001625158[RRM1][KOG1855]Anopheles_gambiae@SMA_ENSANGP00000006836[3][RRM1:100%*][KOG1855:100%*]

Apocrita@PRO_XP_001600355[4][RRM1:100%*][KOG1855:100%*]Tribolium castaneum@SMA_UPI0000D55A0F[3][RRM1:100%*][KOG1855:100%*]

Trichomonas vaginalis_G3@REF_XP_001328836[RRM1]Drosophila melanogaster@PRO_CG3312-PA[5][RRM1:100%*][KOG0128:100%*]

Magnaporthe grisea_70-15@SMA_UPI000021BBA8[RRM2][KOG0123]Chaetomium globosum_CBS_148.51@REF_XP_001222664[2][RRM2:100%][KOG0123:100%]Schizosaccharomyces_pombe@PRO_NP_593427[3][RRM1:100%*][KOG0123:100%*]

Coelomata@REF_XP_001507449[6][RRM1:100%*][KOG1457:100%*]Ricinus communis@PRO_28452_m000049[RRM1][KOG1457]

Medicago truncatula@PRO_IMGA_CU012061_4_1[RRM1]Oryza sativa_japonica_cultivar-group@REF_NP_001063729[RRM1]

Pedobacter sp._BAL39@REF_ZP_01882800[RRM1][PROK][KOG0126]Endopterygota@SMA_Q9VAC9_DROME[21][RRM1:100%***][KOG0109:62%**]

Euteleostomi@PRO_ENSTBEP00000003150[66][RRM1:100%****][RBM:56%***][.LARK:5%*][KOG0109:98%****]Nematostella vectensis@REF_XP_001622030[RRM1][put-sr][KOG0109]

Euteleostomi@SMA_Q4SYG3_TETNG[162][RRM2:93%*****][LARK:56%****][.RBM:21%***][KOG0109:98%*****]Strongylocentrotus purpuratus@PRO_XP_792521[9][RRM1:100%**][put-sr:100%**][KOG0109:100%**]

Clupeocephala@PRO_ENSORLP00000002364[17][RRM2:100%**][KOG0109:100%**]Drosophila melanogaster@REF_NP_659571[RRM1]

Sophophora@SMA_Q7KLX0_DROME[2][RRM1:100%]Bilateria@SMA_ENSCINP00000023722[197][RRM1:85%*****][.RRM2:13%***][LARK:61%****][KOG0109:98%*****]

Ciona intestinalis@PRO_ENSCINP00000017840[RRM1][KOG0109]Danio rerio@PRO_ENSDARP00000065401[3][RRM2:100%*][KOG0109:100%*]

Caenorhabditis@SMA_RNP1_CAEEL[2][RRM1:100%][KOG0109:100%]Ciona intestinalis@PRO_ENSCINP00000017840[RRM2][KOG0109]

Ciona@PRO_ENSCSAVP00000017501[2][RRM1:50%][.RRM2:50%][KOG0109:50%]Trypanosomatidae@PRO_XP_847474[11][RRM1:100%**]

Trichomonas vaginalis_G3@REF_XP_001303000[RRM1][KOG0113]Cryptococcus_neoformans_var._neoformans@PRO_XP_566745_RRM

Physcomitrella patens@PRO_jgi_Phypa1_1_93324[RRM1]Schizosaccharomyces pombe@SMA_MSA1_SCHPO[RRM2][KOG0123]

Trypanosoma@PRO_XP_845376[2][RRM1:50%][.RRM3:50%][KOG0148:50%]Saccharomycetales@PRO_XP_001384462[10][RRM2:90%**][.RRM1:10%][KOG0117:70%*]

Pichia guilliermondii_ATCC_6260@REF_XP_001482891[RRM2]Saccharomycetales@REF_XP_001643628[10][RRM2:100%**][KOG0123:30%*]

Kluyveromyces lactis@PRO_XP_455897[3][RRM2:100%*][KOG0123:100%*]Dictyostelium discoideum_AX4@PRO_XP_641568[3][RRM2:67%][.RRM1:33%][KOG3598:100%*]

Legionella_pneumophila@SMA_Q5X8D2_LEGPA[8][RRM1:100%**][PROK:100%**][put-sr:100%**][KOG0149:100%**]Ostreococcus_lucimarinus@PRO_jgi_Ost9901_3_7602[2][RRM1:100%][KOG0145:100%]

Caenorhabditis@REF_XP_001665847[3][RRM1:100%*][KOG0108:100%*]Aedes aegypti@PRO_AAEL010101-PA[2][RRM1:100%]Anopheles_gambiae@PRO_AGAP007689-PA[2][RRM1:100%]

Ostreococcus_lucimarinus@PRO_jgi_Ost9901_3_32831[2][RRM1:100%]Cryptococcus neoformans_var._neoformans_B-3501A@SMA_Q55Z21_CRYN

Bos taurus@REF_XP_875206[RRM1]Oryza sativa_japonica_cultivar-group@SMA_Q6H4H7_ORYSA[2][RRM1:100%][KOG1520:50%][.KOG0122:50%]

Oryza sativa_japonica_cultivar-group@SMA_Q2QMF0_ORYSA[RRM1][KOG0122]Filobasidiella_neoformans@PRO_XP_569209[4][RRM2:100%*][KOG0144:100%*]

Plesiocystis pacifica_SIR-1@REF_ZP_01911510[RRM1][PROK]Paramecium tetraurelia@REF_XP_001459639[RRM2][KOG0120]Ciona@PRO_ENSCSAVP00000015853[5][RRM2:100%*][KOG0145:100%*]

Ciona@PRO_ENSCINP00000023191[5][RRM3:80%*][.RRM1:20%][KOG0145:100%*]Nematostella vectensis@REF_XP_001634736[RRM3][KOG0145]

Coelomata@PRO_ENSTBEP00000015452[492][RRM3:91%******][.RRM2:6%***][ELAV:80%*****][KOG0145:100%******]Caenorhabditis@REF_XP_001678192[5][RRM3:100%*][KOG0145:100%*]

Nematostella vectensis@REF_XP_001626979[RRM3][KOG0145]Dictyostelium discoideum_AX4@SMA_Q54G90_DICDI[3][RRM3:100%*][KOG0145:100%*]

Saccharomycetales@PRO_NP_984279[13][RRM1:100%**][KOG0921:77%**][.KOG0106:23%*]Entamoeba histolytica_HM-1_IMSS@REF_XP_655235[2][RRM1:100%]

Dictyostelium discoideum_AX4@SMA_Q55CI7_DICDI[RRM1]Caenorhabditis@REF_XP_001676254[5][RRM2:100%*][KOG0148:100%*]Coelomata@PRO_CG4787-PA[243][RRM3:73%*****][.RRM2:16%***][.RRM1:12%***][TIATIAR:75%*****][KOG0148:100%*****] OligoU

12 - ELAV

51 - LARK

50 - LARK

52

81 - La

part of 22 - single-RRM

SR proteins

part of 22 - single-RRM

SR proteins

23 - SRrp

4225

Fungal SR (ScNp13) ?Fig. S9

126

59

84

69

95 73

59

93 74

89

79

72

73

Strongylocentrotus purpuratus@PRO NP 999784[8][RRM1:100%**][KOG4205:100%**]Dictyostelium discoideum_AX4@SMA_Q54D98_DICDI[RRM1][KOG4205]

Eukaryota@PRO_ENSMODP00000031317[717][RRM1:100%******][hnRNP:29%*****][.Musashi:15%****][.Dazap:7%***][KOG4205:100%******]Phytophthora ramorum@PRO_jgi_Phyra1_1_73884[RRM1][KOG4205]

Aureococcus anophagefferens@PRO_jgi_Auran1_6078[RRM1][KOG4205]Strongylocentrotus purpuratus@SMA_UPI0000584744[7][RRM1:100%*][KOG4205:100%*]

Strongylocentrotus purpuratus@SMA_UPI000058437F[RRM1][KOG4205]Strongylocentrotus purpuratus@SMA_UPI0000585178[5][RRM1:100%*][KOG4205:100%*]

Plasmodium@REF_XP_001615026[12][RRM1:100%**][KOG4205:100%**]Ostreococcus_lucimarinus@PRO_jgi_Ost9901_3_24530[2][RRM1:100%][KOG4205:100%]

Oryza_sativa@PRO_NP_001067093[5][RRM1:100%*][KOG4177:100%*]Chlamydomonadales@PRO_jgi_Volca1_107445[2][RRM2:100%][KOG4205:100%]

Physcomitrella patens@PRO_jgi_Phypa1_1_19696[RRM1][KOG4205]Oryza sativa_japonica_cultivar-group@SMA_Q5ZAN1_ORYSA[2][RRM2:100%][KOG4205:100%]

Cryptosporidium_parvum@PRO_XP_626579[3][RRM2:67%][.RRM1:33%][KOG4205:100%*]Cryptosporidium@SMA_Q5CS11_CRYPV[4][RRM2:100%*][KOG4205:100%*]Cryptosporidium@SMA_Q5CEI5_CRYHO[4][RRM2:100%*][KOG4205:100%*]

Ricinus communis@PRO_28976_m000161[RRM2][KOG4205]Filobasidiella_neoformans@PRO_XP_568675[4][RRM2:100%*][KOG4205:100%*]

Endopterygota@PRO_AAEL008257-PA[26][RRM2:100%***][KOG4205:100%***]Viridiplantae@SMA_Q8W4A6_ARATH[35][RRM2:97%***][put-sr:17%*][KOG4205:97%***]

Caenorhabditis@SMA_Q4W5P0_CAEEL[15][RRM1:100%**][KOG4205:100%**]Ascomycota@REF_XP_723052[54][RRM2:100%***][put-sr:6%*][KOG4205:100%***]

Strongylocentrotus purpuratus@PRO_NP_999784[8][RRM2:100%**][KOG4205:100%**]Plasmodium@REF_XP_723811[8][RRM1:100%**][KOG0149:38%*][.KOG4205:38%*][.KOG0113:25%]

Babesia bovis@REF_XP_001609124[RRM1]Theileria@REF_XP_955210[4][RRM1:100%*][KOG0149:50%]

Plasmodium@REF_XP_001615199[6][RRM2:100%*][KOG0149:50%*][.KOG0113:33%][.KOG4205:17%]Theileria@SMA_Q4MZK1_THEPA[3][RRM2:100%*][KOG0149:67%]

Babesia bovis@REF_XP_001609123[RRM1][KOG0149]Embryophyta@PRO_IMGA_AC144431_42_2[12][RRM3:92%**][.RRM2:8%][put-sr:25%*][KOG4205:100%**]

Nematostella vectensis@REF_XP_001637003[RRM2][KOG4205]Coelomata@SMA_UPI000051750E[26][RRM2:100%***][TARDBP:15%*][KOG4205:100%***]

Embryophyta@PRO_jgi_Phypa1_1_112860[11][RRM2:100%**][put-sr:27%*][KOG4205:100%**]Chlamydomonadales@PRO_jgi_Chlre3_105806[2][RRM2:100%][KOG4205:100%]

Chlamydomonadales@PRO_jgi_Volca1_43575[2][RRM3:100%][KOG4205:100%]Encephalitozoon_cuniculi@PRO_NP_597487[2][RRM1:100%][KOG4205:100%]

Nematostella vectensis@REF_XP_001625489[RRM2][KOG4205]Caenorhabditis@REF_XP_001672132[5][RRM1:100%*]

Phytophthora ramorum@PRO_jgi_Phyra1_1_73884[RRM2][KOG4205]Bacillariophyta@PRO_jgi_Phatr2_21039[2][RRM1:100%][KOG4205:100%]

Piroplasmida@REF_XP_001610820[6][RRM1:100%*][put-sr:83%*][KOG4205:100%*]Plasmodium@SMA_Q7RMH6_PLAYO[5][RRM2:100%*][KOG4205:100%*]

Dictyostelium discoideum_AX4@SMA_Q552K5_DICDI[3][RRM1:100%*][KOG3598:100%*]Nematostella vectensis@REF_XP_001641412[RRM1][KOG4205]

Schistosoma japonicum@SMA_Q5DH48_SCHJA[RRM1][KOG4205]Endopterygota@SMA_Q297Q0_DROPS[53][RRM1:100%***][KOG4205:100%***]

Nematostella vectensis@REF_XP_001630480[RRM1][KOG4205]Myotis lucifugus@PRO_ENSMLUP00000003070[RRM1][hnRNP][KOG4205]

Oryctolagus cuniculus@PRO_ENSOCUP00000001170[RRM1][hnRNP][KOG4205]Dictyostelium discoideum_AX4@SMA_Q54D98_DICDI[3][RRM2:100%*][KOG4205:100%*]

Nematostella vectensis@REF_XP_001642130[RRM1][KOG4205]Piroplasmida@REF_XP_001611990[5][RRM2:100%*][KOG4205:100%*]

Ciona@PRO_ENSCINP00000009845[4][RRM1:100%*][KOG0116:100%*]Deuterostomia@REF_NP_001085483[190][RRM1:100%*****][G3BP:85%*****][KOG0116:100%*****]Apis mellifera@PRO_XP_623996[3][RRM1:100%*][KOG0116:100%*]

Tribolium castaneum@PRO_XP_975463[3][RRM1:100%*][KOG0116:100%*]Diptera@SMA_ENSANGP00000007476[2][RRM1:100%][KOG0116:100%]

Anopheles gambiae_str._PEST@SMA_Q5TV30_ANOGA[RRM1]Strongylocentrotus purpuratus@PRO_XP_001176409[7][RRM2:100%*][KOG4205:100%*]

Nematostella vectensis@REF_XP_001634214[RRM1][KOG4205]Canis familiaris@SMA_UPI00005A10B6[RRM1][hnRNP][KOG4205]

Canis familiaris@SMA_UPI00004BDE56[2][RRM1:100%][KOG4205:100%]Sorex araneus@PRO_ENSSARP00000008097[RRM2][hnRNP][KOG4205]

Caenorhabditis@REF_XP_001671843[15][RRM2:100%**][KOG4205:100%**]Bilateria@SMA_RB97D_DROME[955][RRM2:91%******][.RRM1:9%****][hnRNP:57%******][KOG4205:100%******]

Drosophila melanogaster@PRO_CG9654-PA[3][RRM2:100%*][KOG4205:100%*]Ciona intestinalis@PRO_ENSCINP00000012771[RRM2][put-sr][KOG4205]

Ciona@PRO_ENSCINP00000008394[8][RRM2:100%**][KOG4205:100%**]Paracentrotus lividus@SMA_Q6PNM9_PARLI[RRM2][KOG4205]

Caenorhabditis@SMA_Q4W5P0_CAEEL[15][RRM2:100%**][KOG4205:100%**]Physcomitrella patens@PRO_jgi_Phypa1_1_120016[RRM2][KOG4205]

Strongylocentrotus purpuratus@PRO_XP_001183095[5][RRM2:100%*][KOG4205:100%*]Nematostella vectensis@REF_XP_001641412[RRM2][KOG4205]

Eukaryota@SMA_Q5U4T5_XENLA[284][RRM2:86%*****][.RRM1:14%***][Musashi:41%****][.Dazap:18%***][.hnRNP:12%***][KOG4205:100%*****]Apis mellifera@SMA_UPI0000519F31[RRM2][KOG2281]

Ciona@PRO_ENSCSAVP00000001921[5][RRM2:100%*][Musashi:80%*][KOG4205:100%*]Halocynthia roretzi@SMA_Q9UAF2_HALRO[RRM2][Musashi][KOG4205]Ciona@SMA_ENSCINP00000028810[3][RRM2:100%*][KOG4205:100%*]

Ciona@PRO_ENSCSAVP00000016637[4][RRM2:100%*][KOG4205:100%*]Nematostella vectensis@REF_XP_001630480[RRM2][KOG4205]

Euteleostomi@PRO_ENSDARP00000005968[318][RRM2:97%*****][hnRNP:57%*****][KOG4205:100%*****]Endopterygota@SMA_UPI0000514895[54][RRM2:100%***][KOG4205:100%***]

Gammaproteobacteria@SMA_Q60AQ3_METCA[6][RRM1:100%*][PROK:100%*]Aureococcus anophagefferens@PRO_jgi_Auran1_1296[RRM1][KOG0110]Chlamydomonas reinhardtii@PRO_jgi_Chlre3_181993[RRM1]

Eumetazoa@PRO_ENSDNOP00000008593[244][RRM1:100%*****][P54nrb:38%****][.PSP1:16%***][.PSF:16%***][KOG0115:99%*****]Cyanidioschyzon merolae@PRO_gnl_CMER_CML202C[RRM1][put-sr]

Cyanidioschyzon merolae@PRO_gnl_CMER_CMO246C[RRM2][KOG0110]Eukaryota@PRO_IMGA_AC183923_6_1[89][RRM3:70%****][.RRM2:17%**][.RRM1:13%**][put-sr:6%*][KOG0110:100%****]

Thalassiosira pseudonana@PRO_jgi_Thaps3_268689[RRM2][KOG0110]Arabidopsis thaliana@SMA_O49430_ARATH[4][RRM1:100%*][KOG0117:50%][.KOG0127:25%]

eurosids_I@PRO_IMGA_CT963106_6_1[2][RRM1:100%][KOG0117:50%]Trypanosomatidae@PRO_XP_001463723[11][RRM1:82%**][.RRM2:18%][KOG0110:100%**]

Oryza sativa_japonica_cultivar-group@PRO_NP_001053839[3][RRM1:67%][.RRM2:33%][KOG0110:100%*]Phytophthora@PRO_jgi_Physo1_1_129427[2][RRM2:100%][KOG0110:100%]

Caenorhabditis@PRO_T23F6_4_1[6][RRM3:67%*][.RRM2:33%][KOG0110:100%*]Ascomycota@PRO_NP_984131[38][RRM2:100%***][KOG0110:100%***]

Schizosaccharomyces_pombe@PRO_NP_595599[3][RRM2:100%*][KOG0110:100%*]Sordariales@PRO_XP_965014[5][RRM2:100%*][KOG0110:100%*]

Sclerotiniaceae@REF_XP_001548634[2][RRM2:100%][KOG0110:100%]Magnaporthe grisea_70-15@REF_XP_363291[2][RRM2:100%][KOG0110:100%]

Phaeodactylum tricornutum@PRO_jgi_Phatr2_20740[RRM2][KOG0110]Filobasidiella_neoformans@PRO_XP_569873[4][RRM2:75%*][.RRM1:25%][KOG0110:100%*]

Ustilago_maydis@PRO_XP_758493[3][RRM2:100%*][KOG0110:100%*]Entamoeba_histolytica@REF_XP_655058[3][RRM2:100%*][KOG0110:67%][.KOG0123:33%]

Trichomonas vaginalis_G3@REF_XP_001324476[RRM2][KOG0110]Acaryochloris marina_MBIC11017@REF_YP_001521497[RRM1][PROK][KOG0111]

Synechococcus@PRO_YP_473618[6][RRM1:100%*][PROK:100%*][KOG0108:100%*]Piroplasmida@REF_XP_001611590[6][RRM2:100%*][KOG0117:33%][.KOG0116:17%]

Chlamydomonadales@PRO_jgi_Volca1_90315[3][RRM2:67%][.RRM3:33%][KOG0123:67%]Entamoeba histolytica_HM-1_IMSS@REF_XP_653167[3][RRM1:100%*][KOG4209:100%*]

Caenorhabditis briggsae@REF_XP_001678677[RRM1]Entamoeba histolytica_HM-1_IMSS@REF_XP_655803[2][RRM2:100%][KOG0148:100%]

Dictyostelium discoideum_AX4@PRO_XP_643642[3][RRM2:100%*][KOG0148:100%*]Cryptosporidium@PRO_XP_001388131[4][RRM2:100%*][KOG0117:50%][.KOG1015:50%]

Ostreococcus@PRO_jgi_Ost9901_3_27365[3][RRM1:100%*][KOG0123:67%]Strongylocentrotus purpuratus@SMA_UPI0000587E0B[RRM3][KOG0116]

Strongylocentrotus purpuratus@SMA_UPI0000587E0B[RRM1][KOG0116]Ciona@PRO_ENSCSAVP00000005375[6][RRM2:83%*][.RRM1:17%][KOG0116:83%*][.KOG2141:17%]

31

32 33 - p54nrb

PSP1

PSF

35 - G3BP

RBM

30K RRM

hnRNP

Musashi

Dazap

TARDBP

OligoU

Fig. S9

127

52

58

79

100

53 60

59

58

54

93

53

95

77 87

Chlamydomonadales@SMA Q39568 CHLRE[3][RRM2:100%*][KOG0108:67%][ KOG4212:33%]Giardia lamblia_ATCC_50803@SMA_Q7R0B6_GIALA[RRM1][put-sr][KOG0127]

Trypanosomatidae@SMA_Q4FWP9_LEIMA[11][RRM2:100%**][KOG4212:100%**]Saccharomycetaceae@PRO_XP_462023[6][RRM1:100%*][put-sr:83%*][KOG0123:100%*]

Saccharomycetales@PRO_XP_446962[16][RRM1:100%**][put-sr:62%**][KOG0123:50%**][.KOG0127:50%**]Ostreococcus_lucimarinus@PRO_jgi_Ost9901_3_34965[2][RRM1:100%][KOG4212:100%]

Trypanosomatidae@PRO_XP_001465100[11][RRM1:100%**][KOG4212:100%**]Chlamydomonadales@PRO_jgi_Chlre3_184854[2][RRM1:100%][KOG0055:50%]

Bacillariophyta@PRO_jgi_Phatr2_7426[2][RRM1:100%]Volvox carteri@PRO_jgi_Volca1_103054[RRM2][KOG0055]

Filobasidiella_neoformans@REF_XP_773466[5][RRM1:100%*][put-sr:100%*][KOG0147:100%*]Trypanosomatidae@PRO_XP_823301[5][RRM1:100%*][KOG0921:60%*]

Nematostella vectensis@REF_XP_001637595[RRM1][put-sr][KOG4212]Strongylocentrotus purpuratus@PRO_XP_001187716[9][RRM1:100%**][put-sr:89%**][KOG4212:56%*][.KOG4661:44%*]

Schistosoma japonicum@SMA_Q5DC86_SCHJA[RRM1][put-sr][KOG4212]Coelomata@SMA_UPI00005A3D66[197][RRM1:100%*****][hnRNP:39%****][KOG4212:100%*****]Caenorhabditis@SMA_Q9XVS2_CAEEL[2][RRM1:100%][put-sr:100%][KOG4212:100%]

Bilateria@PRO_XP_967263[124][RRM2:82%****][.RRM1:18%***][put-sr:85%****][SR:77%****][KOG0105:100%****]Plasmodium falciparum_3D7@PRO_XP_001347501[RRM2][put-sr][KOG0105]

Theileria@PRO_XP_766386[3][RRM2:100%*][put-sr:100%*][KOG0105:100%*]Fungi/Metazoa_group@REF_XP_001623720[290][RRM2:86%*****][.RRM1:13%***][put-sr:100%*****][SR:59%*****][KOG0105:52%*****][.KOG0106:44%****]

Phytophthora@PRO_jgi_Physo1_1_136493[2][RRM2:100%][put-sr:100%][KOG0105:100%]Phytophthora ramorum@PRO_jgi_Phyra1_1_84100[RRM2][KOG0105]

Plasmodium@PRO_XP_001347332[6][RRM2:100%*][put-sr:83%*][KOG0105:100%*]Babesia bovis@REF_XP_001610592[RRM2][KOG0123]

Theileria@PRO_XP_766728[5][RRM2:100%*][KOG0124:100%*]Nematostella vectensis@REF_XP_001637595[RRM3][put-sr][KOG4212]

Cyanidioschyzon merolae@PRO_gnl_CMER_CMM078C[RRM2][KOG4212]Chordata@PRO_ENSOGAP00000002890[198][RRM3:79%*****][.RRM2:14%***][.RRM1:7%**][hnRNP:45%****][KOG4212:100%*****]

Strongylocentrotus purpuratus@PRO_XP_786244[5][RRM3:100%*][put-sr:80%*][KOG4212:100%*]Endopterygota@REF_XP_001657115[16][RRM3:100%**][hnRNP:6%][KOG4212:100%**]

Caenorhabditis@REF_XP_001668553[3][RRM3:100%*][put-sr:100%*][KOG4212:100%*]Theileria@REF_XP_763694[4][RRM2:100%*][KOG4212:100%*]

Babesia bovis@REF_XP_001610597[RRM2][KOG4212]Dikarya@PRO_XP_568231[30][RRM3:90%***][.RRM2:10%*][put-sr:83%***][KOG4212:90%***][.KOG0147:10%*]

Yarrowia lipolytica@PRO_XP_503927[3][RRM3:100%*][put-sr:100%*][KOG4212:100%*]Saccharomycetales@REF_XP_001483552[11][RRM3:55%*][.RRM2:45%*][put-sr:45%*][KOG0123:64%*][.KOG4212:36%*]

Kluyveromyces lactis@PRO_XP_453283[3][RRM2:100%*][KOG0123:100%*]Saccharomycetales@PRO_YNL004W[14][RRM3:93%**][.RRM2:7%][put-sr:50%*][KOG0123:57%**][.KOG0127:36%*]

Eukaryota@SMA_Q5B6U1_EMENI[102][RRM1:65%****][.RRM2:35%***][put-sr:45%***][KOG4212:86%****][.KOG0123:7%*][.KOG0147:5%*]Candida_glabrata@PRO_XP_446962[3][RRM2:100%*][put-sr:100%*][KOG0127:100%*]

Plasmodium@REF_XP_746250[10][RRM2:90%**][.RRM1:10%][KOG4212:90%**]Schizosaccharomyces pombe_972h-@PRO_NP_594207[2][RRM2:100%][KOG4212:100%]Schizosaccharomyces pombe@SMA_Q9P3U1_SCHPO[RRM2][KOG4212]

Nematostella vectensis@REF_XP_001637595[RRM2][put-sr][KOG4212]Schistosoma japonicum@SMA_Q5DC86_SCHJA[RRM2][put-sr][KOG4212]

Caenorhabditis@PRO_C25A1_4_2[5][RRM2:100%*][put-sr:100%*][KOG4212:100%*]Coelomata@PRO_ENSMLUP00000006206[233][RRM2:88%*****][.RRM1:12%***][hnRNP:36%****][KOG4212:98%*****]

Arabidopsis thaliana@PRO_NP_179762[3][RRM1:100%*][oligoU:100%*]Nematostella vectensis@REF_XP_001627235[RRM1]Phytophthora@PRO_jgi_Physo1_1_141766[2][RRM1:100%][KOG0148:100%]

Guillardia theta@SMA_Q5K249_GUITH[RRM1][KOG0149]Phytophthora@PRO_jgi_Physo1_1_134615[2][RRM1:100%]

Plesiocystis pacifica_SIR-1@REF_ZP_01910335[RRM1][PROK][KOG0921]Chlamydomonadales@PRO_jgi_Volca1_107658[2][RRM1:100%][KOG4205:50%][.KOG0474:50%]

Phaeodactylum tricornutum@PRO_jgi_Phatr2_21039[RRM2][KOG4205]Arabidopsis thaliana@PRO_NP_173298[3][RRM1:100%*][GRSRBP:100%*][KOG0149:100%*]

Oryza sativa_japonica_cultivar-group@SMA_Q8LLX3_ORYSA[RRM1][KOG0148]Magnoliophyta@PRO_NP_001059075[15][RRM1:100%**][put-sr:7%][GRSRBP:53%**][KOG0108:47%*][.KOG0148:33%*][.KOG0111:20%*]

Sorghum bicolor@SMA_GRP1_SORBI[RRM1][GRSRBP][KOG0921]Oryza sativa@SMA_O04432_ORYSA[RRM1][put-sr][KOG0921]

Arabidopsis thaliana@SMA_Q1PES4_ARATH[4][RRM1:100%*][30kRRM:100%*][KOG0149:100%*]Eukaryota@PRO_NP_001058102[212][RRM1:100%*****][RBM:55%****][.30kRRM:17%***][KOG0149:95%*****]

Arabidopsis thaliana@PRO_NP_200183[6][RRM1:100%*][oligoU:100%*][KOG0149:100%*]Phytophthora sojae@PRO_jgi_Physo1_1_139371[RRM2][KOG4205]

Phytophthora sojae@PRO_jgi_Physo1_1_139371[RRM1][KOG4205]Magnoliophyta@SMA_UPI000017A786[34][RRM1:100%***][oligoU:68%***][KOG4205:59%**][.KOG0149:32%**][.KOG2186:9%*]

Oryza_sativa@SMA_Q7XTU5_ORYSA[3][RRM1:100%*][KOG4205:100%*]Oryza sativa_japonica_cultivar-group@SMA_Q2R1J0_ORYSA[RRM1][KOG0148]

Cyanidioschyzon merolae@PRO_gnl_CMER_CMR392C[RRM2][KOG4205]Ostreococcus tauri@PRO_jgi_Ostta4_33731[RRM1]

Ostreococcus tauri@PRO_jgi_Ostta4_33731[RRM2]Aureococcus anophagefferens@PRO_jgi_Auran1_66158[RRM2][put-sr][KOG0149]

Oryza sativa_japonica_cultivar-group@SMA_UPI00000A9C56[2][RRM1:100%][KOG4205:100%]Oryza sativa_japonica_cultivar-group@SMA_Q8GW06_ORYSA[RRM1]

Strongylocentrotus purpuratus@PRO_XP_798256[5][RRM1:100%*][KOG2277:100%*]Xenopus@PRO_ENSXETP00000012439[3][RRM1:100%*][KOG2277:100%*]

Eutheria@SMA_Q5RE94_PONPY[12][RRM1:100%**][KOG2277:100%**]Percomorpha@PRO_ENSORLP00000005442[3][RRM1:100%*][KOG2277:100%*]

Danio rerio@SMA_Q4KMD7_BRARE[RRM1][KOG2277]Oryza sativa_japonica_cultivar-group@PRO_NP_001058805[3][RRM1:100%*][KOG4205:100%*]

Oryza sativa_japonica_cultivar-group@SMA_Q6AU49_ORYSA[4][RRM1:100%*][KOG0149:75%*][.KOG4205:25%]Zea mays@PRO_14684_m000016_AZM5_14964[RRM1][KOG4205]

Ricinus communis@PRO_28976_m000161[RRM1][KOG4205]Piroplasmida@REF_XP_764402[5][RRM1:100%*][KOG4205:100%*]

Ricinus communis@PRO_30170_m013671[RRM1][KOG4205]Arabidopsis thaliana@SMA_Q9SM01_ARATH[3][RRM1:100%*][KOG4205:100%*]

Embryophyta@PRO_jgi_Phypa1_1_156290[11][RRM1:100%**][put-sr:27%*][KOG4205:100%**]Arabidopsis thaliana@SMA_O23189_ARATH[RRM1][KOG4205]

Chlamydomonadales@PRO_jgi_Chlre3_105806[2][RRM1:100%][KOG4205:100%]Nematostella vectensis@REF_XP_001637003[RRM1][KOG4205]

Coelomata@PRO_ENSMLUP00000003881[137][RRM1:100%****][TARDBP:66%****][KOG4205:97%****]Caenorhabditis@SMA_Q20414_CAEEL[2][RRM1:100%][KOG4205:100%]

Strongylocentrotus purpuratus@SMA_UPI00005846A2[6][RRM1:100%*][KOG4205:100%*]Ciona@PRO_ENSCINP00000012771[9][RRM1:100%**][put-sr:11%][KOG4205:100%**]Bilateria@SMA_UPI0000D6301C[874][RRM1:100%******][hnRNP:57%******][KOG4205:100%******]

Cryptosporidium@SMA_Q5CKR7_CRYHO[5][RRM2:100%*][KOG0144:100%*]Plasmodium_falciparum_3D7@SMA_Q8I2Y5_PLAF7[9][RRM2:100%**][KOG0144:100%**]

Cryptosporidium@SMA_Q5CM52_CRYHO[5][RRM2:100%*][KOG4205:100%*]Takifugu rubripes@SMA_UPI000065CE8D[RRM3][KOG4205]

Aureococcus anophagefferens@PRO_jgi_Auran1_9354[RRM1]Ornithorhynchus anatinus@REF_XP_001521058[RRM1]

Tribolium castaneum@PRO_XP_970765[3][RRM1:100%*][KOG0127:100%*]Aureococcus anophagefferens@PRO_jgi_Auran1_9576[RRM1][KOG0149]

Chlamydomonadales@PRO_jgi_Volca1_107445[2][RRM1:100%][KOG4205:100%]Cyanidioschyzon merolae@PRO_gnl_CMER_CMR392C[RRM1][KOG4205]

Nematostella vectensis@REF_XP_001628585[RRM1][KOG4205]Thalassiosira pseudonana@PRO_jgi_Thaps3_25203[2][RRM1:100%][KOG4205:100%]

Phaeodactylum tricornutum@PRO_jgi_Phatr2_41450[RRM1][KOG4205]Ciona intestinalis@PRO_ENSCINP00000029053[2][RRM1:100%][KOG4205:100%]

Ciona intestinalis@PRO_ENSCINP00000006182[RRM1][KOG4205]Ustilago maydis_521@SMA_Q4PBU3_USTMA[3][RRM2:100%*][KOG4205:100%*]

Takifugu rubripes@SMA_UPI000065DA3A[RRM1][KOG0149]Takifugu rubripes@SMA_UPI000065FE7B[RRM1][KOG0149]

Takifugu rubripes@SMA_UPI000065F126[4][RRM1:100%*][KOG0149:100%*]Mus musculus@SMA_UPI0000D66F4E[RRM1][RBM][KOG0149]

Eukaryota@REF_XP_665248[7][RRM1:100%*][KOG4205:100%*]Cryptosporidium@PRO_XP_626025[4][RRM1:100%*][KOG4205:100%*]Chlamydomonadales@PRO_jgi_Volca1_121254[2][RRM2:100%][KOG4205:100%]

Strongylocentrotus purpuratus@PRO_NP_999784[8][RRM1:100%**][KOG4205:100%**]

34

29 - dual-RRM

SR proteins

30 - hnRNP

PDIP

FCA FPA

Fig. S9

128

0.20

52

55

83

78

50

77 54

57

Leptospira@PRO_YP_001385[9][RRM1:100%**][PROK:100%**]Pelobacter carbinolicus_DSM_2380@PRO_YP_357907[3][RRM1:100%*][PROK:100%*][KOG0145:100%*]

Desulfuromonadales@PRO_NP_952377[14][RRM1:100%**][PROK:100%**][KOG0108:43%*][.KOG0145:21%*][.KOG0111:7%][.KOG4207:7%]Pedobacter sp._BAL39@REF_ZP_01882661[RRM1][PROK][KOG0108]

Aureococcus anophagefferens@PRO_jgi_Auran1_60739[RRM1][put-sr][KOG1860]Microscilla marina_ATCC_23134@REF_ZP_01693505[RRM1][PROK][KOG0148]

Vibrio fischeri_ES114@PRO_YP_206444[3][RRM1:100%*][PROK:100%*][KOG0145:100%*]Gammaproteobacteria@REF_ZP_01476992[67][RRM1:100%****][PROK:100%****][KOG0144:21%**][.KOG0108:19%**][.KOG0145:18%**][.KOG0122:9%*]

Dictyostelium discoideum_AX4@PRO_XP_638767[3][RRM1:100%*][KOG0123:100%*]Bacteroides@PRO_YP_001298723[7][RRM1:100%*][PROK:100%*][KOG0108:100%*]

Bacteroidales@PRO_YP_001302325[6][RRM1:100%*][PROK:100%*][KOG0122:67%*][.KOG0123:33%]Methanomicrobiales@PRO_YP_001047169[14][RRM1:100%**][PROK:100%**][KOG0108:43%*][.KOG0116:21%*][.KOG0125:14%]

Ostreococcus tauri@PRO_jgi_Ostta4_19468[RRM1][KOG0127]Oryza sativa_japonica_cultivar-group@SMA_Q6ERT8_ORYSA[RRM1]

Ostreococcus@PRO_jgi_Ost9901_3_12693[3][RRM2:100%*][KOG0127:100%*]Nematostella vectensis@REF_XP_001621824[5][RRM1:100%*][KOG0108:100%*]

Phytophthora@PRO_jgi_Phyra1_1_75647[2][RRM1:100%]Nematostella vectensis@REF_XP_001627237[RRM1][KOG0921]

Proteobacteria@PRO_YP_844222[3][RRM1:100%*][PROK:100%*][KOG0108:100%*]Carboxydothermus hydrogenoformans_Z-2901@SMA_Q3AF33_CARHZ[3][RRM1:100%*][PROK:100%*][KOG0108:100%*]

cellular_organisms@SMA_Q41VF2_DESHA[1326][RRM1:95%*******][.RRM2:5%****][PROK:39%******][put-sr:17%*****][GRSRBP:12%*****][.hnRNP:6%****][.RBMY:5%****][KOG0108:34%******][.KOG0149:11%*****][.KOG0111:10%****][.KOG0116:7%****][.KOG0117:5%****][.KOG0125:5%****]Chloroflexus@SMA_Q3DVT1_CHLAU[5][RRM1:100%*][PROK:100%*][KOG0149:60%*][.KOG0108:40%]

Comamonas testosteroni_KF-1@REF_ZP_01521959[2][RRM1:100%][PROK:100%][KOG0108:50%][.KOG0123:50%]Volvox carteri@PRO_jgi_Volca1_36996[RRM1][KOG0116]Ostreococcus@PRO_jgi_Ost9901_3_34381[3][RRM1:100%*][KOG0145:100%*]

Cyanobacteria@PRO_YP_476186[31][RRM1:100%***][PROK:100%***][KOG0108:32%**][.KOG0122:10%*]Cyanobacteria@PRO_NP_898344[50][RRM1:100%***][PROK:100%***][KOG0108:76%***]

Synechococcus_elongatus@PRO_YP_399809[6][RRM1:100%*][PROK:100%*][KOG0108:100%*]Magnoliophyta@PRO_NP_001060859[12][RRM1:100%**][cpRNP:50%*][KOG0148:42%*][.KOG0110:33%*][.KOG0225:8%]

Magnoliophyta@SMA_Q9FYW5_LYCES[14][RRM1:100%**][put-sr:79%**][snRNP:79%**][KOG0120:100%**]Chlamydomonas reinhardtii@PRO_jgi_Chlre3_145376[RRM2]

Alkalilimnicola ehrlichei_MLHE-1@PRO_YP_741458[3][RRM1:100%*][PROK:100%*]Proteobacteria@SMA_UPI00005F3438[101][RRM1:100%****][PROK:100%****][KOG0108:90%****]

Phaeodactylum tricornutum@PRO_jgi_Phatr2_38474[RRM1]Chlamydomonas reinhardtii@PRO_jgi_Chlre3_174860[RRM2][KOG1240]

Trypanosoma@REF_XP_818775[6][RRM1:100%*]Mariprofundus ferrooxydans_PV-1@REF_ZP_01453708[RRM1][PROK][KOG0108]

Magnoliophyta@PRO_NP_001062073[9][RRM1:100%**][KOG0110:67%*][.KOG0127:33%*]Oryza_sativa@SMA_Q5VSX4_ORYSA[4][RRM1:100%*][KOG0127:75%*]

rosids@PRO_30054_m000821[6][RRM1:100%*][cpRNP:50%*][KOG0127:100%*]Trichomonas vaginalis_G3@REF_XP_001580806[RRM1]

Schizosaccharomyces_pombe@PRO_NP_596721[3][RRM3:100%*][KOG0128:100%*]Trichomonas vaginalis_G3@REF_XP_001325677[2][RRM1:100%][KOG1924:50%]

Schizosaccharomyces_pombe@PRO_NP_596721[3][RRM2:100%*][KOG0128:100%*]Pezizomycotina@SMA_Q01491_OPHUL[15][RRM2:93%**][.RRM1:7%][KOG0128:93%**][.KOG0123:7%]

Ustilago maydis_521@SMA_Q4PC71_USTMA[RRM1][KOG0123]Pichia guilliermondii_ATCC_6260@REF_XP_001485760[RRM2][KOG0123]

Debaryomyces_hansenii@SMA_Q6BM90_DEBHA[3][RRM2:67%][.RRM1:33%][KOG0128:100%*]Eremothecium gossypii@SMA_Q756X0_ASHGO[RRM1][KOG0128]

Saccharomyces cerevisiae@PRO_YMR268C[2][RRM2:100%][KOG0128:100%]Ustilago maydis_521@PRO_XP_761797[3][RRM1:100%*][put-sr:100%*][KOG3257:100%*]Magnoliophyta@PRO_NP_566958[15][RRM2:73%**][.RRM1:27%*][KOG0124:40%*][.KOG0131:33%*][.KOG0123:13%][.KOG0148:7%]

Oryza sativa_japonica_cultivar-group@SMA_Q69UI3_ORYSA[3][RRM2:100%*][KOG0110:100%*]rosids@SMA_Q9MAM6_ARATH[7][RRM2:100%*][cpRNP:86%*][KOG0148:71%*][.KOG0110:14%][.KOG0225:14%]

Aureococcus anophagefferens@PRO_jgi_Auran1_6342[RRM2][KOG0123]Magnoliophyta@PRO_29333_m001057[10][RRM2:90%**][.RRM1:10%][cpRNP:30%*][KOG0131:80%**][.KOG0127:10%][.KOG0148:10%]

Ostreococcus_lucimarinus@PRO_jgi_Ost9901_3_27365[2][RRM3:100%][KOG0123:100%]Chlamydomonadales@PRO_jgi_Volca1_103054[2][RRM3:50%][.RRM2:50%][KOG0055:50%]

Aureococcus anophagefferens@PRO_jgi_Auran1_8994[RRM1][KOG0149]Entamoeba histolytica_HM-1_IMSS@REF_XP_655048[2][RRM2:100%][put-sr:100%][KOG0123:100%]

Dictyostelium discoideum_AX4@PRO_XP_638767[3][RRM2:100%*][KOG0123:100%*]Magnoliophyta@PRO_IMGA_AC119413_25_2[9][RRM2:100%**][cpRNP:33%*][KOG0127:100%**]

Poaceae@PRO_19213_m000022_AZM5_85721[4][RRM2:75%*][.RRM1:25%][KOG0127:75%*]Ricinus communis@PRO_29908_m006094[RRM2][KOG0110]

Arabidopsis thaliana@PRO_NP_192643[6][RRM2:83%*][.RRM1:17%][KOG0110:83%*]Magnoliophyta@PRO_10511_m000028_AZM5_5258[52][RRM1:100%***][cpRNP:29%**][KOG0127:56%***][.KOG0131:33%**][.KOG0145:10%*]

Magnoliophyta@SMA_O81989_HORVU[10][RRM1:100%**][cpRNP:30%*][KOG0131:80%**][.KOG0127:10%]Embryophyta@PRO_jgi_Phypa1_1_134646[17][RRM1:100%**][cpRNP:18%*][KOG0123:59%**][.KOG0127:24%*][.KOG0144:6%][.KOG2029:6%]

Magnoliophyta@SMA_Q6H443_ORYSA[11][RRM1:100%**][KOG0124:55%*][.KOG0131:45%*]Cryptococcus_neoformans_var._neoformans@PRO_XP_572539_RRM

Saccharomycetales@PRO_XP_001386572[28][RRM2:68%**][.RRM1:32%**][put-sr:43%**][KOG0123:64%**][.KOG0127:18%*][.KOG4212:14%*]Yarrowia lipolytica@PRO_XP_505184[3][RRM1:100%*]

Trichocomaceae@REF_XP_001388936[8][RRM1:100%**]Coccidioides immitis_RS@REF_XP_001245337[RRM1][put-sr]

Ajellomyces capsulatus_NAm1@REF_XP_001540919[RRM2]Ostreococcus_lucimarinus@PRO_jgi_Ost9901_3_34965[2][RRM2:100%][KOG4212:100%]

Phytophthora@PRO_jgi_Phyra1_1_75500[2][RRM3:100%][KOG0123:100%]Thalassiosira pseudonana@PRO_jgi_Thaps3_37126[RRM2][KOG0123]

Phaeodactylum tricornutum@PRO_jgi_Phatr2_51303[RRM2][KOG4212]Chlamydomonadales@PRO_jgi_Volca1_78979[3][RRM1:100%*][KOG3070:100%*]Chlamydomonadales@SMA_Q39568_CHLRE[3][RRM2:100%*][KOG0108:67%][.KOG4212:33%]


Fig. S9

129

RRM1 hnRNPr (land plants)

RRM4/5 RBP

RRM4/5/6 RBP

RRM1 CID1RRM1 Rasputin + RRM1 SEB4 + RRM1/2 HRP1

RRM1 SART3 (excl. green plants)

RRM1 SART3 (green plants)

RRM1 U1 snRNPRRM2 SART3[RRM1 peptidyl-prolyl cis-trans isomerase]

RRM2 U1A/U2B snRNP

RRM2 Mei2[RRM1 RBP]

RRM1/2/3 hnRNPm [+RRM1 RRM-containing protein]RRM2 dual RRM SR proteins (excl. plants)

RRM1 LARK

RRM2 dual RRM of plant-specific RS group of SR proteins

RRM1 CAPER/UMH

RRM1 U1A/U2B snRNP

RRM2 U2AF

RRM1 predicted RBP

RRM1 TIF3/eIF3

RRM3 hnRNPr

RRM1 NIFK

RRM1 RBP La

RRM1 RBP

RRM1 splicing factor 2bRRM1 RBP

RRM4 RBP

RRM2 splicing factor SR rich

RRM1 fibrillarin

RRM2 fibrillarin

RRM3 fibrillarin[RRM1 RBP p54 nrb]

RRM3 RBPRRM1 hnRNPr (flowering plants)

RRM1 single RRM SR proteins

[RRM1 cyclophilin-type peptidyl-prolyl cis-trans isomerase][RRM1 RBP RBM8]

[RRM1 CBP20]

RRM? fusillin + RRM2 hnRNPf

RRM2 PUF60 + RRM2 CAPER/UMH [+ RRM1 PUF60]

RRM1 ataxin-2 binding-protein + RRM1 fibrillarin (land plants) + RRM1 SAF-B

RRM2 TIA1/TIAR + RRM1 RBP

RRM1 RBP

RRM1 PABPRRM2 PABP + RRM2 splicing factor 2b (fungi) [+ RRM2 RBP p54 nrb]RRM3 PABP (minor subgroup)RRM4 PABPRRM1 BRUNORRM2 BRUNORRM3 BRUNORRM1 ELAV/HURRM2 ELAV/HURRM3 ELAV/HU

RRM1 hnRNPr (excl. flowering plants)

[RRM1 RBP][RRM1 predicted splicing regulator]

16

17

42

1

2

3

4

5

6

7

8

9

10

11

12

81

13

14

15

19

24

20

29

30

3132

33

34

35

36

37

3839

40

41

44

45

46

4749

50

5152

55

56

59

60

61

62

64

65

67

68

69

70

71

72

73

74

80

82

83

84

85

87

53

54 RRM3 RBP

75

77

RRM1 splicing factor RNPS1

86

prokaryotic RRMs

63

RRM1 Mei243

RRM1 dual RRM SR proteins[RRM1 single RRM Zn-K SR proteins]

RRM1 cyclophilin-type peptidyl-prolyl cis-trans isomerase (SRrp)

1821

22

2325

RRM1 SR45 (green plants)RRM1 splicing factor RNPS1

26

2728

[RRM1 IGF2BP]48

RRM2 RBP

RRM2 LARK

RRM1 RNA15/ZCRB1

RRM1 RNA15/hnRNP/GRSRBP/RBMY

57

58

RRM3 PABP (major subgroup)66

RRM1 TIA1/TIAR76

RRM3 TIA1/TIAR78

RRM3 TIA1/TIAR79

RRM1 hnRNP/RALYL

RRM1 eIF4B

88

= RRM1 of SR proteins

Fig. S10

130

56 RRM2 dual RRM of plant-specific RS group of SR proteins

30b PDIP/FCA/FPA

30a RRM1/2/3 hnRNPm

29 RRM2 dual RRM SR proteins (excl. plants)

24 RRM1 CBP20

misc

misc

22b RRM1 single RRM SR proteins (animals)

22a RRM1 single RRM SR proteins (plants)

23 RRM1 SRrp

20 RRM1 RBP RBM8

27 RRM1 splicing factor RNPS1

26 RRM1 SR45

17 RRM1 single RRM Zn-K SR proteins

16 RRM1 dual RRM SR proteins

57 RRM1 RNA15/ZCRB1


24 RRM1 CBP20

30b PDIP/FCA/FPA

30a RRM1/2/3 hnRNPm



42 RRM1 Mei2


23 RRM1 SRrp

20 RRM1 RBP RBM8

19 RRM1 cyclophilin-type peptidyl-prolyl cis-trans isomerase

misc

16b RRM1 dual RRM SR proteins


16a RRM1 dual RRM SR proteins

misc


26 RRM1 SR45

67 RRM2 CAPER/UMH

43 RRM2 Mei2

40 RRM1 U1A/U2B snRNP


37 RRM2 SART3

38 RRM1 peptidyl-prolyl cis-trans isomerase (cyclophilin)

36 RRM1 U1 snRNP

30 RRM1/2/3 hnRNPm / PDIP/FCA/FPA


84 RRM1 RBP La


26 RRM1 SR45

71 RRM2 fibrillarin (RBM)

20 RRM1 RBP RBM8

24 RRM1 CBP20



23 RRM1 SRrp


42 RRM1 Mei2

33 RRM1 RBP p54 nrb

54 RRM3 RBP

53 RRM2 RBP


20 RRM1 RBP RBM8


26 RRM1 SR45

71 RRM2 fibrillarin (RBM)

63 RRM3 hnRNPr


30b PDIP/FCA/FPA

30a RRM1/2/3 hnRNPm



65 RRM1 TIF3/eIF3

24 RRM1 CBP20


23 RRM1 SRrp



71 RRM2 fibrillarin (RBM)63 RRM3 hnRNPr

41 RRM2 U1A/U2B snRNP


30 RRM1/2/3 hnRNPm / PDIP/FCA/FPA



24 RRM1 CBP20


26 RRM1 SR45


23 RRM1 SRrp


43 RRM2 Mei2


C TREEFINDER (WAG+!4)

B RAXML (WAG+!4)

D RAXML (LG+F+!4)

E large RAXML (WAG+!4)

57 RRM1 RNA15/ZCRB1

34 RRM1 CID1

misc

A PAUP* (MP)

Fig. S11

131

0.25

36

57

56

34 21

7

1

1

7

30

97 56

16

29

11 3

6

8

39 4

6

59

13 18

8

32 14

6

1

18

48 13

2

1

27 18

28 2

33

38

8

13

3

20 6

31

18

1

3

47

1

62

45 38

6

2

1

13

8

26

84

9

7

18

12

19 24

40 48

6

2 1

14

19 1

4 1

48

5

67 4

52 6

24

7

16

3

38

2

2

cellular_organisms@YP_001113853[137][RRM1:100%****][PROK:99%****][KOG0108:58%****][.KOG0116:14%**][.KOG0921:7%**][.KOG0149:7%**][.KOG0111:6%**]

Bacteroidales@YP_213478[13][RRM1:100%**][PROK:100%**][KOG0108:69%**][.KOG0125:31%*]

Embryophyta@jgi_Phypa1_1_28366[17][RRM1:100%**][put-sr:76%**][KOG0127:29%*][.KOG0125:12%][.KOG4661:6%][.KOG0147:6%]

Coelomata@ENSTBEP00000011040[87][RRM1:98%****][put-sr:16%**][KOG4661:100%****]

Gammaproteobacteria@YP_561253[27][RRM1:100%***][PROK:100%***][KOG0108:96%***]

Embryophyta@jgi_Phypa1_1_134646[11][RRM1:100%**][cpRNP:9%][KOG0123:45%*][.KOG0127:36%*][.KOG2029:9%]

Magnoliophyta@10511_m000028_AZM5_5258[15][RRM1:100%**][cpRNP:33%*][KOG0127:53%**][.KOG0131:27%*][.KOG0145:13%][.KOG0108:7%]

Coelomata@ENSTBEP00000015452[229][RRM3:88%*****][.RRM2:9%**][ELAV:82%*****][KOG0145:100%*****]

Embryophyta@NP_001063403[14][RRM1:100%**][KOG0148:100%**]

Cyanobacteria@YP_476186[8][RRM1:100%**][PROK:100%**][KOG0108:38%*][.KOG0122:12%]

Cyanobacteria@NP_898344[17][RRM1:100%**][PROK:100%**][KOG0108:65%**]

Coelomata@ENSORLP00000004891[62][RRM2:94%****][.RRM1:6%*][RBMS:79%***][KOG0145:100%****]

Bilateria@ENSORLP00000014121[125][RRM1:100%****][FOX:75%****][KOG0125:100%****]

Euteleostomi@ENSOANP00000001262[28][RRM1:100%***][RBM:46%**][KOG0127:100%***]

Eukaryota@NP_187747[49][RRM1:100%***][KOG0122:98%***]

Coelomata@ENSMLUP00000006206[100][RRM2:88%****][.RRM1:12%**][put-sr:5%*][hnRNP:28%***][KOG4212:98%****]

Chordata@ENSOGAP00000002890[91][RRM3:80%****][.RRM2:13%**][.RRM1:7%*][hnRNP:37%***][KOG4212:100%****]

Coelomata@ENSOGAP00000009767[86][RRM1:100%****][hnRNP:34%***][KOG4212:100%****]

Eukaryota@jgi_Volca1_109965[18][RRM1:78%**][.RRM2:22%*][put-sr:22%*][KOG4212:61%**][.KOG0123:39%*]

Fungi_Metazoa_group@AGAP004592-PA[123][RRM2:81%****][.RRM1:18%***][put-sr:100%****][SR:60%****][KOG0105:50%****][.KOG0106:46%****]

Bilateria@XP_967263[73][RRM2:78%****][.RRM1:22%**][put-sr:79%****][SR:75%****][KOG0105:100%****]

Euteleostomi@ENSDNOP00000001522[23][RRM1:100%***][RBM:61%**][KOG0144:87%**][.KOG0145:13%*]

Eukaryota@ENSDNOP00000002400[249][RRM4:82%*****][.RRM3:11%***][.RRM2:6%**][PABP:54%****][KOG0123:100%*****]

Eukaryota@XP_964958[72][RRM1:100%****][KOG0226:100%****]

Eukaryota@ENSETEP00000015606[204][RRM3:85%*****][.RRM2:11%***][PABP:66%****][KOG0123:100%*****]

Eukaryota@ENSGALP00000021793[59][RRM1:100%****][cyclophilin:59%***][KOG0111:98%****]

Eukaryota@jgi_Phypa1_1_37849[169][RRM1:100%*****][put-sr:5%**][GRSRBP:33%****][.hnRNP:18%***][.RBMY:15%***][KOG0108:23%***][.KOG0111:23%***][.KOG0149:18%***][.KOG0117:11%**][.KOG0116:9%**]

Euteleostomi@ENSGALP00000012472[36][RRM4:89%***][.RRM2:8%*][nucleolin:56%**][KOG0123:100%***]

Magnoliophyta@NP_181287[9][RRM1:100%**][oligoU:22%][KOG0148:56%*][.KOG0127:22%][.KOG0145:11%][.KOG0113:11%]

Eukaryota@XP_391240[27][RRM2:67%**][.RRM1:33%**][cpRNP:19%*][KOG0127:48%**][.KOG0108:22%*][.KOG0131:15%*][.KOG0149:7%][.KOG0145:7%]

Coelomata@AGAP006798-PA[81][RRM1:100%****][put-sr:99%****][KOG0122:26%***][.KOG0125:25%**][.KOG0147:14%**][.KOG0108:9%*]

Eukaryota@jgi_Physo1_1_108557[316][RRM2:91%*****][.RRM1:9%***][PABP:46%****][KOG0123:79%*****][.KOG0131:21%****]

Embryophyta@29727_m000492[13][RRM3:92%**][.RRM2:8%][oligoU:46%*][KOG0148:100%**]

Eukaryota@IMGA_AC144483_30_2[123][RRM2:83%****][.RRM1:17%***][TIATIAR:58%****][.oligoU:6%*][KOG0148:99%****]

Eukaryota@ENSMUSP00000030730[72][RRM2:85%****][.RRM1:15%**][oligoU:10%*][KOG0148:58%***][.KOG0123:25%**][.KOG0131:14%**]

Embryophyta@NP_001067623[8][RRM1:100%**][KOG0117:100%**]

Bilateria@ENSORLP00000004891[130][RRM1:100%****][RBMS:72%****][KOG0145:99%****]

Eukaryota@NP_001058102[93][RRM1:100%****][RBM:52%***][.30kRRM:13%**][KOG0149:96%****]

Magnoliophyta@NP_001042672[10][RRM1:100%**][oligoU:50%*][KOG4205:80%**][.KOG0149:20%]

Coelomata@SINFRUP00000146060[58][RRM1:100%****][TARDBP:72%***][KOG4205:98%****]

Endopterygota@CG16901-PC[19][RRM1:100%**][KOG4205:100%**]

Eukaryota@ENSMODP00000031317[289][RRM1:100%*****][hnRNP:28%****][.Musashi:13%***][.Dazap:9%***][KOG4205:99%*****]

Bilateria@ENSRNOP00000022054[326][RRM1:100%*****][hnRNP:54%*****][KOG4205:100%*****]

Ciona@ENSCINP00000012771[9][RRM1:100%**][put-sr:11%][KOG4205:100%**]

Eukaryota@AGAP006656-PA[121][RRM2:88%****][.RRM1:12%**][Musashi:36%***][.Dazap:21%***][.hnRNP:10%**][KOG4205:100%****]

Endopterygota@AAEL008257-PA[8][RRM2:100%**][KOG4205:100%**]

Deuterostomia@ENSMODP00000011218[78][RRM1:100%****][G3BP:82%****][KOG0116:100%****]

Viridiplantae@NP_851001[17][RRM2:100%**][put-sr:12%][KOG4205:94%**][.KOG1833:6%]

Euteleostomi@ENSEEUP00000005436[64][RRM1:95%****]

Coelomata@AAEL001684-PA[39][RRM1:100%***][KOG0125:21%**]

Endopterygota@XP_001121454[19][RRM2:100%**][KOG4205:100%**]

Mammalia@ENSETEP00000003776[19][RRM1:100%**][LA:95%**][KOG4213:100%**]

Euteleostomi@ENSDARP00000005968[129][RRM2:95%****][.RRM1:5%*][hnRNP:57%****][KOG4205:100%****]

Coelomata@CG6354-PB[373][RRM2:95%*****][hnRNP:53%*****][KOG4205:100%*****]

Ciona@ENSCINP00000008394[8][RRM2:100%**][KOG4205:100%**]

Embryophyta@NP_001062111[8][RRM1:100%**][put-sr:62%*][KOG4849:38%*][.KOG4246:12%][.KOG0113:12%][.KOG4676:12%]

Eukaryota@IMGA_AC183923_6_1[34][RRM3:74%***][.RRM1:15%*][.RRM2:12%*][put-sr:6%][KOG0110:100%***]

Euteleostomi@ENSSTOP00000002132[31][RRM1:100%***][SART3:68%***][KOG0128:100%***]

Coelomata@ENSDARP00000093407[32][RRM2:88%***][.RRM1:12%*][KOG0108:12%*][.KOG3001:6%][.KOG0123:6%][.KOG0126:6%]

Coelomata@XP_001182806[39][RRM1:100%***][KOG0108:13%*][.KOG0116:8%*][.KOG0921:5%]

Euteleostomi@ENSSARP00000000775[28][RRM1:100%***][eIF4B:54%**]

Eukaryota@ENSMLUP00000011758[47][RRM1:100%***][put-sr:91%***][UMH:64%***][.CAPER:15%*][KOG0147:100%***]

Eukaryota@ENSCSAVP00000003369[89][RRM1:100%****][put-sr:17%**][PABP:26%***][KOG4209:100%****]

Viridiplantae@jgi_Chlre3_99594[25][RRM1:100%***][KOG0123:8%]

Chordata@ENSETEP00000010530[36][RRM1:50%**][.RRM2:50%**][put-sr:100%***][SRrp:75%***][KOG4676:100%***]

Eukaryota@8925_m000027_AZM5_1178[67][RRM1:100%****][put-sr:84%****][SR:61%***][KOG4207:61%***][.KOG4368:24%**]

Embryophyta@30076_m004622[9][RRM1:100%**][FCAFPA:22%][KOG0144:100%**]

Deuterostomia@ENSDNOP00000008593[94][RRM1:100%****][P54nrb:28%***][.PSP1:21%**][.PSF:18%**][KOG0115:99%****]

Endopterygota@CG10328-PA[9][RRM1:100%**][P54nrb:33%*][KOG0115:100%**]

Euteleostomi@GSTENP00013801001[29][RRM1:100%***][LA:59%**][KOG1855:100%***]

Euteleostomi@ENSGACP00000016696[19][RRM3:79%**][.RRM4:11%][.RRM1:11%][RBM:58%**][KOG0127:100%**]

Eukaryota@ENSMODP00000034858[66][RRM1:100%****][KOG0121:100%****]

Eukaryota@jgi_Phatr2_8132[54][RRM1:100%***][KOG0114:100%***]

Embryophyta@jgi_Phypa1_1_217831[15][RRM3:93%**][.RRM1:7%][KOG0117:100%**]

Euteleostomi@ENSSTOP00000002923[18][RRM1:100%**][KOG4205:11%]

Eukaryota@NP_001053839[55][RRM6:42%***][.RRM5:35%**][.RRM4:11%*][.RRM3:9%*][KOG0110:100%****]

Embryophyta@30128_m008555[15][RRM1:100%**][KOG4660:100%**]

Euteleostomi@GSTENP00022906001[41][RRM3:83%***][.RRM2:10%*][.RRM1:7%*][nucleolin:54%***][KOG0123:93%***]

Euteleostomi@ENSMODP00000021210[32][RRM2:97%***][nucleolin:59%**][KOG0123:100%***]

Chordata@ENSOGAP00000005376[31][RRM2:90%***][.RRM3:6%][RBM:39%**][KOG0127:100%***]

Embryophyta@29742_m001371[15][RRM2:80%**][.RRM1:20%*][put-sr:87%**][SR:67%**][KOG0106:100%**]

Coelomata@ENSCINP00000003632[126][RRM2:70%****][.RRM1:30%***][hnRNP:37%***][.GRSRBP:15%**][KOG4211:100%****]

Euteleostomi@ENSOCUP00000014007[29][RRM2:97%***][SART3:69%**][KOG0128:100%***]

Coelomata@ENSMUSP00000057332[45][RRM1:100%***][put-sr:100%***][RNPS1:64%***][KOG4209:87%***]

Viridiplantae@jgi_Phypa1_1_105411[8][RRM1:100%**][put-sr:100%**][SR:25%][KOG0117:12%][.KOG0462:12%]

Chordata@ENSETEP00000001114[45][RRM1:100%***][put-sr:96%***][SRrp:82%***][KOG0111:29%**][.KOG0415:13%*]

Viridiplantae@NP_001046448[23][RRM1:100%***][put-sr:91%***][SR:35%**][KOG4207:13%*][.KOG0127:13%*][.KOG0110:9%]

Eukaryota@ENSGALP00000022397[157][RRM1:100%*****][put-sr:75%****][SR:59%****][KOG0107:66%****]

Euteleostomi@ENSOANP00000024755[113][RRM1:100%****][hnRNP:36%***][.RALYL:15%**]

Eukaryota@ENSOANP00000021053[127][RRM1:100%****][put-sr:91%****][SR:61%****][KOG0106:55%****][.KOG0105:37%***]

Embryophyta@NP_194280[13][RRM1:100%**][put-sr:77%**][SR:62%**][KOG0106:100%**]

Eukaryota@ENSTBEP00000007356[92][RRM1:100%****][put-sr:82%****][SR:65%****][KOG0105:100%****]

Eukaryota@ENSGACP00000013006[79][RRM2:96%****][snRNP:30%***][KOG4206:100%****]

Ascomycota@YDL224C[8][RRM1:88%*][.RRM2:12%][KOG3598:12%][.KOG1457:12%]

Bilateria@ENSLAFP00000012959[197][RRM3:93%*****][.RRM2:5%**][hnRNP:36%****][KOG0117:100%*****]

Endopterygota@CG8597-PE[8][RRM2:100%**][LARK:62%*][KOG0109:100%**]

Coelomata@ENSXETP00000008271[74][RRM1:100%****][LARK:61%***][KOG0109:97%****]

Euteleostomi@ENSDNOP00000012760[63][RRM2:94%****][.RRM1:6%*][LARK:65%***][.RBM:21%**][KOG0109:97%****]

Clupeocephala@ENSORLP00000002364[10][RRM2:100%**][KOG0109:100%**]

Clupeocephala@ENSGACP00000025151[11][RRM1:100%**][KOG0109:100%**]

Mammalia@ENSTBEP00000003150[16][RRM1:100%**][RBM:94%**][KOG0109:100%**]

Eukaryota@jgi_Ostta4_3181[66][RRM1:100%****][put-sr:47%***][cyclophilin:32%***][KOG0415:97%****]

Deuterostomia@XP_001178221[30][RRM1:100%***][put-sr:63%**][snRNP:70%***][KOG0113:100%***]

Coelomata@XP_974651[54][RRM2:83%***][.RRM1:17%**][put-sr:87%***][RBM:37%**][KOG0112:100%***]

Coelomata@ENSMMUP00000010529[37][RRM3:54%**][.RRM2:41%**][.RRM1:5%][put-sr:92%***][KOG0112:84%***][.KOG3598:8%*]

Eukaryota@GSTENP00007343001[69][RRM1:100%****][FCAFPA:10%*][KOG0533:99%****]

Coelomata@XP_782270[24][RRM1:100%***][Bruno:42%**][KOG0144:100%***]

Bilateria@ENSXETP00000031370[81][RRM1:100%****][Bruno:42%***][KOG0146:84%****][.KOG0144:16%**]

Bilateria@ENSGALP00000025475[210][RRM1:100%*****][hnRNP:33%****][KOG0117:100%*****]

Bilateria@AGAP009477-PA[250][RRM2:73%*****][.RRM1:27%****][Bruno:59%****][KOG0144:56%****][.KOG0146:44%****]

Embryophyta@jgi_Phypa1_1_115029[9][RRM2:100%**][KOG0144:100%**]

Embryophyta@29889_m003323[11][RRM2:100%**][FCAFPA:18%][KOG0144:100%**]

Eukaryota@NP_001063859[35][RRM1:100%***][ZCRB1:69%***][KOG0108:40%**][.KOG0122:9%*][.KOG0117:6%][.KOG0107:6%]

Eukaryota@jgi_Volca1_104604[49][RRM1:100%***][put-sr:78%***][KOG0151:100%***]

Coelomata@XP_975014[28][RRM1:100%***][RBM:86%***][KOG0153:100%***]

Eutheria@ENSETEP00000000464[10][RRM1:100%**][put-sr:100%**][KOG0132:100%**]

Euteleostomi@ENSOANP00000013028[22][RRM1:100%***]

Euteleostomi@ENSMODP00000018834[25][RRM1:100%***][put-sr:64%**][KOG0147:48%**][.KOG0132:12%*]

Diptera@AGAP003899-PA[15][RRM2:100%**][KOG0145:100%**]

Bilateria@CG3151-PE[218][RRM2:92%*****][.RRM1:7%**][ELAV:84%*****][KOG0145:100%*****]

Tetrapoda@ENSXETP00000004736[17][RRM2:59%**][.RRM1:41%*][PTBP:94%**][KOG1190:100%**]

Embryophyta@IMGA_AC141435_12_2[17][RRM2:76%**][.RRM1:24%*][KOG4660:100%**]

Coelomata@ENSORLP00000008206[18][RRM1:100%**][snRNP:83%**][KOG4206:100%**]

Diptera@AAEL011150-PA[15][RRM1:100%**][KOG0145:100%**]

Bilateria@ENSORLP00000021434[219][RRM1:100%*****][ELAV:79%*****][KOG0145:100%*****]

Euteleostomi@ENSXETP00000044031[49][RRM2:76%***][.RRM1:24%**][KOG0145:41%**][.KOG0123:14%*][.KOG0110:14%*]

Coelomata@ENSTBEP00000005385[105][RRM2:86%****][.RRM1:14%**][P54nrb:30%***][.PSP1:24%***][.PSF:21%***][KOG0115:100%****]

Gammaproteobacteria@YP_001083500[11][RRM1:100%**][PROK:100%**][KOG0145:27%*][.KOG0108:18%][.KOG0144:9%][.KOG0122:9%]

Euteleostomi@GSTENP00029551001[21][RRM1:100%***][put-sr:10%][KOG0110:100%***]

Ascomycota@XP_001386803[10][RRM4:90%**][.RRM2:10%][KOG0110:100%**]

Euteleostomi@ENSGALP00000013474[20][RRM5:85%**][.RRM4:5%][.RRM3:5%][.RRM2:5%][put-sr:10%][KOG0110:100%**]

Eukaryota@ENSXETP00000023927[236][RRM1:100%*****][PABP:55%****][KOG0123:100%*****]

Eukaryota@NP_001064759[59][RRM1:100%****][snRNP:8%*][KOG0131:100%****]

Deuterostomia@ENSXETP00000012868[47][RRM1:100%***][KOG4454:60%***][.KOG0131:40%**]

Eukaryota@jgi_Volca1_82970[75][RRM2:91%****][.RRM1:9%*][put-sr:80%****][snRNP:53%***][KOG0120:100%****]

Eukaryota@AAEL002461-PA[78][RRM1:100%****][put-sr:29%***][KOG0126:100%****]

Euteleostomi@ENSDARP00000069729[82][RRM1:100%****][KOG1995:77%****][.KOG0921:16%**][.KOG2044:5%*]

Amniota@ENSMODP00000004174[11][RRM4:55%*][.RRM3:36%*][.RRM2:9%][put-sr:100%**][KOG0112:100%**]

Eukaryota@YHR086W[51][RRM3:76%***][.RRM2:20%**][oligoU:10%*][KOG0148:90%***]

Eukaryota@ENSOANP00000006980[251][RRM3:67%*****][.RRM2:24%****][.RRM1:10%***][Bruno:50%****][KOG0144:55%****][.KOG0146:45%****]

Eukaryota@CG6937-PA[73][RRM1:100%****][put-sr:5%*][KOG4208:99%****]

Eukaryota@jgi_Physo1_1_143842[43][RRM1:100%***][put-sr:47%**][snRNP:14%*][KOG0113:100%***]

Embryophyta@29900_m001607[13][RRM2:100%**][oligoU:38%*][KOG4205:77%**][.KOG0149:23%*]

Eukaryota@ENSDARP00000064611[84][RRM1:100%****][KOG0108:99%****]

Eukaryota@jgi_Thaps3_18841[52][RRM1:100%***][put-sr:56%***][RBM:42%***][KOG0130:100%***]

Embryophyta@NP_188026[13][RRM1:100%**][oligoU:38%*][KOG0148:100%**]

Bilateria@ENSSARP00000011721[82][RRM1:100%****][TIATIAR:80%****][KOG0148:100%****]

Dikarya@XP_960425[12][RRM3:100%**][PABP:17%][KOG0123:100%**]

Eukaryota@ENSFCAP00000006163[84][RRM2:88%****][.RRM1:12%**][put-sr:86%****][UMH:39%***][.CAPER:8%*][KOG0147:100%****]

Bilateria@ENSCSAVP00000007991[62][RRM2:95%****][.RRM1:5%*][UMH:74%***][KOG0124:100%****]

Bilateria@Y47G6A_20a[64][RRM1:100%****][UMH:73%***][KOG0124:100%****]

Coelomata@CG4787-PA[102][RRM3:74%****][.RRM2:16%**][.RRM1:11%**][TIATIAR:75%****][KOG0148:100%****] part of 79 - TIA TIAR OligoU

67 - UMH

5 - PABP

76 - TIA TIAR OligoU

20 - RBM

part of 79 - TIA TIAR OligoU

Part of 36 - snRNP82

9 - Bruno78 - OligoU

61

6964 - snRNP

4746

49

3 - PABP

59

1

Part of 4 - p54rnb

10 - ELAV

43

Part of 11 - ELAV RBMS

14 - RBM13

57 - ZCRB18 - Bruno

FCA FPA

2 - hnRNP

7 - Bruno FCA FPA

Part of 30 - PDIP FCA FPA

5453 - RBM

55

Part of 36 - snRNP38 - Cyclophilin

50 -51- 52 - LARK

Part of 63 - hnRNP

41 - snRNP

16 - dual RRM SR proteins

86 - hnRNP/RALYL17 - single-RRM Zn-K SR proteins

18

22a - single RRM SR proteins (plants)23 - SRrp

26 - SR4527 - RNPS1

37 - SART380 - hnRNP

56 - green plant-specific RS group of SR proteins71 - RBM

4260

Part of 63 - hnRNP

4424

72 - RBM81 - La

Part of 33 - p54nrb

22b - single RRM SR proteins (animals)85 - SRrp

83 - PABP75 - CAPER UMH

87 - eIF-4B

73 - SART3Part of 32

35 - G3BP

RBM

30K-RRM

hnRNP

Musashi

Dazap

TARDBP

OligoU

84 - La

62

77 - TIA TIAR OligoU

4 - PABP PSP1 PSF p54rnb missing

19 - cyclophilin66 - PaBP

6 - PABP

29 - dual-RRM

SR proteins

Part of 30

- hnRNP

6570 - RBM

Part of 68 - FOXPart of 11 - ELAV RBMS

12 - ELAV

Part of 68


28

Fig. S12

132

52 60

94 59

96

57

97

58

63

55

93

100 69

98 53

70

50

74

57 98

93

92

98

99

73

71 91

70

52

71

55

96

70 92

71

54

75 58

84

81

80 85

72

64

X t i li @ENSXETP00000057107[2][RRM1 100%][ t 100%][SR 100%][KOG0106 100%][SR 40]Ciona intestinalis@ENSCINP00000014783[RRM1][put-sr][KOG0106]

Caenorhabditis elegans@W02B12_3a[3][RRM1:100%*][put-sr:33%][SR:100%*][KOG0106:100%*][CeSRp75/rsp-1]Caenorhabditis elegans@W02B12_2[RRM1][put-sr][SR][KOG0106][CeSRp40/rsp-2]

Xenopus tropicalis@ENSXETP00000031465[2][RRM1:100%][put-sr:100%][KOG0105:100%]Ciona savignyi@ENSCSAVP00000019399[RRM1][put-sr][KOG0106]

Ciona intestinalis@ENSCINP00000022868[RRM1][KOG0106]Ciona savignyi@ENSCSAVP00000004366[3][RRM1:100%*][put-sr:100%*][KOG0106:100%*]Ciona intestinalis@ENSCINP00000010131[3][RRM1:100%*][put-sr:100%*][KOG0106:100%*]

Ciona intestinalis@ENSCINP00000016525[RRM1][put-sr][KOG0106]Theria@ENSBTAP00000017699[12][RRM1:100%**][put-sr:100%**][SR:100%**][KOG0106:50%*][.KOG0105:50%*][SRp75]Myotis lucifugus@ENSMLUP00000013443[RRM1][put-sr][SR][KOG0105][SRp75]Tetraodon nigroviridis@GSTENP00010110001[RRM1][put-sr][KOG0598]Smegmamorpha@ENSGACP00000003112[3][RRM1:100%*][put-sr:100%*][KOG0106:100%*]

Danio rerio@ENSDARP00000025299[RRM1][put-sr][KOG0105]Danio rerio@ENSDARP00000094522[RRM1][put-sr]

Danio rerio@ENSDARP00000095990[2][RRM1:100%][put-sr:100%][SR:50%][KOG0105:100%][SRp55]Oryzias latipes@ENSORLP00000004399[RRM1][put-sr][KOG0105]Tetraodontidae@SINFRUP00000158023[2][RRM1:100%][put-sr:100%][KOG3766:50%][.KOG0105:50%]

Danio rerio@ENSDARP00000022089[RRM1][put-sr][KOG0105]Gasterosteus aculeatus@ENSGACP00000008092[3][RRM1:100%*][put-sr:100%*][KOG0105:100%*]

Xenopus tropicalis@ENSXETP00000054329[RRM1][put-sr][KOG0105]Monodelphis domestica@ENSMODP00000030967[2][RRM1:100%][put-sr:100%][SR:100%][KOG0106:50%][.KOG0105:50%][SRp55]Cavia porcellus@ENSCPOP00000010577[RRM1][put-sr][SR][KOG0106][SRp55]Eutheria@ENSDNOP00000006506[3][RRM1:100%*][put-sr:67%][SR:100%*][KOG0105:67%][.KOG0106:33%][SRp55]Echinops telfairi@ENSETEP00000005046[RRM1][put-sr][SR][KOG0105][SRp55]Murinae@ENSMUSP00000017065[2][RRM1:100%][put-sr:100%][SR:100%][KOG0105:100%][SRp55]

Bos taurus@ENSBTAP00000011240[RRM1][put-sr][SR][KOG0105][SRp55]Oryza sativa_japonica_cultivar-group@NP_001052061[RRM1][put-sr][SR][KOG0106][RSp29]

Arabidopsis thaliana@NP_182184[RRM1][put-sr][SR][KOG0106][RSp31a]Arabidopsis thaliana@NP_567120[RRM1][put-sr][SR][KOG0106][RSp31]

Ricinus communis@29742_m001371[RRM1][KOG0106]Physcomitrella patens@jgi_Phypa1_1_167387[RRM1][put-sr][KOG0106]Oryza sativa_japonica_cultivar-group@NP_001045729[RRM1][put-sr][SR][KOG0106][RSp33]

Zea mays@8514_m000507_c0216K08[RRM1][SR][KOG0106][RSp33]Zea mays@10633_m000022_AZM5_5503[RRM1][KOG0106]

Ricinus communis@30147_m014308[RRM1][put-sr][KOG0106]Medicago truncatula@IMGA_AC152177_25_1[RRM1][put-sr][KOG0106]

Arabidopsis thaliana@NP_194280[RRM1][put-sr][SR][KOG0106][RSp40/SRp35]Arabidopsis thaliana@NP_851174[2][RRM1:100%][put-sr:100%][SR:100%][KOG0106:100%][RSp41]

Ostreococcus lucimarinus@jgi_Ost9901_3_8794[RRM1][KOG0105]Caenorhabditis elegans@Y111B2A_18_1[3][RRM1:100%*][put-sr:100%*][SR:100%*][KOG0105:100%*][CeSF2/ASF/rsp-3]

Phytophthora sojae@jgi_Physo1_1_142377[RRM1][put-sr][KOG0105]Phytophthora ramorum@jgi_Phyra1_1_46108[RRM1][KOG0105]

Volvox carteri@jgi_Volca1_45192[RRM1][put-sr][KOG0105]Chlamydomonas reinhardtii@jgi_Chlre3_129159[RRM1][put-sr][KOG0105]

Phytophthora ramorum@jgi_Phyra1_1_84100[RRM1][KOG0105]Phytophthora sojae@jgi_Physo1_1_138982[RRM1][KOG0105]

Volvox carteri@jgi_Volca1_72532[RRM1][put-sr][KOG0105]Chlamydomonas reinhardtii@jgi_Chlre3_120469[RRM1][KOG0105]

Oryza sativa_japonica_cultivar-group@NP_001060608[RRM1][put-sr][SR][KOG0105][SRp33a]Arabidopsis thaliana@NP_190512[2][RRM1:100%][put-sr:100%][SR:100%][KOG0105:100%][SRp34a]Medicago truncatula@IMGA_CT868739_2_1[RRM1][put-sr][SR][KOG0105][SRp34a]Ricinus communis@29827_m002610[RRM1][put-sr][KOG0105]

Physcomitrella patens@jgi_Phypa1_1_140978[RRM1][put-sr][KOG0105]Physcomitrella patens@jgi_Phypa1_1_113630[RRM1][put-sr][KOG0105]Physcomitrella patens@jgi_Phypa1_1_205547[RRM1][put-sr][KOG0105]

Oryza sativa_japonica_cultivar-group@NP_001050082[RRM1][put-sr][SR][KOG0105][SRp32]Oryza sativa_japonica_cultivar-group@NP_001055323[RRM1][put-sr][SR][KOG0105][SRp33b]

Arabidopsis thaliana@NP_683288[2][RRM1:100%][put-sr:100%][SR:100%][KOG0105:100%][SRp30]Arabidopsis thaliana@NP_850933[3][RRM1:100%*][put-sr:100%*][SR:100%*][KOG0105:100%*][SR1/SRp34]

Arabidopsis thaliana@NP_567235[2][RRM1:100%][put-sr:50%][SR:100%][KOG0105:100%][SRp34b]Medicago truncatula@IMGA_AC134522_46_2[2][RRM1:100%][put-sr:100%][KOG0105:100%]Medicago truncatula@IMGA_AC144541_27_2[RRM1][put-sr][KOG0105]

Ricinus communis@29986_m001610[RRM1][put-sr][SR][KOG0105][SRp33a]Medicago truncatula@IMGA_AC174141_23_1[RRM1][put-sr][KOG0105]

Ricinus communis@30128_m008837[RRM1][put-sr][KOG0105]Ricinus communis@30128_m008840[RRM1][put-sr][KOG0105]

Plasmodium falciparum_3D7@XP_001351730[RRM1][put-sr][KOG0105]Plasmodium falciparum_3D7@XP_001347501[RRM1][put-sr][KOG0105]

Theileria parva_strain_Muguga@XP_766386[RRM1][put-sr][KOG0105]Ciona savignyi@ENSCSAVP00000010348[2][RRM1:100%][put-sr:100%][KOG0105:100%]

Ciona intestinalis@ENSCINP00000015147[RRM1][put-sr][KOG0105]Danio rerio@ENSDARP00000091488[2][RRM1:100%][put-sr:100%][KOG0105:100%]

Takifugu rubripes@SINFRUP00000145791[RRM1][put-sr][SR][KOG0105][SRp30c]Gasterosteus aculeatus@ENSGACP00000022361[2][RRM1:100%][put-sr:100%][KOG0105:100%]

Xenopus tropicalis@ENSXETP00000026703[RRM1][put-sr][SR][KOG0105][SRp30c]Monodelphis domestica@ENSMODP00000003831[RRM1][put-sr][SR][KOG0105][SRp30c]

Mus musculus@ENSMUSP00000031513[RRM1][put-sr][SR][KOG0105][SRp30c]Bos taurus@ENSBTAP00000016997[RRM1][put-sr][SR][KOG0105][SRp30c]Tupaia belangeri@ENSTBEP00000007356[RRM1][put-sr][SR][KOG0105][SRp30c]

Myotis lucifugus@ENSMLUP00000009421[RRM1][put-sr][SR][KOG0105][SRp30c]Eutheria@ENSCAFP00000015146[7][RRM1:100%*][put-sr:100%*][SR:86%*][KOG0105:100%*][SRp30c]

Oryctolagus cuniculus@ENSOCUP00000009368[RRM1][KOG0105]Nasonia vitripennis@XP_001605411[RRM1][put-sr][KOG0105]Apis mellifera@XP_393525[RRM1][put-sr][KOG0105]Diptera@AAEL006473-PA[3][RRM1:100%*][put-sr:100%*][KOG0105:100%*]

Tribolium castaneum@XP_967263[RRM1][put-sr][KOG0105]Oryzias latipes@ENSORLP00000006698[RRM1][put-sr][SR][KOG0105][ASF/SF2]Gasterosteus aculeatus@ENSGACP00000027276[RRM1][put-sr][SR][KOG0105][ASF/SF2]

Takifugu rubripes@SINFRUP00000151768[RRM1][put-sr][SR][KOG0105][ASF/SF2]Danio rerio@ENSDARP00000074866[2][RRM1:100%][put-sr:100%][SR:100%][KOG0105:100%][ASF/SF2]Gasterosteus aculeatus@ENSGACP00000014666[RRM1][SR][KOG0105][ASF/SF2]Oryzias latipes@ENSORLP00000005758[RRM1][put-sr][SR][KOG0105][ASF/SF2]Tetraodontidae@SINFRUP00000136750[2][RRM1:100%][put-sr:100%][SR:100%][KOG0105:100%][ASF/SF2]

Otolemur garnettii@ENSOGAP00000012982[RRM1][SR][KOG0105][ASF/SF2]Tupaia belangeri@ENSTBEP00000013333[RRM1][SR][KOG0105][ASF/SF2]Tetrapoda@ENSBTAP00000019644[17][RRM1:100%**][put-sr:53%**][SR:100%**][KOG0105:100%**][ASF/SF2]

Macaca mulatta@ENSMMUP00000004343[RRM1][SR][KOG0105][ASF/SF2]Echinops telfairi@ENSETEP00000004344[RRM1][SR][KOG0105][ASF/SF2]

ASF-like

"plant"

SRp75

SRp55

RS "plant"

SRp30c

ASF/SF2

N5

N6

Fig. S13

133

95

92

56

56

99 81

95

100 79

58 77

72 53

88

94

93

61

90

72 72

75

67 69

100

84 59

55

100

99

60

62 66

63

69

98

87

95

70

72 67

97

65

77

87

50

Th l i i d @j i Th 3 32790[RRM1][KOG0122]Chlamydomonas reinhardtii@jgi_Chlre3_112621[RRM1][KOG0122]Ostreococcus lucimarinus@jgi_Ost9901_3_6420[RRM1][KOG0122]

Ostreococcus tauri@jgi_Ostta4_5527[RRM1][KOG0122]Physcomitrella patens@jgi_Phypa1_1_196691[RRM1][KOG0122]Physcomitrella patens@jgi_Phypa1_1_164814[RRM1][KOG0122]


Ricinus communis@29973_m000409[RRM1][KOG0122]Medicago truncatula@IMGA_AC174277_12_1[2][RRM1:100%][KOG0122:100%]

Medicago truncatula@IMGA_AC144431_18_2[RRM1][KOG0122]Arabidopsis thaliana@NP_187747[RRM1][TIF3][KOG0122][TIF3]

Arabidopsis thaliana@NP_196219[RRM1][TIF3][KOG0122][TIF3]Ciona savignyi@ENSCSAVP00000018514[RRM1][put-sr]

Strongylocentrotus purpuratus@XP_001178467[2][RRM1:100%][put-sr:100%]Drosophila melanogaster@CG5655-PA[RRM1][put-sr][KOG0107]

Anopheles gambiae@AGAP009142-PA[RRM1][put-sr][KOG0921]Tribolium castaneum@XP_969323[RRM1][put-sr][KOG0107]

Nasonia vitripennis@XP_001605989[RRM1][put-sr][KOG0107]Apis mellifera@XP_396951[RRM1][put-sr][KOG0107]

Phytophthora@jgi_Phyra1_1_75301[2][RRM1:100%][put-sr:100%][KOG0105:100%]Strongylocentrotus purpuratus@XP_001178394[2][RRM1:100%][put-sr:100%][KOG0116:100%]

Caenorhabditis elegans@C33H5_12a_1[5][RRM1:100%*][put-sr:40%][SR:100%*][KOG0107:60%*][.KOG0116:40%][CeSRp20/rsp-6]Chlamydomonas reinhardtii@jgi_Chlre3_132362[RRM1][KOG0107]

Chlamydomonas reinhardtii@jgi_Chlre3_192053[RRM1][put-sr][KOG0107]Volvox carteri@jgi_Volca1_121301[RRM1][put-sr][KOG0107]

Physcomitrella patens@jgi_Phypa1_1_143810[2][RRM1:100%][KOG0107:100%]Oryza sativa_japonica_cultivar-group@NP_001048352[RRM1][put-sr][SR][RSZp21b]

Oryza sativa_japonica_cultivar-group@NP_001057018[RRM1][put-sr][SR][RSZp21a]Oryza sativa_japonica_cultivar-group@NP_001047400[RRM1][put-sr][SR][KOG0107][RSZp23]

Arabidopsis thaliana@NP_973901[2][RRM1:100%][SR:100%][SRZ21/RSZ21]Arabidopsis thaliana@NP_194886[2][RRM1:100%][put-sr:100%][SR:100%][KOG0107:100%][SRZ22/RSZ22]

Arabidopsis thaliana@NP_180035[RRM1][put-sr][SR][RSZ22a]Ricinus communis@28610_m000073[RRM1][SR][KOG0107][SRZ21/RSZ21]

Ricinus communis@29848_m004475[RRM1][put-sr][SR][SRZ22/RSZ22]Medicago truncatula@IMGA_CR936368_17_2[RRM1][put-sr][KOG0107]

Ciona intestinalis@ENSCINP00000026132[3][RRM1:100%*][put-sr:100%*][KOG0415:67%]Ciona savignyi@ENSCSAVP00000012556[4][RRM1:100%*][put-sr:100%*]

Tribolium castaneum@XP_968789[RRM1][put-sr][KOG4368]Apis mellifera@XP_001122800[RRM1][put-sr][KOG0107]

Anopheles gambiae@AGAP008303-PA[RRM1][put-sr]Drosophila melanogaster@CG10203-PA[RRM1][put-sr][SR][KOG0107][9G8]Ciona intestinalis@ENSCINP00000022204[2][RRM1:100%][put-sr:100%][KOG0107:100%]Ciona savignyi@ENSCSAVP00000004510[RRM1][put-sr]

Strongylocentrotus purpuratus@XP_788595[2][RRM1:100%][put-sr:100%]Strongylocentrotus purpuratus@XP_001180596[2][RRM1:100%][put-sr:100%]

Apis mellifera@XP_001123058[2][RRM1:100%][put-sr:50%][KOG0107:100%]Endopterygota@XP_001599712[6][RRM1:100%*][put-sr:17%][KOG0107:83%*][.KOG2490:17%]Culicidae@AAEL001356-PA[3][RRM1:100%*][put-sr:100%*][KOG0108:67%][.KOG0107:33%]Drosophila melanogaster@CG1987-PA[RRM1][put-sr][KOG0107]Drosophila melanogaster@CG17136-PD[4][RRM1:100%*][put-sr:50%][KOG0107:100%*]

Danio rerio@ENSDARP00000051184[2][RRM1:100%][put-sr:100%]Percomorpha@ENSGACP00000016280[4][RRM1:100%*][put-sr:100%*][KOG0107:50%][.KOG4368:25%]

Oryzias latipes@ENSORLP00000000921[3][RRM1:100%*][put-sr:100%*][KOG4368:33%][.KOG0107:33%]Danio rerio@ENSDARP00000070952[RRM1][SR][KOG0107][9G8]Xenopus tropicalis@ENSXETP00000054077[2][RRM1:100%][put-sr:100%][SR:100%][9G8]Mammalia@ENSBTAP00000033048[27][RRM1:100%***][put-sr:78%***][SR:93%***][KOG0107:81%***][9G8]Spermophilus tridecemlineatus@ENSSTOP00000003936[RRM1][put-sr]

Gallus gallus@ENSGALP00000022397[RRM1][put-sr][SR][9G8]Gallus gallus@ENSGALP00000038155[RRM1][put-sr][SR][9G8]

Rattus norvegicus@ENSRNOP00000058047[RRM1][put-sr]Rattus norvegicus@ENSRNOP00000011102[RRM1][put-sr][SR][KOG0107][9G8]

Gallus gallus@ENSGALP00000022386[RRM1][put-sr][SR][9G8]Monodelphis domestica@ENSMODP00000010787[RRM1][put-sr][SR][KOG0107][9G8]

Canis familiaris@ENSCAFP00000009434[RRM1][put-sr][KOG0107]Rattus norvegicus@ENSRNOP00000040587[RRM1][put-sr][SR][KOG0107][9G8]

Xenopus tropicalis@ENSXETP00000033870[RRM1][KOG0107]Xenopus tropicalis@ENSXETP00000018945[RRM1][KOG0107]

Strongylocentrotus purpuratus@XP_789661[2][RRM1:100%][put-sr:100%][KOG0116:100%]Strongylocentrotus purpuratus@XP_001178879[2][RRM1:100%][put-sr:100%][KOG0107:100%]

Danio rerio@ENSDARP00000076899[2][RRM1:100%][put-sr:50%][SR:100%][KOG0107:100%][SRp20]Gasterosteus aculeatus@ENSGACP00000001355[RRM1][put-sr][SR][KOG0107][SRp20]

Oryzias latipes@ENSORLP00000000358[RRM1][put-sr][SR][KOG0107][SRp20]Danio rerio@ENSDARP00000035207[2][RRM1:100%][put-sr:50%][SR:100%][KOG0107:100%][SRp20]

Takifugu rubripes@SINFRUP00000136850[RRM1][SR][KOG0107][SRp20]Tetraodon nigroviridis@GSTENP00027331001[RRM1][SR][KOG0107][SRp20]

Gasterosteus aculeatus@ENSGACP00000001909[3][RRM1:100%*][put-sr:100%*][SR:100%*][KOG0107:100%*][SRp20]Oryzias latipes@ENSORLP00000024888[RRM1][put-sr][SR][KOG0107][SRp20]

Takifugu rubripes@SINFRUP00000147448[RRM1][put-sr][SR][KOG0107][SRp20]Mus musculus@ENSMUSP00000100538[RRM1][put-sr][SR][KOG0107][SRp20]Tetrapoda@ENSBTAP00000004154[28][RRM1:100%***][put-sr:68%**][SR:100%***][KOG0107:100%***][SRp20]Eutheria@ENSEEUP00000001001[3][RRM1:100%*][put-sr:100%*]

Arabidopsis thaliana@NP_190918[RRM1][put-sr][SR][KOG0107][RSZ32]Arabidopsis thaliana@NP_850280[RRM1][put-sr][SR][KOG0107][RSZ33]

Oryza sativa_japonica_cultivar-group@NP_001042066[RRM1][put-sr][SR][KOG0109][RSZ37a]Oryza sativa_japonica_cultivar-group@NP_001054731[RRM1][put-sr][SR][RSZ39]

Ricinus communis@29805_m001527[RRM1][put-sr][KOG0109]Oryza sativa_japonica_cultivar-group@NP_001054489[RRM1][put-sr][SR][KOG0109][RSZ36]

Oryza sativa_japonica_cultivar-group@NP_001049771[RRM1][put-sr][SR][KOG0109][RSZ37b]Nasonia vitripennis@XP_001603815[2][RRM1:100%][put-sr:100%][KOG0105:100%]


Tribolium castaneum@XP_966697[RRM1][put-sr][KOG0106]Aedes aegypti@AAEL012621-PA[RRM1][put-sr][KOG0105]

Diptera@AGAP004592-PA[7][RRM1:100%*][put-sr:71%*][SR:86%*][KOG0105:57%*][.KOG0106:43%*]Aedes aegypti@AAEL000769-PA[RRM1][put-sr][KOG0106]

Caenorhabditis elegans@T28D9_2a[3][RRM1:100%*][put-sr:100%*][SR:100%*][KOG0106:100%*][CeSC35-2/rsp-5]Cryptococcus neoformans_var._neoformans_JEC21@XP_567562[RRM1][KOG0106]


Strongylocentrotus purpuratus@XP_001180940[2][RRM1:100%][put-sr:100%][KOG0106:100%]Danio rerio@ENSDARP00000043311[RRM1][put-sr][KOG0106]

Xenopus tropicalis@ENSXETP00000038885[RRM1][put-sr][KOG0106]Gasterosteus aculeatus@ENSGACP00000015556[RRM1][put-sr][KOG0106]Tetraodon nigroviridis@GSTENP00035800001[RRM1][put-sr][KOG0106]

Takifugu rubripes@SINFRUP00000169885[RRM1][put-sr][KOG0106]Gallus gallus@ENSGALP00000015427[RRM1][put-sr][KOG0106]

Gallus gallus@ENSGALP00000037225[RRM1][KOG0106]Oryzias latipes@ENSORLP00000011623[3][RRM1:100%*][put-sr:67%][SR:33%][KOG0106:100%*]

Gasterosteus aculeatus@ENSGACP00000010395[2][RRM1:100%][put-sr:100%][SR:50%][KOG0106:100%][SRp40]Tetraodontidae@SINFRUP00000132279[2][RRM1:100%][put-sr:50%][SR:50%][KOG0106:100%]

Danio rerio@ENSDARP00000069997[3][RRM1:100%*][put-sr:67%][SR:33%][KOG0106:100%*][SRp40]Ornithorhynchus anatinus@ENSOANP00000021051[RRM1][put-sr][SR][KOG0105][SRp40]

Ornithorhynchus anatinus@ENSOANP00000021052[RRM1][put-sr][SR][KOG0106][SRp40]Ornithorhynchus anatinus@ENSOANP00000021053[RRM1][put-sr][SR][KOG0106][SRp40]Afrotheria@ENSETEP00000016575[2][RRM1:100%][put-sr:100%][SR:100%][KOG0106:100%][SRp40]Amniota@ENSBTAP00000015408[24][RRM1:100%***][put-sr:96%***][SR:100%***][KOG0106:54%**][.KOG0105:46%**][SRp40]

Sorex araneus@ENSSARP00000000971[RRM1][put-sr][SR][KOG0105][SRp40]Catarrhini@ENSP00000342294[3][RRM1:100%*][put-sr:100%*][SR:100%*][KOG0106:100%*][SRp40]

Xenopus tropicalis@ENSXETP00000057107[2][RRM1:100%][put-sr:100%][SR:100%][KOG0106:100%][SRp40]

SRp20

RS2Z "plant"

RSZ "plant"

9G8

SRp40

N3

N4

Fig. S13

134

57

57 50 84

67

96

59 69

83

52

79 52

100

82

99 50

94

100 99

57

100

93

58

83

99

95

98

91

56 72

57 94

77 98

90 96

60

59 81

86 77

54 94

89

100

65 62

G t t l t @ENSGACP00000002897[RRM1][ t ][KOG0415]Tetraodon nigroviridis@GSTENP00010468001[RRM1][SRrp][KOG4207][SRp38]

Takifugu rubripes@SINFRUP00000150947[RRM1][put-sr]Oryzias latipes@ENSORLP00000009635[RRM1][SRrp][KOG4207][SRp38]

Xenopus tropicalis@ENSXETP00000011851[RRM1][put-sr]Mus musculus@ENSMUSP00000103794[RRM1][put-sr][SRrp][KOG0111][SRrp35]Echinops telfairi@ENSETEP00000001114[RRM1][put-sr]Catarrhini@ENSP00000358479[3][RRM1:100%*][put-sr:100%*][SRrp:100%*][SRrp35]

Erinaceus europaeus@ENSEEUP00000010036[RRM1][put-sr][SRrp][SRrp35]Cavia porcellus@ENSCPOP00000009809[RRM1][put-sr][SRrp][SRrp35]

Monodelphis domestica@ENSMODP00000022797[RRM1][put-sr][SRrp][SRrp35]Canis familiaris@ENSCAFP00000019234[RRM1][put-sr][SRrp][SRp38]Eutheria@ENSBTAP00000010616[19][RRM1:100%**][put-sr:100%**][SRrp:100%**][KOG0111:58%**][.KOG0415:21%*][SRp38]

Canis familiaris@ENSCAFP00000004604[RRM1][put-sr][SRrp][SRp38]Eutheria@ENSEEUP00000013029[3][RRM1:100%*][put-sr:100%*][SRrp:100%*][SRp38]Monodelphis domestica@ENSMODP00000016281[RRM1][put-sr][SRrp][SRp38]Rattus norvegicus@ENSRNOP00000011154[2][RRM1:100%][put-sr:100%][SRrp:100%][SRp38]Gallus gallus@ENSGALP00000006566[RRM1][put-sr][SRrp][SRp38]

Drosophila melanogaster@CG5442-PB[RRM1][put-sr][SR][KOG4207][SC35]Aedes aegypti@AAEL010340-PB[2][RRM1:100%][put-sr:100%][KOG4207:100%]

Anopheles gambiae@AGAP009742-PA[RRM1][put-sr][KOG4207]Tribolium castaneum@XP_969931[RRM1][put-sr]Apis mellifera@XP_393352[RRM1][put-sr]

Caenorhabditis elegans@EEED8_7b[2][RRM1:100%][put-sr:50%][SR:100%][KOG4207:50%][CeSC35/rsp-4]Strongylocentrotus purpuratus@XP_785989[2][RRM1:100%][put-sr:100%][KOG4207:100%]Strongylocentrotus purpuratus@XP_001180179[4][RRM1:100%*][KOG4207:100%*]Ciona intestinalis@ENSCINP00000008678[RRM1][put-sr][KOG4207]

Ciona savignyi@ENSCSAVP00000015651[RRM1][put-sr][KOG4207]Oryzias latipes@ENSORLP00000023350[RRM1][put-sr][SR][KOG4368][SC35]

Takifugu rubripes@SINFRUP00000176738[RRM1][put-sr][SR][KOG4207][SC35]Percomorpha@ENSGACP00000004058[2][RRM1:100%][put-sr:100%][SR:100%][SC35]Clupeocephala@ENSDARP00000074623[3][RRM1:100%*][put-sr:100%*][SR:67%][KOG4207:100%*][SC35]

Oryzias latipes@ENSORLP00000001513[RRM1][put-sr][SR][KOG4207][SC35]Bos taurus@ENSBTAP00000012614[2][RRM1:100%][put-sr:100%][KOG4207:100%]

Rattus norvegicus@ENSRNOP00000045342[2][RRM1:100%][KOG4207:100%]Mus musculus@ENSMUSP00000078984[RRM1][KOG4207]

Danio rerio@ENSDARP00000015569[RRM1][put-sr][SR][KOG4207][SC35]Xenopus tropicalis@ENSXETP00000054042[RRM1][put-sr][SR][SC35]

Homo sapiens@ENSP00000381889[RRM1][put-sr][KOG4207]Macaca mulatta@ENSMMUP00000010035[RRM1][put-sr][SR][SRp46]

Mammalia@ENSBTAP00000024299[19][RRM1:100%**][put-sr:95%**][SR:100%**][KOG4368:74%**][.KOG4207:26%*][SC35]Dasypus novemcinctus@ENSDNOP00000000330[RRM1][put-sr][SR][KOG4368][SC35]

Erinaceus europaeus@ENSEEUP00000008808[RRM1][put-sr][SR][SC35]Homo sapiens@ENSP00000350877[RRM1][KOG4207]Macaca mulatta@ENSMMUP00000034012[RRM1][SR][KOG4207][SC35]Pan troglodytes@ENSPTRP00000032751[RRM1][KOG4207]

Ostreococcus lucimarinus@jgi_Ost9901_3_8174[RRM1][KOG4207]Tribolium castaneum@XP_970765[RRM2][KOG0127]

Ostreococcus lucimarinus@jgi_Ost9901_3_9858[RRM1][KOG0108]Ostreococcus tauri@jgi_Ostta4_7793[RRM1][KOG0108]

Cyanidioschyzon merolae@gnl_CMER_CML202C[RRM1][put-sr]Zea mays@8925_m000027_AZM5_1178[RRM1][KOG4207]

Oryza sativa_japonica_cultivar-group@NP_001062094[RRM1][put-sr][SR][KOG0415][SC35a]Zea mays@20810_m000015_AZM5_89637[2][RRM1:100%][put-sr:50%][SR:50%][KOG4207:100%][SC35a]

Oryza sativa_japonica_cultivar-group@NP_001050263[RRM1][put-sr][SR][KOG4207][SC35c]Physcomitrella patens@jgi_Phypa1_1_172957[RRM1][put-sr][KOG0415]

Physcomitrella patens@jgi_Phypa1_1_122960[RRM1][put-sr][KOG4207]Oryza sativa_japonica_cultivar-group@NP_001060322[RRM1][put-sr][SR][KOG4207][SC35b]

Medicago truncatula@IMGA_AC144459_24_2[2][RRM1:100%][put-sr:100%][KOG4207:100%]Ricinus communis@29581_m000256[RRM1][put-sr][KOG4207]

Arabidopsis thaliana@NP_201225[2][RRM1:100%][put-sr:100%][SR:100%][KOG4207:100%][SC35]Neurospora crassa_OR74A@XP_965346[RRM1][KOG0110]

Yarrowia lipolytica@XP_500351[RRM2][KOG0123]Theileria parva_strain_Muguga@XP_765374[RRM2]Methylococcus capsulatus_str._Bath@YP_113294[RRM1][PROK]

Nitrosococcus oceani_ATCC_19707@YP_344593[RRM1][PROK]Aureococcus anophagefferens@jgi_Auran1_9404[RRM1][KOG0122]

Aureococcus anophagefferens@jgi_Auran1_9375[RRM1][KOG0122]Aureococcus anophagefferens@jgi_Auran1_9018[RRM1]

Aureococcus anophagefferens@jgi_Auran1_17018[RRM1][KOG0111]Cryptosporidium parvum_Iowa_II@XP_626081[RRM1][KOG0122]

Chlamydomonas reinhardtii@jgi_Chlre3_184151[RRM1][KOG0921]Volvox carteri@jgi_Volca1_103546[RRM1][KOG0116]



Aureococcus anophagefferens@jgi_Auran1_17889[RRM1][KOG4207]Yarrowia lipolytica@XP_503515[RRM1][KOG0122]

Candida glabrata_CBS138@XP_446998[RRM1][KOG0122]Saccharomyces cerevisiae@YDR429C[RRM1][KOG0122]

Ashbya gossypii_ATCC_10895@NP_984285[RRM1][KOG0122]Pichia stipitis_CBS_6054@XP_001388004[RRM1][KOG0122]

Debaryomyces hansenii_CBS767@XP_458660[RRM1][KOG0122]Aedes aegypti@AAEL010807-PA[RRM1][put-sr][KOG1080]

Oryzias latipes@ENSORLP00000016244[RRM1][KOG1080]Tetraodon nigroviridis@GSTENP00000272001[RRM1]

Mus musculus@ENSMUSP00000098297[RRM1]Macaca mulatta@ENSMMUP00000016612[RRM1]Eutheria@ENSBTAP00000022553[3][RRM1:100%*][KOG1080:100%*]



Gibberella zeae_PH-1@XP_385241[RRM1][KOG0122]Leishmania infantum_JPCM5@XP_001468615[RRM1]


Caenorhabditis elegans@F22B5_2[RRM1][KOG0122]Cyanidioschyzon merolae@gnl_CMER_CMH159C[RRM1][KOG0122]

Dictyostelium discoideum_AX4@XP_641693[RRM1][KOG0122]Gasterosteus aculeatus@ENSGACP00000018150[RRM1][KOG0122]Clupeocephala@ENSDARP00000027672[2][RRM1:100%][KOG0122:100%]Tetrapoda@ENSBTAP00000003545[10][RRM1:100%**][KOG0122:100%**]Takifugu rubripes@SINFRUP00000147763[RRM1][KOG0122]

Tetraodon nigroviridis@GSTENP00034383001[RRM1][KOG0122]Strongylocentrotus purpuratus@XP_791582[2][RRM1:100%][KOG0122:100%]Ciona intestinalis@ENSCINP00000000359[RRM1][KOG0122]



Drosophila melanogaster@CG8636-PA[RRM1][KOG0122]Aedes aegypti@AAEL006851-PA[2][RRM1:100%][KOG0122:100%]

Anopheles gambiae@AGAP007668-PA[RRM1][KOG0122]Phytophthora sojae@jgi_Physo1_1_108333[RRM1][KOG0122]

Phytophthora ramorum@jgi_Phyra1_1_79758[RRM1][KOG0122]Phaeodactylum tricornutum@jgi_Phatr2_16281[RRM1][KOG0122]

Aureococcus anophagefferens@jgi_Auran1_9314[2][RRM1:100%][KOG0585:50%][.KOG0122:50%]Thalassiosira pseudonana@jgi_Thaps3_32790[RRM1][KOG0122]

SC35 "plant"

SRrp

SC35

Fig. S13

135

0.27

95

76

98

97

96 97

97

97

75

61

60

56 54

75

57 72

57

93

98

77

98

89

86

88

94

84 83

67

59

98 59

78

93 79

57 96

55


Caenorhabditis elegans@F26A3_2[RRM1][KOG0121]Phytophthora ramorum@jgi_Phyra1_1_46906[RRM1][KOG0121]

Cyanidioschyzon merolae@gnl_CMER_CMQ282C[RRM1][KOG0121]Cryptosporidium parvum_Iowa_II@XP_627536[RRM1][KOG0121]

Encephalitozoon cuniculi_GB-M1@NP_597585[RRM1][KOG0121]Pichia stipitis_CBS_6054@XP_001387884[RRM1][KOG0121]

Debaryomyces hansenii_CBS767@XP_458582[RRM1][KOG0121]Kluyveromyces lactis@XP_451996[RRM1][KOG0121]Candida glabrata_CBS138@XP_445241[RRM1][KOG0121]

Ashbya gossypii_ATCC_10895@NP_985498[RRM1][KOG0121]Saccharomyces cerevisiae@YPL178W[RRM1][KOG0121]

Plasmodium falciparum_3D7@XP_001351463[RRM1][KOG0121]Leishmania infantum_JPCM5@XP_001466901[RRM1][KOG0121]

Trypanosoma brucei_TREU927@XP_845318[RRM1][KOG0121]Theileria parva_strain_Muguga@XP_766484[RRM1][KOG0121]


Oryza sativa_japonica_cultivar-group@NP_001047412[RRM1][KOG0121]Arabidopsis thaliana@NP_199233[2][RRM1:100%][KOG0121:100%]

Ricinus communis@29983_m003140[RRM1][KOG0121]Ostreococcus lucimarinus@jgi_Ost9901_3_43898[RRM1][KOG0121]

Ostreococcus tauri@jgi_Ostta4_21085[RRM1][KOG0121]Drosophila melanogaster@CG12357-PA[RRM1][KOG0121]

Aedes aegypti@AAEL006135-PA[RRM1][KOG0121]Anopheles gambiae@AGAP002547-PA[RRM1][KOG0121]

Ciona savignyi@ENSCSAVP00000009906[RRM1][KOG0121]Ciona intestinalis@ENSCINP00000006257[2][RRM1:100%][KOG0121:100%]Nasonia vitripennis@XP_001600470[RRM1][KOG0121]


Strongylocentrotus purpuratus@XP_001187788[2][RRM1:100%][KOG0121:100%]Tribolium castaneum@XP_975066[RRM1][KOG0121]


Aspergillus fumigatus_Af293@XP_755191[RRM1][KOG0121]Gibberella zeae_PH-1@XP_385664[RRM1][KOG0121]

Eutheria@ENSBTAP00000011684[11][RRM1:100%**][KOG0121:100%**]Sorex araneus@ENSSARP00000012929[RRM1][KOG0121]

Cavia porcellus@ENSCPOP00000002703[RRM1][KOG0121]Loxodonta africana@ENSLAFP00000005354[RRM1][KOG0121]

Spermophilus tridecemlineatus@ENSSTOP00000001416[RRM1][KOG0121]Oryctolagus cuniculus@ENSOCUP00000012352[RRM1][KOG0121]Monodelphis domestica@ENSMODP00000029243[RRM1][KOG0121]

Monodelphis domestica@ENSMODP00000034858[2][RRM1:100%][KOG0121:100%]Monodelphis domestica@ENSMODP00000019849[RRM1][KOG0121]

Gallus gallus@ENSGALP00000011061[RRM1][KOG0121]Gallus gallus@ENSGALP00000009225[RRM1][KOG0121]Xenopus tropicalis@ENSXETP00000041997[RRM1][KOG0121]

Erinaceus europaeus@ENSEEUP00000004164[RRM1][KOG0121]Equus caballus@XP_001492661[RRM1][KOG0121]

Canis familiaris@ENSCAFP00000026571[RRM1][KOG0121]Oryzias latipes@ENSORLP00000014087[RRM1][KOG0121]Danio rerio@ENSDARP00000020688[RRM1][KOG0121]

Gasterosteus aculeatus@ENSGACP00000008263[RRM1][KOG0121]Tetraodon nigroviridis@GSTENP00011485001[RRM1][KOG0121]

Takifugu rubripes@SINFRUP00000128783[RRM1][KOG0121]Aureococcus anophagefferens@jgi_Auran1_17068[RRM1][KOG4207]

Phytophthora sojae@jgi_Physo1_1_136528[RRM1][put-sr]Phytophthora ramorum@jgi_Phyra1_1_75322[RRM1][KOG3208]

Cryptosporidium parvum_Iowa_II@XP_628282[RRM1][put-sr][KOG4207]Cryptosporidium parvum_Iowa_II@XP_627626[RRM1][put-sr][KOG0111]


Chlamydomonas reinhardtii@jgi_Chlre3_116256[RRM1][put-sr]Volvox carteri@jgi_Volca1_121229[RRM1][put-sr][KOG0415]

Arabidopsis thaliana@NP_187966[RRM1][put-sr][SR][SCL30a]Arabidopsis thaliana@NP_001031195[2][RRM1:100%][put-sr:100%][SR:100%][KOG0110:100%][SR33/SCL33]Ricinus communis@30084_m000177[RRM1][put-sr]

Ricinus communis@27553_m000316[RRM1][put-sr]Medicago truncatula@IMGA_AC146760_9_2[RRM1][put-sr]

Oryza sativa_japonica_cultivar-group@NP_001060372[RRM1][put-sr][SR][SCL25]Oryza sativa_japonica_cultivar-group@NP_001050213[RRM1][put-sr][KOG4207]

Physcomitrella patens@jgi_Phypa1_1_141868[RRM1]Physcomitrella patens@jgi_Phypa1_1_108464[RRM1][put-sr]

Oryza sativa_japonica_cultivar-group@NP_001050168[RRM1][put-sr]Ricinus communis@29726_m003960[RRM1][put-sr]

Arabidopsis thaliana@NP_197382[RRM1][put-sr][SR][KOG0127][SCL28]Oryza sativa_japonica_cultivar-group@NP_001068546[RRM1][put-sr][KOG0127]

Oryza sativa_japonica_cultivar-group@NP_001046448[RRM1][put-sr][SR][SCL30a]Oryza sativa_japonica_cultivar-group@NP_001067091[RRM1][put-sr][SR][SCL30b]

Ricinus communis@27383_m000159[RRM1][put-sr][KOG0127]Medicago truncatula@IMGA_CR962128_15_2[RRM1][put-sr]

Arabidopsis thaliana@NP_567021[RRM1][put-sr][SR][KOG0122][SCL30]Phytophthora sojae@jgi_Physo1_1_138511[RRM1][put-sr]

Phaeodactylum tricornutum@jgi_Phatr2_12366[RRM1]Thalassiosira pseudonana@jgi_Thaps3_23196[RRM1][KOG4207]

Chlamydomonas reinhardtii@jgi_Chlre3_188086[RRM1][put-sr]Volvox carteri@jgi_Volca1_120666[RRM1][put-sr]


Ciona savignyi@ENSCSAVP00000008618[RRM1][put-sr][KOG0111]Gasterosteus aculeatus@ENSGACP00000018038[RRM1][put-sr]Danio rerio@ENSDARP00000091866[RRM1][put-sr]

Danio rerio@ENSDARP00000031512[RRM1][put-sr][KOG0415]Gasterosteus aculeatus@ENSGACP00000002897[RRM1][put-sr][KOG0415]

SCL

N2

Fig. S13

136

64 76

96

95

97

63

93

98 57

99 54

75

66

99

98

99

95

94

70 92

78

62

60

62

67

56

97

72 98

63

63

62

85

73 91

73 70

57

64

G t t l t @ENSGACP00000010395[2][RRM1 100%][ t 100%][SR 50%][KOG0106 100%][SR 40]Tetraodontidae@SINFRUP00000132279[2][RRM1:100%][put-sr:50%][SR:50%][KOG0106:100%]

Danio rerio@ENSDARP00000069997[3][RRM1:100%*][put-sr:67%][SR:33%][KOG0106:100%*][SRp40]Ciona intestinalis@ENSCINP00000014783[RRM1][put-sr][KOG0106]

Caenorhabditis elegans@W02B12_3a[3][RRM1:100%*][put-sr:33%][SR:100%*][KOG0106:100%*][CeSRp75/rsp-1]Caenorhabditis elegans@W02B12_2[RRM1][put-sr][SR][KOG0106][CeSRp40/rsp-2]

Theria@ENSBTAP00000017699[12][RRM1:100%**][put-sr:100%**][SR:100%**][KOG0106:50%*][.KOG0105:50%*][SRp75]Myotis lucifugus@ENSMLUP00000013443[RRM1][put-sr][SR][KOG0105][SRp75]

Xenopus tropicalis@ENSXETP00000031465[2][RRM1:100%][put-sr:100%][KOG0105:100%]Ciona savignyi@ENSCSAVP00000019399[RRM1][put-sr][KOG0106]

Ciona intestinalis@ENSCINP00000022868[RRM1][KOG0106]Ciona savignyi@ENSCSAVP00000004366[3][RRM1:100%*][put-sr:100%*][KOG0106:100%*]

Ciona intestinalis@ENSCINP00000016525[RRM1][put-sr][KOG0106]Ciona intestinalis@ENSCINP00000010131[3][RRM1:100%*][put-sr:100%*][KOG0106:100%*]

Tetraodon nigroviridis@GSTENP00010110001[RRM1][put-sr][KOG0598]Smegmamorpha@ENSGACP00000003112[3][RRM1:100%*][put-sr:100%*][KOG0106:100%*]



Gasterosteus aculeatus@ENSGACP00000008092[3][RRM1:100%*][put-sr:100%*][KOG0105:100%*]Danio rerio@ENSDARP00000022089[RRM1][put-sr][KOG0105]

Xenopus tropicalis@ENSXETP00000054329[RRM1][put-sr][KOG0105]Monodelphis domestica@ENSMODP00000030967[2][RRM1:100%][put-sr:100%][SR:100%][KOG0106:50%][.KOG0105:50%][SRp55]Murinae@ENSMUSP00000017065[2][RRM1:100%][put-sr:100%][SR:100%][KOG0105:100%][SRp55]

Bos taurus@ENSBTAP00000011240[RRM1][put-sr][SR][KOG0105][SRp55]Eutheria@ENSDNOP00000006506[3][RRM1:100%*][put-sr:67%][SR:100%*][KOG0105:67%][.KOG0106:33%][SRp55]

Echinops telfairi@ENSETEP00000005046[RRM1][put-sr][SR][KOG0105][SRp55]Cavia porcellus@ENSCPOP00000010577[RRM1][put-sr][SR][KOG0106][SRp55]

Oryza sativa_japonica_cultivar-group@NP_001052061[RRM1][put-sr][SR][KOG0106][RSp29]Ricinus communis@29742_m001371[RRM1][KOG0106]


Physcomitrella patens@jgi_Phypa1_1_167387[RRM1][put-sr][KOG0106]Oryza sativa_japonica_cultivar-group@NP_001045729[RRM1][put-sr][SR][KOG0106][RSp33]

Zea mays@10633_m000022_AZM5_5503[RRM1][KOG0106]Zea mays@8514_m000507_c0216K08[RRM1][SR][KOG0106][RSp33]


Arabidopsis thaliana@NP_851174[2][RRM1:100%][put-sr:100%][SR:100%][KOG0106:100%][RSp41]Arabidopsis thaliana@NP_194280[RRM1][put-sr][SR][KOG0106][RSp40/SRp35]



Caenorhabditis elegans@Y111B2A_18_1[3][RRM1:100%*][put-sr:100%*][SR:100%*][KOG0105:100%*][CeSF2/ASF/rsp-3]Volvox carteri@jgi_Volca1_45192[RRM1][put-sr][KOG0105]

Chlamydomonas reinhardtii@jgi_Chlre3_129159[RRM1][put-sr][KOG0105]Phytophthora ramorum@jgi_Phyra1_1_46108[RRM1][KOG0105]

Phytophthora sojae@jgi_Physo1_1_142377[RRM1][put-sr][KOG0105]Oryza sativa_japonica_cultivar-group@NP_001060608[RRM1][put-sr][SR][KOG0105][SRp33a]

Physcomitrella patens@jgi_Phypa1_1_140978[RRM1][put-sr][KOG0105]Physcomitrella patens@jgi_Phypa1_1_113630[RRM1][put-sr][KOG0105]

Physcomitrella patens@jgi_Phypa1_1_205547[RRM1][put-sr][KOG0105]Arabidopsis thaliana@NP_190512[2][RRM1:100%][put-sr:100%][SR:100%][KOG0105:100%][SRp34a]Ricinus communis@29827_m002610[RRM1][put-sr][KOG0105]Medicago truncatula@IMGA_CT868739_2_1[RRM1][put-sr][SR][KOG0105][SRp34a]

Ricinus communis@29986_m001610[RRM1][put-sr][SR][KOG0105][SRp33a]Ricinus communis@30128_m008840[RRM1][put-sr][KOG0105]


Medicago truncatula@IMGA_AC134522_46_2[2][RRM1:100%][put-sr:100%][KOG0105:100%]Medicago truncatula@IMGA_AC144541_27_2[RRM1][put-sr][KOG0105]

Arabidopsis thaliana@NP_850933[3][RRM1:100%*][put-sr:100%*][SR:100%*][KOG0105:100%*][SR1/SRp34]Arabidopsis thaliana@NP_567235[2][RRM1:100%][put-sr:50%][SR:100%][KOG0105:100%][SRp34b]Arabidopsis thaliana@NP_683288[2][RRM1:100%][put-sr:100%][SR:100%][KOG0105:100%][SRp30]

Oryza sativa_japonica_cultivar-group@NP_001055323[RRM1][put-sr][SR][KOG0105][SRp33b]Oryza sativa_japonica_cultivar-group@NP_001050082[RRM1][put-sr][SR][KOG0105][SRp32]


Ciona savignyi@ENSCSAVP00000010348[2][RRM1:100%][put-sr:100%][KOG0105:100%]Ciona intestinalis@ENSCINP00000015147[RRM1][put-sr][KOG0105]

Danio rerio@ENSDARP00000091488[2][RRM1:100%][put-sr:100%][KOG0105:100%]Takifugu rubripes@SINFRUP00000145791[RRM1][put-sr][SR][KOG0105][SRp30c]

Gasterosteus aculeatus@ENSGACP00000022361[2][RRM1:100%][put-sr:100%][KOG0105:100%]Xenopus tropicalis@ENSXETP00000026703[RRM1][put-sr][SR][KOG0105][SRp30c]

Myotis lucifugus@ENSMLUP00000009421[RRM1][put-sr][SR][KOG0105][SRp30c]Eutheria@ENSCAFP00000015146[7][RRM1:100%*][put-sr:100%*][SR:86%*][KOG0105:100%*][SRp30c]

Tupaia belangeri@ENSTBEP00000007356[RRM1][put-sr][SR][KOG0105][SRp30c]Monodelphis domestica@ENSMODP00000003831[RRM1][put-sr][SR][KOG0105][SRp30c]

Mus musculus@ENSMUSP00000031513[RRM1][put-sr][SR][KOG0105][SRp30c]Bos taurus@ENSBTAP00000016997[RRM1][put-sr][SR][KOG0105][SRp30c]Oryctolagus cuniculus@ENSOCUP00000009368[RRM1][KOG0105]

Diptera@AAEL006473-PA[3][RRM1:100%*][put-sr:100%*][KOG0105:100%*]Tribolium castaneum@XP_967263[RRM1][put-sr][KOG0105]Nasonia vitripennis@XP_001605411[RRM1][put-sr][KOG0105]

Apis mellifera@XP_393525[RRM1][put-sr][KOG0105]Oryzias latipes@ENSORLP00000006698[RRM1][put-sr][SR][KOG0105][ASF/SF2]

Takifugu rubripes@SINFRUP00000151768[RRM1][put-sr][SR][KOG0105][ASF/SF2]Gasterosteus aculeatus@ENSGACP00000027276[RRM1][put-sr][SR][KOG0105][ASF/SF2]

Danio rerio@ENSDARP00000074866[2][RRM1:100%][put-sr:100%][SR:100%][KOG0105:100%][ASF/SF2]Gasterosteus aculeatus@ENSGACP00000014666[RRM1][SR][KOG0105][ASF/SF2]Tetraodontidae@SINFRUP00000136750[2][RRM1:100%][put-sr:100%][SR:100%][KOG0105:100%][ASF/SF2]Oryzias latipes@ENSORLP00000005758[RRM1][put-sr][SR][KOG0105][ASF/SF2]

Macaca mulatta@ENSMMUP00000004343[RRM1][SR][KOG0105][ASF/SF2]Echinops telfairi@ENSETEP00000004344[RRM1][SR][KOG0105][ASF/SF2]

Tetrapoda@ENSBTAP00000019644[17][RRM1:100%**][put-sr:53%**][SR:100%**][KOG0105:100%**][ASF/SF2]Tupaia belangeri@ENSTBEP00000013333[RRM1][SR][KOG0105][ASF/SF2]

Otolemur garnettii@ENSOGAP00000012982[RRM1][SR][KOG0105][ASF/SF2]

SRp75

ASF/SF2

SRp30c

ASF-like "plant"

RS "plant"

SRp55

N5

N6

Fig. S14

137

93

85 78

59 97

93

99 81

86 87

95

92

99 77

95

100

98

97

72

99

60 67

64

87

70 82

55 85

79

83

100 60

60

79

98

99

98

54

81

79 60

97

66

93

55

Ci i t ti li @ENSCINP00000000359[RRM1][KOG0122]Tetrapoda@ENSBTAP00000003545[10][RRM1:100%**][KOG0122:100%**]Clupeocephala@ENSDARP00000027672[2][RRM1:100%][KOG0122:100%]

Gasterosteus aculeatus@ENSGACP00000018150[RRM1][KOG0122]Tetraodon nigroviridis@GSTENP00034383001[RRM1][KOG0122]Takifugu rubripes@SINFRUP00000147763[RRM1][KOG0122]



Drosophila melanogaster@CG8636-PA[RRM1][KOG0122]Anopheles gambiae@AGAP007668-PA[RRM1][KOG0122]

Aedes aegypti@AAEL006851-PA[2][RRM1:100%][KOG0122:100%]Plasmodium falciparum_3D7@XP_001351730[RRM1][put-sr][KOG0105]

Ostreococcus lucimarinus@jgi_Ost9901_3_8794[RRM1][KOG0105]Phytophthora@jgi_Phyra1_1_75301[2][RRM1:100%][put-sr:100%][KOG0105:100%]

Caenorhabditis elegans@C33H5_12a_1[5][RRM1:100%*][put-sr:40%][SR:100%*][KOG0107:60%*][.KOG0116:40%][CeSRp20/rsp-6]Chlamydomonas reinhardtii@jgi_Chlre3_132362[RRM1][KOG0107]

Volvox carteri@jgi_Volca1_121301[RRM1][put-sr][KOG0107]Chlamydomonas reinhardtii@jgi_Chlre3_192053[RRM1][put-sr][KOG0107]


Oryza sativa_japonica_cultivar-group@NP_001047400[RRM1][put-sr][SR][KOG0107][RSZp23]Oryza sativa_japonica_cultivar-group@NP_001057018[RRM1][put-sr][SR][RSZp21a]

Ricinus communis@28610_m000073[RRM1][SR][KOG0107][SRZ21/RSZ21]Medicago truncatula@IMGA_CR936368_17_2[RRM1][put-sr][KOG0107]

Ricinus communis@29848_m004475[RRM1][put-sr][SR][SRZ22/RSZ22]Arabidopsis thaliana@NP_180035[RRM1][put-sr][SR][RSZ22a]


Ciona savignyi@ENSCSAVP00000018514[RRM1][put-sr]Strongylocentrotus purpuratus@XP_001178467[2][RRM1:100%][put-sr:100%]

Drosophila melanogaster@CG5655-PA[RRM1][put-sr][KOG0107]Anopheles gambiae@AGAP009142-PA[RRM1][put-sr][KOG0921]

Tribolium castaneum@XP_969323[RRM1][put-sr][KOG0107]Nasonia vitripennis@XP_001605989[RRM1][put-sr][KOG0107]

Apis mellifera@XP_396951[RRM1][put-sr][KOG0107]Strongylocentrotus purpuratus@XP_001178394[2][RRM1:100%][put-sr:100%][KOG0116:100%]Ciona savignyi@ENSCSAVP00000012556[4][RRM1:100%*][put-sr:100%*]

Ciona intestinalis@ENSCINP00000026132[3][RRM1:100%*][put-sr:100%*][KOG0415:67%]Strongylocentrotus purpuratus@XP_789661[2][RRM1:100%][put-sr:100%][KOG0116:100%]Strongylocentrotus purpuratus@XP_001178879[2][RRM1:100%][put-sr:100%][KOG0107:100%]

Strongylocentrotus purpuratus@XP_001180596[2][RRM1:100%][put-sr:100%]Ciona savignyi@ENSCSAVP00000004510[RRM1][put-sr]Ciona intestinalis@ENSCINP00000022204[2][RRM1:100%][put-sr:100%][KOG0107:100%]

Drosophila melanogaster@CG10203-PA[RRM1][put-sr][SR][KOG0107][9G8]Anopheles gambiae@AGAP008303-PA[RRM1][put-sr]Tribolium castaneum@XP_968789[RRM1][put-sr][KOG4368]

Apis mellifera@XP_001122800[RRM1][put-sr][KOG0107]Xenopus tropicalis@ENSXETP00000033870[RRM1][KOG0107]

Xenopus tropicalis@ENSXETP00000018945[RRM1][KOG0107]Eutheria@ENSEEUP00000001001[3][RRM1:100%*][put-sr:100%*]

Gasterosteus aculeatus@ENSGACP00000001909[3][RRM1:100%*][put-sr:100%*][SR:100%*][KOG0107:100%*][SRp20]Takifugu rubripes@SINFRUP00000147448[RRM1][put-sr][SR][KOG0107][SRp20]

Oryzias latipes@ENSORLP00000024888[RRM1][put-sr][SR][KOG0107][SRp20]Tetrapoda@ENSBTAP00000004154[28][RRM1:100%***][put-sr:68%**][SR:100%***][KOG0107:100%***][SRp20]

Mus musculus@ENSMUSP00000100538[RRM1][put-sr][SR][KOG0107][SRp20]Danio rerio@ENSDARP00000035207[2][RRM1:100%][put-sr:50%][SR:100%][KOG0107:100%][SRp20]

Oryzias latipes@ENSORLP00000000358[RRM1][put-sr][SR][KOG0107][SRp20]Tetraodon nigroviridis@GSTENP00027331001[RRM1][SR][KOG0107][SRp20]

Takifugu rubripes@SINFRUP00000136850[RRM1][SR][KOG0107][SRp20]Gasterosteus aculeatus@ENSGACP00000001355[RRM1][put-sr][SR][KOG0107][SRp20]Danio rerio@ENSDARP00000076899[2][RRM1:100%][put-sr:50%][SR:100%][KOG0107:100%][SRp20]

Strongylocentrotus purpuratus@XP_788595[2][RRM1:100%][put-sr:100%]Apis mellifera@XP_001123058[2][RRM1:100%][put-sr:50%][KOG0107:100%]Endopterygota@XP_001599712[6][RRM1:100%*][put-sr:17%][KOG0107:83%*][.KOG2490:17%]

Culicidae@AAEL001356-PA[3][RRM1:100%*][put-sr:100%*][KOG0108:67%][.KOG0107:33%]Drosophila melanogaster@CG17136-PD[4][RRM1:100%*][put-sr:50%][KOG0107:100%*]

Drosophila melanogaster@CG1987-PA[RRM1][put-sr][KOG0107]Percomorpha@ENSGACP00000016280[4][RRM1:100%*][put-sr:100%*][KOG0107:50%][.KOG4368:25%]

Oryzias latipes@ENSORLP00000000921[3][RRM1:100%*][put-sr:100%*][KOG4368:33%][.KOG0107:33%]Danio rerio@ENSDARP00000051184[2][RRM1:100%][put-sr:100%]

Gallus gallus@ENSGALP00000022386[RRM1][put-sr][SR][9G8]Spermophilus tridecemlineatus@ENSSTOP00000003936[RRM1][put-sr]

Monodelphis domestica@ENSMODP00000010787[RRM1][put-sr][SR][KOG0107][9G8]Rattus norvegicus@ENSRNOP00000040587[RRM1][put-sr][SR][KOG0107][9G8]

Canis familiaris@ENSCAFP00000009434[RRM1][put-sr][KOG0107]Xenopus tropicalis@ENSXETP00000054077[2][RRM1:100%][put-sr:100%][SR:100%][9G8]Mammalia@ENSBTAP00000033048[27][RRM1:100%***][put-sr:78%***][SR:93%***][KOG0107:81%***][9G8]

Danio rerio@ENSDARP00000070952[RRM1][SR][KOG0107][9G8]Rattus norvegicus@ENSRNOP00000058047[RRM1][put-sr]

Rattus norvegicus@ENSRNOP00000011102[RRM1][put-sr][SR][KOG0107][9G8]Gallus gallus@ENSGALP00000022397[RRM1][put-sr][SR][9G8]Gallus gallus@ENSGALP00000038155[RRM1][put-sr][SR][9G8]

Arabidopsis thaliana@NP_850280[RRM1][put-sr][SR][KOG0107][RSZ33]Arabidopsis thaliana@NP_190918[RRM1][put-sr][SR][KOG0107][RSZ32]

Oryza sativa_japonica_cultivar-group@NP_001054731[RRM1][put-sr][SR][RSZ39]Oryza sativa_japonica_cultivar-group@NP_001042066[RRM1][put-sr][SR][KOG0109][RSZ37a]

Ricinus communis@29805_m001527[RRM1][put-sr][KOG0109]Oryza sativa_japonica_cultivar-group@NP_001049771[RRM1][put-sr][SR][KOG0109][RSZ37b]

Oryza sativa_japonica_cultivar-group@NP_001054489[RRM1][put-sr][SR][KOG0109][RSZ36]Caenorhabditis elegans@T28D9_2a[3][RRM1:100%*][put-sr:100%*][SR:100%*][KOG0106:100%*][CeSC35-2/rsp-5]

Tribolium castaneum@XP_969451[RRM1][put-sr][KOG0105]Nasonia vitripennis@XP_001603815[2][RRM1:100%][put-sr:100%][KOG0105:100%]


Aedes aegypti@AAEL000769-PA[RRM1][put-sr][KOG0106]Diptera@AGAP004592-PA[7][RRM1:100%*][put-sr:71%*][SR:86%*][KOG0105:57%*][.KOG0106:43%*]

Aedes aegypti@AAEL012621-PA[RRM1][put-sr][KOG0105]Cryptococcus neoformans_var._neoformans_JEC21@XP_567562[RRM1][KOG0106]


Strongylocentrotus purpuratus@XP_001180940[2][RRM1:100%][put-sr:100%][KOG0106:100%]Gallus gallus@ENSGALP00000037225[RRM1][KOG0106]

Gallus gallus@ENSGALP00000015427[RRM1][put-sr][KOG0106]Oryzias latipes@ENSORLP00000011623[3][RRM1:100%*][put-sr:67%][SR:33%][KOG0106:100%*]

Xenopus tropicalis@ENSXETP00000038885[RRM1][put-sr][KOG0106]Gasterosteus aculeatus@ENSGACP00000015556[RRM1][put-sr][KOG0106]

Danio rerio@ENSDARP00000043311[RRM1][put-sr][KOG0106]Tetraodon nigroviridis@GSTENP00035800001[RRM1][put-sr][KOG0106]

Takifugu rubripes@SINFRUP00000169885[RRM1][put-sr][KOG0106]Sorex araneus@ENSSARP00000000971[RRM1][put-sr][SR][KOG0105][SRp40]Catarrhini@ENSP00000342294[3][RRM1:100%*][put-sr:100%*][SR:100%*][KOG0106:100%*][SRp40]

Xenopus tropicalis@ENSXETP00000057107[2][RRM1:100%][put-sr:100%][SR:100%][KOG0106:100%][SRp40]Amniota@ENSBTAP00000015408[24][RRM1:100%***][put-sr:96%***][SR:100%***][KOG0106:54%**][.KOG0105:46%**][SRp40]Afrotheria@ENSETEP00000016575[2][RRM1:100%][put-sr:100%][SR:100%][KOG0106:100%][SRp40]

Ornithorhynchus anatinus@ENSOANP00000021053[RRM1][put-sr][SR][KOG0106][SRp40]Ornithorhynchus anatinus@ENSOANP00000021052[RRM1][put-sr][SR][KOG0106][SRp40]

Ornithorhynchus anatinus@ENSOANP00000021051[RRM1][put-sr][SR][KOG0105][SRp40]Gasterosteus aculeatus@ENSGACP00000010395[2][RRM1:100%][put-sr:100%][SR:50%][KOG0106:100%][SRp40]

RS2Z "plant"

SRp40

RSZ "plant"

SRp20

9G8

N3

N4

Fig. S14

138

54 76

74

90

76

99

100 57

99

100

82

71 58

99

88 92

94

84

92

56 85

77 99

100

63

95

57 54

94

99

98

89

62

100

92 94

58

81

69 91

85

97

98

74 67

98

59

71

Ci i i@ENSCSAVP00000008618[RRM1][ t ][KOG0111]Gasterosteus aculeatus@ENSGACP00000018038[RRM1][put-sr]

Danio rerio@ENSDARP00000031512[RRM1][put-sr][KOG0415]Danio rerio@ENSDARP00000091866[RRM1][put-sr]Gasterosteus aculeatus@ENSGACP00000002897[RRM1][put-sr][KOG0415]

Tetraodon nigroviridis@GSTENP00010468001[RRM1][SRrp][KOG4207][SRp38]Takifugu rubripes@SINFRUP00000150947[RRM1][put-sr]

Oryzias latipes@ENSORLP00000009635[RRM1][SRrp][KOG4207][SRp38]Xenopus tropicalis@ENSXETP00000011851[RRM1][put-sr]

Mus musculus@ENSMUSP00000103794[RRM1][put-sr][SRrp][KOG0111][SRrp35]Echinops telfairi@ENSETEP00000001114[RRM1][put-sr]

Catarrhini@ENSP00000358479[3][RRM1:100%*][put-sr:100%*][SRrp:100%*][SRrp35]Erinaceus europaeus@ENSEEUP00000010036[RRM1][put-sr][SRrp][SRrp35]

Monodelphis domestica@ENSMODP00000022797[RRM1][put-sr][SRrp][SRrp35]Cavia porcellus@ENSCPOP00000009809[RRM1][put-sr][SRrp][SRrp35]

Canis familiaris@ENSCAFP00000019234[RRM1][put-sr][SRrp][SRp38]Eutheria@ENSBTAP00000010616[19][RRM1:100%**][put-sr:100%**][SRrp:100%**][KOG0111:58%**][.KOG0415:21%*][SRp38]

Canis familiaris@ENSCAFP00000004604[RRM1][put-sr][SRrp][SRp38]Eutheria@ENSEEUP00000013029[3][RRM1:100%*][put-sr:100%*][SRrp:100%*][SRp38]

Monodelphis domestica@ENSMODP00000016281[RRM1][put-sr][SRrp][SRp38]Rattus norvegicus@ENSRNOP00000011154[2][RRM1:100%][put-sr:100%][SRrp:100%][SRp38]Gallus gallus@ENSGALP00000006566[RRM1][put-sr][SRrp][SRp38]

Phytophthora sojae@jgi_Physo1_1_138511[RRM1][put-sr]Thalassiosira pseudonana@jgi_Thaps3_23196[RRM1][KOG4207]

Phaeodactylum tricornutum@jgi_Phatr2_12366[RRM1]Phytophthora sojae@jgi_Physo1_1_136528[RRM1][put-sr]

Phytophthora ramorum@jgi_Phyra1_1_75322[RRM1][KOG3208]Volvox carteri@jgi_Volca1_121229[RRM1][put-sr][KOG0415]

Chlamydomonas reinhardtii@jgi_Chlre3_116256[RRM1][put-sr]Oryza sativa_japonica_cultivar-group@NP_001068546[RRM1][put-sr][KOG0127]

Oryza sativa_japonica_cultivar-group@NP_001067091[RRM1][put-sr][SR][SCL30b]Oryza sativa_japonica_cultivar-group@NP_001046448[RRM1][put-sr][SR][SCL30a]


Arabidopsis thaliana@NP_567021[RRM1][put-sr][SR][KOG0122][SCL30]Physcomitrella patens@jgi_Phypa1_1_141868[RRM1]

Physcomitrella patens@jgi_Phypa1_1_108464[RRM1][put-sr]Oryza sativa_japonica_cultivar-group@NP_001050168[RRM1][put-sr]

Ricinus communis@29726_m003960[RRM1][put-sr]Arabidopsis thaliana@NP_197382[RRM1][put-sr][SR][KOG0127][SCL28]

Arabidopsis thaliana@NP_187966[RRM1][put-sr][SR][SCL30a]Arabidopsis thaliana@NP_001031195[2][RRM1:100%][put-sr:100%][SR:100%][KOG0110:100%][SR33/SCL33]

Ricinus communis@30084_m000177[RRM1][put-sr]Ricinus communis@27553_m000316[RRM1][put-sr]

Medicago truncatula@IMGA_AC146760_9_2[RRM1][put-sr]Oryza sativa_japonica_cultivar-group@NP_001060372[RRM1][put-sr][SR][SCL25]

Oryza sativa_japonica_cultivar-group@NP_001050213[RRM1][put-sr][KOG4207]Aureococcus anophagefferens@jgi_Auran1_9018[RRM1]


Aedes aegypti@AAEL010807-PA[RRM1][put-sr][KOG1080]Oryzias latipes@ENSORLP00000016244[RRM1][KOG1080]

Tetraodon nigroviridis@GSTENP00000272001[RRM1]Mus musculus@ENSMUSP00000098297[RRM1]Eutheria@ENSBTAP00000022553[3][RRM1:100%*][KOG1080:100%*]Macaca mulatta@ENSMMUP00000016612[RRM1]


Cyanidioschyzon merolae@gnl_CMER_CML202C[RRM1][put-sr]Aureococcus anophagefferens@jgi_Auran1_17068[RRM1][KOG4207]

Tribolium castaneum@XP_970765[RRM2][KOG0127]Ostreococcus lucimarinus@jgi_Ost9901_3_8174[RRM1][KOG4207]

Zea mays@20810_m000015_AZM5_89637[2][RRM1:100%][put-sr:50%][SR:50%][KOG4207:100%][SC35a]Oryza sativa_japonica_cultivar-group@NP_001050263[RRM1][put-sr][SR][KOG4207][SC35c]

Zea mays@8925_m000027_AZM5_1178[RRM1][KOG4207]Oryza sativa_japonica_cultivar-group@NP_001062094[RRM1][put-sr][SR][KOG0415][SC35a]


Oryza sativa_japonica_cultivar-group@NP_001060322[RRM1][put-sr][SR][KOG4207][SC35b]Medicago truncatula@IMGA_AC144459_24_2[2][RRM1:100%][put-sr:100%][KOG4207:100%]

Ricinus communis@29581_m000256[RRM1][put-sr][KOG4207]Arabidopsis thaliana@NP_201225[2][RRM1:100%][put-sr:100%][SR:100%][KOG4207:100%][SC35]

Neurospora crassa_OR74A@XP_965346[RRM1][KOG0110]Nitrosococcus oceani_ATCC_19707@YP_344593[RRM1][PROK]

Methylococcus capsulatus_str._Bath@YP_113294[RRM1][PROK]Cryptosporidium parvum_Iowa_II@XP_626081[RRM1][KOG0122]

Volvox carteri@jgi_Volca1_103546[RRM1][KOG0116]Chlamydomonas reinhardtii@jgi_Chlre3_184151[RRM1][KOG0921]




Leishmania infantum_JPCM5@XP_001468615[RRM1]Yarrowia lipolytica@XP_503515[RRM1][KOG0122]



Gibberella zeae_PH-1@XP_385241[RRM1][KOG0122]Caenorhabditis elegans@F22B5_2[RRM1][KOG0122]


Dictyostelium discoideum_AX4@XP_641693[RRM1][KOG0122]Pichia stipitis_CBS_6054@XP_001388004[RRM1][KOG0122]

Debaryomyces hansenii_CBS767@XP_458660[RRM1][KOG0122]Candida glabrata_CBS138@XP_446998[RRM1][KOG0122]

Saccharomyces cerevisiae@YDR429C[RRM1][KOG0122]Ashbya gossypii_ATCC_10895@NP_984285[RRM1][KOG0122]

Chlamydomonas reinhardtii@jgi_Chlre3_112621[RRM1][KOG0122]Physcomitrella patens@jgi_Phypa1_1_164814[RRM1][KOG0122]Physcomitrella patens@jgi_Phypa1_1_196691[RRM1][KOG0122]


Medicago truncatula@IMGA_AC144431_18_2[RRM1][KOG0122]Ricinus communis@29973_m000409[RRM1][KOG0122]


Medicago truncatula@IMGA_AC174277_12_1[2][RRM1:100%][KOG0122:100%]Arabidopsis thaliana@NP_196219[RRM1][TIF3][KOG0122][TIF3]

Arabidopsis thaliana@NP_187747[RRM1][TIF3][KOG0122][TIF3]Phytophthora ramorum@jgi_Phyra1_1_79758[RRM1][KOG0122]

Phytophthora sojae@jgi_Physo1_1_108333[RRM1][KOG0122]Phaeodactylum tricornutum@jgi_Phatr2_16281[RRM1][KOG0122]

Thalassiosira pseudonana@jgi_Thaps3_32790[RRM1][KOG0122]Aureococcus anophagefferens@jgi_Auran1_9314[2][RRM1:100%][KOG0585:50%][.KOG0122:50%]

Cyanidioschyzon merolae@gnl_CMER_CMH159C[RRM1][KOG0122]Strongylocentrotus purpuratus@XP_791582[2][RRM1:100%][KOG0122:100%]

Ciona intestinalis@ENSCINP00000000359[RRM1][KOG0122]

SC35 "plant"

SCL

SRrp

N2

Fig. S14

139

0.15

98

92

100

96

62

52

97 98

86 50

95

55 89

52

100

67

58 72

74

69 52 57

53

83

50

94

86

100

92

100

55 52

89

100 99

74

64

63

92

96 80

Aureococcus anophagefferens@jgi_Auran1_17018[RRM1][KOG0111]Ostreococcus lucimarinus@jgi_Ost9901_3_43898[RRM1][KOG0121]

Ostreococcus tauri@jgi_Ostta4_21085[RRM1][KOG0121]Thalassiosira pseudonana@jgi_Thaps3_19374[RRM1][KOG0121]

Phaeodactylum tricornutum@jgi_Phatr2_13520[RRM1][KOG0121]Encephalitozoon cuniculi_GB-M1@NP_597585[RRM1][KOG0121]

Cryptosporidium parvum_Iowa_II@XP_627536[RRM1][KOG0121]Trypanosoma brucei_TREU927@XP_845318[RRM1][KOG0121]

Leishmania infantum_JPCM5@XP_001466901[RRM1][KOG0121]Theileria parva_strain_Muguga@XP_766484[RRM1][KOG0121]


Erinaceus europaeus@ENSEEUP00000004164[RRM1][KOG0121]Equus caballus@XP_001492661[RRM1][KOG0121]Canis familiaris@ENSCAFP00000026571[RRM1][KOG0121]

Phytophthora ramorum@jgi_Phyra1_1_46906[RRM1][KOG0121]Caenorhabditis elegans@F26A3_2[RRM1][KOG0121]

Drosophila melanogaster@CG12357-PA[RRM1][KOG0121]Anopheles gambiae@AGAP002547-PA[RRM1][KOG0121]

Aedes aegypti@AAEL006135-PA[RRM1][KOG0121]Oryza sativa_japonica_cultivar-group@NP_001047412[RRM1][KOG0121]Ricinus communis@29983_m003140[RRM1][KOG0121]

Arabidopsis thaliana@NP_199233[2][RRM1:100%][KOG0121:100%]Dictyostelium discoideum_AX4@XP_637361[RRM1][KOG0121]

Schizosaccharomyces pombe_972h-@NP_596414[RRM1][KOG0121]Gibberella zeae_PH-1@XP_385664[RRM1][KOG0121]

Aspergillus fumigatus_Af293@XP_755191[RRM1][KOG0121]Plasmodium falciparum_3D7@XP_001351463[RRM1][KOG0121]

Cyanidioschyzon merolae@gnl_CMER_CMQ282C[RRM1][KOG0121]Pichia stipitis_CBS_6054@XP_001387884[RRM1][KOG0121]

Debaryomyces hansenii_CBS767@XP_458582[RRM1][KOG0121]Kluyveromyces lactis@XP_451996[RRM1][KOG0121]

Candida glabrata_CBS138@XP_445241[RRM1][KOG0121]Saccharomyces cerevisiae@YPL178W[RRM1][KOG0121]

Ashbya gossypii_ATCC_10895@NP_985498[RRM1][KOG0121]Ciona savignyi@ENSCSAVP00000009906[RRM1][KOG0121]

Ciona intestinalis@ENSCINP00000006257[2][RRM1:100%][KOG0121:100%]Strongylocentrotus purpuratus@XP_001187788[2][RRM1:100%][KOG0121:100%]



Xenopus tropicalis@ENSXETP00000041997[RRM1][KOG0121]Gallus gallus@ENSGALP00000009225[RRM1][KOG0121]

Oryzias latipes@ENSORLP00000014087[RRM1][KOG0121]Danio rerio@ENSDARP00000020688[RRM1][KOG0121]

Gasterosteus aculeatus@ENSGACP00000008263[RRM1][KOG0121]Tetraodon nigroviridis@GSTENP00011485001[RRM1][KOG0121]

Takifugu rubripes@SINFRUP00000128783[RRM1][KOG0121]Eutheria@ENSBTAP00000011684[11][RRM1:100%**][KOG0121:100%**]Sorex araneus@ENSSARP00000012929[RRM1][KOG0121]Loxodonta africana@ENSLAFP00000005354[RRM1][KOG0121]

Cavia porcellus@ENSCPOP00000002703[RRM1][KOG0121]Oryctolagus cuniculus@ENSOCUP00000012352[RRM1][KOG0121]

Spermophilus tridecemlineatus@ENSSTOP00000001416[RRM1][KOG0121]Gallus gallus@ENSGALP00000011061[RRM1][KOG0121]

Monodelphis domestica@ENSMODP00000029243[RRM1][KOG0121]Monodelphis domestica@ENSMODP00000019849[RRM1][KOG0121]Monodelphis domestica@ENSMODP00000034858[2][RRM1:100%][KOG0121:100%]

Yarrowia lipolytica@XP_500351[RRM2][KOG0123]Drosophila melanogaster@CG5442-PB[RRM1][put-sr][SR][KOG4207][SC35]

Tribolium castaneum@XP_969931[RRM1][put-sr]Apis mellifera@XP_393352[RRM1][put-sr]Anopheles gambiae@AGAP009742-PA[RRM1][put-sr][KOG4207]

Aedes aegypti@AAEL010340-PB[2][RRM1:100%][put-sr:100%][KOG4207:100%]Caenorhabditis elegans@EEED8_7b[2][RRM1:100%][put-sr:50%][SR:100%][KOG4207:50%][CeSC35/rsp-4]

Strongylocentrotus purpuratus@XP_001180179[4][RRM1:100%*][KOG4207:100%*]Strongylocentrotus purpuratus@XP_785989[2][RRM1:100%][put-sr:100%][KOG4207:100%]

Ciona savignyi@ENSCSAVP00000015651[RRM1][put-sr][KOG4207]Ciona intestinalis@ENSCINP00000008678[RRM1][put-sr][KOG4207]

Rattus norvegicus@ENSRNOP00000045342[2][RRM1:100%][KOG4207:100%]Mus musculus@ENSMUSP00000078984[RRM1][KOG4207]

Percomorpha@ENSGACP00000004058[2][RRM1:100%][put-sr:100%][SR:100%][SC35]Takifugu rubripes@SINFRUP00000176738[RRM1][put-sr][SR][KOG4207][SC35]Oryzias latipes@ENSORLP00000023350[RRM1][put-sr][SR][KOG4368][SC35]

Oryzias latipes@ENSORLP00000001513[RRM1][put-sr][SR][KOG4207][SC35]Clupeocephala@ENSDARP00000074623[3][RRM1:100%*][put-sr:100%*][SR:67%][KOG4207:100%*][SC35]

Danio rerio@ENSDARP00000015569[RRM1][put-sr][SR][KOG4207][SC35]Xenopus tropicalis@ENSXETP00000054042[RRM1][put-sr][SR][SC35]

Macaca mulatta@ENSMMUP00000010035[RRM1][put-sr][SR][SRp46]Homo sapiens@ENSP00000381889[RRM1][put-sr][KOG4207]

Bos taurus@ENSBTAP00000012614[2][RRM1:100%][put-sr:100%][KOG4207:100%]Mammalia@ENSBTAP00000024299[19][RRM1:100%**][put-sr:95%**][SR:100%**][KOG4368:74%**][.KOG4207:26%*][SC35]

Dasypus novemcinctus@ENSDNOP00000000330[RRM1][put-sr][SR][KOG4368][SC35]Erinaceus europaeus@ENSEEUP00000008808[RRM1][put-sr][SR][SC35]

Homo sapiens@ENSP00000350877[RRM1][KOG4207]Pan troglodytes@ENSPTRP00000032751[RRM1][KOG4207]

Macaca mulatta@ENSMMUP00000034012[RRM1][SR][KOG4207][SC35]Cryptosporidium parvum_Iowa_II@XP_628282[RRM1][put-sr][KOG4207]


Cryptosporidium parvum_Iowa_II@XP_627626[RRM1][put-sr][KOG0111]Volvox carteri@jgi_Volca1_120666[RRM1][put-sr]

Chlamydomonas reinhardtii@jgi_Chlre3_188086[RRM1][put-sr]Volvox carteri@jgi_Volca1_73973[RRM1][put-sr][KOG4207]

Chlamydomonas reinhardtii@jgi_Chlre3_113900[RRM1][KOG4207]Ciona savignyi@ENSCSAVP00000008618[RRM1][put-sr][KOG0111]

SC35

Fig. S14

140

0.10

100

77

52

83

100

67 88

79

53

76

57

59

100

Volvox carteri@jgi_Volca1_105177[RRM1][put-sr][KOG0462]Phytophthora sojae@jgi_Physo1_1_138873[RRM1][put-sr][KOG1611]

Phytophthora ramorum@jgi_Phyra1_1_78424[RRM1][put-sr]Physcomitrella patens@jgi_Phypa1_1_166555[RRM1][put-sr]Physcomitrella patens@jgi_Phypa1_1_105411[RRM1][put-sr]

Oryza sativa_japonica_cultivar-group@NP_001054414[RRM1][put-sr][KOG0117]Oryza sativa_japonica_cultivar-group@NP_001045458[RRM1][put-sr]

Ricinus communis@30169_m006358[RRM1][put-sr]Arabidopsis thaliana@NP_173107[2][RRM1:100%][put-sr:100%][SR:100%][SR45]

Dictyostelium discoideum_AX4@XP_636445[RRM1][put-sr]Ciona savignyi@ENSCSAVP00000002175[RRM1][put-sr]

Ciona intestinalis@ENSCINP00000028346[RRM1][put-sr]Caenorhabditis elegans@K02F3_11_2[2][RRM1:100%][put-sr:100%][KOG4209:100%]

Cryptococcus neoformans_var._neoformans_JEC21@XP_569824[RRM1][put-sr]Schizosaccharomyces pombe_972h-@NP_596549[RRM1][put-sr]

Magnaporthe grisea_70-15@XP_001522188[RRM1][put-sr]Neurospora crassa_OR74A@XP_958016[RRM1][put-sr]

Gibberella zeae_PH-1@XP_388712[RRM1]Strongylocentrotus purpuratus@XP_800344[2][RRM1:100%][put-sr:100%][KOG4209:100%]

Nasonia vitripennis@XP_001604831[RRM1][put-sr][KOG1311]Apis mellifera@XP_624099[RRM1][put-sr]

Tribolium castaneum@XP_975044[RRM1][put-sr][KOG4209]Anopheles gambiae@AGAP009570-PA[RRM1][put-sr][KOG4209]

Drosophila melanogaster@CG16788-PA[RRM1][put-sr]Drosophila melanogaster@CG41105-PC[RRM1][put-sr]

Gasterosteus aculeatus@ENSGACP00000014885[RRM1][put-sr][RNPS1][KOG4209][RNPS1]Takifugu rubripes@SINFRUP00000147394[RRM1][put-sr][RNPS1][KOG4209][RNPS1]

Oryzias latipes@ENSORLP00000010076[RRM1][put-sr][RNPS1][KOG4209][RNPS1]Danio rerio@ENSDARP00000016052[RRM1][put-sr][RNPS1][KOG4209][RNPS1]Oryzias latipes@ENSORLP00000023176[RRM1][put-sr][RNPS1][KOG4209][RNPS1]

Tetraodon nigroviridis@GSTENP00014231001[RRM1][put-sr][RNPS1][KOG4209][RNPS1]Gasterosteus aculeatus@ENSGACP00000007466[2][RRM1:100%][put-sr:100%][RNPS1:50%][KOG4209:100%][RNPS1]

Gallus gallus@ENSGALP00000015093[RRM1][put-sr][RNPS1][KOG4209][RNPS1]Xenopus tropicalis@ENSXETP00000052845[RRM1][put-sr][RNPS1][KOG4209][RNPS1]

Bos taurus@ENSBTAP00000043081[RRM1][put-sr][KOG4209]Rattus norvegicus@ENSRNOP00000045977[RRM1][put-sr][KOG4209]

Rattus norvegicus@ENSRNOP00000038996[RRM1][put-sr][KOG4209]Eutheria@ENSBTAP00000013151[18][RRM1:100%**][put-sr:100%**][RNPS1:100%**][KOG4209:100%**][RNPS1]

Monodelphis domestica@ENSMODP00000019828[RRM1][put-sr][RNPS1][KOG4209][RNPS1]Rattus norvegicus@ENSRNOP00000046403[RRM1][put-sr][RNPS1][KOG4209][RNPS1]

Rattus norvegicus@ENSRNOP00000011681[RRM1][put-sr][KOG4209]Mus musculus@ENSMUSP00000057332[RRM1][put-sr][KOG4209]

RNPS1

SR45

Fig. S15

141

0.11

76

74

51 70

89

100

100

76 87

87

60

86

70

100 62

59 60

Volvox carteri@jgi_Volca1_105177[RRM1][put-sr][KOG0462]Physcomitrella patens@jgi_Phypa1_1_105411[RRM1][put-sr]

Physcomitrella patens@jgi_Phypa1_1_166555[RRM1][put-sr]Oryza sativa_japonica_cultivar-group@NP_001054414[RRM1][put-sr][KOG0117]

Oryza sativa_japonica_cultivar-group@NP_001045458[RRM1][put-sr]Ricinus communis@30169_m006358[RRM1][put-sr]Arabidopsis thaliana@NP_173107[2][RRM1:100%][put-sr:100%][SR:100%][SR45]

Dictyostelium discoideum_AX4@XP_636445[RRM1][put-sr]Ciona savignyi@ENSCSAVP00000002175[RRM1][put-sr]

Ciona intestinalis@ENSCINP00000028346[RRM1][put-sr]Caenorhabditis elegans@K02F3_11_2[2][RRM1:100%][put-sr:100%][KOG4209:100%]

Cryptococcus neoformans_var._neoformans_JEC21@XP_569824[RRM1][put-sr]Schizosaccharomyces pombe_972h-@NP_596549[RRM1][put-sr]

Phytophthora sojae@jgi_Physo1_1_138873[RRM1][put-sr][KOG1611]Phytophthora ramorum@jgi_Phyra1_1_78424[RRM1][put-sr]

Magnaporthe grisea_70-15@XP_001522188[RRM1][put-sr]Neurospora crassa_OR74A@XP_958016[RRM1][put-sr]

Gibberella zeae_PH-1@XP_388712[RRM1]Strongylocentrotus purpuratus@XP_800344[2][RRM1:100%][put-sr:100%][KOG4209:100%]

Nasonia vitripennis@XP_001604831[RRM1][put-sr][KOG1311]Apis mellifera@XP_624099[RRM1][put-sr]

Drosophila melanogaster@CG16788-PA[RRM1][put-sr]Drosophila melanogaster@CG41105-PC[RRM1][put-sr]

Tribolium castaneum@XP_975044[RRM1][put-sr][KOG4209]Anopheles gambiae@AGAP009570-PA[RRM1][put-sr][KOG4209]

Gallus gallus@ENSGALP00000015093[RRM1][put-sr][RNPS1][KOG4209][RNPS1]Xenopus tropicalis@ENSXETP00000052845[RRM1][put-sr][RNPS1][KOG4209][RNPS1]

Oryzias latipes@ENSORLP00000023176[RRM1][put-sr][RNPS1][KOG4209][RNPS1]Tetraodon nigroviridis@GSTENP00014231001[RRM1][put-sr][RNPS1][KOG4209][RNPS1]

Gasterosteus aculeatus@ENSGACP00000007466[2][RRM1:100%][put-sr:100%][RNPS1:50%][KOG4209:100%][RNPS1]Danio rerio@ENSDARP00000016052[RRM1][put-sr][RNPS1][KOG4209][RNPS1]Oryzias latipes@ENSORLP00000010076[RRM1][put-sr][RNPS1][KOG4209][RNPS1]

Takifugu rubripes@SINFRUP00000147394[RRM1][put-sr][RNPS1][KOG4209][RNPS1]Gasterosteus aculeatus@ENSGACP00000014885[RRM1][put-sr][RNPS1][KOG4209][RNPS1]

Bos taurus@ENSBTAP00000043081[RRM1][put-sr][KOG4209]Rattus norvegicus@ENSRNOP00000038996[RRM1][put-sr][KOG4209]

Rattus norvegicus@ENSRNOP00000045977[RRM1][put-sr][KOG4209]Monodelphis domestica@ENSMODP00000019828[RRM1][put-sr][RNPS1][KOG4209][RNPS1]

Eutheria@ENSBTAP00000013151[18][RRM1:100%**][put-sr:100%**][RNPS1:100%**][KOG4209:100%**][RNPS1]Rattus norvegicus@ENSRNOP00000046403[RRM1][put-sr][RNPS1][KOG4209][RNPS1]

Rattus norvegicus@ENSRNOP00000011681[RRM1][put-sr][KOG4209]Mus musculus@ENSMUSP00000057332[RRM1][put-sr][KOG4209]

SR45

RNPS1

Fig. S16

142

51

75 50

80

92 91

75

58 67

65

56 76

67 80

76

66 66

61

81

63

Danio rerio@ENSDARP00000002874[RRM2][put-sr][KOG0105]Theria@ENSBTAP00000046374[8][RRM2:100%**][put-sr:100%**][SR:100%**][KOG0105:100%**][ASF/SF2]

Oryzias latipes@ENSORLP00000005758[RRM2][put-sr][SR][KOG0105][ASF/SF2]Takifugu rubripes@SINFRUP00000151768[RRM2][put-sr][SR][KOG0105][ASF/SF2]Tetraodontidae@SINFRUP00000136750[2][RRM2:100%][put-sr:100%][SR:100%][KOG0105:100%][ASF/SF2]

Gasterosteus aculeatus@ENSGACP00000027276[RRM2][put-sr][SR][KOG0105][ASF/SF2]Xenopus tropicalis@ENSXETP00000019608[RRM2][put-sr][SR][KOG0105][ASF/SF2]Euteleostomi@ENSDARP00000074866[6][RRM1:67%*][.RRM2:33%][put-sr:100%*][SR:100%*][KOG0105:100%*][ASF/SF2]

Gasterosteus aculeatus@ENSGACP00000014666[RRM2][SR][KOG0105][ASF/SF2]Ornithorhynchus anatinus@ENSOANP00000011650[RRM1][SR][KOG0105][ASF/SF2]Eutheria@ENSBTAP00000019644[10][RRM2:90%**][.RRM1:10%][SR:100%**][KOG0105:100%**][ASF/SF2]

Macaca mulatta@ENSMMUP00000004343[RRM2][SR][KOG0105][ASF/SF2]Mus musculus@ENSMUSP00000103553[RRM2][SR][KOG0105][ASF/SF2]

Rattus norvegicus@ENSRNOP00000052565[RRM2][SR][KOG0105][ASF/SF2]Schizosaccharomyces pombe_972h-@NP_594570[RRM2][put-sr][KOG0106]

Danio rerio@ENSDARP00000084873[2][RRM2:100%][put-sr:100%][KOG0106:100%]Takifugu rubripes@SINFRUP00000132279[RRM2][put-sr][KOG0106]Eutheria@ENSBTAP00000015408[22][RRM2:95%***][.RRM1:5%][put-sr:100%***][SR:100%***][KOG0106:50%**][.KOG0105:50%**][SRp40]Tetrapoda@ENSGALP00000015326[6][RRM2:100%*][put-sr:100%*][SR:100%*][KOG0106:83%*][.KOG0105:17%][SRp40]

Xenopus tropicalis@ENSXETP00000038885[RRM2][put-sr][KOG0106]Gallus gallus@ENSGALP00000015427[RRM2][put-sr][KOG0106]

Danio rerio@ENSDARP00000043311[RRM2][put-sr][KOG0106]Tetraodontidae@SINFRUP00000169885[2][RRM2:100%][put-sr:100%][KOG0106:100%]

Oryzias latipes@ENSORLP00000011623[RRM2][put-sr][KOG0106]Gasterosteus aculeatus@ENSGACP00000015556[RRM2][put-sr][KOG0106]Ciona intestinalis@ENSCINP00000014783[RRM2][put-sr][KOG0106]

Strongylocentrotus purpuratus@XP_001180940[2][RRM2:100%][put-sr:100%][KOG0106:100%]Tribolium castaneum@XP_969451[RRM2][put-sr][KOG0105]

Ciona intestinalis@ENSCINP00000016525[RRM2][put-sr][KOG0106]Ciona intestinalis@ENSCINP00000010229[3][RRM2:100%*][put-sr:100%*][KOG0106:100%*]

Ciona savignyi@ENSCSAVP00000004366[3][RRM2:100%*][put-sr:100%*][KOG0106:100%*]Tribolium castaneum@XP_966697[RRM2][put-sr][KOG0106]

Apis mellifera@XP_391860[RRM2][put-sr][KOG0105]Nasonia vitripennis@XP_001603815[2][RRM2:100%][put-sr:100%][KOG0105:100%]Drosophila melanogaster@CG10851-PA[3][RRM2:100%*][put-sr:100%*][SR:100%*][KOG0105:67%][.KOG0106:33%][SRp55]

Aedes aegypti@AAEL012621-PA[RRM2][put-sr][KOG0105]Anopheles gambiae@AGAP004592-PA[RRM2][put-sr][KOG0105]

Gallus gallus@ENSGALP00000002147[2][RRM1:50%][.RRM2:50%][put-sr:100%][SR:100%][KOG0106:50%][.KOG0105:50%][SRp75]Afrotheria@ENSETEP00000007936[2][RRM1:50%][.RRM2:50%][put-sr:100%][SR:100%][KOG0106:50%][.KOG0105:50%][SRp75]Mammalia@ENSBTAP00000017699[17][RRM2:59%**][.RRM1:41%*][put-sr:100%**][SR:88%**][KOG0105:53%**][.KOG0106:41%*][SRp75]

Danio rerio@ENSDARP00000025299[RRM2][put-sr][KOG0105]Tetraodontidae@SINFRUP00000181560[3][RRM2:67%][.RRM4:33%][put-sr:100%*][KOG0598:100%*]

Gasterosteus aculeatus@ENSGACP00000003112[RRM2][put-sr][KOG0106]Oryzias latipes@ENSORLP00000011823[2][RRM2:100%][put-sr:100%][KOG0106:100%]

Xenopus tropicalis@ENSXETP00000054329[RRM2][put-sr][KOG0105]Danio rerio@ENSDARP00000095990[2][RRM2:100%][put-sr:100%][SR:50%][KOG0105:100%][SRp55]

Xenopus tropicalis@ENSXETP00000031474[2][RRM2:100%][put-sr:100%][KOG0105:100%]Amniota@ENSGALP00000001460[3][RRM1:67%][.RRM2:33%][put-sr:100%*][SR:100%*][KOG0105:100%*][SRp55]Cavia porcellus@ENSCPOP00000010577[RRM2][put-sr][SR][KOG0106][SRp55]

Otolemur garnettii@ENSOGAP00000012965[RRM1][put-sr][SR][KOG0105][SRp55]Theria@ENSBTAP00000011240[18][RRM1:50%**][.RRM2:50%**][put-sr:100%**][SR:94%**][KOG0105:78%**][.KOG0106:22%*][SRp55]

Echinops telfairi@ENSETEP00000005046[RRM2][put-sr][SR][KOG0105][SRp55]Oryzias latipes@ENSORLP00000004399[RRM2][put-sr][KOG0105]

Tetraodon nigroviridis@GSTENP00022576001[RRM2][put-sr][KOG3766]Takifugu rubripes@SINFRUP00000158023[RRM2][put-sr][KOG0105]


RRM2

RRM2

SRp40

SRp55

SRp75

Fig. S17

143

69 52 87

51

53 50 92

66

100

60

60

58

53

100

98

99

59

53

83

95

64 72

96

98 62

71 59

95100

73

91 91

79 82

71

99

88

93

62

50

51

77

76

69

95

79

100

60

64

51 51

74

95

79 73

92

61 71

74

50

Ciona savignyi@ENSCSAVP00000001354[2][RRM1:50%][ RRM3:50%][KOG4212:100%]Rattus norvegicus@ENSRNOP00000007103[2][RRM3:100%][KOG4212:100%]Mus musculus@ENSMUSP00000106126[4][RRM3:100%*][KOG4212:100%*]

Cavia porcellus@ENSCPOP00000009504[RRM2][KOG4212]Amniota@ENSBTAP00000035742[18][RRM3:89%**][.RRM1:6%][.RRM2:6%][KOG4212:100%**]Otolemur garnettii@ENSOGAP00000009767[RRM3][KOG4212]

Xenopus tropicalis@ENSXETP00000039881[RRM3][KOG4212]Gasterosteus aculeatus@ENSGACP00000022130[2][RRM3:100%][KOG4212:100%]

Oryzias latipes@ENSORLP00000003410[3][RRM3:100%*][KOG4212:100%*]Danio rerio@ENSDARP00000076939[3][RRM3:67%][.RRM1:33%][KOG4212:100%*]Takifugu rubripes@SINFRUP00000133120[RRM3][KOG4212]

Tetraodon nigroviridis@GSTENP00018073001[RRM1][KOG4212]Xenopus tropicalis@ENSXETP00000003694[5][RRM3:100%*][KOG4212:100%*]

Gallus gallus@ENSGALP00000000511[2][RRM3:100%][hnRNP:50%][KOG4212:100%][hnRNP_M]Danio rerio@ENSDARP00000082808[2][RRM3:50%][.RRM2:50%][KOG4212:100%]

Gasterosteus aculeatus@ENSGACP00000013576[2][RRM3:100%][KOG4212:100%]Oryzias latipes@ENSORLP00000006803[RRM3][KOG4212]

Tetraodontidae@SINFRUP00000183106[2][RRM3:50%][.RRM2:50%][KOG4212:100%]Mammalia@ENSMODP00000004659[5][RRM1:40%][.RRM3:40%][.RRM2:20%][hnRNP:100%*][KOG4212:100%*][hnRNP_M]

Cavia porcellus@ENSCPOP00000013686[RRM2][hnRNP][KOG4212][hnRNP_M]Tupaia belangeri@ENSTBEP00000007557[RRM3][hnRNP][KOG4212][hnRNP_M]

Sorex araneus@ENSSARP00000000242[RRM3][hnRNP][KOG4212][hnRNP_M]Eutheria@ENSBTAP00000028022[21][RRM3:86%**][.RRM2:14%*][hnRNP:90%**][KOG4212:100%***][HNRP_M]Otolemur garnettii@ENSOGAP00000002890[RRM3][hnRNP][KOG4212][hnRNP_M]

Bos taurus@ENSBTAP00000047141[2][RRM2:100%][KOG4212:100%]Rattus norvegicus@ENSRNOP00000056410[3][RRM3:100%*][hnRNP:100%*][KOG4212:100%*][hnRNP_M]

Loxodonta africana@ENSLAFP00000011385[RRM2][hnRNP][KOG4212][hnRNP_M]Felis catus@ENSFCAP00000014117[RRM3][hnRNP][KOG4212][hnRNP_M]

Ostreococcus lucimarinus@jgi_Ost9901_3_34965[RRM1][KOG4212]Trypanosoma brucei_TREU927@XP_827596[RRM1][KOG4212]Leishmania infantum_JPCM5@XP_001465100[RRM1][KOG4212]


Chlamydomonas reinhardtii@jgi_Chlre3_184854[RRM1]Volvox carteri@jgi_Volca1_103054[RRM1][KOG0055]

Volvox carteri@jgi_Volca1_109965[RRM1][KOG4212]Volvox carteri@jgi_Volca1_103054[RRM2][KOG0055]


Thalassiosira pseudonana@jgi_Thaps3_37126[RRM1][KOG0123]Trypanosoma brucei_TREU927@XP_823301[RRM1][KOG0921]

Cyanidioschyzon merolae@gnl_CMER_CMM217C[RRM1][KOG4212]Plasmodium falciparum_3D7@XP_001347353[RRM1][KOG4212]

Cryptosporidium parvum_Iowa_II@XP_628165[RRM1][KOG4212]Phytophthora ramorum@jgi_Phyra1_1_75500[RRM2][KOG0123]


Cyanidioschyzon merolae@gnl_CMER_CMM078C[RRM1][KOG4212]Phytophthora ramorum@jgi_Phyra1_1_75500[RRM1][KOG0123]

Phytophthora sojae@jgi_Physo1_1_141148[RRM1][KOG0123]Cryptococcus neoformans_var._neoformans_JEC21@XP_568231[RRM1][put-sr][KOG0147]

Yarrowia lipolytica@XP_503927[RRM1][put-sr][KOG4212]Neurospora crassa_OR74A@XP_959532[RRM1][put-sr][KOG4212]

Aspergillus fumigatus_Af293@XP_751108[RRM1][put-sr][KOG4212]Schizosaccharomyces pombe_972h-@NP_594207[RRM1][KOG4212]

Strongylocentrotus purpuratus@XP_001187716[4][RRM1:100%*][put-sr:100%*][KOG4212:50%][.KOG4661:50%]Drosophila melanogaster@CG9373-PA[RRM1][KOG4212]

Tribolium castaneum@XP_974319[RRM1][KOG4212]Nasonia vitripennis@XP_001603370[RRM1][KOG4212]

Apis mellifera@XP_395436[RRM1][KOG4212]Aedes aegypti@AAEL003670-PA[RRM1][KOG4212]

Anopheles gambiae@AGAP001460-PA[RRM1][KOG4212]Ciona intestinalis@ENSCINP00000006201[RRM1][KOG4212]

Ciona savignyi@ENSCSAVP00000001355[RRM1][KOG4212]Ciona savignyi@ENSCSAVP00000001356[RRM1][put-sr][KOG4212]

Takifugu rubripes@SINFRUP00000183106[RRM1][KOG4212]Gasterosteus aculeatus@ENSGACP00000013583[2][RRM1:100%][KOG4212:100%]

Danio rerio@ENSDARP00000082808[RRM1][KOG4212]Oryzias latipes@ENSORLP00000006803[RRM1][KOG4212]Rattus norvegicus@ENSRNOP00000048850[RRM1][hnRNP][KOG4212][hnRNP_M]

Rattus norvegicus@ENSRNOP00000010809[RRM1][hnRNP][KOG4212][hnRNP_M]Rattus norvegicus@ENSRNOP00000056410[RRM1][hnRNP][KOG4212][hnRNP_M]

Gallus gallus@ENSGALP00000000509[2][RRM1:100%][hnRNP:50%][KOG4212:100%]Theria@ENSCAFP00000027344[24][RRM1:100%***][hnRNP:92%***][KOG4212:100%***][hnRNP_M]

Myotis lucifugus@ENSMLUP00000006124[RRM1][hnRNP][KOG4212][hnRNP_M]Monodelphis domestica@ENSMODP00000004247[RRM1][hnRNP][KOG4212][HNRP_M]Bos taurus@ENSBTAP00000011559[RRM1][hnRNP][KOG4212][hnRNP_M]

Xenopus tropicalis@ENSXETP00000039881[RRM1][KOG4212]Danio rerio@ENSDARP00000076939[RRM1][KOG4212]

Danio rerio@ENSDARP00000076941[RRM1][KOG4212]Oryzias latipes@ENSORLP00000003410[RRM1][KOG4212]

Oryzias latipes@ENSORLP00000003405[2][RRM1:100%][KOG4212:100%]Takifugu rubripes@SINFRUP00000133120[RRM1][KOG4212]

Tetraodon nigroviridis@GSTENP00018074001[RRM1][KOG4212]Gasterosteus aculeatus@ENSGACP00000022128[RRM1][KOG4212]

Gasterosteus aculeatus@ENSGACP00000022130[RRM1][KOG4212]Eutheria@ENSBTAP00000035744[2][RRM1:100%][KOG4212:100%]

Otolemur garnettii@ENSOGAP00000009767[RRM1][KOG4212]Amniota@ENSBTAP00000035742[23][RRM1:100%***][KOG4212:100%***]

Loxodonta africana@ENSLAFP00000010861[RRM1][KOG4212]Monodelphis domestica@ENSMODP00000003337[RRM1][KOG4212]

Ornithorhynchus anatinus@ENSOANP00000011737[2][RRM1:100%][KOG4212:100%]Theileria parva_strain_Muguga@XP_766728[RRM2][KOG0124]


Phytophthora sojae@jgi_Physo1_1_136493[RRM2][put-sr][KOG0105]Phytophthora ramorum@jgi_Phyra1_1_75301[RRM2][put-sr][KOG0105]

Plasmodium falciparum_3D7@XP_001347501[RRM2][put-sr][KOG0105]Theileria parva_strain_Muguga@XP_766386[RRM2][put-sr][KOG0105]

Strongylocentrotus purpuratus@XP_788257[2][RRM1:100%][put-sr:100%][KOG0105:100%]Aedes aegypti@AAEL006473-PA[RRM2][put-sr][KOG0105]

Drosophila melanogaster@CG6987-PA[RRM2][put-sr][KOG0105]Anopheles gambiae@AGAP010496-PA[RRM2][put-sr][KOG0105]


Tribolium castaneum@XP_967263[RRM2][put-sr][KOG0105]Ciona savignyi@ENSCSAVP00000005983[RRM1][put-sr][KOG0105]

Ciona intestinalis@ENSCINP00000000458[RRM1][put-sr][KOG0105]Ciona savignyi@ENSCSAVP00000010348[2][RRM2:100%][put-sr:100%][KOG0105:100%]Ciona intestinalis@ENSCINP00000015147[RRM2][put-sr][KOG0105]Caenorhabditis elegans@Y111B2A_18_2[3][RRM2:100%*][put-sr:100%*][SR:100%*][KOG0105:100%*][CeSF2/ASF/rsp-3]

Xenopus tropicalis@ENSXETP00000026703[RRM2][put-sr][SR][KOG0105][SRp30c]Bos taurus@ENSBTAP00000016997[RRM2][put-sr][SR][KOG0105][SRp30c]Eutheria@ENSCAFP00000015146[11][RRM2:55%*][.RRM1:45%*][put-sr:100%**][SR:91%**][KOG0105:100%**][SRp30c]Catarrhini@ENSP00000229390[3][RRM2:67%][.RRM1:33%][put-sr:100%*][SR:100%*][KOG0105:100%*][SRp30c]Tupaia belangeri@ENSTBEP00000007356[RRM2][put-sr][SR][KOG0105][SRp30c]Monodelphis domestica@ENSMODP00000003831[RRM2][put-sr][SR][KOG0105][SRp30c]

Gasterosteus aculeatus@ENSGACP00000022358[2][RRM2:100%][put-sr:100%][KOG0105:100%]Danio rerio@ENSDARP00000091488[RRM2][put-sr][KOG0105]

Danio rerio@ENSDARP00000002874[RRM2][put sr][KOG0105]

RRM3

hnRNP M

RRM1

hnRNP M

RRM2

ASF-like

AnimalFig. S17

144

68

81

99

83 72

57 86

100

81

64

100

97

61

64

73

61

70

91

78

74 88

93

89

70

83

99

100

50

98

100

50 70

53 51

62

81

87

69 70

57 71

64

51

95

85 77

92

80

61

67 64

63

100

82

98 97

92

Apis mellifera@XP 001121250[RRM1][KOG0533]Nasonia vitripennis@XP_001605125[RRM1][KOG0433]

Tribolium castaneum@XP_971598[RRM1][KOG0533]Aedes aegypti@AAEL005114-PA[2][RRM1:100%][KOG0533:100%]

Anopheles gambiae@AGAP006733-PA[RRM1][KOG0533]Ciona savignyi@ENSCSAVP00000005567[RRM1][KOG0533]

Ciona intestinalis@ENSCINP00000024858[RRM1][KOG0533]Gasterosteus aculeatus@ENSGACP00000024021[3][RRM1:100%*][KOG0533:100%*]

Oryzias latipes@ENSORLP00000002010[RRM1][KOG0533]Takifugu rubripes@SINFRUP00000132916[RRM1][KOG0533]

Tetraodon nigroviridis@GSTENP00026384001[RRM1][KOG0533]Tetraodon nigroviridis@GSTENP00007343001[RRM1][KOG0533]Myotis lucifugus@ENSMLUP00000006845[RRM1][KOG0533]

Myotis lucifugus@ENSMLUP00000013791[RRM1][KOG0533]Myotis lucifugus@ENSMLUP00000008945[4][RRM1:100%*][KOG0533:100%*]

Myotis lucifugus@ENSMLUP00000014758[2][RRM1:100%][KOG0533:100%]Tetrapoda@ENSBTAP00000011202[16][RRM1:100%**][KOG0533:100%**]Homo sapiens@ENSP00000383553[RRM1][KOG0533]

Mus musculus@ENSMUSP00000080242[RRM1][KOG0533]Gasterosteus aculeatus@ENSGACP00000017621[RRM1][put-sr][KOG0533]

Oryzias latipes@ENSORLP00000015435[RRM1][KOG0533]Tetraodon nigroviridis@GSTENP00021828001[RRM1][KOG0533]

Takifugu rubripes@SINFRUP00000169188[RRM1][KOG0533]Trypanosoma brucei_TREU927@XP_827596[RRM2][KOG4212]

Leishmania infantum_JPCM5@XP_001465100[RRM2][KOG4212]Debaryomyces hansenii_CBS767@XP_462023[RRM1][put-sr][KOG0123]

Pichia stipitis_CBS_6054@XP_001386572[RRM1][put-sr][KOG0123]Ashbya gossypii_ATCC_10895@NP_982524[RRM1][KOG0127]

Candida glabrata_CBS138@XP_445179[RRM1][put-sr][KOG0123]Saccharomyces cerevisiae@YCL011C[RRM1][put-sr][KOG0123]

Candida glabrata_CBS138@XP_446962[RRM1][put-sr][KOG0127]Saccharomyces cerevisiae@YNL004W[RRM1][KOG0127]


Schizosaccharomyces pombe_972h-@NP_594207[RRM3][KOG4212]Ustilago maydis_521@XP_759231[RRM3][put-sr][KOG4212]

Cryptococcus neoformans_var._neoformans_JEC21@XP_568231[RRM3][put-sr][KOG0147]Neurospora crassa_OR74A@XP_959532[RRM3][put-sr][KOG4212]

Aspergillus fumigatus_Af293@XP_751108[RRM3][put-sr][KOG4212]Yarrowia lipolytica@XP_503927[RRM3][put-sr][KOG4212]

Candida albicans_SC5314@XP_888678[RRM2][KOG4212]Debaryomyces hansenii_CBS767@XP_462023[RRM3][put-sr][KOG0123]

Pichia stipitis_CBS_6054@XP_001386572[RRM3][put-sr][KOG0123]Ashbya gossypii_ATCC_10895@NP_982524[RRM3][KOG0127]

Kluyveromyces lactis@XP_453283[RRM2][KOG0123]Saccharomyces cerevisiae@YNL004W[RRM3][KOG0127]

Saccharomyces cerevisiae@YCL011C[RRM3][put-sr][KOG0123]Candida glabrata_CBS138@XP_445179[RRM3][put-sr][KOG0123]


Volvox carteri@jgi_Volca1_78979[RRM1][KOG3070]Ostreococcus lucimarinus@jgi_Ost9901_3_34965[RRM2][KOG4212]



Ostreococcus tauri@jgi_Ostta4_7882[RRM1]Ostreococcus lucimarinus@jgi_Ost9901_3_27365[RRM1][KOG0123]

Yarrowia lipolytica@XP_503927[RRM2][put-sr][KOG4212]Strongylocentrotus purpuratus@XP_001188339[4][RRM2:100%*][put-sr:100%*][KOG4661:50%][.KOG4212:50%]

Ciona savignyi@ENSCSAVP00000001355[2][RRM2:100%][put-sr:50%][KOG4212:100%]Ciona intestinalis@ENSCINP00000006201[2][RRM1:50%][.RRM2:50%][KOG4212:100%]

Caenorhabditis elegans@C25A1_4_2[2][RRM2:100%][put-sr:100%][KOG4212:100%]Apocrita@XP_395436[2][RRM2:100%][KOG4212:100%]

Tribolium castaneum@XP_974319[RRM2][KOG4212]Drosophila melanogaster@CG9373-PA[RRM2][KOG4212]

Aedes aegypti@AAEL003670-PA[RRM2][KOG4212]Anopheles gambiae@AGAP001460-PA[RRM2][KOG4212]

Gasterosteus aculeatus@ENSGACP00000013576[2][RRM2:100%][KOG4212:100%]Danio rerio@ENSDARP00000082789[3][RRM1:67%][.RRM2:33%][KOG4212:100%*]

Oryzias latipes@ENSORLP00000006803[RRM2][KOG4212]Tetraodon nigroviridis@GSTENP00028898001[RRM1][KOG4212]Takifugu rubripes@SINFRUP00000183106[RRM2][KOG4212]

Xenopus tropicalis@ENSXETP00000057903[5][RRM2:100%*][KOG4212:100%*]Gallus gallus@ENSGALP00000000509[2][RRM2:100%][hnRNP:50%][KOG4212:100%]Mammalia@ENSMODP00000032153[4][RRM2:75%*][.RRM1:25%][hnRNP:100%*][KOG4212:100%*][HNRP_M]Eutheria@ENSBTAP00000011559[22][RRM2:86%**][.RRM1:14%*][hnRNP:91%**][KOG4212:100%***][hnRNP_M]

Oryctolagus cuniculus@ENSOCUP00000000477[RRM1][hnRNP][KOG4212][hnRNP_M]Mus musculus@ENSMUSP00000110027[2][RRM2:100%][hnRNP:100%][KOG4212:100%][HNRP_M]

Tetraodon nigroviridis@GSTENP00018074001[RRM2][KOG4212]Oryzias latipes@ENSORLP00000003408[3][RRM2:100%*][KOG4212:100%*]

Takifugu rubripes@SINFRUP00000133120[RRM2][KOG4212]Gasterosteus aculeatus@ENSGACP00000022130[2][RRM2:100%][KOG4212:100%]

Danio rerio@ENSDARP00000076941[2][RRM2:100%][KOG4212:100%]Xenopus tropicalis@ENSXETP00000039881[RRM2][KOG4212]

Ornithorhynchus anatinus@ENSOANP00000011736[2][RRM2:100%][KOG4212:100%]Myotis lucifugus@ENSMLUP00000006206[RRM1][KOG4212]

Sorex araneus@ENSSARP00000002953[RRM2][KOG4212]Amniota@ENSBTAP00000035742[26][RRM2:92%***][.RRM1:8%][KOG4212:100%***]Spermophilus tridecemlineatus@ENSSTOP00000006938[RRM2][KOG4212]Monodelphis domestica@ENSMODP00000003337[RRM2][KOG4212]

Cryptococcus neoformans_var._neoformans_JEC21@XP_572539[4][RRM2:100%*][KOG4212:100%*]Pichia stipitis_CBS_6054@XP_001386572[RRM2][put-sr][KOG0123]

Candida albicans_SC5314@XP_888678[RRM1][KOG4212]Debaryomyces hansenii_CBS767@XP_462023[RRM2][put-sr][KOG0123]

Ustilago maydis_521@XP_758699[RRM2][KOG4212]Cryptococcus neoformans_var._neoformans_JEC21@XP_567941[4][RRM1:100%*][KOG4212:100%*]

Ustilago maydis_521@XP_758699[RRM1][KOG4212]Ustilago maydis_521@XP_759231[RRM2][put-sr][KOG4212]

Schizosaccharomyces pombe_972h-@NP_594207[RRM2][KOG4212]Plasmodium falciparum_3D7@XP_001347353[RRM2][KOG4212]


Aspergillus fumigatus_Af293@XP_751108[RRM2][put-sr][KOG4212]Saccharomyces cerevisiae@YNL004W[RRM2][KOG0127]

Ashbya gossypii_ATCC_10895@NP_982524[RRM2][KOG0127]Kluyveromyces lactis@XP_453283[RRM1][KOG0123]

Candida glabrata_CBS138@XP_446962[RRM2][put-sr][KOG0127]Saccharomyces cerevisiae@YCL011C[RRM2][put-sr][KOG0123]

Candida glabrata_CBS138@XP_445179[RRM2][put-sr][KOG0123]Volvox carteri@jgi_Volca1_103054[RRM3][KOG0055]

Chlamydomonas reinhardtii@jgi_Chlre3_95535[RRM2]Cyanidioschyzon merolae@gnl_CMER_CMM078C[RRM2][KOG4212]

Strongylocentrotus purpuratus@XP_786244[2][RRM3:100%][put-sr:100%][KOG4212:100%]Drosophila melanogaster@CG9373-PA[RRM3][KOG4212]

Anopheles gambiae@AGAP001460-PA[RRM3][KOG4212]Nasonia vitripennis@XP_001603370[RRM3][KOG4212]

Apis mellifera@XP_395436[RRM3][KOG4212]Ciona intestinalis@ENSCINP00000006201[RRM3][KOG4212]

Ciona savignyi@ENSCSAVP00000001354[2][RRM1:50%][.RRM3:50%][KOG4212:100%]

RRM2

hnRNP M

Fig. S17

145

0.13

98

71

52

80

81

62 92

100

65

97 99

63 81

100

92 93

61

99

97

70

84 50

59

92 63

62

62

68

78

Cryptosporidium parvum_Iowa_II@XP_628165[RRM2][KOG4212]Neurospora crassa_OR74A@XP_956471[RRM1][KOG0533]

Gibberella zeae_PH-1@XP_391006[RRM1][KOG0533]Schizosaccharomyces pombe_972h-@NP_595715[RRM1][KOG0533]


Pichia stipitis_CBS_6054@XP_001387082[RRM1][KOG0533]Debaryomyces hansenii_CBS767@XP_462132[RRM1][KOG0533]

Saccharomyces cerevisiae@YDR381W[RRM1][KOG0533]Candida glabrata_CBS138@XP_444903[RRM1][KOG0533]

Kluyveromyces lactis@XP_454070[RRM1][KOG0533]Ashbya gossypii_ATCC_10895@NP_985696[RRM1][KOG0533]

Tupaia belangeri@ENSTBEP00000009485[RRM1][PDIP][KOG0533][PDIP3]Oryzias latipes@ENSORLP00000018556[RRM1]

Tetraodon nigroviridis@GSTENP00020488001[RRM1]Cyanidioschyzon merolae@gnl_CMER_CMH135C[RRM1]

Drosophila melanogaster@CG6961-PA[2][RRM1:100%][KOG0533:100%]Anopheles gambiae@AGAP000924-PA[RRM1]

Aedes aegypti@AAEL008938-PB[2][RRM1:100%]Tribolium castaneum@XP_969371[RRM1]

Nasonia vitripennis@XP_001600231[RRM1]Phytophthora ramorum@jgi_Phyra1_1_97175[RRM1][KOG0533]

Phytophthora sojae@jgi_Physo1_1_157747[RRM1][put-sr][KOG0533]Yarrowia lipolytica@XP_505140[RRM1][KOG0533]

Ustilago maydis_521@XP_757147[RRM1][KOG0533]Aspergillus fumigatus_Af293@XP_753805[RRM1][KOG0533]

Neurospora crassa_OR74A@XP_958422[RRM1][put-sr][KOG0533]Gibberella zeae_PH-1@XP_387031[RRM1][KOG0533]


Dictyostelium discoideum_AX4@XP_638266[RRM1][KOG0533]Volvox carteri@jgi_Volca1_90392[RRM1][KOG0533]

Chlamydomonas reinhardtii@jgi_Chlre3_168261[RRM1][KOG0533]Ostreococcus tauri@jgi_Ostta4_36431[RRM1][KOG0533]

Oryza sativa_japonica_cultivar-group@NP_001049725[RRM1][KOG0533]Arabidopsis thaliana@NP_200803[3][RRM1:100%*][FCAFPA:100%*][KOG0533:100%*][AtREF]

Arabidopsis thaliana@NP_195873[RRM1][FCAFPA][KOG0533][AtREF]Ricinus communis@29876_m000260[RRM1][KOG0533]






Ricinus communis@29005_m000257[RRM1][KOG0533]Medicago truncatula@IMGA_CT963094_22_1[RRM1][KOG0533]

Arabidopsis thaliana@NP_001078676[2][RRM1:100%][FCAFPA:100%][KOG0533:100%][AtREF]Arabidopsis thaliana@NP_564871[RRM1][FCAFPA][KOG0533][AtREF]

Drosophila melanogaster@CG1101-PA[RRM1][KOG0533]Strongylocentrotus purpuratus@XP_782040[2][RRM1:100%][KOG0533:100%]

Apis mellifera@XP_001121250[RRM1][KOG0533]

Fig. S17

146

55 63

67 53

93

92 95

81

57

78 83

69

58

74 74

64 80

84

57

65 59

55

90

55

74

Aedes aegypti@AAEL006473-PA[RRM2][put-sr][KOG0105]Theria@ENSBTAP00000046374[8][RRM2:100%**][put-sr:100%**][SR:100%**][KOG0105:100%**][ASF/SF2]

Gasterosteus aculeatus@ENSGACP00000027276[RRM2][put-sr][SR][KOG0105][ASF/SF2]Oryzias latipes@ENSORLP00000005758[RRM2][put-sr][SR][KOG0105][ASF/SF2]Tetraodontidae@SINFRUP00000136750[2][RRM2:100%][put-sr:100%][SR:100%][KOG0105:100%][ASF/SF2]Takifugu rubripes@SINFRUP00000151768[RRM2][put-sr][SR][KOG0105][ASF/SF2]

Xenopus tropicalis@ENSXETP00000019608[RRM2][put-sr][SR][KOG0105][ASF/SF2]Euteleostomi@ENSDARP00000074866[6][RRM1:67%*][.RRM2:33%][put-sr:100%*][SR:100%*][KOG0105:100%*][ASF/SF2]

Gasterosteus aculeatus@ENSGACP00000014666[RRM2][SR][KOG0105][ASF/SF2]Ornithorhynchus anatinus@ENSOANP00000011650[RRM1][SR][KOG0105][ASF/SF2]Eutheria@ENSBTAP00000019644[10][RRM2:90%**][.RRM1:10%][SR:100%**][KOG0105:100%**][ASF/SF2]

Macaca mulatta@ENSMMUP00000004343[RRM2][SR][KOG0105][ASF/SF2]Rattus norvegicus@ENSRNOP00000052565[RRM2][SR][KOG0105][ASF/SF2]Mus musculus@ENSMUSP00000103553[RRM2][SR][KOG0105][ASF/SF2]

Schizosaccharomyces pombe_972h-@NP_594570[RRM2][put-sr][KOG0106]Danio rerio@ENSDARP00000084873[2][RRM2:100%][put-sr:100%][KOG0106:100%]

Takifugu rubripes@SINFRUP00000132279[RRM2][put-sr][KOG0106]Tetrapoda@ENSGALP00000015326[6][RRM2:100%*][put-sr:100%*][SR:100%*][KOG0106:83%*][.KOG0105:17%][SRp40]Eutheria@ENSBTAP00000015408[22][RRM2:95%***][.RRM1:5%][put-sr:100%***][SR:100%***][KOG0106:50%**][.KOG0105:50%**][SRp40]Xenopus tropicalis@ENSXETP00000038885[RRM2][put-sr][KOG0106]Gallus gallus@ENSGALP00000015427[RRM2][put-sr][KOG0106]

Danio rerio@ENSDARP00000043311[RRM2][put-sr][KOG0106]Tetraodontidae@SINFRUP00000169885[2][RRM2:100%][put-sr:100%][KOG0106:100%]

Oryzias latipes@ENSORLP00000011623[RRM2][put-sr][KOG0106]Gasterosteus aculeatus@ENSGACP00000015556[RRM2][put-sr][KOG0106]

Ciona intestinalis@ENSCINP00000014783[RRM2][put-sr][KOG0106]Tribolium castaneum@XP_969451[RRM2][put-sr][KOG0105]

Ciona intestinalis@ENSCINP00000016525[RRM2][put-sr][KOG0106]Ciona savignyi@ENSCSAVP00000004366[3][RRM2:100%*][put-sr:100%*][KOG0106:100%*]

Ciona intestinalis@ENSCINP00000010229[3][RRM2:100%*][put-sr:100%*][KOG0106:100%*]Tribolium castaneum@XP_966697[RRM2][put-sr][KOG0106]Nasonia vitripennis@XP_001603815[2][RRM2:100%][put-sr:100%][KOG0105:100%]

Apis mellifera@XP_391860[RRM2][put-sr][KOG0105]Drosophila melanogaster@CG10851-PA[3][RRM2:100%*][put-sr:100%*][SR:100%*][KOG0105:67%][.KOG0106:33%][SRp55]

Anopheles gambiae@AGAP004592-PA[RRM2][put-sr][KOG0105]Aedes aegypti@AAEL012621-PA[RRM2][put-sr][KOG0105]

Strongylocentrotus purpuratus@XP_001180940[2][RRM2:100%][put-sr:100%][KOG0106:100%]Gallus gallus@ENSGALP00000002147[2][RRM1:50%][.RRM2:50%][put-sr:100%][SR:100%][KOG0106:50%][.KOG0105:50%][SRp75]Mammalia@ENSBTAP00000017699[17][RRM2:59%**][.RRM1:41%*][put-sr:100%**][SR:88%**][KOG0105:53%**][.KOG0106:41%*][SRp75]Afrotheria@ENSETEP00000007936[2][RRM1:50%][.RRM2:50%][put-sr:100%][SR:100%][KOG0106:50%][.KOG0105:50%][SRp75]

Oryzias latipes@ENSORLP00000011823[2][RRM2:100%][put-sr:100%][KOG0106:100%]Gasterosteus aculeatus@ENSGACP00000003112[RRM2][put-sr][KOG0106]

Tetraodontidae@SINFRUP00000181560[3][RRM2:67%][.RRM4:33%][put-sr:100%*][KOG0598:100%*]Danio rerio@ENSDARP00000025299[RRM2][put-sr][KOG0105]

Xenopus tropicalis@ENSXETP00000054329[RRM2][put-sr][KOG0105]Xenopus tropicalis@ENSXETP00000031474[2][RRM2:100%][put-sr:100%][KOG0105:100%]

Danio rerio@ENSDARP00000095990[2][RRM2:100%][put-sr:100%][SR:50%][KOG0105:100%][SRp55]Oryzias latipes@ENSORLP00000004399[RRM2][put-sr][KOG0105]



Amniota@ENSGALP00000001460[3][RRM1:67%][.RRM2:33%][put-sr:100%*][SR:100%*][KOG0105:100%*][SRp55]Cavia porcellus@ENSCPOP00000010577[RRM2][put-sr][SR][KOG0106][SRp55]Theria@ENSBTAP00000011240[18][RRM1:50%**][.RRM2:50%**][put-sr:100%**][SR:94%**][KOG0105:78%**][.KOG0106:22%*][SRp55]

Otolemur garnettii@ENSOGAP00000012965[RRM1][put-sr][SR][KOG0105][SRp55]Echinops telfairi@ENSETEP00000005046[RRM2][put-sr][SR][KOG0105][SRp55]

RRM2

SRp40

SRp55

SRp75

RRM2

Fig. S18

147

88 51

92

60 61

55 61

63 74

52 78

58

66

74

98

99

100

98

87

58

65 76

94

98 71

70 67

86100

79

84 91

79 83

53 60

99

89

86

60

54

91

77

67

94

97

90 99

83

100

52

95 62

58

72

91 73

61

71 55

71

94

Gasterosteus aculeatus@ENSGACP00000013576[2][RRM2:100%][KOG4212:100%]Danio rerio@ENSDARP00000082789[3][RRM1:67%][.RRM2:33%][KOG4212:100%*]

Oryzias latipes@ENSORLP00000006803[RRM2][KOG4212]Tetraodon nigroviridis@GSTENP00028898001[RRM1][KOG4212]Takifugu rubripes@SINFRUP00000183106[RRM2][KOG4212]

Xenopus tropicalis@ENSXETP00000057903[5][RRM2:100%*][KOG4212:100%*]Gallus gallus@ENSGALP00000000509[2][RRM2:100%][hnRNP:50%][KOG4212:100%]Mammalia@ENSMODP00000032153[4][RRM2:75%*][.RRM1:25%][hnRNP:100%*][KOG4212:100%*][HNRP_M]Oryctolagus cuniculus@ENSOCUP00000000477[RRM1][hnRNP][KOG4212][hnRNP_M]Eutheria@ENSBTAP00000011559[22][RRM2:86%**][.RRM1:14%*][hnRNP:91%**][KOG4212:100%***][hnRNP_M]

Mus musculus@ENSMUSP00000110027[2][RRM2:100%][hnRNP:100%][KOG4212:100%][HNRP_M]Tetraodon nigroviridis@GSTENP00018074001[RRM2][KOG4212]

Takifugu rubripes@SINFRUP00000133120[RRM2][KOG4212]Oryzias latipes@ENSORLP00000003408[3][RRM2:100%*][KOG4212:100%*]Gasterosteus aculeatus@ENSGACP00000022130[2][RRM2:100%][KOG4212:100%]

Danio rerio@ENSDARP00000076941[2][RRM2:100%][KOG4212:100%]Xenopus tropicalis@ENSXETP00000039881[RRM2][KOG4212]

Ornithorhynchus anatinus@ENSOANP00000011736[2][RRM2:100%][KOG4212:100%]Myotis lucifugus@ENSMLUP00000006206[RRM1][KOG4212]Amniota@ENSBTAP00000035742[26][RRM2:92%***][.RRM1:8%][KOG4212:100%***]Sorex araneus@ENSSARP00000002953[RRM2][KOG4212]

Spermophilus tridecemlineatus@ENSSTOP00000006938[RRM2][KOG4212]Monodelphis domestica@ENSMODP00000003337[RRM2][KOG4212]

Trypanosoma brucei_TREU927@XP_823301[RRM1][KOG0921]Cyanidioschyzon merolae@gnl_CMER_CMM217C[RRM1][KOG4212]


Volvox carteri@jgi_Volca1_103054[RRM1][KOG0055]Chlamydomonas reinhardtii@jgi_Chlre3_184854[RRM1]

Volvox carteri@jgi_Volca1_109965[RRM1][KOG4212]Ostreococcus lucimarinus@jgi_Ost9901_3_34965[RRM1][KOG4212]


Aureococcus anophagefferens@jgi_Auran1_32583[RRM1][KOG0123]Volvox carteri@jgi_Volca1_103054[RRM2][KOG0055]

Aureococcus anophagefferens@jgi_Auran1_32583[RRM2][KOG0123]Thalassiosira pseudonana@jgi_Thaps3_37126[RRM1][KOG0123]

Phaeodactylum tricornutum@jgi_Phatr2_51303[RRM1][KOG4212]Cyanidioschyzon merolae@gnl_CMER_CMM078C[RRM1][KOG4212]

Phytophthora sojae@jgi_Physo1_1_141148[RRM1][KOG0123]Phytophthora ramorum@jgi_Phyra1_1_75500[RRM1][KOG0123]



Cryptococcus neoformans_var._neoformans_JEC21@XP_568231[RRM1][put-sr][KOG0147]Schizosaccharomyces pombe_972h-@NP_594207[RRM1][KOG4212]

Yarrowia lipolytica@XP_503927[RRM1][put-sr][KOG4212]Neurospora crassa_OR74A@XP_959532[RRM1][put-sr][KOG4212]

Aspergillus fumigatus_Af293@XP_751108[RRM1][put-sr][KOG4212]Strongylocentrotus purpuratus@XP_001187716[4][RRM1:100%*][put-sr:100%*][KOG4212:50%][.KOG4661:50%]

Drosophila melanogaster@CG9373-PA[RRM1][KOG4212]Tribolium castaneum@XP_974319[RRM1][KOG4212]


Anopheles gambiae@AGAP001460-PA[RRM1][KOG4212]Aedes aegypti@AAEL003670-PA[RRM1][KOG4212]

Ciona intestinalis@ENSCINP00000006201[RRM1][KOG4212]Ciona savignyi@ENSCSAVP00000001356[RRM1][put-sr][KOG4212]

Ciona savignyi@ENSCSAVP00000001355[RRM1][KOG4212]Takifugu rubripes@SINFRUP00000183106[RRM1][KOG4212]

Gasterosteus aculeatus@ENSGACP00000013583[2][RRM1:100%][KOG4212:100%]Oryzias latipes@ENSORLP00000006803[RRM1][KOG4212]

Danio rerio@ENSDARP00000082808[RRM1][KOG4212]Rattus norvegicus@ENSRNOP00000048850[RRM1][hnRNP][KOG4212][hnRNP_M]

Rattus norvegicus@ENSRNOP00000056410[RRM1][hnRNP][KOG4212][hnRNP_M]Rattus norvegicus@ENSRNOP00000010809[RRM1][hnRNP][KOG4212][hnRNP_M]Monodelphis domestica@ENSMODP00000004247[RRM1][hnRNP][KOG4212][HNRP_M]Bos taurus@ENSBTAP00000011559[RRM1][hnRNP][KOG4212][hnRNP_M]

Theria@ENSCAFP00000027344[24][RRM1:100%***][hnRNP:92%***][KOG4212:100%***][hnRNP_M]Myotis lucifugus@ENSMLUP00000006124[RRM1][hnRNP][KOG4212][hnRNP_M]Gallus gallus@ENSGALP00000000509[2][RRM1:100%][hnRNP:50%][KOG4212:100%]

Xenopus tropicalis@ENSXETP00000039881[RRM1][KOG4212]Danio rerio@ENSDARP00000076939[RRM1][KOG4212]

Danio rerio@ENSDARP00000076941[RRM1][KOG4212]Oryzias latipes@ENSORLP00000003410[RRM1][KOG4212]

Oryzias latipes@ENSORLP00000003405[2][RRM1:100%][KOG4212:100%]Takifugu rubripes@SINFRUP00000133120[RRM1][KOG4212]

Tetraodon nigroviridis@GSTENP00018074001[RRM1][KOG4212]Gasterosteus aculeatus@ENSGACP00000022128[RRM1][KOG4212]

Gasterosteus aculeatus@ENSGACP00000022130[RRM1][KOG4212]Otolemur garnettii@ENSOGAP00000009767[RRM1][KOG4212]Eutheria@ENSBTAP00000035744[2][RRM1:100%][KOG4212:100%]

Loxodonta africana@ENSLAFP00000010861[RRM1][KOG4212]Amniota@ENSBTAP00000035742[23][RRM1:100%***][KOG4212:100%***]

Ornithorhynchus anatinus@ENSOANP00000011737[2][RRM1:100%][KOG4212:100%]Monodelphis domestica@ENSMODP00000003337[RRM1][KOG4212]

Plasmodium falciparum_3D7@XP_001347353[RRM2][KOG4212]Nasonia vitripennis@XP_001603370[RRM3][KOG4212]

Apis mellifera@XP_395436[RRM3][KOG4212]Drosophila melanogaster@CG9373-PA[RRM3][KOG4212]

Anopheles gambiae@AGAP001460-PA[RRM3][KOG4212]Theileria parva_strain_Muguga@XP_766728[RRM2][KOG0124]


Phytophthora ramorum@jgi_Phyra1_1_75301[RRM2][put-sr][KOG0105]Phytophthora sojae@jgi_Physo1_1_136493[RRM2][put-sr][KOG0105]


Danio rerio@ENSDARP00000091488[RRM2][put-sr][KOG0105]Danio rerio@ENSDARP00000002874[RRM2][put-sr][KOG0105]

Gasterosteus aculeatus@ENSGACP00000022358[2][RRM2:100%][put-sr:100%][KOG0105:100%]Xenopus tropicalis@ENSXETP00000026703[RRM2][put-sr][SR][KOG0105][SRp30c]

Monodelphis domestica@ENSMODP00000003831[RRM2][put-sr][SR][KOG0105][SRp30c]Tupaia belangeri@ENSTBEP00000007356[RRM2][put-sr][SR][KOG0105][SRp30c]Eutheria@ENSCAFP00000015146[11][RRM2:55%*][.RRM1:45%*][put-sr:100%**][SR:91%**][KOG0105:100%**][SRp30c]Catarrhini@ENSP00000229390[3][RRM2:67%][.RRM1:33%][put-sr:100%*][SR:100%*][KOG0105:100%*][SRp30c]Bos taurus@ENSBTAP00000016997[RRM2][put-sr][SR][KOG0105][SRp30c]

Caenorhabditis elegans@Y111B2A_18_2[3][RRM2:100%*][put-sr:100%*][SR:100%*][KOG0105:100%*][CeSF2/ASF/rsp-3]Ciona savignyi@ENSCSAVP00000010348[2][RRM2:100%][put-sr:100%][KOG0105:100%]Ciona intestinalis@ENSCINP00000015147[RRM2][put-sr][KOG0105]

Ciona savignyi@ENSCSAVP00000005983[RRM1][put-sr][KOG0105]Ciona intestinalis@ENSCINP00000000458[RRM1][put-sr][KOG0105]

Strongylocentrotus purpuratus@XP_788257[2][RRM1:100%][put-sr:100%][KOG0105:100%]Nasonia vitripennis@XP_001605411[RRM2][put-sr][KOG0105]


Anopheles gambiae@AGAP010496-PA[RRM2][put-sr][KOG0105]Drosophila melanogaster@CG6987-PA[RRM2][put-sr][KOG0105]

Aedes aegypti@AAEL006473 PA[RRM2][put sr][KOG0105] RRM2

ASF-like

Animal

RRM1

hnRNP M

Fig. S18

148

80 75

76

82 56

69

74100

52

77

61

84

96

78

79 94

95

87

73

91

100

98

54

60 91

71

99

97

100

58 62

89 70

100

95

80

92

75 51 88

55 58

52 52 98

95

50

67

56

66

83

87

61

99

73 93

54

70

98

Ciona intestinalis@ENSCINP00000024858[RRM1][KOG0533]Oryzias latipes@ENSORLP00000002010[RRM1][KOG0533]

Gasterosteus aculeatus@ENSGACP00000024021[3][RRM1:100%*][KOG0533:100%*]Takifugu rubripes@SINFRUP00000132916[RRM1][KOG0533]

Tetraodon nigroviridis@GSTENP00007343001[RRM1][KOG0533]Tetraodon nigroviridis@GSTENP00026384001[RRM1][KOG0533]

Strongylocentrotus purpuratus@XP_782040[2][RRM1:100%][KOG0533:100%]Nasonia vitripennis@XP_001605125[RRM1][KOG0433]


Anopheles gambiae@AGAP006733-PA[RRM1][KOG0533]Aedes aegypti@AAEL005114-PA[2][RRM1:100%][KOG0533:100%]

Tetraodon nigroviridis@GSTENP00021828001[RRM1][KOG0533]Mus musculus@ENSMUSP00000080242[RRM1][KOG0533]Gasterosteus aculeatus@ENSGACP00000017621[RRM1][put-sr][KOG0533]

Takifugu rubripes@SINFRUP00000169188[RRM1][KOG0533]Oryzias latipes@ENSORLP00000015435[RRM1][KOG0533]Tetrapoda@ENSBTAP00000011202[16][RRM1:100%**][KOG0533:100%**]Homo sapiens@ENSP00000383553[RRM1][KOG0533]

Myotis lucifugus@ENSMLUP00000006845[RRM1][KOG0533]Myotis lucifugus@ENSMLUP00000013791[RRM1][KOG0533]

Myotis lucifugus@ENSMLUP00000008945[4][RRM1:100%*][KOG0533:100%*]Myotis lucifugus@ENSMLUP00000014758[2][RRM1:100%][KOG0533:100%]

Schizosaccharomyces pombe_972h-@NP_594207[RRM3][KOG4212]Ustilago maydis_521@XP_759231[RRM3][put-sr][KOG4212]


Aspergillus fumigatus_Af293@XP_751108[RRM3][put-sr][KOG4212]Yarrowia lipolytica@XP_503927[RRM3][put-sr][KOG4212]

Candida albicans_SC5314@XP_888678[RRM2][KOG4212]Pichia stipitis_CBS_6054@XP_001386572[RRM3][put-sr][KOG0123]

Debaryomyces hansenii_CBS767@XP_462023[RRM3][put-sr][KOG0123]Kluyveromyces lactis@XP_453283[RRM2][KOG0123]

Ashbya gossypii_ATCC_10895@NP_982524[RRM3][KOG0127]Saccharomyces cerevisiae@YNL004W[RRM3][KOG0127]




Pichia stipitis_CBS_6054@XP_001386572[RRM1][put-sr][KOG0123]Debaryomyces hansenii_CBS767@XP_462023[RRM1][put-sr][KOG0123]

Candida glabrata_CBS138@XP_445179[RRM1][put-sr][KOG0123]Ashbya gossypii_ATCC_10895@NP_982524[RRM1][KOG0127]

Saccharomyces cerevisiae@YCL011C[RRM1][put-sr][KOG0123]Saccharomyces cerevisiae@YNL004W[RRM1][KOG0127]

Candida glabrata_CBS138@XP_446962[RRM1][put-sr][KOG0127]Ostreococcus tauri@jgi_Ostta4_7882[RRM1]

Ostreococcus lucimarinus@jgi_Ost9901_3_27365[RRM1][KOG0123]Volvox carteri@jgi_Volca1_78979[RRM1][KOG3070]


Volvox carteri@jgi_Volca1_103054[RRM3][KOG0055]Chlamydomonas reinhardtii@jgi_Chlre3_95535[RRM2]

Cyanidioschyzon merolae@gnl_CMER_CMM078C[RRM2][KOG4212]Ostreococcus lucimarinus@jgi_Ost9901_3_34965[RRM2][KOG4212]

Saccharomyces cerevisiae@YNL004W[RRM2][KOG0127]Kluyveromyces lactis@XP_453283[RRM1][KOG0123]

Ashbya gossypii_ATCC_10895@NP_982524[RRM2][KOG0127]Candida glabrata_CBS138@XP_446962[RRM2][put-sr][KOG0127]


Cryptococcus neoformans_var._neoformans_JEC21@XP_572539[4][RRM2:100%*][KOG4212:100%*]Pichia stipitis_CBS_6054@XP_001386572[RRM2][put-sr][KOG0123]

Debaryomyces hansenii_CBS767@XP_462023[RRM2][put-sr][KOG0123]Candida albicans_SC5314@XP_888678[RRM1][KOG4212]

Yarrowia lipolytica@XP_503927[RRM2][put-sr][KOG4212]Phytophthora sojae@jgi_Physo1_1_141148[RRM3][KOG0123]

Phytophthora ramorum@jgi_Phyra1_1_75500[RRM3][KOG0123]Thalassiosira pseudonana@jgi_Thaps3_37126[RRM2][KOG0123]

Phaeodactylum tricornutum@jgi_Phatr2_51303[RRM2][KOG4212]Schizosaccharomyces pombe_972h-@NP_594207[RRM2][KOG4212]Ustilago maydis_521@XP_758699[RRM2][KOG4212]

Ustilago maydis_521@XP_758699[RRM1][KOG4212]Cryptococcus neoformans_var._neoformans_JEC21@XP_567941[4][RRM1:100%*][KOG4212:100%*]

Ustilago maydis_521@XP_759231[RRM2][put-sr][KOG4212]Cryptococcus neoformans_var._neoformans_JEC21@XP_568231[RRM2][put-sr][KOG0147]

Neurospora crassa_OR74A@XP_959532[RRM2][put-sr][KOG4212]Aspergillus fumigatus_Af293@XP_751108[RRM2][put-sr][KOG4212]

Strongylocentrotus purpuratus@XP_786244[2][RRM3:100%][put-sr:100%][KOG4212:100%]Ciona savignyi@ENSCSAVP00000001354[2][RRM1:50%][.RRM3:50%][KOG4212:100%]

Ciona intestinalis@ENSCINP00000006201[RRM3][KOG4212]Gasterosteus aculeatus@ENSGACP00000022130[2][RRM3:100%][KOG4212:100%]

Tetraodon nigroviridis@GSTENP00018073001[RRM1][KOG4212]Takifugu rubripes@SINFRUP00000133120[RRM3][KOG4212]

Oryzias latipes@ENSORLP00000003410[3][RRM3:100%*][KOG4212:100%*]Danio rerio@ENSDARP00000076939[3][RRM3:67%][.RRM1:33%][KOG4212:100%*]

Rattus norvegicus@ENSRNOP00000007103[2][RRM3:100%][KOG4212:100%]Mus musculus@ENSMUSP00000106126[4][RRM3:100%*][KOG4212:100%*]

Cavia porcellus@ENSCPOP00000009504[RRM2][KOG4212]Amniota@ENSBTAP00000035742[18][RRM3:89%**][.RRM1:6%][.RRM2:6%][KOG4212:100%**]Otolemur garnettii@ENSOGAP00000009767[RRM3][KOG4212]

Xenopus tropicalis@ENSXETP00000039881[RRM3][KOG4212]Danio rerio@ENSDARP00000082808[2][RRM3:50%][.RRM2:50%][KOG4212:100%]

Gasterosteus aculeatus@ENSGACP00000013576[2][RRM3:100%][KOG4212:100%]Tetraodontidae@SINFRUP00000183106[2][RRM3:50%][.RRM2:50%][KOG4212:100%]

Oryzias latipes@ENSORLP00000006803[RRM3][KOG4212]Xenopus tropicalis@ENSXETP00000003694[5][RRM3:100%*][KOG4212:100%*]

Gallus gallus@ENSGALP00000000511[2][RRM3:100%][hnRNP:50%][KOG4212:100%][hnRNP_M]Mammalia@ENSMODP00000004659[5][RRM1:40%][.RRM3:40%][.RRM2:20%][hnRNP:100%*][KOG4212:100%*][hnRNP_M]

Cavia porcellus@ENSCPOP00000013686[RRM2][hnRNP][KOG4212][hnRNP_M]Tupaia belangeri@ENSTBEP00000007557[RRM3][hnRNP][KOG4212][hnRNP_M]

Eutheria@ENSBTAP00000028022[21][RRM3:86%**][.RRM2:14%*][hnRNP:90%**][KOG4212:100%***][HNRP_M]Sorex araneus@ENSSARP00000000242[RRM3][hnRNP][KOG4212][hnRNP_M]

Loxodonta africana@ENSLAFP00000011385[RRM2][hnRNP][KOG4212][hnRNP_M]Felis catus@ENSFCAP00000014117[RRM3][hnRNP][KOG4212][hnRNP_M]

Otolemur garnettii@ENSOGAP00000002890[RRM3][hnRNP][KOG4212][hnRNP_M]Rattus norvegicus@ENSRNOP00000056410[3][RRM3:100%*][hnRNP:100%*][KOG4212:100%*][hnRNP_M]

Bos taurus@ENSBTAP00000047141[2][RRM2:100%][KOG4212:100%]Strongylocentrotus purpuratus@XP_001188339[4][RRM2:100%*][put-sr:100%*][KOG4661:50%][.KOG4212:50%]

Ciona savignyi@ENSCSAVP00000001355[2][RRM2:100%][put-sr:50%][KOG4212:100%]Ciona intestinalis@ENSCINP00000006201[2][RRM1:50%][.RRM2:50%][KOG4212:100%]

Apocrita@XP_395436[2][RRM2:100%][KOG4212:100%]Tribolium castaneum@XP_974319[RRM2][KOG4212]

Caenorhabditis elegans@C25A1_4_2[2][RRM2:100%][put-sr:100%][KOG4212:100%]Drosophila melanogaster@CG9373-PA[RRM2][KOG4212]

Anopheles gambiae@AGAP001460-PA[RRM2][KOG4212]Aedes aegypti@AAEL003670-PA[RRM2][KOG4212]

Gasterosteus aculeatus@ENSGACP00000013576[2][RRM2:100%][KOG4212:100%]

RRM2 and RRM3

hnRNP M

Fig. S18

149

0.14

92

90 91

67 65

94

61

70

85

61 97

100

59

100

97 99

64 63

88

97 58

86 51

62

86

88

71

100 77

71

Cyanidioschyzon merolae@gnl_CMER_CMH135C[RRM1]Cryptosporidium parvum_Iowa_II@XP_628165[RRM2][KOG4212]


Yarrowia lipolytica@XP_505140[RRM1][KOG0533]Ustilago maydis_521@XP_757147[RRM1][KOG0533]Aspergillus fumigatus_Af293@XP_753805[RRM1][KOG0533]

Neurospora crassa_OR74A@XP_958422[RRM1][put-sr][KOG0533]Gibberella zeae_PH-1@XP_387031[RRM1][KOG0533]

Neurospora crassa_OR74A@XP_956471[RRM1][KOG0533]Gibberella zeae_PH-1@XP_391006[RRM1][KOG0533]


Cryptococcus neoformans_var._neoformans_JEC21@XP_572037[RRM1][KOG0533]Pichia stipitis_CBS_6054@XP_001387082[RRM1][KOG0533]

Debaryomyces hansenii_CBS767@XP_462132[RRM1][KOG0533]Saccharomyces cerevisiae@YDR381W[RRM1][KOG0533]

Candida glabrata_CBS138@XP_444903[RRM1][KOG0533]Kluyveromyces lactis@XP_454070[RRM1][KOG0533]

Ashbya gossypii_ATCC_10895@NP_985696[RRM1][KOG0533]Phytophthora sojae@jgi_Physo1_1_157747[RRM1][put-sr][KOG0533]

Phytophthora ramorum@jgi_Phyra1_1_97175[RRM1][KOG0533]Tupaia belangeri@ENSTBEP00000009485[RRM1][PDIP][KOG0533][PDIP3]

Tetraodon nigroviridis@GSTENP00020488001[RRM1]Oryzias latipes@ENSORLP00000018556[RRM1]

Drosophila melanogaster@CG6961-PA[2][RRM1:100%][KOG0533:100%]Tribolium castaneum@XP_969371[RRM1]

Nasonia vitripennis@XP_001600231[RRM1]Anopheles gambiae@AGAP000924-PA[RRM1]

Aedes aegypti@AAEL008938-PB[2][RRM1:100%]Dictyostelium discoideum_AX4@XP_638266[RRM1][KOG0533]

Volvox carteri@jgi_Volca1_90392[RRM1][KOG0533]Chlamydomonas reinhardtii@jgi_Chlre3_168261[RRM1][KOG0533]Ostreococcus tauri@jgi_Ostta4_36431[RRM1][KOG0533]


Ricinus communis@29005_m000257[RRM1][KOG0533]Medicago truncatula@IMGA_CT963094_22_1[RRM1][KOG0533]

Arabidopsis thaliana@NP_001078676[2][RRM1:100%][FCAFPA:100%][KOG0533:100%][AtREF]Arabidopsis thaliana@NP_564871[RRM1][FCAFPA][KOG0533][AtREF]

Arabidopsis thaliana@NP_195873[RRM1][FCAFPA][KOG0533][AtREF]Oryza sativa_japonica_cultivar-group@NP_001049725[RRM1][KOG0533]

Arabidopsis thaliana@NP_200803[3][RRM1:100%*][FCAFPA:100%*][KOG0533:100%*][AtREF]Ricinus communis@29876_m000260[RRM1][KOG0533]





Drosophila melanogaster@CG1101-PA[RRM1][KOG0533]Ciona savignyi@ENSCSAVP00000005567[RRM1][KOG0533]

Ciona intestinalis@ENSCINP00000024858[RRM1][KOG0533]

Fig. S18

150

59

74

80

60

97

70

98 52

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66

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59

75

71

68 92

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71 53

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92

86

76 97

80 57

57

51

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Tribolium castaneum@XP 966697[RRM1][put-sr][KOG0106]Strongylocentrotus purpuratus@XP_001180940[2][RRM1:100%][put-sr:100%][KOG0106:100%]

Oryzias latipes@ENSORLP00000011623[3][RRM1:100%*][put-sr:67%][SR:33%][KOG0106:100%*]Danio rerio@ENSDARP00000043311[RRM1][put-sr][KOG0106]

Gasterosteus aculeatus@ENSGACP00000015556[RRM1][put-sr][KOG0106]Xenopus tropicalis@ENSXETP00000038885[RRM1][put-sr][KOG0106]

Takifugu rubripes@SINFRUP00000169885[RRM1][put-sr][KOG0106]Tetraodon nigroviridis@GSTENP00035800001[RRM1][put-sr][KOG0106]

Sorex araneus@ENSSARP00000000971[RRM1][put-sr][SR][KOG0105][SRp40]Catarrhini@ENSP00000342294[3][RRM1:100%*][put-sr:100%*][SR:100%*][KOG0106:100%*][SRp40]

Xenopus tropicalis@ENSXETP00000057107[2][RRM1:100%][put-sr:100%][SR:100%][KOG0106:100%][SRp40]Amniota@ENSBTAP00000015408[24][RRM1:100%***][put-sr:96%***][SR:100%***][KOG0106:54%**][.KOG0105:46%**][SRp40]Afrotheria@ENSETEP00000016575[2][RRM1:100%][put-sr:100%][SR:100%][KOG0106:100%][SRp40]


Ornithorhynchus anatinus@ENSOANP00000021051[RRM1][put-sr][SR][KOG0105][SRp40]Gasterosteus aculeatus@ENSGACP00000010395[2][RRM1:100%][put-sr:100%][SR:50%][KOG0106:100%][SRp40]

Tetraodontidae@SINFRUP00000132279[2][RRM1:100%][put-sr:50%][SR:50%][KOG0106:100%]Danio rerio@ENSDARP00000069997[3][RRM1:100%*][put-sr:67%][SR:33%][KOG0106:100%*][SRp40]


Tetraodon nigroviridis@GSTENP00010110001[RRM1][put-sr][KOG0598]Smegmamorpha@ENSGACP00000003112[3][RRM1:100%*][put-sr:100%*][KOG0106:100%*]



Danio rerio@ENSDARP00000022089[RRM1][put-sr][KOG0105]Gasterosteus aculeatus@ENSGACP00000008092[3][RRM1:100%*][put-sr:100%*][KOG0105:100%*]

Xenopus tropicalis@ENSXETP00000054329[RRM1][put-sr][KOG0105]Monodelphis domestica@ENSMODP00000030967[2][RRM1:100%][put-sr:100%][SR:100%][KOG0106:50%][.KOG0105:50%][SRp55]Cavia porcellus@ENSCPOP00000010577[RRM1][put-sr][SR][KOG0106][SRp55]Eutheria@ENSDNOP00000006506[3][RRM1:100%*][put-sr:67%][SR:100%*][KOG0105:67%][.KOG0106:33%][SRp55]

Echinops telfairi@ENSETEP00000005046[RRM1][put-sr][SR][KOG0105][SRp55]Murinae@ENSMUSP00000017065[2][RRM1:100%][put-sr:100%][SR:100%][KOG0105:100%][SRp55]



Ricinus communis@29742_m001371[RRM1][KOG0106]Physcomitrella patens@jgi_Phypa1_1_167387[RRM1][put-sr][KOG0106]

Oryza sativa_japonica_cultivar-group@NP_001045729[RRM1][put-sr][SR][KOG0106][RSp33]Zea mays@8514_m000507_c0216K08[RRM1][SR][KOG0106][RSp33]

Zea mays@10633_m000022_AZM5_5503[RRM1][KOG0106]Ricinus communis@30147_m014308[RRM1][put-sr][KOG0106]

Medicago truncatula@IMGA_AC152177_25_1[RRM1][put-sr][KOG0106]Arabidopsis thaliana@NP_851174[2][RRM1:100%][put-sr:100%][SR:100%][KOG0106:100%][RSp41]

Arabidopsis thaliana@NP_194280[RRM1][put-sr][SR][KOG0106][RSp40/SRp35]Oryza sativa_japonica_cultivar-group@NP_001055323[RRM1][put-sr][SR][KOG0105][SRp33b]

Oryza sativa_japonica_cultivar-group@NP_001050082[RRM1][put-sr][SR][KOG0105][SRp32]Oryza sativa_japonica_cultivar-group@NP_001060608[RRM1][put-sr][SR][KOG0105][SRp33a]

Arabidopsis thaliana@NP_190512[2][RRM1:100%][put-sr:100%][SR:100%][KOG0105:100%][SRp34a]Ricinus communis@29827_m002610[RRM1][put-sr][KOG0105]Medicago truncatula@IMGA_CT868739_2_1[RRM1][put-sr][SR][KOG0105][SRp34a]


Physcomitrella patens@jgi_Phypa1_1_113630[RRM1][put-sr][KOG0105]Arabidopsis thaliana@NP_683288[2][RRM1:100%][put-sr:100%][SR:100%][KOG0105:100%][SRp30]

Ricinus communis@29986_m001610[RRM1][put-sr][SR][KOG0105][SRp33a]Ricinus communis@30128_m008840[RRM1][put-sr][KOG0105]

Medicago truncatula@IMGA_AC174141_23_1[RRM1][put-sr][KOG0105]Ricinus communis@30128_m008837[RRM1][put-sr][KOG0105]

Medicago truncatula@IMGA_AC144541_27_2[RRM1][put-sr][KOG0105]Medicago truncatula@IMGA_AC134522_46_2[2][RRM1:100%][put-sr:100%][KOG0105:100%]

Arabidopsis thaliana@NP_567235[2][RRM1:100%][put-sr:50%][SR:100%][KOG0105:100%][SRp34b]Arabidopsis thaliana@NP_850933[3][RRM1:100%*][put-sr:100%*][SR:100%*][KOG0105:100%*][SR1/SRp34]

Xenopus tropicalis@ENSXETP00000026703[RRM1][put-sr][SR][KOG0105][SRp30c]Danio rerio@ENSDARP00000091488[2][RRM1:100%][put-sr:100%][KOG0105:100%]

Takifugu rubripes@SINFRUP00000145791[RRM1][put-sr][SR][KOG0105][SRp30c]Gasterosteus aculeatus@ENSGACP00000022361[2][RRM1:100%][put-sr:100%][KOG0105:100%]

Monodelphis domestica@ENSMODP00000003831[RRM1][put-sr][SR][KOG0105][SRp30c]Mus musculus@ENSMUSP00000031513[RRM1][put-sr][SR][KOG0105][SRp30c]

Bos taurus@ENSBTAP00000016997[RRM1][put-sr][SR][KOG0105][SRp30c]Tupaia belangeri@ENSTBEP00000007356[RRM1][put-sr][SR][KOG0105][SRp30c]Eutheria@ENSCAFP00000015146[7][RRM1:100%*][put-sr:100%*][SR:86%*][KOG0105:100%*][SRp30c]

Myotis lucifugus@ENSMLUP00000009421[RRM1][put-sr][SR][KOG0105][SRp30c]Oryctolagus cuniculus@ENSOCUP00000009368[RRM1][KOG0105]

Tribolium castaneum@XP_967263[RRM1][put-sr][KOG0105]Diptera@AAEL006473-PA[3][RRM1:100%*][put-sr:100%*][KOG0105:100%*]

Apis mellifera@XP_393525[RRM1][put-sr][KOG0105]Nasonia vitripennis@XP_001605411[RRM1][put-sr][KOG0105]

Oryzias latipes@ENSORLP00000006698[RRM1][put-sr][SR][KOG0105][ASF/SF2]Gasterosteus aculeatus@ENSGACP00000027276[RRM1][put-sr][SR][KOG0105][ASF/SF2]

Takifugu rubripes@SINFRUP00000151768[RRM1][put-sr][SR][KOG0105][ASF/SF2]Danio rerio@ENSDARP00000074866[2][RRM1:100%][put-sr:100%][SR:100%][KOG0105:100%][ASF/SF2]

Gasterosteus aculeatus@ENSGACP00000014666[RRM1][SR][KOG0105][ASF/SF2]Oryzias latipes@ENSORLP00000005758[RRM1][put-sr][SR][KOG0105][ASF/SF2]Tetraodontidae@SINFRUP00000136750[2][RRM1:100%][put-sr:100%][SR:100%][KOG0105:100%][ASF/SF2]

Macaca mulatta@ENSMMUP00000004343[RRM1][SR][KOG0105][ASF/SF2]Tetrapoda@ENSBTAP00000019644[17][RRM1:100%**][put-sr:53%**][SR:100%**][KOG0105:100%**][ASF/SF2]

Echinops telfairi@ENSETEP00000004344[RRM1][SR][KOG0105][ASF/SF2]Otolemur garnettii@ENSOGAP00000012982[RRM1][SR][KOG0105][ASF/SF2]

Tupaia belangeri@ENSTBEP00000013333[RRM1][SR][KOG0105][ASF/SF2]

ASF/SF2

SRp30c

ASF-like "plant"

SRp75

SRp40

SRp55

RS

N6

N5

Fig. S19

151

98

100 98

77

59

100 81

80

55

96

92 95

98

93

89

83

57

54 59

95

54 57

82

58

88

65

64

96

68

100 70

66 85

70 50

66

94

68 55

57

91

82 62

63

72

62

95

54

58 77

62

85

64

74

81

98

83

93

81

Oryzias latipes@ENSORLP00000001513[RRM1][put-sr][SR][KOG4207][SC35]Danio rerio@ENSDARP00000015569[RRM1][put-sr][SR][KOG4207][SC35]

Xenopus tropicalis@ENSXETP00000054042[RRM1][put-sr][SR][SC35]Homo sapiens@ENSP00000381889[RRM1][put-sr][KOG4207]

Macaca mulatta@ENSMMUP00000010035[RRM1][put-sr][SR][SRp46]Mammalia@ENSBTAP00000024299[19][RRM1:100%**][put-sr:95%**][SR:100%**][KOG4368:74%**][.KOG4207:26%*][SC35]


Homo sapiens@ENSP00000350877[RRM1][KOG4207]Macaca mulatta@ENSMMUP00000034012[RRM1][SR][KOG4207][SC35]

Pan troglodytes@ENSPTRP00000032751[RRM1][KOG4207]Chlamydomonas reinhardtii@jgi_Chlre3_188086[RRM1][put-sr]

Volvox carteri@jgi_Volca1_120666[RRM1][put-sr]Chlamydomonas reinhardtii@jgi_Chlre3_113900[RRM1][KOG4207]

Volvox carteri@jgi_Volca1_73973[RRM1][put-sr][KOG4207]Oryza sativa_japonica_cultivar-group@NP_001068546[RRM1][put-sr][KOG0127]

Oryza sativa_japonica_cultivar-group@NP_001067091[RRM1][put-sr][SR][SCL30b]Oryza sativa_japonica_cultivar-group@NP_001046448[RRM1][put-sr][SR][SCL30a]


Arabidopsis thaliana@NP_567021[RRM1][put-sr][SR][KOG0122][SCL30]Physcomitrella patens@jgi_Phypa1_1_141868[RRM1]

Physcomitrella patens@jgi_Phypa1_1_108464[RRM1][put-sr]Oryza sativa_japonica_cultivar-group@NP_001050168[RRM1][put-sr]Arabidopsis thaliana@NP_197382[RRM1][put-sr][SR][KOG0127][SCL28]

Ricinus communis@29726_m003960[RRM1][put-sr]Chlamydomonas reinhardtii@jgi_Chlre3_116256[RRM1][put-sr]

Volvox carteri@jgi_Volca1_121229[RRM1][put-sr][KOG0415]Arabidopsis thaliana@NP_187966[RRM1][put-sr][SR][SCL30a]

Arabidopsis thaliana@NP_001031195[2][RRM1:100%][put-sr:100%][SR:100%][KOG0110:100%][SR33/SCL33]Ricinus communis@30084_m000177[RRM1][put-sr]

Ricinus communis@27553_m000316[RRM1][put-sr]Medicago truncatula@IMGA_AC146760_9_2[RRM1][put-sr]

Oryza sativa_japonica_cultivar-group@NP_001050213[RRM1][put-sr][KOG4207]Oryza sativa_japonica_cultivar-group@NP_001060372[RRM1][put-sr][SR][SCL25]

Ciona savignyi@ENSCSAVP00000008618[RRM1][put-sr][KOG0111]Gasterosteus aculeatus@ENSGACP00000018038[RRM1][put-sr]

Danio rerio@ENSDARP00000031512[RRM1][put-sr][KOG0415]Danio rerio@ENSDARP00000091866[RRM1][put-sr]Gasterosteus aculeatus@ENSGACP00000002897[RRM1][put-sr][KOG0415]

Tetraodon nigroviridis@GSTENP00010468001[RRM1][SRrp][KOG4207][SRp38]Oryzias latipes@ENSORLP00000009635[RRM1][SRrp][KOG4207][SRp38]

Takifugu rubripes@SINFRUP00000150947[RRM1][put-sr]Canis familiaris@ENSCAFP00000019234[RRM1][put-sr][SRrp][SRp38]Eutheria@ENSBTAP00000010616[19][RRM1:100%**][put-sr:100%**][SRrp:100%**][KOG0111:58%**][.KOG0415:21%*][SRp38]

Canis familiaris@ENSCAFP00000004604[RRM1][put-sr][SRrp][SRp38]Eutheria@ENSEEUP00000013029[3][RRM1:100%*][put-sr:100%*][SRrp:100%*][SRp38]

Monodelphis domestica@ENSMODP00000016281[RRM1][put-sr][SRrp][SRp38]Rattus norvegicus@ENSRNOP00000011154[2][RRM1:100%][put-sr:100%][SRrp:100%][SRp38]Gallus gallus@ENSGALP00000006566[RRM1][put-sr][SRrp][SRp38]

Xenopus tropicalis@ENSXETP00000011851[RRM1][put-sr]Echinops telfairi@ENSETEP00000001114[RRM1][put-sr]Mus musculus@ENSMUSP00000103794[RRM1][put-sr][SRrp][KOG0111][SRrp35]



Chlamydomonas reinhardtii@jgi_Chlre3_132362[RRM1][KOG0107]Volvox carteri@jgi_Volca1_121301[RRM1][put-sr][KOG0107]

Chlamydomonas reinhardtii@jgi_Chlre3_192053[RRM1][put-sr][KOG0107]Physcomitrella patens@jgi_Phypa1_1_143810[2][RRM1:100%][KOG0107:100%]

Oryza sativa_japonica_cultivar-group@NP_001048352[RRM1][put-sr][SR][RSZp21b]Oryza sativa_japonica_cultivar-group@NP_001057018[RRM1][put-sr][SR][RSZp21a]Oryza sativa_japonica_cultivar-group@NP_001047400[RRM1][put-sr][SR][KOG0107][RSZp23]


Arabidopsis thaliana@NP_180035[RRM1][put-sr][SR][RSZ22a]Ricinus communis@28610_m000073[RRM1][SR][KOG0107][SRZ21/RSZ21]


Apis mellifera@XP_001123058[2][RRM1:100%][put-sr:50%][KOG0107:100%]Endopterygota@XP_001599712[6][RRM1:100%*][put-sr:17%][KOG0107:83%*][.KOG2490:17%]

Culicidae@AAEL001356-PA[3][RRM1:100%*][put-sr:100%*][KOG0108:67%][.KOG0107:33%]Drosophila melanogaster@CG1987-PA[RRM1][put-sr][KOG0107]

Drosophila melanogaster@CG17136-PD[4][RRM1:100%*][put-sr:50%][KOG0107:100%*]Percomorpha@ENSGACP00000016280[4][RRM1:100%*][put-sr:100%*][KOG0107:50%][.KOG4368:25%]


Spermophilus tridecemlineatus@ENSSTOP00000003936[RRM1][put-sr]Danio rerio@ENSDARP00000070952[RRM1][SR][KOG0107][9G8]

Gallus gallus@ENSGALP00000038155[RRM1][put-sr][SR][9G8]Rattus norvegicus@ENSRNOP00000011102[RRM1][put-sr][SR][KOG0107][9G8]

Rattus norvegicus@ENSRNOP00000058047[RRM1][put-sr]Mammalia@ENSBTAP00000033048[27][RRM1:100%***][put-sr:78%***][SR:93%***][KOG0107:81%***][9G8]

Xenopus tropicalis@ENSXETP00000054077[2][RRM1:100%][put-sr:100%][SR:100%][9G8]Gallus gallus@ENSGALP00000022386[RRM1][put-sr][SR][9G8]


Canis familiaris@ENSCAFP00000009434[RRM1][put-sr][KOG0107]Apis mellifera@XP_001122800[RRM1][put-sr][KOG0107]

Tribolium castaneum@XP_968789[RRM1][put-sr][KOG4368]Anopheles gambiae@AGAP008303-PA[RRM1][put-sr]

Drosophila melanogaster@CG10203-PA[RRM1][put-sr][SR][KOG0107][9G8]Ciona savignyi@ENSCSAVP00000004510[RRM1][put-sr]Ciona intestinalis@ENSCINP00000022204[2][RRM1:100%][put-sr:100%][KOG0107:100%]

Eutheria@ENSEEUP00000001001[3][RRM1:100%*][put-sr:100%*]Mus musculus@ENSMUSP00000100538[RRM1][put-sr][SR][KOG0107][SRp20]Tetrapoda@ENSBTAP00000004154[28][RRM1:100%***][put-sr:68%**][SR:100%***][KOG0107:100%***][SRp20]



Oryzias latipes@ENSORLP00000000358[RRM1][put-sr][SR][KOG0107][SRp20]Gasterosteus aculeatus@ENSGACP00000001355[RRM1][put-sr][SR][KOG0107][SRp20]Danio rerio@ENSDARP00000076899[2][RRM1:100%][put-sr:50%][SR:100%][KOG0107:100%][SRp20]Tetraodon nigroviridis@GSTENP00027331001[RRM1][SR][KOG0107][SRp20]

Takifugu rubripes@SINFRUP00000136850[RRM1][SR][KOG0107][SRp20]Arabidopsis thaliana@NP_850280[RRM1][put-sr][SR][KOG0107][RSZ33]

Arabidopsis thaliana@NP_190918[RRM1][put-sr][SR][KOG0107][RSZ32]Oryza sativa_japonica_cultivar-group@NP_001042066[RRM1][put-sr][SR][KOG0109][RSZ37a]

Oryza sativa_japonica_cultivar-group@NP_001054731[RRM1][put-sr][SR][RSZ39]Ricinus communis@29805_m001527[RRM1][put-sr][KOG0109]

Oryza sativa_japonica_cultivar-group@NP_001049771[RRM1][put-sr][SR][KOG0109][RSZ37b]Oryza sativa_japonica_cultivar-group@NP_001054489[RRM1][put-sr][SR][KOG0109][RSZ36]

Nasonia vitripennis@XP_001603815[2][RRM1:100%][put-sr:100%][KOG0105:100%]Tribolium castaneum@XP_969451[RRM1][put-sr][KOG0105]

Aedes aegypti@AAEL000769-PA[RRM1][put-sr][KOG0106]Apis mellifera@XP_391860[RRM1][put-sr][KOG0105]

Diptera@AGAP004592-PA[7][RRM1:100%*][put-sr:71%*][SR:86%*][KOG0105:57%*][.KOG0106:43%*]Tribolium castaneum@XP_966697[RRM1][put sr][KOG0106]

RS2Z "plant"

SRp20

RSZ "plant"

9G8

SRrp

SCL

SC35

N2

N4

N3

Fig. S19

152

0.12 70

96

94 99

67 67

97

64 50 53

91

66 78

67

74

83

99

100

89 99

59

96

99

72 73

60 76

100

66 61

57

57

56 73 87

54

96

56

54

95

70

55

63

77

67

99

98

56 64

66

65



Cyanidioschyzon merolae@gnl_CMER_CMQ282C[RRM1][KOG0121]Oryza sativa_japonica_cultivar-group@NP_001047412[RRM1][KOG0121]

Arabidopsis thaliana@NP_199233[2][RRM1:100%][KOG0121:100%]Ricinus communis@29983_m003140[RRM1][KOG0121]


Aspergillus fumigatus_Af293@XP_755191[RRM1][KOG0121]Gibberella zeae_PH-1@XP_385664[RRM1][KOG0121]

Strongylocentrotus purpuratus@XP_001187788[2][RRM1:100%][KOG0121:100%]Apis mellifera@XP_397316[RRM1][KOG0121]

Tribolium castaneum@XP_975066[RRM1][KOG0121]Ciona intestinalis@ENSCINP00000006257[2][RRM1:100%][KOG0121:100%]

Ciona savignyi@ENSCSAVP00000009906[RRM1][KOG0121]Anopheles gambiae@AGAP002547-PA[RRM1][KOG0121]

Aedes aegypti@AAEL006135-PA[RRM1][KOG0121]Drosophila melanogaster@CG12357-PA[RRM1][KOG0121]



Cavia porcellus@ENSCPOP00000002703[RRM1][KOG0121]Loxodonta africana@ENSLAFP00000005354[RRM1][KOG0121]Spermophilus tridecemlineatus@ENSSTOP00000001416[RRM1][KOG0121]

Oryctolagus cuniculus@ENSOCUP00000012352[RRM1][KOG0121]Monodelphis domestica@ENSMODP00000029243[RRM1][KOG0121]

Monodelphis domestica@ENSMODP00000034858[2][RRM1:100%][KOG0121:100%]Monodelphis domestica@ENSMODP00000019849[RRM1][KOG0121]

Gallus gallus@ENSGALP00000011061[RRM1][KOG0121]Xenopus tropicalis@ENSXETP00000041997[RRM1][KOG0121]

Oryzias latipes@ENSORLP00000014087[RRM1][KOG0121]Danio rerio@ENSDARP00000020688[RRM1][KOG0121]

Takifugu rubripes@SINFRUP00000128783[RRM1][KOG0121]Gasterosteus aculeatus@ENSGACP00000008263[RRM1][KOG0121]

Tetraodon nigroviridis@GSTENP00011485001[RRM1][KOG0121]Volvox carteri@jgi_Volca1_103546[RRM1][KOG0116]

Chlamydomonas reinhardtii@jgi_Chlre3_184151[RRM1][KOG0921]Ustilago maydis_521@XP_760099[RRM1][KOG0122]





Oryza sativa_japonica_cultivar-group@NP_001048346[RRM1][KOG0122]Oryza sativa_japonica_cultivar-group@NP_001048347[RRM1][KOG0122]Medicago truncatula@IMGA_AC174277_12_1[2][RRM1:100%][KOG0122:100%]

Arabidopsis thaliana@NP_196219[RRM1][TIF3][KOG0122][TIF3]Arabidopsis thaliana@NP_187747[RRM1][TIF3][KOG0122][TIF3]

Chlamydomonas reinhardtii@jgi_Chlre3_112621[RRM1][KOG0122]Phytophthora ramorum@jgi_Phyra1_1_79758[RRM1][KOG0122]


Thalassiosira pseudonana@jgi_Thaps3_32790[RRM1][KOG0122]Aureococcus anophagefferens@jgi_Auran1_9314[2][RRM1:100%][KOG0585:50%][.KOG0122:50%]

Strongylocentrotus purpuratus@XP_791582[2][RRM1:100%][KOG0122:100%]Ciona intestinalis@ENSCINP00000000359[RRM1][KOG0122]

Gasterosteus aculeatus@ENSGACP00000018150[RRM1][KOG0122]Clupeocephala@ENSDARP00000027672[2][RRM1:100%][KOG0122:100%]Tetrapoda@ENSBTAP00000003545[10][RRM1:100%**][KOG0122:100%**]

Takifugu rubripes@SINFRUP00000147763[RRM1][KOG0122]Tetraodon nigroviridis@GSTENP00034383001[RRM1][KOG0122]

Cyanidioschyzon merolae@gnl_CMER_CML202C[RRM1][put-sr]Oryza sativa_japonica_cultivar-group@NP_001060322[RRM1][put-sr][SR][KOG4207][SC35b]


Arabidopsis thaliana@NP_201225[2][RRM1:100%][put-sr:100%][SR:100%][KOG4207:100%][SC35]Physcomitrella patens@jgi_Phypa1_1_172957[RRM1][put-sr][KOG0415]

Physcomitrella patens@jgi_Phypa1_1_122960[RRM1][put-sr][KOG4207]Zea mays@8925_m000027_AZM5_1178[RRM1][KOG4207]

Oryza sativa_japonica_cultivar-group@NP_001062094[RRM1][put-sr][SR][KOG0415][SC35a]Oryza sativa_japonica_cultivar-group@NP_001050263[RRM1][put-sr][SR][KOG4207][SC35c]

Zea mays@20810_m000015_AZM5_89637[2][RRM1:100%][put-sr:50%][SR:50%][KOG4207:100%][SC35a]Drosophila melanogaster@CG5442-PB[RRM1][put-sr][SR][KOG4207][SC35]


Aedes aegypti@AAEL010340-PB[2][RRM1:100%][put-sr:100%][KOG4207:100%]Strongylocentrotus purpuratus@XP_001180179[4][RRM1:100%*][KOG4207:100%*]

Strongylocentrotus purpuratus@XP_785989[2][RRM1:100%][put-sr:100%][KOG4207:100%]Ciona savignyi@ENSCSAVP00000015651[RRM1][put-sr][KOG4207]

Ciona intestinalis@ENSCINP00000008678[RRM1][put-sr][KOG4207]Oryzias latipes@ENSORLP00000023350[RRM1][put-sr][SR][KOG4368][SC35]

Takifugu rubripes@SINFRUP00000176738[RRM1][put-sr][SR][KOG4207][SC35]Percomorpha@ENSGACP00000004058[2][RRM1:100%][put-sr:100%][SR:100%][SC35]Clupeocephala@ENSDARP00000074623[3][RRM1:100%*][put-sr:100%*][SR:67%][KOG4207:100%*][SC35]

Oryzias latipes@ENSORLP00000001513[RRM1][put sr][SR][KOG4207][SC35] SC35

SC35

"plant"

N1

Fig. S19

153

61

50 51

58

84

70

96

76

97 74

57

66

91

79

58

98 69

100 50

72

52

78

60100

83 92

73

61

64

65

90

67 93

66

62

87

91

75 94

61

55

81 77

60

89

84

87

57

55

Apis mellifera@XP 391860[RRM1][put-sr][KOG0105]Strongylocentrotus purpuratus@XP_001180940[2][RRM1:100%][put-sr:100%][KOG0106:100%]

Danio rerio@ENSDARP00000043311[RRM1][put-sr][KOG0106]Xenopus tropicalis@ENSXETP00000038885[RRM1][put-sr][KOG0106]


Gasterosteus aculeatus@ENSGACP00000015556[RRM1][put-sr][KOG0106]Oryzias latipes@ENSORLP00000011623[3][RRM1:100%*][put-sr:67%][SR:33%][KOG0106:100%*]

Gasterosteus aculeatus@ENSGACP00000010395[2][RRM1:100%][put-sr:100%][SR:50%][KOG0106:100%][SRp40]Tetraodontidae@SINFRUP00000132279[2][RRM1:100%][put-sr:50%][SR:50%][KOG0106:100%]

Danio rerio@ENSDARP00000069997[3][RRM1:100%*][put-sr:67%][SR:33%][KOG0106:100%*][SRp40]Ornithorhynchus anatinus@ENSOANP00000021051[RRM1][put-sr][SR][KOG0105][SRp40]


Sorex araneus@ENSSARP00000000971[RRM1][put-sr][SR][KOG0105][SRp40]Amniota@ENSBTAP00000015408[24][RRM1:100%***][put-sr:96%***][SR:100%***][KOG0106:54%**][.KOG0105:46%**][SRp40]Afrotheria@ENSETEP00000016575[2][RRM1:100%][put-sr:100%][SR:100%][KOG0106:100%][SRp40]

Catarrhini@ENSP00000342294[3][RRM1:100%*][put-sr:100%*][SR:100%*][KOG0106:100%*][SRp40]Xenopus tropicalis@ENSXETP00000057107[2][RRM1:100%][put-sr:100%][SR:100%][KOG0106:100%][SRp40]


Smegmamorpha@ENSGACP00000003112[3][RRM1:100%*][put-sr:100%*][KOG0106:100%*]Tetraodon nigroviridis@GSTENP00010110001[RRM1][put-sr][KOG0598]

Danio rerio@ENSDARP00000094522[RRM1][put-sr]Danio rerio@ENSDARP00000025299[RRM1][put-sr][KOG0105]



Xenopus tropicalis@ENSXETP00000054329[RRM1][put-sr][KOG0105]Monodelphis domestica@ENSMODP00000030967[2][RRM1:100%][put-sr:100%][SR:100%][KOG0106:50%][.KOG0105:50%][SRp55]Cavia porcellus@ENSCPOP00000010577[RRM1][put-sr][SR][KOG0106][SRp55]Eutheria@ENSDNOP00000006506[3][RRM1:100%*][put-sr:67%][SR:100%*][KOG0105:67%][.KOG0106:33%][SRp55]

Echinops telfairi@ENSETEP00000005046[RRM1][put-sr][SR][KOG0105][SRp55]Murinae@ENSMUSP00000017065[2][RRM1:100%][put-sr:100%][SR:100%][KOG0105:100%][SRp55]



Ricinus communis@29742_m001371[RRM1][KOG0106]Physcomitrella patens@jgi_Phypa1_1_167387[RRM1][put-sr][KOG0106]

Oryza sativa_japonica_cultivar-group@NP_001045729[RRM1][put-sr][SR][KOG0106][RSp33]Zea mays@10633_m000022_AZM5_5503[RRM1][KOG0106]

Zea mays@8514_m000507_c0216K08[RRM1][SR][KOG0106][RSp33]Ricinus communis@30147_m014308[RRM1][put-sr][KOG0106]

Medicago truncatula@IMGA_AC152177_25_1[RRM1][put-sr][KOG0106]Arabidopsis thaliana@NP_851174[2][RRM1:100%][put-sr:100%][SR:100%][KOG0106:100%][RSp41]

Arabidopsis thaliana@NP_194280[RRM1][put-sr][SR][KOG0106][RSp40/SRp35]Oryza sativa_japonica_cultivar-group@NP_001055323[RRM1][put-sr][SR][KOG0105][SRp33b]

Oryza sativa_japonica_cultivar-group@NP_001050082[RRM1][put-sr][SR][KOG0105][SRp32]Oryza sativa_japonica_cultivar-group@NP_001060608[RRM1][put-sr][SR][KOG0105][SRp33a]


Physcomitrella patens@jgi_Phypa1_1_205547[RRM1][put-sr][KOG0105]Arabidopsis thaliana@NP_190512[2][RRM1:100%][put-sr:100%][SR:100%][KOG0105:100%][SRp34a]Ricinus communis@29827_m002610[RRM1][put-sr][KOG0105]Medicago truncatula@IMGA_CT868739_2_1[RRM1][put-sr][SR][KOG0105][SRp34a]

Arabidopsis thaliana@NP_683288[2][RRM1:100%][put-sr:100%][SR:100%][KOG0105:100%][SRp30]Medicago truncatula@IMGA_AC144541_27_2[RRM1][put-sr][KOG0105]

Medicago truncatula@IMGA_AC134522_46_2[2][RRM1:100%][put-sr:100%][KOG0105:100%]Ricinus communis@29986_m001610[RRM1][put-sr][SR][KOG0105][SRp33a]

Ricinus communis@30128_m008837[RRM1][put-sr][KOG0105]Ricinus communis@30128_m008840[RRM1][put-sr][KOG0105]

Arabidopsis thaliana@NP_567235[2][RRM1:100%][put-sr:50%][SR:100%][KOG0105:100%][SRp34b]Medicago truncatula@IMGA_AC174141_23_1[RRM1][put-sr][KOG0105]

Arabidopsis thaliana@NP_850933[3][RRM1:100%*][put-sr:100%*][SR:100%*][KOG0105:100%*][SR1/SRp34]Xenopus tropicalis@ENSXETP00000026703[RRM1][put-sr][SR][KOG0105][SRp30c]

Danio rerio@ENSDARP00000091488[2][RRM1:100%][put-sr:100%][KOG0105:100%]Takifugu rubripes@SINFRUP00000145791[RRM1][put-sr][SR][KOG0105][SRp30c]

Gasterosteus aculeatus@ENSGACP00000022361[2][RRM1:100%][put-sr:100%][KOG0105:100%]Myotis lucifugus@ENSMLUP00000009421[RRM1][put-sr][SR][KOG0105][SRp30c]

Eutheria@ENSCAFP00000015146[7][RRM1:100%*][put-sr:100%*][SR:86%*][KOG0105:100%*][SRp30c]Tupaia belangeri@ENSTBEP00000007356[RRM1][put-sr][SR][KOG0105][SRp30c]

Monodelphis domestica@ENSMODP00000003831[RRM1][put-sr][SR][KOG0105][SRp30c]Mus musculus@ENSMUSP00000031513[RRM1][put-sr][SR][KOG0105][SRp30c]

Bos taurus@ENSBTAP00000016997[RRM1][put-sr][SR][KOG0105][SRp30c]Oryctolagus cuniculus@ENSOCUP00000009368[RRM1][KOG0105]

Diptera@AAEL006473-PA[3][RRM1:100%*][put-sr:100%*][KOG0105:100%*]Tribolium castaneum@XP_967263[RRM1][put-sr][KOG0105]


Oryzias latipes@ENSORLP00000006698[RRM1][put-sr][SR][KOG0105][ASF/SF2]Takifugu rubripes@SINFRUP00000151768[RRM1][put-sr][SR][KOG0105][ASF/SF2]

Gasterosteus aculeatus@ENSGACP00000027276[RRM1][put-sr][SR][KOG0105][ASF/SF2]Danio rerio@ENSDARP00000074866[2][RRM1:100%][put-sr:100%][SR:100%][KOG0105:100%][ASF/SF2]

Gasterosteus aculeatus@ENSGACP00000014666[RRM1][SR][KOG0105][ASF/SF2]Tetraodontidae@SINFRUP00000136750[2][RRM1:100%][put-sr:100%][SR:100%][KOG0105:100%][ASF/SF2]Oryzias latipes@ENSORLP00000005758[RRM1][put-sr][SR][KOG0105][ASF/SF2]

Macaca mulatta@ENSMMUP00000004343[RRM1][SR][KOG0105][ASF/SF2]Tetrapoda@ENSBTAP00000019644[17][RRM1:100%**][put-sr:53%**][SR:100%**][KOG0105:100%**][ASF/SF2]

Echinops telfairi@ENSETEP00000004344[RRM1][SR][KOG0105][ASF/SF2]Tupaia belangeri@ENSTBEP00000013333[RRM1][SR][KOG0105][ASF/SF2]

Otolemur garnettii@ENSOGAP00000012982[RRM1][SR][KOG0105][ASF/SF2]

ASF-like

"plant"

SRp30c

ASF/SF2

RS

SRp55

SRp75

SRp40

N5

N6

Fig. S20

154

58 56

100 98

69

69

61 73

58

83

88

73

100

100

63 84

100

96

87

93

98

87 94

82

73

51

58

62

100 72

82 87

53

80

99

70 81

86

94

84 58

64

75

84

97

54

72 86

63 56

91

84

85

99

85

96

95

60 50 88

Clupeocephala@ENSDARP00000074623[3][RRM1:100%*][put-sr:100%*][SR:67%][KOG4207:100%*][SC35]Oryzias latipes@ENSORLP00000001513[RRM1][put-sr][SR][KOG4207][SC35]Percomorpha@ENSGACP00000004058[2][RRM1:100%][put-sr:100%][SR:100%][SC35]Takifugu rubripes@SINFRUP00000176738[RRM1][put-sr][SR][KOG4207][SC35]Oryzias latipes@ENSORLP00000023350[RRM1][put-sr][SR][KOG4368][SC35]Mammalia@ENSBTAP00000024299[19][RRM1:100%**][put-sr:95%**][SR:100%**][KOG4368:74%**][.KOG4207:26%*][SC35]


Homo sapiens@ENSP00000350877[RRM1][KOG4207]Pan troglodytes@ENSPTRP00000032751[RRM1][KOG4207]

Macaca mulatta@ENSMMUP00000034012[RRM1][SR][KOG4207][SC35]Ciona savignyi@ENSCSAVP00000008618[RRM1][put-sr][KOG0111]

Gasterosteus aculeatus@ENSGACP00000018038[RRM1][put-sr]Danio rerio@ENSDARP00000091866[RRM1][put-sr]

Danio rerio@ENSDARP00000031512[RRM1][put-sr][KOG0415]Gasterosteus aculeatus@ENSGACP00000002897[RRM1][put-sr][KOG0415]

Tetraodon nigroviridis@GSTENP00010468001[RRM1][SRrp][KOG4207][SRp38]Takifugu rubripes@SINFRUP00000150947[RRM1][put-sr]Oryzias latipes@ENSORLP00000009635[RRM1][SRrp][KOG4207][SRp38]

Echinops telfairi@ENSETEP00000001114[RRM1][put-sr]Mus musculus@ENSMUSP00000103794[RRM1][put-sr][SRrp][KOG0111][SRrp35]



Canis familiaris@ENSCAFP00000004604[RRM1][put-sr][SRrp][SRp38]Eutheria@ENSBTAP00000010616[19][RRM1:100%**][put-sr:100%**][SRrp:100%**][KOG0111:58%**][.KOG0415:21%*][SRp38]Canis familiaris@ENSCAFP00000019234[RRM1][put-sr][SRrp][SRp38]

Eutheria@ENSEEUP00000013029[3][RRM1:100%*][put-sr:100%*][SRrp:100%*][SRp38]Monodelphis domestica@ENSMODP00000016281[RRM1][put-sr][SRrp][SRp38]Rattus norvegicus@ENSRNOP00000011154[2][RRM1:100%][put-sr:100%][SRrp:100%][SRp38]

Xenopus tropicalis@ENSXETP00000011851[RRM1][put-sr]Gallus gallus@ENSGALP00000006566[RRM1][put-sr][SRrp][SRp38]


Volvox carteri@jgi_Volca1_120666[RRM1][put-sr]Chlamydomonas reinhardtii@jgi_Chlre3_188086[RRM1][put-sr]

Volvox carteri@jgi_Volca1_121229[RRM1][put-sr][KOG0415]Chlamydomonas reinhardtii@jgi_Chlre3_116256[RRM1][put-sr]

Arabidopsis thaliana@NP_187966[RRM1][put-sr][SR][SCL30a]Arabidopsis thaliana@NP_001031195[2][RRM1:100%][put-sr:100%][SR:100%][KOG0110:100%][SR33/SCL33]

Ricinus communis@30084_m000177[RRM1][put-sr]Ricinus communis@27553_m000316[RRM1][put-sr]

Medicago truncatula@IMGA_AC146760_9_2[RRM1][put-sr]Oryza sativa_japonica_cultivar-group@NP_001060372[RRM1][put-sr][SR][SCL25]

Oryza sativa_japonica_cultivar-group@NP_001050213[RRM1][put-sr][KOG4207]Physcomitrella patens@jgi_Phypa1_1_108464[RRM1][put-sr]

Physcomitrella patens@jgi_Phypa1_1_141868[RRM1]Oryza sativa_japonica_cultivar-group@NP_001050168[RRM1][put-sr]

Ricinus communis@29726_m003960[RRM1][put-sr]Arabidopsis thaliana@NP_197382[RRM1][put-sr][SR][KOG0127][SCL28]

Oryza sativa_japonica_cultivar-group@NP_001068546[RRM1][put-sr][KOG0127]Oryza sativa_japonica_cultivar-group@NP_001046448[RRM1][put-sr][SR][SCL30a]

Oryza sativa_japonica_cultivar-group@NP_001067091[RRM1][put-sr][SR][SCL30b]Ricinus communis@27383_m000159[RRM1][put-sr][KOG0127]

Medicago truncatula@IMGA_CR962128_15_2[RRM1][put-sr]Arabidopsis thaliana@NP_567021[RRM1][put-sr][SR][KOG0122][SCL30]

Chlamydomonas reinhardtii@jgi_Chlre3_132362[RRM1][KOG0107]Volvox carteri@jgi_Volca1_121301[RRM1][put-sr][KOG0107]

Chlamydomonas reinhardtii@jgi_Chlre3_192053[RRM1][put-sr][KOG0107]Ricinus communis@28610_m000073[RRM1][SR][KOG0107][SRZ21/RSZ21]


Oryza sativa_japonica_cultivar-group@NP_001057018[RRM1][put-sr][SR][RSZp21a]Oryza sativa_japonica_cultivar-group@NP_001047400[RRM1][put-sr][SR][KOG0107][RSZp23]


Arabidopsis thaliana@NP_180035[RRM1][put-sr][SR][RSZ22a]Arabidopsis thaliana@NP_973901[2][RRM1:100%][SR:100%][SRZ21/RSZ21]

Arabidopsis thaliana@NP_194886[2][RRM1:100%][put-sr:100%][SR:100%][KOG0107:100%][SRZ22/RSZ22]Apis mellifera@XP_001123058[2][RRM1:100%][put-sr:50%][KOG0107:100%]Endopterygota@XP_001599712[6][RRM1:100%*][put-sr:17%][KOG0107:83%*][.KOG2490:17%]

Culicidae@AAEL001356-PA[3][RRM1:100%*][put-sr:100%*][KOG0108:67%][.KOG0107:33%]Drosophila melanogaster@CG17136-PD[4][RRM1:100%*][put-sr:50%][KOG0107:100%*]

Drosophila melanogaster@CG1987-PA[RRM1][put-sr][KOG0107]Percomorpha@ENSGACP00000016280[4][RRM1:100%*][put-sr:100%*][KOG0107:50%][.KOG4368:25%]


Gallus gallus@ENSGALP00000022386[RRM1][put-sr][SR][9G8]Spermophilus tridecemlineatus@ENSSTOP00000003936[RRM1][put-sr]

Xenopus tropicalis@ENSXETP00000054077[2][RRM1:100%][put-sr:100%][SR:100%][9G8]Mammalia@ENSBTAP00000033048[27][RRM1:100%***][put-sr:78%***][SR:93%***][KOG0107:81%***][9G8]


Canis familiaris@ENSCAFP00000009434[RRM1][put-sr][KOG0107]Danio rerio@ENSDARP00000070952[RRM1][SR][KOG0107][9G8]

Gallus gallus@ENSGALP00000038155[RRM1][put-sr][SR][9G8]Rattus norvegicus@ENSRNOP00000011102[RRM1][put-sr][SR][KOG0107][9G8]

Rattus norvegicus@ENSRNOP00000058047[RRM1][put-sr]Tribolium castaneum@XP_968789[RRM1][put-sr][KOG4368]

Apis mellifera@XP_001122800[RRM1][put-sr][KOG0107]Drosophila melanogaster@CG10203-PA[RRM1][put-sr][SR][KOG0107][9G8]

Anopheles gambiae@AGAP008303-PA[RRM1][put-sr]Ciona savignyi@ENSCSAVP00000004510[RRM1][put-sr]Ciona intestinalis@ENSCINP00000022204[2][RRM1:100%][put-sr:100%][KOG0107:100%]

Mus musculus@ENSMUSP00000100538[RRM1][put-sr][SR][KOG0107][SRp20]Tetrapoda@ENSBTAP00000004154[28][RRM1:100%***][put-sr:68%**][SR:100%***][KOG0107:100%***][SRp20]Eutheria@ENSEEUP00000001001[3][RRM1:100%*][put-sr:100%*]



Oryzias latipes@ENSORLP00000000358[RRM1][put-sr][SR][KOG0107][SRp20]Tetraodon nigroviridis@GSTENP00027331001[RRM1][SR][KOG0107][SRp20]

Takifugu rubripes@SINFRUP00000136850[RRM1][SR][KOG0107][SRp20]Gasterosteus aculeatus@ENSGACP00000001355[RRM1][put-sr][SR][KOG0107][SRp20]Danio rerio@ENSDARP00000076899[2][RRM1:100%][put-sr:50%][SR:100%][KOG0107:100%][SRp20]

Ricinus communis@29805_m001527[RRM1][put-sr][KOG0109]Oryza sativa_japonica_cultivar-group@NP_001054731[RRM1][put-sr][SR][RSZ39]

Oryza sativa_japonica_cultivar-group@NP_001054489[RRM1][put-sr][SR][KOG0109][RSZ36]Oryza sativa_japonica_cultivar-group@NP_001049771[RRM1][put-sr][SR][KOG0109][RSZ37b]

Oryza sativa_japonica_cultivar-group@NP_001042066[RRM1][put-sr][SR][KOG0109][RSZ37a]Arabidopsis thaliana@NP_190918[RRM1][put-sr][SR][KOG0107][RSZ32]

Arabidopsis thaliana@NP_850280[RRM1][put-sr][SR][KOG0107][RSZ33]Tribolium castaneum@XP_969451[RRM1][put-sr][KOG0105]

Nasonia vitripennis@XP_001603815[2][RRM1:100%][put-sr:100%][KOG0105:100%]Aedes aegypti@AAEL000769-PA[RRM1][put-sr][KOG0106]

Diptera@AGAP004592-PA[7][RRM1:100%*][put-sr:71%*][SR:86%*][KOG0105:57%*][.KOG0106:43%*]Tribolium castaneum@XP_966697[RRM1][put-sr][KOG0106]

Apis mellifera@XP_391860[RRM1][put sr][KOG0105]

RS2Z "plant"

SRp20

9G8

RSZ

"plant"

SRrp

SCL

SC35

N1

N2

N3

N4

Fig. S20

155

0.11 69

98

91 99

56

70 70

99

65

54

55

85

63 71

50

58

56

68

93

99

100

83 99

99

99

78 79

60 72

100

70

65

52

82

77

99

56

73

96

53 52

90 52

86

77

100

97

98

69

55

96

83



Cyanidioschyzon merolae@gnl_CMER_CMQ282C[RRM1][KOG0121]Oryza sativa_japonica_cultivar-group@NP_001047412[RRM1][KOG0121]


Anopheles gambiae@AGAP002547-PA[RRM1][KOG0121]Drosophila melanogaster@CG12357-PA[RRM1][KOG0121]

Aedes aegypti@AAEL006135-PA[RRM1][KOG0121]Dictyostelium discoideum_AX4@XP_637361[RRM1][KOG0121]

Schizosaccharomyces pombe_972h-@NP_596414[RRM1][KOG0121]Gibberella zeae_PH-1@XP_385664[RRM1][KOG0121]

Aspergillus fumigatus_Af293@XP_755191[RRM1][KOG0121]Strongylocentrotus purpuratus@XP_001187788[2][RRM1:100%][KOG0121:100%]



Ciona savignyi@ENSCSAVP00000009906[RRM1][KOG0121]Ciona intestinalis@ENSCINP00000006257[2][RRM1:100%][KOG0121:100%]


Loxodonta africana@ENSLAFP00000005354[RRM1][KOG0121]Cavia porcellus@ENSCPOP00000002703[RRM1][KOG0121]

Spermophilus tridecemlineatus@ENSSTOP00000001416[RRM1][KOG0121]Oryctolagus cuniculus@ENSOCUP00000012352[RRM1][KOG0121]

Monodelphis domestica@ENSMODP00000019849[RRM1][KOG0121]Monodelphis domestica@ENSMODP00000034858[2][RRM1:100%][KOG0121:100%]

Monodelphis domestica@ENSMODP00000029243[RRM1][KOG0121]Gallus gallus@ENSGALP00000011061[RRM1][KOG0121]

Xenopus tropicalis@ENSXETP00000041997[RRM1][KOG0121]Oryzias latipes@ENSORLP00000014087[RRM1][KOG0121]Danio rerio@ENSDARP00000020688[RRM1][KOG0121]

Takifugu rubripes@SINFRUP00000128783[RRM1][KOG0121]Tetraodon nigroviridis@GSTENP00011485001[RRM1][KOG0121]

Gasterosteus aculeatus@ENSGACP00000008263[RRM1][KOG0121]Volvox carteri@jgi_Volca1_103546[RRM1][KOG0116]

Chlamydomonas reinhardtii@jgi_Chlre3_184151[RRM1][KOG0921]Schizosaccharomyces pombe_972h-@NP_595727[RRM1][KOG0122]

Ustilago maydis_521@XP_760099[RRM1][KOG0122]Aspergillus fumigatus_Af293@XP_755320[RRM1][KOG0122]




Chlamydomonas reinhardtii@jgi_Chlre3_112621[RRM1][KOG0122]Oryza sativa_japonica_cultivar-group@NP_001048346[RRM1][KOG0122]

Oryza sativa_japonica_cultivar-group@NP_001048347[RRM1][KOG0122]Medicago truncatula@IMGA_AC174277_12_1[2][RRM1:100%][KOG0122:100%]

Arabidopsis thaliana@NP_187747[RRM1][TIF3][KOG0122][TIF3]Arabidopsis thaliana@NP_196219[RRM1][TIF3][KOG0122][TIF3]


Phaeodactylum tricornutum@jgi_Phatr2_16281[RRM1][KOG0122]Thalassiosira pseudonana@jgi_Thaps3_32790[RRM1][KOG0122]

Aureococcus anophagefferens@jgi_Auran1_9314[2][RRM1:100%][KOG0585:50%][.KOG0122:50%]Strongylocentrotus purpuratus@XP_791582[2][RRM1:100%][KOG0122:100%]

Ciona intestinalis@ENSCINP00000000359[RRM1][KOG0122]Tetraodon nigroviridis@GSTENP00034383001[RRM1][KOG0122]Takifugu rubripes@SINFRUP00000147763[RRM1][KOG0122]

Gasterosteus aculeatus@ENSGACP00000018150[RRM1][KOG0122]Tetrapoda@ENSBTAP00000003545[10][RRM1:100%**][KOG0122:100%**]Clupeocephala@ENSDARP00000027672[2][RRM1:100%][KOG0122:100%]

Cyanidioschyzon merolae@gnl_CMER_CML202C[RRM1][put-sr]Oryza sativa_japonica_cultivar-group@NP_001050263[RRM1][put-sr][SR][KOG4207][SC35c]

Zea mays@20810_m000015_AZM5_89637[2][RRM1:100%][put-sr:50%][SR:50%][KOG4207:100%][SC35a]Zea mays@8925_m000027_AZM5_1178[RRM1][KOG4207]

Oryza sativa_japonica_cultivar-group@NP_001062094[RRM1][put-sr][SR][KOG0415][SC35a]Physcomitrella patens@jgi_Phypa1_1_172957[RRM1][put-sr][KOG0415]

Physcomitrella patens@jgi_Phypa1_1_122960[RRM1][put-sr][KOG4207]Oryza sativa_japonica_cultivar-group@NP_001060322[RRM1][put-sr][SR][KOG4207][SC35b]


Arabidopsis thaliana@NP_201225[2][RRM1:100%][put-sr:100%][SR:100%][KOG4207:100%][SC35]Drosophila melanogaster@CG5442-PB[RRM1][put-sr][SR][KOG4207][SC35]


Aedes aegypti@AAEL010340-PB[2][RRM1:100%][put-sr:100%][KOG4207:100%]Strongylocentrotus purpuratus@XP_001180179[4][RRM1:100%*][KOG4207:100%*]

Strongylocentrotus purpuratus@XP_785989[2][RRM1:100%][put-sr:100%][KOG4207:100%]Ciona savignyi@ENSCSAVP00000015651[RRM1][put-sr][KOG4207]

Ciona intestinalis@ENSCINP00000008678[RRM1][put-sr][KOG4207]Danio rerio@ENSDARP00000015569[RRM1][put-sr][SR][KOG4207][SC35]

Xenopus tropicalis@ENSXETP00000054042[RRM1][put-sr][SR][SC35]Macaca mulatta@ENSMMUP00000010035[RRM1][put-sr][SR][SRp46]

Homo sapiens@ENSP00000381889[RRM1][put-sr][KOG4207]Clupeocephala@ENSDARP00000074623[3][RRM1:100% ][put sr:100% ][SR:67%][KOG4207:100% ][SC35]

SC35

SC35

"plant"

Fig. S20

156

0

1

2

3

4

bit

s

1

L2

LK

3

V4

LD

5

N6

VIL

7

ST

8

T

FY

9

G

SR

10

T11

A

TS

12AP

13

ED

14

S

C

DT

15

L16

S

L

KYFR

17

Y

A

PR

18

S

A

CLV

19

F20

ADE

21

RK

22

CY

23

G

24

DKER

25

V

26

LVG

27

D

28

IV

29

R

FY

30

I

31

P

32

R

33

ED

34

PHKR

35

HFRY

36

ST

37

GRK

38

ADE

39

PS

40

R

41

G

42

S

F

43

A

44

F

45 46

V

47

R

48

YF

49

N

L

F

PYKH

50

YD

51

REAK

52

S

E

DR

53

ED

54

A

55

SH

QE

56

KD

57

A

58

EL

IVM

59

N

AED

60

G

SRA

61

LM

62

D

63

W

A

G

64

M

KNRA

65

W

R

D

T

E

MLV

66

M

FPYVL

67

GD

68

V

A

C

G

69

P

L

G

R

70

V

NAKE

71

V

AI

L

72

P

VDTMR

73

Q

G

LV

0

1

2

3

4

bit

s

1

L

2

FL

3

IFV

4

SR

5

N

6

IL

7

SRP

8

KRHL

9

TSD

10

TAC

11

STR

12

GTQAP

13

NDE

14

ED

15

VI

L16

QR

17

K

H

G

A

VI

R

18

YTSP

19

TAF

20

QGE

21HKQR

22YF

23

G24

ARVP

25

ILV

26

RK

27

D28

VI

29

Y30

IL

31

P

32

KR

33

ND

34

FY

35

QNHY

36

ST

37

RG

38

L

QDE

39

LP

40

R

41

G

42

LF

43

AG

44

F

45 46

IV

47

KEQ

48

YF

49

YSLARMV

50

HEYD

51

TSAP

52

S

Q

D

RKEYA

53

ED

54

A

55

MGESA

56

VKDE

57

A

58

MRQK

59

RKQHY

60

Y

Q

E

SRCH

61

LM

62

ND

63

RHG

64

E

SRYKQ

65

S

M

TL

IV

66

VF

IL

67

S

Q

FGAL

68

G

69

R

70

VE

71

VL

I

72

RAST

73

IV

RRM1 SC35

RRM1 SCL

RRM1 SRrp

63 domains

21 domains

41 domains

A. RRM1 of Single RRM SR proteins

�1 �2 �3 �4�1 �2L1 L2 L3 L4 L5

0

1

2

3

4

bit

s

1

L

2

F

3

IV

4

R

5

N

6

SIV

7

TG

SA

8

D

9

V

NEAD

10

IST

11

R

12

PS

13

E

14

D

15

L

16

PR

17

R

18

E

19

F

20

V

G

21

R22

FY

23

G24

SP

25

VI

26

SV

27

D28

V29

Y30

IV

31P

32VL

33

D34

YF

35

Y36

ST

37

R38

HQR

39

SP

40

R41

G

42

F

43

A

44

Y

45

FL

46

S

FIV

47

ETI

Q

48

YIF

49

V

PD

QE

50

D

51

V

52

R

53

D

54

A

55

E

56

D

57

A

58

L

59

YH

60

ASN

61

ML

62

ND

63

KR

64

NK

65

W

66

VI

67

C

68

G

69

R

70

Y

Q

71

I

72

E

73

VI

RNP2 RNP1

Fig. S21

157

0

1

2

3

4

bit

s

1

LIV

2

Y

3

IV

4

G

5

N

6

L

7

PD

8

SAP

9

GDR

10

AIV

11

RSAT

12

SAE

13

GER

14

DE

15

IVL

16

RE

17

TD

18

DE

19

F

20

VHKER

21

SMRAV

22

YF

23

G24

RV

25

IVL

26

R27

TNS

28

IV

29W

30

V31

GA

32

R33

RK

34

P35

P36

G

37

YF

38

A

39

F

40

VML

I

41

ED

42

MF

43

ED

44

D

45

S

L

PKEDR

46

R

47

D

48

A

49

RLED

50

D

51

A

52

LVI

53

HSR

54

KEDA

55

VIL

56

ND

57

RG

58

MFK

59

KQN

60 61 62

G

63

W

64

R

65

V

66

E

67

IFL

0

1

2

3

4

bit

s

1

V2

Y3

V4

G5

DN

6

L7

E

G8

NT

9

G10

VA

11S

AG

12

RK

13

R

G14

E15

L16

KE

17

R18

SA

19

LF

20

G

S

21

Y

22

Y

23

G

24

SP

25

L

26

R

27

ST

28

V

29

W

30

VI

31

VA

32

KR

33

N

34

P

35

AP

36

G

37

F

38

PA

39

F

40

V

41

E

42

YF

43

E

44

D

45

TAP

46

TR

47

HD

48

A

49

KE

50

PD

51

V

SLA

52

LV

53

L

G

QKR

54

S

RD

G

55

S

ML

56

KG

D

57

S

G

58

RK

59

I

LV

60

LI

61

C

62

G

63

A

S

64

GR

65

MV

66

R

67

V

0

1

2

3

4

bit

s

1

L

2

Y

3

V

4

G

5

HR

6

IL

7

AS

8

LS

9

R

10

T

11

R

12

ATS

13

ER

14

D

15

L

16

E

17

N

DRY

18

HL

19

F

20

GS

21

KR

22

Y

23

G

24

R

25

IV

26

R

27

Y

FED

28

V

29

ED

30

LM

31

K

32 33 34 35

NHR

36

ED

37

FY

38

GA

39

F40

IV

41

E42

F43

GS

44

D45

AP

46

R

47

D

48

A

49

NED

50

ED

51

A

52

R

53

LHY

54

H

DYN

55

L

56

D

57

G

58

KR

59

KD

60

Y

LVF

61

D

62

G

63

S

64

DR

65

MI

66

TL

I

67

V

0

1

2

3

4

bit

s

1

V

2

Y

3

V

4

G

5

N

6

L

7

G

8

SN

9

SN

10

G11

N12

K13

ST

14

DE

15

L16

E17

W

SR

18

SA

19

F20

G21

Y22

Y23

G24

P25

L26

R27

T

S28

V29

W

30

V

31

A

32

R

33

N

34

P

35

P

36

G

37

F

38

A

39

F

40

V

41

E

42

F

43

E

44

D

45

SP

46

R

47

D

48

A

49

SNTA

50

D

51

A

52

V

53

KR

54

E

55

L

56

D

57

G

58

R

59

HT

60

ML

61

C

62

G

63

C

64

R

65

V

66

R

67

V

RRM1 9G8

RRM1 SRp20

RRM1 RS2Z

RRM1 RSZ

47 domains

45 domains

16 domains

7 domains

B. RRM1 of Single RRM ZnK-like SR proteins

L5L4L3L2L1�2�1 �4�3�2�1

RNP2 RNP1

Fig. S21

158

0

1

2

3

4

bit

s

1

IV

2

YF

3

VI

4

G

5

HKR

6

L

7

NS

8

YP

9

SRNHQA

10

VA

11

R

12

E

13

RK

14

D

15

IV

16

QE

17

KR

18

F

19

F

20

R

GSK

21

G22

FY

23

G24

KR

25

LI

26

K

MLR

27

DE

28

VI

29

ND

30M

L31

K32 33 34 35 36 37

K

RN

38

G39

YF

40

G

41

F

42

V

43

E

44

F

45

DE

46

D

47

Y

T

NHSLP

48

R

49

D

50

A

51

ED

52

D

53

V

A

54

Y

V

55

E

Y

56

DE

57

L

58

DN

59

S

G

60

K

61

DE

62

L

63

VL

C

64 65 66

NGS

67

KE

68

R

69

Y

V

70

M

IT

71

VI

0

1

2

3

4

bit

s

1

V

I2

Y3

V4

E

G5

N6

L7

Q

P8

VSAMTP

9

D10

VI

11G

QR

12SET

13

RK

14

ED

15

VL

I

16

K

QE

17

V

D18

M

VL

19

F20

D

FHY

21

R

K

22

FY

23

G

24

TKRA

25

VI

26

S

I

TR

27

T

FED

28

VI

29

ED

30

L

31

K

32

N

33

Q

L

NR

34

S

HR

35

W

SG

36

A

TLG

37

R

AI

VP

38

L

P

39

F

40

A

41

F

42

IV

43

S

QRE

44

F

45

Q

N

DE

46

S

N

E

D

47

L

AP

48

R

49

D

50

SA

51

H

G

DE

52

N

D

53

V

A

54

IV

55

KFHY

56

E

AG

57

R

58

ND

59

G

60

Y

61

V

E

GD

62

FY

63

Y

E

GD

64 65 66

S

DQG

67

SCY

68

KR

69

L

70

R

71

V

0

1

2

3

4

bit

s

1

IV

2

YF

3

VC

4

G

5

N

6

LF

7

DE

8

FY

9

ED

10

CVTA

11

R

12

IHEQ

13

GS

14

DE

15

VIL

16

DE

17

R

18

L

19

F

20

Y

KD

GSR

21

ERK

22

FY

23

G

24

KR

25

IV

26

KDE

27

R

28

IV

29

D

30

LM

31

K

32 33 34 35 36 37

TAS

38

G39

YF

40SA

41F

42

IV

43

Y44

FM

45

E46

D47

E48

R

49

D

50

GA

51

ADE

52

AED

53

A

54

I

55

HSR

56

KHGRA

57

TL

58

D

59

GNR

60

YTMF

I

61

TSPDE

62

YF

63

G

64

PYR

65

QE

DTGK

66

KRG

67

R

68

KR

69

IL

70

KSR

71

V

0

1

2

3

4

bit

s

1

VL

I

2

Y

3

V

4

G

5

N

6

L

7

P

8

SAG

9

D

10

VI

11

R12

WQKLE

13

WSHCR

14

E15

IV

16

KE

17

HD

18

IL

19

F20

MSY

21K

22FY

23

G24

LHRP

25

VI

26

TMLAV

27

HREQD

28

VI

29

ED

30

L

31

RK

32

NLVI

33

P

34

P

35

KR

36

TP

37

P

38

CG

39

FY

40

CA

41

F

42

LI

V

43

VQE

44

F

45

KDE

46

ENHD

47

TGSPA

48

LCR

49

ND

50

A

51

QDE

52

ED

53

A

54

CI

55

C

A

KHYR

56

EYG

57

CR

58

HD

59

G

60

Y

61

KND

62

LF

63

ND

64 65 66

G

67

F

YNHC

68

QHR

69

L

70

LR

71

V

RRM1 ASF-like (animals)

RRM1 ASF-like (plants)

RRM1 RS

RRM1 SRp40-55-75

55 domains

24 domains

91 domains

13 domains

C. RRM1 of Dual RRM SR proteins

L5L4L3L2L1�2�1 �4�3�2�1

RNP2 RNP1

Fig. S21

159

0

1

2

3

4

bit

s

1

L

2

VH

3

IV

4

GD

5

NHCS

6

L7

TS

8

R9

N10

V11

TN

12E

13

TGDA

14

H15

IL

16

RK

17

E18

I

19

F

20

ESG

21

LCN

22

YF

23

G

24

VE

25

LIV

26

KIV

27

SNH

28

V

29

E

30

IL

31

SA

32

M

33

D

34

R

35 36

V

S

M

TA

37

V

38

N

39

L

40

P

41

KR

42

G

43

FHY

44

AG

45

HY

46

IV

47

E

48

YF

49

EK

50 51

HR

52

V

G

E

TA

53

D

54

A

55

E

56

RK

57

A

58

QL

59

DAL

60

FHY

61

LM

62

ND

63

NG

64

AG

65

Q

66

I

67

D

68

G

69

KN

70

IAV

71

V

72

SRK

73

LVA

0

1

2

3

4

bit

s

1

CL

IV

2

TYH

3

VL

I

4

KE

A

G

5

KHGR

6

SL

7

PST

8

PK

GR

9

T

QK

IN

10

TI

V

11

NIT

12

ERK

13

ED

14

H15

VL

I16

V

R

L

H

F

T

QM

17

E18

I19

F20

TA

G

S21

H

SIT

22FY

23

R

G24

R

Q

P

N

D

EAK

25

L

VI

26

TS

RK

27

N

H

KASM

28

VI

29

ED

30

L

IFM

31

RA

P

32

S

R

K

I

A

PMV

33

NDE

34

HKR

35

Y

A

FIVLM

36

R

Q

N

L

FYH

37

QG

AP

38

R

PA

NH

39

V

P

H

QMFL

40

T

CGS

41

Q

RK

42

C

G

43

V

S

H

FY

44

VCA

45

FY

46

IV

47

DE

48

YF

49

V

TS

A

ME

50

R

D

A

STN

51

SHAP

52

GNED

53

G

DE

54

CA

55

DAQE

56

SNK

57

TA

58

I

VML

59

K

60

YH

61

M

62

ND

63

G

64

G

65

Q

66

I

67

D

68

G

69

K

Q

70

QL

E

71

I

72

SR

MT

73

VA

RRM1 SR45

RRM1 RNPS1

8 domains

43 domains

D. RRM1 of RNPS1-like proteins

L5L4L3L2L1�2�1 �4�3�2�1

RNP2 RNP1

Fig. S21

160

�2

0

1

2

3

4

bit

s

1

MI

L

2

FLY

3

IV

4

SARG

5

GN

6

V

M

IL

7 8

T

DANSP

9

RY

10

ADSKNR

11

M

LTAV

12

R

SKTHN

13

TQNDE

14

T

QDESAG

15

TAQHED

16

MIVL

17

T

L

E

A

QGKR

18

N

S

DVQAE

19

M

H

FAVL

20

LMF

21

Q

RSGAE

22

V

P

K

DAQE

23

R

QHFY

24

W

G

25

V

KQTPE

26

F

LIV

27

N

28

T

RN

L

GAS

29

ACV

30

V

N

STKR

31

VI

L

32

P

MIV

33

V

E

ILTMRK

34

V

R

N

G

E

QD

35

P

QKR

36

Y

H

D

ARKE

37

ST

38

QN

RG

39

L

EQKR

40

TP

RS

41

RK

42

K

G43

YF

44

AG

45

F46

AIV

47K

IDVE

48

ILM

49

I

G

D

SEAP

50

A

KTEDNS

51

P

V

SKADE

52

R

N

GDSEA

53

Q

AGDE

54

V

L

E

GA

55

S

N

IAEDKQ

56

V

P

T

ENAK

57

VA

58

LM

I

59

SNEDVAK

60

Q

N

SD

KEA

61

M

E

AL

62

HDN

63

T

QEDG

64

V

Q

S

YTFAK

65

V

R

T

P

DSKNE

66

I

LVYF

67

V

L

K

GDMAEQ

68

D

A

TKQEG

69

QNSKR

70

V

S

R

G

QNPKT

71

V

MI

L

72

S

A

VRK

73

LIV

0

1

2

3

4

bit

s

1

VI

L

2

Y

3

VI

4

G

5

N

6

L

7

P

8

KP

9

REQ

10

S

DVNGET

11

M

LVI

F

12

T

S

K

DNE

13

V

SEQPR

14

EAQK

15

DAE

16

FL

17

V

AQDE

18

N

G

E

D

SKTA

19

M

F

IQVL

20

IFL

21

S

R

Q

N

TKA

22

Q

PG

AES

23

EI

AV

24

TNSG

25

KAED

26

AVSG

27GVI

28KTSR

29

LATF

30

K31

T

SVLA

32

IV

33

RKFTL

34

D35

KR

36

R

DKE

37

T

38

KG

39

V

S

GEAK

40

SC

41

R

42

G

43

F

44

AG

45

F

46

LVA

47

NT

48

S

LA

ITV

49

E

AKSDN

50

STND

51

PDE

52

QNDKE

53

M

IALQNV

54

TSA

55

EQND

56

S

EQLA

57

YF

ILV

58

I

59

QE

60

ARQK

61

YFL

62

N

63

N

G

64

TH

YRQKF

65

T

Q

MSDE

66

YVF

67

R

M

QKGN

68

EDG

69

VTNS

70

S

Q

ATPNK

71

IL

72

KR

73

LIV

0

1

2

3

4

bit

s

1

V

M

LI

2

S

LFY

3

IV

4

A

RG

5

G

SN

6

M

I

L7

P8

V

D

NASP

9

E

RWQFY

10

G

A

K

N

TQ

EDSR

11

M

ILFTAV

12

D

K

HRSNET

13

A

P

SRDQE

14

S

KQGADE

15

T

SHAQED

16

FIVL

17

I

T

EQKR

18

T

K

S

DQAE

19

T

F

S

Q

I

AVL

20

MLF

21

KTGESA

22

D

PASQE

23

A

VHFY

24

S

G

25

DSQPKATE

26

SGIV

27

E

I

T

K

28

A

T

K

ENRS

29

I

T

FCAV

30

A

T

H

NQSRK

31

AVI

L

32

MVP

I

33

V

I

RKMLT

34

ED

35

P

QKR

36

L

RFKDE

37

ST

38

RKG

39

AEQKR

40

MPCRKS

41

L

KR

42

S

G

43

L

C

YF

44

AG

45

YS

F

46

L

AIV

47

R

V

NDTE

48

Y

T

I

LVM

49

DN

EGSPA

50

A

ETNSD

51

Q

P

KS

ADE

52

N

G

KDSEA

53

VQGADE

54

T

GEA

55

T

R

N

AEKDQ

56

L

Q

T

N

SEKA

57

LIVA

58

V

ALM

I

59

V

S

Q

NKADE

60

Q

S

DEKGA

61

Y

AFML

62

HQDN

63

Q

NEDG

64

S

Y

FVQTKA

65

K

Q

TPNSDE

66

IVYWLF

67

A

E

K

DNQGM

68

T

K

N

DQEG

69

T

KNSR

70

Q

K

N

A

D

S

PT

71

V

MI

L

72

A

N

TVKR

73

LIV

0

1

2

3

4

bit

s

1

VL

I

2

FY

3

F

IV

4

G

5

SN

6

L

7 8

VASP

9

WFY

10

KA

E

TDQRS

11

F

MI

TVA

12

D

SRET

13

A

SRDQE

14

N

QADE

15

T

H

SQED

16

IVL

17

L

E

K

T

IQR

18

K

S

G

AQDE

19

T

SAVL

20

VF

21

TGESA

22

T

D

SAPEQ

23

HFY

24

A

G

25

P

KQTASE

26

IV

27

V

E

A

L

S

DTK

28

Q

KRNS

29

I

S

CAV

30

V

A

NRQSK

31

VI

L32

VM

IP

33

Y

S

N

I

VMLT

34

ED

35

KR

36

L

FDE

37ST

38R

K

G39

QKR

40

A

V

L

MPKS

41

KR

42

G43

LF

44

AG

45

F46

IV

47

DE

48

VLM

49

D

N

EPSGA

50

A

T

ENSD

51

S

N

K

AED

52

T

N

G

DSEA

53

S

I

G

V

QADE

54

GAE

55

N

KETRADQ

56

R

Q

STEKA

57

I

M

VA

58

A

MI

59

T

S

Q

NADE

60

K

SEDGA

61

V

A

ML

62

HQDN

63

ENDG

64

Y

S

R

KVQTA

65

N

Q

PTSDE

66

Y

M

VIFLW

67

RNK

DGM

68

N

G

69

R

70

Q

N

E

T

SADP

71

V

M

IL

72

M

NVTKR

73

IV

0

1

2

3

4

bit

s

1

VL

I

2

FY

3

IV

4

G

5

N

6

L7

P

8

N

KPS

9

R

WEQYF

10

G

S

N

TK

QEDR

11

L

T

IFVA

12

SDNTE

13

S

VP

REQ

14

DAQKE

15

T

H

ASED

16

FIVL

17L

K

D

T

I

E

18L

K

G

Q

TDEA

19

I

FQAVL

20

LF

21

Q

TKSA

22

T

A

PQSE

23

R

EI

AFVY

24

WSG

25

N

K

ATSDE

26

A

SGV

27

L

ATVSI

K

28

Q

TKSNR

29

I

A

TFVC

30

T

VAQSK

31

S

VI

AL

32

IVP

33

R

K

IF

VTL

34

ED

35

KR

36

KDE

37

ST

38

KG

39

G

QEAKR

40

S

VL

MPCK

41

R

42

G

43

F

44

GA

45

F

46

LIAV

47

NDTE

48

I

TLVM

49

V

DGESNA

50

A

ETNSD

51

S

A

PDE

52

T

Q

N

DSKEA

53

N

L

I

VAQDE

54

AE

55

S

KE

NATQD

56

TQLESKA

57

Y

F

ILVA

58

I

59

T

S

AQDE

60

S

EQGKDA

61

A

YFL

62

NDQ

63

NDG

64

Y

R

KQFTVA

65

M

SDTE

66

V

M

LFW

67

Q

F

KGNM

68

NEDG

69

VTNSR

70

E

N

Q

M

A

KDP

71

IL

72

S

KR

73

LIV

all prokaryotic RRM domains across tree

all cyanobacterial RRM domains across tree

prokaryotic RRM domains in prok-1 subtree

prokaryotic RRM domains in prok-2 subtree

prokaryotic RRM domains in prok-3 subtree (cyanobacteria)

259 domains

95 domains

27 domains

138 domains

76 domains

RNP2 RNP1

L5L4L3L2L1�2�1 �4�3�1

Fig. S22

161

9G8 ZnK

RSZ ZnK

RS2Z ZnK (right)

RS2Z ZnK (left)

C-�-X-C-G-±-X-G-H-X-X-X-�-C

45 domains

22 domains

13 domains

13 domains

0

1

2

3

4

bit

s

1

DG

2

HR

3

C

4

YF

5

N

6

C

7

G

8

VM

I

9

ED

10

G11

H12

W

13

VHA

14

R

15

ND

16

C

17

TK

18

A

0

1

2

3

4

bit

s

1

D2

KR

3

C4

Y

5

QE

6

C

7

G

8

G

DE

9

Q

TRK

10

G

11

H

12

FY

13

A

14

RY

15

HD

16

Y

C

17

S

R

Q

YH

18

KE

R

0

1

2

3

4

bit

s

1

SML

2

RK

3

C4

Y5

E6

C7

G

8

E

9

S

LI

ATP

10

G

11

H

12

IF

13

A

14

R

15

DE

16

C

17

NVR

18

RSNL

0

1

2

3

4

bit

s

1

DN

2

RK

3

C

4

FY

5

GR

6

C7

G8

DE

9

LR

10

G

11

H

12

I

13

LE

14

R

15

EDN

16

C

17

RQK

18

N

Fig. S23

162

Word density cumulative distributions <plotdist> - page 1

0

10

20

30

40

50

60

70

80

90

100

0 1 2 3 4 5 6 7 8 9

cum

ulat

ive

freq

uenc

y (%

)

max word density (24-AA window)

E after last domain

9g8 (47)asf-like-anim (55)

asf-like-plt (23)rnps1 (39)

rs (13)rs2z (7)rsz (14)

sc35 (53)scl (21)sr45 (8)

srp20 (44)srp40-55-75-ins (97)

srrp (42) 0

10

20

30

40

50

60

70

80

90

100

0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22

cum

ulat

ive

freq

uenc

y (%

)


G after last domain



rs (13)rs2z (7)rsz (14)

sc35 (53)scl (21)sr45 (8)

srp20 (44)srp40-55-75-ins (97)

srrp (42)

0

10

20

30

40

50

60

70

80

90

100

0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19

cum

ulat

ive

freq

uenc

y (%

)


G before RRM 1



rs (13)rs2z (7)rsz (14)

sc35 (53)scl (21)sr45 (8)

srp20 (44)srp40-55-75-ins (97)

srrp (42) 0

10

20

30

40

50

60

70

80

90

100

0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24

cum

ulat

ive

freq

uenc

y (%

)


G between RRM 1 and RRM 2

asf-like-anim (50)asf-like-plt (23)

rs (12)srp40-55-75-ins (74)

Fig. S24

163


0

10

20

30

40

50

60

70

80

90

100

0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19

cum

ulat

ive

freq

uenc

y (%

)


G between RRM 1 and ZNK 1

9g8 (44)rs2z (7)rsz (13)

0

10

20

30

40

50

60

70

80

90

100

0 1 2 3 4 5 6 7 8 9 10

cum

ulat

ive

freq

uenc

y (%

)


K after last domain



rs (13)rs2z (7)rsz (14)

sc35 (53)scl (21)sr45 (8)

srp20 (44)srp40-55-75-ins (97)

srrp (42)

0

10

20

30

40

50

60

70

80

90

100

0 1 2 3 4 5 6 7 8 9 10 11 12 13 14

cum

ulat

ive

freq

uenc

y (%

)


P after last domain



rs (13)rs2z (7)rsz (14)

sc35 (53)scl (21)sr45 (8)

srp20 (44)srp40-55-75-ins (97)

srrp (42) 0

10

20

30

40

50

60

70

80

90

100

0 1 2 3 4 5 6 7 8 9 10 11 12 13

cum

ulat

ive

freq

uenc

y (%

)


P before RRM 1



rs (13)rs2z (7)rsz (14)

sc35 (53)scl (21)sr45 (8)

srp20 (44)srp40-55-75-ins (97)

srrp (42)

Fig. S24

164


0

10

20

30

40

50

60

70

80

90

100

0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24

cum

ulat

ive

freq

uenc

y (%

)


R after last domain



rs (13)rs2z (7)rsz (14)

sc35 (53)scl (21)sr45 (8)

srp20 (44)srp40-55-75-ins (97)

srrp (42) 0

10

20

30

40

50

60

70

80

90

100

0 1 2 3 4 5 6 7 8 9 10 11 12 13

cum

ulat

ive

freq

uenc

y (%

)


R before RRM 1



rs (13)rs2z (7)rsz (14)

sc35 (53)scl (21)sr45 (8)

srp20 (44)srp40-55-75-ins (97)

srrp (42)

0

10

20

30

40

50

60

70

80

90

100

0 1 2 3 4 5 6 7 8 9 10 11

cum

ulat

ive

freq

uenc

y (%

)


R between RRM 1 and RRM 2


rs (12)srp40-55-75-ins (74)

0

10

20

30

40

50

60

70

80

90

100

0 1 2 3 4 5 6

cum

ulat

ive

freq

uenc

y (%

)


R between RRM 1 and ZNK 1

9g8 (44)rs2z (7)rsz (13)

Fig. S24

165


0

10

20

30

40

50

60

70

80

90

100

0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15

cum

ulat

ive

freq

uenc

y (%

)


S after last domain



rs (13)rs2z (7)rsz (14)

sc35 (53)scl (21)sr45 (8)

srp20 (44)srp40-55-75-ins (97)

srrp (42) 0

10

20

30

40

50

60

70

80

90

100

0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22

cum

ulat

ive

freq

uenc

y (%

)


S before RRM 1



rs (13)rs2z (7)rsz (14)

sc35 (53)scl (21)sr45 (8)

srp20 (44)srp40-55-75-ins (97)

srrp (42)

0

10

20

30

40

50

60

70

80

90

100

0 1 2 3 4 5 6 7 8 9 10

cum

ulat

ive

freq

uenc

y (%

)


S between RRM 1 and RRM 2


rs (12)srp40-55-75-ins (74)

0

10

20

30

40

50

60

70

80

90

100

0 1 2 3 4 5

cum

ulat

ive

freq

uenc

y (%

)


S between RRM 1 and ZNK 1

9g8 (44)rs2z (7)rsz (13)

Fig. S24

166


0

10

20

30

40

50

60

70

80

90

100

0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22

cum

ulat

ive

freq

uenc

y (%

)


[GGG] between RRM 1 and RRM 2


rs (12)srp40-55-75-ins (74)

0

10

20

30

40

50

60

70

80

90

100

0 1 2 3 4 5 6 7 8 9 10 11 12

cum

ulat

ive

freq

uenc

y (%

)


[GGG] between RRM 1 and ZNK 1

9g8 (44)rs2z (7)rsz (13)

0

10

20

30

40

50

60

70

80

90

100

0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23

cum

ulat

ive

freq

uenc

y (%

)


[GG] between RRM 1 and RRM 2


rs (12)srp40-55-75-ins (74)

0

10

20

30

40

50

60

70

80

90

100

0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15

cum

ulat

ive

freq

uenc

y (%

)


[GG] between RRM 1 and ZNK 1

9g8 (44)rs2z (7)rsz (13)

Fig. S24

167


0

10

20

30

40

50

60

70

80

90

100

0 1 2 3 4 5 6 7 8

cum

ulat

ive

freq

uenc

y (%

)


[GR] before RRM 1



rs (13)rs2z (7)rsz (14)

sc35 (53)scl (21)sr45 (8)

srp20 (44)srp40-55-75-ins (97)

srrp (42) 0

10

20

30

40

50

60

70

80

90

100

0 1 2 3 4 5 6 7 8 9 10

cum

ulat

ive

freq

uenc

y (%

)


[GR] between RRM 1 and RRM 2


rs (12)srp40-55-75-ins (74)

0

10

20

30

40

50

60

70

80

90

100

0 1 2 3 4 5 6 7 8 9

cum

ulat

ive

freq

uenc

y (%

)


[GR] between RRM 1 and ZNK 1

9g8 (44)rs2z (7)rsz (13)

0

10

20

30

40

50

60

70

80

90

100

0 1 2 3 4 5 6 7 8 9 10 11 12 13 14

cum

ulat

ive

freq

uenc

y (%

)


[GS] before RRM 1



rs (13)rs2z (7)rsz (14)

sc35 (53)scl (21)sr45 (8)

srp20 (44)srp40-55-75-ins (97)

srrp (42)

Fig. S24

168


0

10

20

30

40

50

60

70

80

90

100

0 1 2 3 4 5 6

cum

ulat

ive

freq

uenc

y (%

)


[GS] between RRM 1 and RRM 2


rs (12)srp40-55-75-ins (74)

0

10

20

30

40

50

60

70

80

90

100

0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17

cum

ulat

ive

freq

uenc

y (%

)


[KS] after last domain



rs (13)rs2z (7)rsz (14)

sc35 (53)scl (21)sr45 (8)

srp20 (44)srp40-55-75-ins (97)

srrp (42)

0

10

20

30

40

50

60

70

80

90

100

0 1 2 3 4 5

cum

ulat

ive

freq

uenc

y (%

)


[PPP] after last domain



rs (13)rs2z (7)rsz (14)

sc35 (53)scl (21)sr45 (8)

srp20 (44)srp40-55-75-ins (97)

srrp (42) 0

10

20

30

40

50

60

70

80

90

100

0 1 2 3 4 5 6 7 8 9

cum

ulat

ive

freq

uenc

y (%

)


[PP] after last domain



rs (13)rs2z (7)rsz (14)

sc35 (53)scl (21)sr45 (8)

srp20 (44)srp40-55-75-ins (97)

srrp (42)

Fig. S24

169


0

10

20

30

40

50

60

70

80

90

100

0 1 2 3 4 5 6 7 8 9

cum

ulat

ive

freq

uenc

y (%

)


[PRS] after last domain



rs (13)rs2z (7)rsz (14)

sc35 (53)scl (21)sr45 (8)

srp20 (44)srp40-55-75-ins (97)

srrp (42) 0

10

20

30

40

50

60

70

80

90

100

0 1 2 3 4 5 6 7 8 9 10 11 12

cum

ulat

ive

freq

uenc

y (%

)


[PS] after last domain



rs (13)rs2z (7)rsz (14)

sc35 (53)scl (21)sr45 (8)

srp20 (44)srp40-55-75-ins (97)

srrp (42)

0

10

20

30

40

50

60

70

80

90

100

0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23

cum

ulat

ive

freq

uenc

y (%

)


[RR] after last domain



rs (13)rs2z (7)rsz (14)

sc35 (53)scl (21)sr45 (8)

srp20 (44)srp40-55-75-ins (97)

srrp (42) 0

10

20

30

40

50

60

70

80

90

100

0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21

cum

ulat

ive

freq

uenc

y (%

)


[RS] after last domain



rs (13)rs2z (7)rsz (14)

sc35 (53)scl (21)sr45 (8)

srp20 (44)srp40-55-75-ins (97)

srrp (42)

Fig. S24

170


0

10

20

30

40

50

60

70

80

90

100

0 1 2 3 4 5 6 7 8 9 10 11 12 13 14

cum

ulat

ive

freq

uenc

y (%

)


[RS] before RRM 1



rs (13)rs2z (7)rsz (14)

sc35 (53)scl (21)sr45 (8)

srp20 (44)srp40-55-75-ins (97)

srrp (42) 0

10

20

30

40

50

60

70

80

90

100

0 1 2 3

cum

ulat

ive

freq

uenc

y (%

)


[RS] between RRM 1 and ZNK 1

9g8 (44)rs2z (7)rsz (13)

0

10

20

30

40

50

60

70

80

90

100

0 1 2 3 4 5

cum

ulat

ive

freq

uenc

y (%

)


[SSS] after last domain



rs (13)rs2z (7)rsz (14)

sc35 (53)scl (21)sr45 (8)

srp20 (44)srp40-55-75-ins (97)

srrp (42) 0

10

20

30

40

50

60

70

80

90

100

0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17

cum

ulat

ive

freq

uenc

y (%

)


[SSS] before RRM 1



rs (13)rs2z (7)rsz (14)

sc35 (53)scl (21)sr45 (8)

srp20 (44)srp40-55-75-ins (97)

srrp (42)

Fig. S24

171


0

10

20

30

40

50

60

70

80

90

100

0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19

cum

ulat

ive

freq

uenc

y (%

)


[SS] before RRM 1



rs (13)rs2z (7)rsz (14)

sc35 (53)scl (21)sr45 (8)

srp20 (44)srp40-55-75-ins (97)

srrp (42) 0

10

20

30

40

50

60

70

80

90

100

0 1 2 3 4 5 6 7 8

cum

ulat

ive

freq

uenc

y (%

)


[ST] before RRM 1



rs (13)rs2z (7)rsz (14)

sc35 (53)scl (21)sr45 (8)

srp20 (44)srp40-55-75-ins (97)

srrp (42)

Fig. S24

172

0

4

8

12

16

20

0 50 100 150 200

com

posi

tion

A. SC35

0

8

16

24

cons

erva

tion

N CRRM1

0

4

8

12

0 50 100 150 200

com

posi

tion

B. SCL

0

8

16

24

cons

erva

tion

N CRRM1

0

4

8

12

0 50 100 150 200 250

com

posi

tion

C. SRrp

0

10

20

30

cons

erva

tion

N CRRM1

0

4

8

12

16

0 50 100 150 200

com

posi

tion

D. 9G8

0

10

20

30

cons

erva

tion

N CZ1RRM1

0

4

8

12

16

0 20 40 60 80 100 120 140 160

com

posi

tion

E. SRp20

0

10

20

30

cons

erva

tion

N CRRM1

0

4

8

12

0 20 40 60 80 100 120 140 160 180

com

posi

tion

F. RSZ

0

8

16

24

cons

erva

tion

N CRRM1 ZNK1

0

4

8

12

16

0 50 100 150 200 250 300

com

posi

tion

G. RS2Z

0

10

20

30

cons

erva

tion

N CZ1 Z2RRM1

0

4

8

12

16

20

0 50 100 150 200

com

posi

tion

H. ASF/SF2

0

8

16

24

cons

erva

tion

N CRRM2RRM1

RS

RS

RS

G

G

R

S

KS

KP

R

PS

R

GR E

S

P

G

GG

GR

R

S P

RS

R

SRS

PK KS

RS

G

P

R

S

GR

RS

R

S

G

P

RS

R

S

Fig. S25

173

0

3

6

9

0 50 100 150 200

com

posi

tion

I. SRp30c

0

8

16

24

cons

erva

tion

N CRRM2RRM1

0

4

8

12

16

0 50 100 150 200 250

com

posi

tion

J. ASF-like (plants)

0

8

16

24

cons

erva

tion

N CRRM1 RRM2

0

4

8

12

16

20

0 50 100 150 200 250

com

posi

tion

K. SRp40

0

8

16

24

cons

erva

tion

N CRRM1 RRM2

0

4

8

12

16

20

0 50 100 150 200 250 300

com

posi

tion

L. SRp55

0

8

16

24

cons

erva

tion

N CRRM2RRM1

0

4

8

12

16

0 50 100 150 200 250 300 350 400 450

com

posi

tion

M. SRp75

0

8

16

24

cons

erva

tion

N CRRM2RRM1

0

5

10

0 50 100 150 200 250 300 350

com

posi

tion

N. RS

0

8

16

24

cons

erva

tion

N CRRM2RRM1

0

4

8

12

16

0 50 100 150 200 250 300 350 400

com

posi

tion

O. SR45

0

8

16

24

cons

erva

tion

N CRRM1

0

4

8

12

16

20

0 50 100 150 200 250 300

com

posi

tion

P. RNPS1

0

8

16

24

cons

erva

tion

N CRRM1

G

P

R

S

RS RS

G

S

R

KKS

RS

G

R S KS

SS

R

E

PS

RS

RS

R

S

GK

KS

RS

K

P

R

S

PPSS

SSS

RS

G

K

R

S

KS

S

SS

SSS

ST

P

R

PPRS

Fig. S25

174

98

90

100 86

67

82

100

100

100 77

72

99

100

100 68

100

99 84

68 85

60

100

55

98 55

100

61

55 52

100

65 71

79

51

asflkpl-Volvox carteri@jgi Volca1 72532 RRM 1[KOG0105]asflkan-Caenorhabditis elegans@Y111B2A_18_3_RRM_1[SR|CeSF2/ASF/rsp-3][KOG0105]

asflkpl-Chlamydomonas reinhardtii@jgi_Chlre3_129159_RRM_1[KOG0105]asflkpl-Volvox carteri@jgi_Volca1_45192_RRM_1[KOG0105]

asflkpl-Chlorella sp._NC64A@jgi_ChlNC64A_1_36976_estExt_Genewise1Plus___RRM_1[KOG0105]asflkpl-Oryza sativa_japonica_cultivar_group@NP_001060608_RRM_1[SR|SRp33a][KOG0105]

asflkpl-Populus trichocarpa@jgi_Poptr1_1_250704_gw1_XV_140_1_RRM_1[SR|SRp34a][KOG0105]asflkpl-Populus trichocarpa@jgi_Poptr1_1_421685_gw1_XII_145_1_RRM_1[SR|SRp34a][KOG0105]

asflkpl-Arabidopsis thaliana@NP_001078264_RRM_1[SR|SRp34a][KOG0105]asflkpl-Arabidopsis thaliana@NP_190512_RRM_1[SR|SRp34a][KOG0105]

asflkpl-Physcomitrella patens@jgi_Phypa1_1_140978_RRM_1[KOG0105]asflkpl-Physcomitrella patens@jgi_Phypa1_1_113630_RRM_1[KOG0105]

asflkpl-Physcomitrella patens@jgi_Phypa1_1_205547_RRM_1[KOG0105]asflkpl-Selaginella moellendorfii@jgi_Selmo1_36388_gw1_41_236_1_RRM_1[KOG0105]

asflkpl-Populus trichocarpa@jgi_Poptr1_1_811208_fgenesh4_pm___RRM_1[KOG0105]asflkpl-Populus trichocarpa@jgi_Poptr1_1_773626_fgenesh4_pg___RRM_1[SR|SRp30][KOG0105]

asflkpl-Populus trichocarpa@jgi_Poptr1_1_409414_gw1_II_749_1_RRM_1[KOG0105]asflkpl-Populus trichocarpa@jgi_Poptr1_1_664446_grail3_0061020502_RRM_1[SR|SRp33a][KOG0105]

asflkpl-Sorghum bicolor_BTx623@jgi_Sorbi1_5049442_Sb01g035680_RRM_1[SR|SRp32][KOG0105]asflkpl-Oryza sativa_japonica_cultivar_group@NP_001050082_RRM_1[SR|SRp32][KOG0105]

asflkpl-Selaginella moellendorfii@jgi_Selmo1_119951_e_gw1_61_278_1_RRM_1[KOG0105]asflkpl-Selaginella moellendorfii@jgi_Selmo1_97566_e_gw1_19_485_1_RRM_1[KOG0105]

asflkpl-Sorghum bicolor_BTx623@jgi_Sorbi1_5035702_Sb03g013010_RRM_1[SR|SR20][KOG0105]asflkan-Mus musculus@ENSMUSP00000031513_RRM_1[SR|SRp30c][KOG0105]

asflkan-Homo sapiens@ENSP00000229390_RRM_1[SR|SRp30c][KOG0105]asflkan-Drosophila melanogaster@CG6987_PA_RRM_1[KOG0105]

asflkan-Homo sapiens@ENSP00000258962_RRM_1[SR|ASF/SF2][KOG0105]asflkan-Mus musculus@ENSMUSP00000078792_RRM_1[SR|ASF/SF2][KOG0105]asflkan-Mus musculus@ENSMUSP00000103553_RRM_1[SR|ASF/SF2][KOG0105]

asflkpl-Oryza sativa_japonica_cultivar_group@NP_001055323_RRM_1[SR|SRp33b][KOG0105]asflkpl-Arabidopsis thaliana@NP_683288_RRM_1[SR|SRp30][KOG0105]asflkpl-Arabidopsis thaliana@NP_172386_RRM_1[SR|SRp30][KOG0105]

asflkpl-Arabidopsis thaliana@NP_849537_RRM_1[SR|SRp34b][KOG0105]asflkpl-Arabidopsis thaliana@NP_567235_RRM_1[SR|SRp34b][KOG0105]

asflkpl-Arabidopsis thaliana@NP_850933_RRM_1[SR|SR1/SRp34][KOG0105]asflkpl-Arabidopsis thaliana@NP_850934_RRM_1[SR|SR1/SRp34][KOG0105]

9g8-Caenorhabditis elegans@C33H5_12c_RRM_1[SR|CeSRp20/rsp-6][KOG0107]9g8-Caenorhabditis elegans@C33H5_12b_1_RRM_1[SR|CeSRp20/rsp-6][KOG0107]9g8-Caenorhabditis elegans@C33H5_12a_2_RRM_1[SR|CeSRp20/rsp-6][KOG0116]

9g8-Drosophila melanogaster@CG1987_PA_RRM_1[KOG0107]9g8-Drosophila melanogaster@CG17136_PD_RRM_1[KOG0107]9g8-Drosophila melanogaster@CG17136_PB_RRM_1[KOG0107]9g8-Drosophila melanogaster@CG17136_PC_RRM_1[KOG0107]

srp20-Drosophila melanogaster@CG10203_PA_RRM_1[SR|9G8][KOG0107]srp20-Mus musculus@ENSMUSP00000100538_RRM_1[SR|SRp20][KOG0107]

srp20-Mus musculus@ENSMUSP00000110365_RRM_1[SR|SRp20][KOG0107]srp20-Homo sapiens@ENSP00000344762_RRM_1[SR|SRp20][KOG0107]srp20-Mus musculus@ENSMUSP00000049025_RRM_1[SR|SRp20][KOG0107]srp20-Homo sapiens@ENSP00000362820_RRM_1[SR|SRp20][KOG0107]

9g8-Homo sapiens@ENSP00000325905_RRM_1[SR|9G8]9g8-Mus musculus@ENSMUSP00000066393_RRM_1[SR|9G8][KOG0107]9g8-Homo sapiens@ENSP00000368134_RRM_1[SR|9G8][KOG0107]9g8-Homo sapiens@ENSP00000368146_RRM_1[SR|9G8][KOG0107]9g8-Mus musculus@ENSMUSP00000070983_RRM_1[SR|9G8][KOG0107]9g8-Mus musculus@ENSMUSP00000108040_RRM_1[SR|9G8][KOG0107]

9g8-Drosophila melanogaster@CG5655_PA_RRM_1[KOG0107]rsz-Chlorella sp._NC64A@jgi_ChlNC64A_1_139931_IGS_gm_27_00109_RRM_1[KOG0107]

rsz-Chlamydomonas reinhardtii@jgi_Chlre3_132362_RRM_1[KOG0107]rsz-Chlamydomonas reinhardtii@jgi_Chlre3_192053_RRM_1[KOG0107]

rsz-Volvox carteri@jgi_Volca1_121301_RRM_1[KOG0107]rsz-Chlorella sp._NC64A@jgi_ChlNC64A_1_135849_IGS_gm_14_00382_RRM_1

rsz-Populus trichocarpa@jgi_Poptr1_1_248500_gw1_XIX_900_1_RRM_1[SR|SRZ21/RSZ21][KOG0107]rsz-Physcomitrella patens@jgi_Phypa1_1_143810_RRM_1[KOG0107]rsz-Physcomitrella patens@jgi_Phypa1_1_151194_RRM_1[KOG0107]

rsz-Oryza sativa_japonica_cultivar_group@NP_001057018_RRM_1[SR|RSZp21a]rsz-Oryza sativa_japonica_cultivar_group@NP_001047400_RRM_1[SR|RSZp23][KOG0107]

rsz-Sorghum bicolor_BTx623@jgi_Sorbi1_5061430_Sb10g005960_RRM_1[SR|RSZp21a]rsz-Sorghum bicolor_BTx623@jgi_Sorbi1_5056021_Sb04g035540_RRM_1[SR|RSZp21b]

rsz-Oryza sativa_japonica_cultivar_group@NP_001048352_RRM_1[SR|RSZp21b]rsz-Selaginella moellendorfii@jgi_Selmo1_172361_estExt_Genewise1Plus___RRM_1[KOG0107]rsz-Selaginella moellendorfii@jgi_Selmo1_68846_gw1_3_1555_1_RRM_1[KOG0107]

rsz-Populus trichocarpa@jgi_Poptr1_1_261622_gw1_XVIII_2163_1_RRM_1[KOG0116]rsz-Populus trichocarpa@jgi_Poptr1_1_583120_eugene3_01470005_RRM_1[SR|RSZ22a]rsz-Populus trichocarpa@jgi_Poptr1_1_583122_eugene3_01470007_RRM_1[SR|RSZp21a][KOG0107]

rsz-Arabidopsis thaliana@NP_180035_RRM_1[SR|RSZ22a]rsz-Arabidopsis thaliana@NP_194886_RRM_1[SR|SRZ22/RSZ22][KOG0107]

rsz-Arabidopsis thaliana@NP_564208_RRM_1[SR|SRZ21/RSZ21]

9G8SRp20

RSZ

"plant"

ASF-like

"animal"

ASF-like

"plant"

N3

N4

Fig. S26

175

90

81

51 57

50

91

83 78

99

99 86

52

94

83 78

85 58

97

100

98

95

98 98

100 69

99

95

74

80

90

82

74

100

96100

100

92 92

77

100 77

100

51

68

91

97

83

100 67

88

56

98 87

95

98

100

scl-Chlamydomonas reinhardtii@jgi Chlre3 116256 RRM 1scl-Selaginella moellendorfii@jgi_Selmo1_8401_gw1_62_42_1_RRM_1[KOG4207]

scl-Physcomitrella patens@jgi_Phypa1_1_108464_RRM_1scl-Physcomitrella patens@jgi_Phypa1_1_141868_RRM_1

scl-Sorghum bicolor_BTx623@jgi_Sorbi1_5056881_Sb05g027700_RRM_1scl-Arabidopsis thaliana@NP_567021_RRM_1[SR|SCL30][KOG0122]

scl-Populus trichocarpa@jgi_Poptr1_1_656109_grail3_0049021701_RRM_1[KOG0122]scl-Populus trichocarpa@jgi_Poptr1_1_227475_gw1_X_2172_1_RRM_1[KOG0127]

scl-Oryza sativa_japonica_cultivar_group@NP_001068546_RRM_1[KOG0127]scl-Sorghum bicolor_BTx623@jgi_Sorbi1_5047478_Sb0514s002010_RRM_1[KOG0110]

scl-Oryza sativa_japonica_cultivar_group@NP_001046448_RRM_1[SR|SCL30a]scl-Oryza sativa_japonica_cultivar_group@NP_001067091_RRM_1[SR|SCL30b]

scl-Selaginella moellendorfii@jgi_Selmo1_8339_gw1_49_32_1_RRM_1[KOG4207]scl-Oryza sativa_japonica_cultivar_group@NP_001050168_RRM_1

scl-Sorghum bicolor_BTx623@jgi_Sorbi1_5049384_Sb01g034590_RRM_1[KOG0127]scl-Populus trichocarpa@jgi_Poptr1_1_814124_estExt_fgenesh4_kg___RRM_1

scl-Arabidopsis thaliana@NP_197382_RRM_1[SR|SCL28][KOG0127]scl-Populus trichocarpa@jgi_Poptr1_1_420699_gw1_VIII_2127_1_RRM_1[SR|SCL28]

scl-Selaginella moellendorfii@jgi_Selmo1_102070_e_gw1_25_62_1_RRM_1[KOG0148]scl-Selaginella moellendorfii@jgi_Selmo1_79810_e_gw1_3_146_1_RRM_1[KOG4207]

scl-Populus trichocarpa@jgi_Poptr1_1_256035_gw1_XVI_1974_1_RRM_1[SR|SCL25][KOG0111]scl-Populus trichocarpa@jgi_Poptr1_1_547618_eugene3_00010059_RRM_1

scl-Arabidopsis thaliana@NP_187966_RRM_1[SR|SCL30a]scl-Arabidopsis thaliana@NP_564685_RRM_1[SR|SR33/SCL33][KOG0110]scl-Arabidopsis thaliana@NP_001031195_RRM_1[SR|SR33/SCL33][KOG0110]

scl-Oryza sativa_japonica_cultivar_group@NP_001060372_RRM_1[SR|SCL25]scl-Sorghum bicolor_BTx623@jgi_Sorbi1_5052097_Sb02g040350_RRM_1[SR|SCL25]

scl-Sorghum bicolor_BTx623@jgi_Sorbi1_5049360_Sb01g034200_RRM_1scl-Oryza sativa_japonica_cultivar_group@NP_001050213_RRM_1[KOG4207]

2rs-Chlorella sp._NC64A@jgi_ChlNC64A_1_25380_e_gw1_15_148_1_RRM_22rs-Cyanidioschyzon merolae@gnl_CMER_CMO009C_RRM_22rs-Chlamydomonas reinhardtii@jgi_Chlre3_120019_RRM_2[KOG0106]

2rs-Chlamydomonas reinhardtii@jgi_Chlre3_80366_RRM_2[KOG0106]2rs-Volvox carteri@jgi_Volca1_80657_RRM_1

2rs-Sorghum bicolor_BTx623@jgi_Sorbi1_5054582_Sb04g001910_RRM_22rs-Oryza sativa_japonica_cultivar_group@NP_001045729_RRM_2

2rs-Oryza sativa_japonica_cultivar_group@NP_001052061_RRM_22rs-Sorghum bicolor_BTx623@jgi_Sorbi1_5056945_Sb06g001100_RRM_2

2rs-Arabidopsis thaliana@NP_973702_RRM_12rs-Arabidopsis thaliana@NP_182184_RRM_2

2rs-Populus trichocarpa@jgi_Poptr1_1_552308_eugene3_00021623_RRM_22rs-Populus trichocarpa@jgi_Poptr1_1_245070_gw1_XIV_1813_1_RRM_2

2rs-Arabidopsis thaliana@NP_567120_RRM_22rs-Sorghum bicolor_BTx623@jgi_Sorbi1_5030607_Sb01g049590_RRM_2


2rs-Arabidopsis thaliana@NP_974616_RRM_1[SR|RSp40/SRp35][KOG0106]2rs-Arabidopsis thaliana@NP_194280_RRM_22rs-Arabidopsis thaliana@NP_001078447_RRM_1

2rs-Physcomitrella patens@jgi_Phypa1_1_167387_RRM_22rs-Selaginella moellendorfii@jgi_Selmo1_124209_e_gw1_74_375_1_RRM_22rs-Selaginella moellendorfii@jgi_Selmo1_82477_e_gw1_5_1267_1_RRM_2

2rs-Populus trichocarpa@jgi_Poptr1_1_423171_gw1_XII_1631_1_RRM_22rs-Populus trichocarpa@jgi_Poptr1_1_253698_gw1_XV_3134_1_RRM_2

2rs-Populus trichocarpa@jgi_Poptr1_1_411608_gw1_II_2943_1_RRM_22rs-Populus trichocarpa@jgi_Poptr1_1_244286_gw1_XIV_1029_1_RRM_2

rs2z-Arabidopsis thaliana@NP_850280_RRM_1[SR|RSZ33][KOG0107]rs2z-Arabidopsis thaliana@NP_190918_RRM_1[SR|RSZ32][KOG0107]

rs2z-Oryza sativa_japonica_cultivar_group@NP_001042066_RRM_1[SR|RSZ37a][KOG0109]rs2z-Sorghum bicolor_BTx623@jgi_Sorbi1_5052652_Sb03g005500_RRM_1[KOG0109]

rs2z-Sorghum bicolor_BTx623@jgi_Sorbi1_5059999_Sb09g001910_RRM_1[SR|RSZ36][KOG0109]rs2z-Sorghum bicolor_BTx623@jgi_Sorbi1_5060000_Sb09g001920_RRM_1[SR|RSZ36][KOG0106]

rs2z-Oryza sativa_japonica_cultivar_group@NP_001054489_RRM_1[SR|RSZ36][KOG0109]rs2z-Oryza sativa_japonica_cultivar_group@NP_001049771_RRM_1[SR|RSZ37b][KOG0109]

rs2z-Populus trichocarpa@jgi_Poptr1_1_667717_grail3_0004036801_RRM_1[SR|RSZ37b][KOG0107]rs2z-Populus trichocarpa@jgi_Poptr1_1_653760_grail3_0013007302_RRM_1[SR|RSZ37b][KOG0107]

rs2z-Oryza sativa_japonica_cultivar_group@NP_001054731_RRM_1[SR|RSZ39]rs2z-Sorghum bicolor_BTx623@jgi_Sorbi1_5045949_Sb09g004685_RRM_1[KOG0106]

rs2z-Sorghum bicolor_BTx623@jgi_Sorbi1_5045954_Sb09g004726_RRM_1[KOG0107]rs2z-Sorghum bicolor_BTx623@jgi_Sorbi1_5045953_Sb09g004723_RRM_1[KOG0109]

srp457-Caenorhabditis elegans@T28D9_2d_RRM_1[SR|CeSC35-2/rsp-5][KOG0106]srp457-Caenorhabditis elegans@T28D9_2a_RRM_1[SR|CeSC35-2/rsp-5][KOG0106]srp457-Caenorhabditis elegans@T28D9_2b_RRM_1[SR|CeSC35-2/rsp-5][KOG0106]

srp457-Homo sapiens@ENSP00000342294_RRM_1[SR|SRp40][KOG0106]srp457-Mus musculus@ENSMUSP00000021562_RRM_1[SR|SRp40][KOG0106]srp457-Mus musculus@ENSMUSP00000105985_RRM_1[SR|SRp40][KOG0106]srp457-Mus musculus@ENSMUSP00000105983_RRM_1[SR|SRp40][KOG0106]srp457-Homo sapiens@ENSP00000377892_RRM_1[SR|SRp40][KOG0105]

srp457-Homo sapiens@ENSP00000362900_RRM_1[SR|SRp75][KOG0105]srp457-Mus musculus@ENSMUSP00000061474_RRM_1[SR|SRp75][KOG0105]

srp457-Mus musculus@ENSMUSP00000017065_RRM_1[SR|SRp55][KOG0105]srp457-Homo sapiens@ENSP00000244020_RRM_1[SR|SRp55][KOG0105]srp457-Homo sapiens@ENSP00000362251_RRM_1[SR|SRp55][KOG0106]

srp457-Caenorhabditis elegans@W02B12_2_RRM_1[SR|CeSRp40/rsp-2][KOG0106]srp457-Caenorhabditis elegans@W02B12_3a_RRM_1[SR|CeSRp75/rsp-1][KOG0106]srp457-Caenorhabditis elegans@W02B12_3b_RRM_1[SR|CeSRp75/rsp-1][KOG0106]srp457-Caenorhabditis elegans@W02B12_3c_RRM_1[SR|CeSRp75/rsp-1][KOG0106]

srp457-Drosophila melanogaster@CG10851_PB_RRM_1[SR|SRp55][KOG0106]srp457-Drosophila melanogaster@CG10851_PC_RRM_1[SR|SRp55][KOG0105]srp457-Drosophila melanogaster@CG10851_PE_RRM_1[SR|SRp55][KOG0105]srp457-Drosophila melanogaster@CG10851_PF_RRM_1[SR|Hrp45][KOG0106]srp457-Drosophila melanogaster@CG10851_PD_RRM_1[SR|Hrp45][KOG0106]

asflkpl-Ostreococcus lucimarinus@jgi_Ost9901_3_8794_RRM_1[KOG0105]asflkpl-Ostreococcus sp._RCC809@jgi_OstRCC809_1_16551_gw1_5_1077_1_RRM_1[KOG0105]

rs-Chlorella sp._NC64A@jgi_ChlNC64A_1_25380_e_gw1_15_148_1_RRM_1[KOG0106]rs-Cyanidioschyzon merolae@gnl_CMER_CMO009C_RRM_1

rs-Sorghum bicolor_BTx623@jgi_Sorbi1_5056945_Sb06g001100_RRM_1[SR|RSp29][KOG0106]rs-Oryza sativa_japonica_cultivar_group@NP_001052061_RRM_1[SR|RSp29][KOG0106]

rs-Populus trichocarpa@jgi_Poptr1_1_245070_gw1_XIV_1813_1_RRM_1[KOG0106]rs-Populus trichocarpa@jgi_Poptr1_1_552308_eugene3_00021623_RRM_1[KOG0106]

rs-Arabidopsis thaliana@NP_567120_RRM_1[SR|RSp31][KOG0106]rs-Sorghum bicolor_BTx623@jgi_Sorbi1_5030607_Sb01g049590_RRM_1[KOG0106]

rs-Arabidopsis thaliana@NP_182184_RRM_1[SR|RSp31a][KOG0106]rs-Physcomitrella patens@jgi_Phypa1_1_167387_RRM_1[KOG0106]

rs-Selaginella moellendorfii@jgi_Selmo1_82477_e_gw1_5_1267_1_RRM_1[KOG0106]rs-Selaginella moellendorfii@jgi_Selmo1_124209_e_gw1_74_375_1_RRM_1[KOG0106]

rs-Populus trichocarpa@jgi_Poptr1_1_253698_gw1_XV_3134_1_RRM_1[KOG0106]rs-Populus trichocarpa@jgi_Poptr1_1_423171_gw1_XII_1631_1_RRM_1[KOG0106]

rs-Sorghum bicolor_BTx623@jgi_Sorbi1_5054582_Sb04g001910_RRM_1[KOG0106]rs-Oryza sativa_japonica_cultivar_group@NP_001045729_RRM_1[SR|RSp33][KOG0106]rs-Populus trichocarpa@jgi_Poptr1_1_244286_gw1_XIV_1029_1_RRM_1[KOG0106]

rs-Populus trichocarpa@jgi_Poptr1_1_644386_grail3_0033034501_RRM_1[SR|RSp33][KOG0106]rs-Populus trichocarpa@jgi_Poptr1_1_411608_gw1_II_2943_1_RRM_1[SR|RSp33][KOG0106]

rs-Arabidopsis thaliana@NP_194280_RRM_1[SR|RSp40/SRp35][KOG0106]rs-Arabidopsis thaliana@NP_851174_RRM_1[SR|RSp41][KOG0106]rs-Arabidopsis thaliana@NP_200017_RRM_1[SR|RSp41][KOG0106]

rs-Chlamydomonas reinhardtii@jgi_Chlre3_120019_RRM_1rs-Chlamydomonas reinhardtii@jgi_Chlre3_80366_RRM_1

asflkpl-Chlamydomonas reinhardtii@jgi_Chlre3_120469_RRM_1[KOG0105]asflkpl Volvox carteri@jgi_Volca1_72532_RRM_1[KOG0105]

SRp40

SRp55

SRp75

RRM1

RS "plant"

RS2Z

"plant"

SCL

RRM2

RS

"plant"

N6Fig. S26

176

0.12

76

99 97

55

65

100

73

100

97 63

52

70

93

83

87

100 53

100 75 61

51

93

68

57

66

66100

100

100

98

75

90

100

rnps1-Caenorhabditis elegans@K02F3_11_1_RRM_1[KOG4209]rnps1-Drosophila melanogaster@CG41105_PC_RRM_1

rnps1-Drosophila melanogaster@CG16788_PA_RRM_1rnps1-Mus musculus@ENSMUSP00000057332_RRM_1[KOG4209]

rnps1-Homo sapiens@ENSP00000380275_RRM_1[RNPS1|RNPS1][KOG4209]rnps1-Mus musculus@ENSMUSP00000111025_RRM_1[RNPS1|RNPS1][KOG4209]rnps1-Mus musculus@ENSMUSP00000111028_RRM_1[RNPS1|RNPS1][KOG4209]

sr45-Volvox carteri@jgi_Volca1_105177_RRM_1[KOG0462]sr45-Chlorella sp._NC64A@jgi_ChlNC64A_1_138910_IGS_gm_22_00151_RRM_1

sr45-Micromonas pusilla_RCC299@jgi_MicpuN3_63440_EuGene_1300010090_RRM_1sr45-Micromonas pusilla_CCMP1545@jgi_MicpuC2_9037_gw1_7_479_1_RRM_1

sr45-Selaginella moellendorfii@jgi_Selmo1_446044_estExt_fgenesh2_pg___RRM_1[KOG0122]sr45-Selaginella moellendorfii@jgi_Selmo1_424875_fgenesh2_pg___RRM_1[KOG0122]

sr45-Physcomitrella patens@jgi_Phypa1_1_166555_RRM_1sr45-Physcomitrella patens@jgi_Phypa1_1_105411_RRM_1

sr45-Populus trichocarpa@jgi_Poptr1_1_823076_estExt_fgenesh4_pg___RRM_1sr45-Arabidopsis thaliana@NP_173107_RRM_1[SR|SR45]sr45-Arabidopsis thaliana@NP_973844_RRM_1[SR|SR45]

sr45-Oryza sativa_japonica_cultivar_group@NP_001054414_RRM_1[KOG0117]sr45-Oryza sativa_japonica_cultivar_group@NP_001045458_RRM_1

sr45-Sorghum bicolor_BTx623@jgi_Sorbi1_5054420_Sb03g046480_RRM_1sc35-Micromonas pusilla_CCMP1545@jgi_MicpuC2_9129_gw1_3_931_1_RRM_1[KOG4207]

sc35-Micromonas pusilla_RCC299@jgi_MicpuN3_91839_estExt_Genewise2___RRM_1[KOG4207]sc35-Ostreococcus sp._RCC809@jgi_OstRCC809_1_16908_gw1_5_1114_1_RRM_1[KOG4207]

sc35-Ostreococcus lucimarinus@jgi_Ost9901_3_8174_RRM_1[KOG4207]sc35-Drosophila melanogaster@CG5442_PB_RRM_1[SR|SC35][KOG4207]

sc35-Caenorhabditis elegans@EEED8_7a_RRM_1[SR|CeSC35/rsp-4]sc35-Caenorhabditis elegans@EEED8_7b_RRM_1[SR|CeSC35/rsp-4][KOG4207]

sc35-Mus musculus@ENSMUSP00000078984_RRM_1[KOG4207]sc35-Homo sapiens@ENSP00000381889_RRM_1[KOG4207]

sc35-Mus musculus@ENSMUSP00000090059_RRM_1[SR|SC35][KOG4368]sc35-Homo sapiens@ENSP00000293233_RRM_1[SR|SC35][KOG4368]sc35-Homo sapiens@ENSP00000353089_RRM_1[SR|SC35][KOG4368]sc35-Mus musculus@ENSMUSP00000072182_RRM_1[SR|SC35][KOG4207]

sc35-Oryza sativa_japonica_cultivar_group@NP_001060322_RRM_1[SR|SC35b][KOG4207]sc35-Arabidopsis thaliana@NP_851261_RRM_1[SR|SC35][KOG4207]

sc35-Populus trichocarpa@jgi_Poptr1_1_672394_grail3_1445000102_RRM_1[SR|SC35a][KOG4207]sc35-Populus trichocarpa@jgi_Poptr1_1_645719_grail3_0067008905_RRM_1[SR|SC35b][KOG4207]

sc35-Populus trichocarpa@jgi_Poptr1_1_709848_estExt_Genewise1___RRM_1[KOG4207]sc35-Populus trichocarpa@jgi_Poptr1_1_559112_eugene3_00050727_RRM_1[SR|SC35a][KOG4207]

sc35-Oryza sativa_japonica_cultivar_group@NP_001062094_RRM_1[SR|SC35a][KOG0415]sc35-Oryza sativa_japonica_cultivar_group@NP_001050263_RRM_1[SR|SC35c][KOG4207]

sc35-Sorghum bicolor_BTx623@jgi_Sorbi1_5029845_Sb01g033710_RRM_1[KOG4207]sc35-Sorghum bicolor_BTx623@jgi_Sorbi1_5059167_Sb07g029000_RRM_1[KOG0147]

sc35-Selaginella moellendorfii@jgi_Selmo1_134332_e_gw1_124_43_1_RRM_1[SR|SC35a][KOG4207]sc35-Cyanidioschyzon merolae@gnl_CMER_CML202C_RRM_1

sc35-Physcomitrella patens@jgi_Phypa1_1_122960_RRM_1[KOG4207]sc35-Physcomitrella patens@jgi_Phypa1_1_172957_RRM_1[KOG0415]

sc35-Selaginella moellendorfii@jgi_Selmo1_7952_gw1_7_122_1_RRM_1[SR|SC35a][KOG4207]scl-Micromonas pusilla_RCC299@jgi_MicpuN3_74643_gw2_11_587_1_RRM_1[KOG0107]

scl-Micromonas pusilla_CCMP1545@jgi_MicpuC2_11901_gw1_8_619_1_RRM_1[KOG4207]scl-Ostreococcus sp._RCC809@jgi_OstRCC809_1_16959_gw1_4_1177_1_RRM_1[KOG0108]

scl-Ostreococcus lucimarinus@jgi_Ost9901_3_9858_RRM_1[KOG0108]scl-Ostreococcus tauri@jgi_Ostta4_7793_RRM_1[KOG0108]

scl-Chlorella sp._NC64A@jgi_ChlNC64A_1_135593_IGS_gm_14_00126_RRM_1[KOG4207]srrp-Homo sapiens@ENSP00000358479_RRM_1[SRrp|SRrp35]

srrp-Mus musculus@ENSMUSP00000103794_RRM_1[SRrp|SRrp35][KOG0111]srrp-Mus musculus@ENSMUSP00000095455_RRM_1[SRrp|SRp38]srrp-Mus musculus@ENSMUSP00000101479_RRM_1[SRrp|SRp38][KOG0415]srrp-Homo sapiens@ENSP00000340764_RRM_1[SRrp|SRp38][KOG0111]srrp-Mus musculus@ENSMUSP00000030438_RRM_1[SRrp|SRp38][KOG0111]srrp-Homo sapiens@ENSP00000363577_RRM_1[SRrp|SRp38][KOG0111]srrp-Mus musculus@ENSMUSP00000099603_RRM_1[SRrp|SRp38][KOG0111]srrp-Mus musculus@ENSMUSP00000030437_RRM_1[SRrp|SRp38][KOG0415]srrp-Homo sapiens@ENSP00000345293_RRM_1[SRrp|SRp38]srrp-Homo sapiens@ENSP00000363573_RRM_1[SRrp|SRp38][KOG0415]srrp-Homo sapiens@ENSP00000342913_RRM_1[SRrp|SRp38][KOG0111]srrp-Homo sapiens@ENSP00000363576_RRM_1[SRrp|SRp38][KOG0111]

scl-Volvox carteri@jgi_Volca1_120666_RRM_1scl-Chlamydomonas reinhardtii@jgi_Chlre3_188086_RRM_1

scl-Volvox carteri@jgi_Volca1_73973_RRM_1[KOG4207]scl-Chlamydomonas reinhardtii@jgi_Chlre3_113900_RRM_1[KOG4207]

scl-Chlorella sp._NC64A@jgi_ChlNC64A_1_17896_gw1_13_295_1_RRM_1scl-Volvox carteri@jgi_Volca1_121229_RRM_1[KOG0415]

scl Chlamydomonas reinhardtii@jgi_Chlre3_116256_RRM_1

SC35

SRrp

RNPS1

SR45

N1

N2

Fig. S26

177

88

100 81

100

56

70

100

81

100

100 72

89

99

92

63

91 86

88

100 67

99 89

95

83 50

93

100

100

97

99 97

100 94

96

99 54

52

60

90

80

asflkpl-Populus trichocarpa@jgi Poptr1 1 421685 gw1 XII 145 1 RRM 1[SR|SRp34a][KOG0105]asflkpl-Populus trichocarpa@jgi_Poptr1_1_250704_gw1_XV_140_1_RRM_1[SR|SRp34a][KOG0105]



asflkpl-Selaginella moellendorfii@jgi_Selmo1_36388_gw1_41_236_1_RRM_1[KOG0105]asflkpl-Physcomitrella patens@jgi_Phypa1_1_205547_RRM_1[KOG0105]



asflkpl-Sorghum bicolor_BTx623@jgi_Sorbi1_5035702_Sb03g013010_RRM_1[SR|SR20][KOG0105]asflkpl-Oryza sativa_japonica_cultivar_group@NP_001055323_RRM_1[SR|SRp33b][KOG0105]

asflkpl-Populus trichocarpa@jgi_Poptr1_1_811208_fgenesh4_pm____RRM_1asflkpl-Populus trichocarpa@jgi_Poptr1_1_773626_fgenesh4_pg___RRM_1[SR|SRp30][KOG0105]

asflkpl-Arabidopsis thaliana@NP_683288_RRM_1[SR|SRp30][KOG0105]asflkpl-Arabidopsis thaliana@NP_172386_RRM_1[SR|SRp30][KOG0105]

asflkpl-Populus trichocarpa@jgi_Poptr1_1_409414_gw1_II_749_1_RRM_1[KOG0105]asflkpl-Populus trichocarpa@jgi_Poptr1_1_664446_grail3_0061020502_RRM_1[SR|SRp33a][KOG0105]asflkpl-Arabidopsis thaliana@NP_849537_RRM_1[SR|SRp34b][KOG0105]asflkpl-Arabidopsis thaliana@NP_567235_RRM_1[SR|SRp34b][KOG0105]asflkpl-Arabidopsis thaliana@NP_850934_RRM_1[SR|SR1/SRp34][KOG0105]asflkpl-Arabidopsis thaliana@NP_850933_RRM_1[SR|SR1/SRp34][KOG0105]

asflkpl-Ostreococcus sp._RCC809@jgi_OstRCC809_1_16551_gw1_5_1077_1_RRM_1[KOG0105]asflkpl-Ostreococcus lucimarinus@jgi_Ost9901_3_8794_RRM_1[KOG0105]

rs-Sorghum bicolor_BTx623@jgi_Sorbi1_5056945_Sb06g001100_RRM_1[SR|RSp29][KOG0106]rs-Oryza sativa_japonica_cultivar_group@NP_001052061_RRM_1[SR|RSp29][KOG0106]

rs-Populus trichocarpa@jgi_Poptr1_1_245070_gw1_XIV_1813_1_RRM_1[KOG0106]rs-Populus trichocarpa@jgi_Poptr1_1_552308_eugene3_00021623_RRM_1[KOG0106]rs-Arabidopsis thaliana@NP_567120_RRM_1[SR|RSp31][KOG0106]

rs-Sorghum bicolor_BTx623@jgi_Sorbi1_5030607_Sb01g049590_RRM_1[KOG0106]rs-Arabidopsis thaliana@NP_182184_RRM_1[SR|RSp31a][KOG0106]


rs-Populus trichocarpa@jgi_Poptr1_1_423171_gw1_XII_1631_1_RRM_1[KOG0106]rs-Populus trichocarpa@jgi_Poptr1_1_253698_gw1_XV_3134_1_RRM_1[KOG0106]

rs-Physcomitrella patens@jgi_Phypa1_1_167387_RRM_1[KOG0106]rs-Selaginella moellendorfii@jgi_Selmo1_124209_e_gw1_74_375_1_RRM_1[KOG0106]rs-Selaginella moellendorfii@jgi_Selmo1_82477_e_gw1_5_1267_1_RRM_1[KOG0106]rs-Sorghum bicolor_BTx623@jgi_Sorbi1_5054582_Sb04g001910_RRM_1[KOG0106]

rs-Oryza sativa_japonica_cultivar_group@NP_001045729_RRM_1[SR|RSp33][KOG0106]rs-Populus trichocarpa@jgi_Poptr1_1_244286_gw1_XIV_1029_1_RRM_1[KOG0106]

rs-Populus trichocarpa@jgi_Poptr1_1_644386_grail3_0033034501_RRM_1[SR|RSp33][KOG0106]rs-Populus trichocarpa@jgi_Poptr1_1_411608_gw1_II_2943_1_RRM_1[SR|RSp33][KOG0106]

rs-Chlorella sp._NC64A@jgi_ChlNC64A_1_25380_e_gw1_15_148_1_RRM_1[KOG0106]rs-Chlamydomonas reinhardtii@jgi_Chlre3_80366_RRM_1

rs-Chlamydomonas reinhardtii@jgi_Chlre3_120019_RRM_1rs-Cyanidioschyzon merolae@gnl_CMER_CMO009C_RRM_1

2rs-Chlorella sp._NC64A@jgi_ChlNC64A_1_25380_e_gw1_15_148_1_RRM_22rs-Cyanidioschyzon merolae@gnl_CMER_CMO009C_RRM_2


2rs-Chlamydomonas reinhardtii@jgi_Chlre3_80366_RRM_2[KOG0106]2rs-Sorghum bicolor_BTx623@jgi_Sorbi1_5054582_Sb04g001910_RRM_2


2rs-Oryza sativa_japonica_cultivar_group@NP_001052061_RRM_22rs-Populus trichocarpa@jgi_Poptr1_1_245070_gw1_XIV_1813_1_RRM_2

2rs-Populus trichocarpa@jgi_Poptr1_1_552308_eugene3_00021623_RRM_22rs-Sorghum bicolor_BTx623@jgi_Sorbi1_5030607_Sb01g049590_RRM_2

2rs-Arabidopsis thaliana@NP_567120_RRM_22rs-Arabidopsis thaliana@NP_182184_RRM_22rs-Arabidopsis thaliana@NP_973702_RRM_1




2rs-Populus trichocarpa@jgi_Poptr1_1_244286_gw1_XIV_1029_1_RRM_22rs-Populus trichocarpa@jgi_Poptr1_1_411608_gw1_II_2943_1_RRM_22rs-Populus trichocarpa@jgi_Poptr1_1_253698_gw1_XV_3134_1_RRM_22rs-Populus trichocarpa@jgi_Poptr1_1_423171_gw1_XII_1631_1_RRM_2

ASF-like

"plant"

RRM1

RS

"plant"

RRM2

RS "plant"

Fig. S27

178

67 75

77

50

90 65

100

95

92 72

99 86

91

94 85

69

71

88

59

93

92

58

100

79100

100

92 93

72

100 88

93 62

100

50

81

67

51 97

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59 56 88

87 62

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99

60

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62 80

62 51

100

100

56

53 64

87

58

100

100

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96 71

66

88

62

scl-Chlamydomonas reinhardtii@jgi Chlre3 116256 RRM 1scl-Oryza sativa_japonica_cultivar_group@NP_001068546_RRM_1[KOG0127]

scl-Sorghum bicolor_BTx623@jgi_Sorbi1_5056881_Sb05g027700_RRM_1scl-Sorghum bicolor_BTx623@jgi_Sorbi1_5047478_Sb0514s002010_RRM_1[KOG0110]scl-Oryza sativa_japonica_cultivar_group@NP_001067091_RRM_1[SR|SCL30b]scl-Oryza sativa_japonica_cultivar_group@NP_001046448_RRM_1[SR|SCL30a]

scl-Arabidopsis thaliana@NP_567021_RRM_1[SR|SCL30][KOG0122]scl-Populus trichocarpa@jgi_Poptr1_1_227475_gw1_X_2172_1_RRM_1[KOG0127]

scl-Populus trichocarpa@jgi_Poptr1_1_656109_grail3_0049021701_RRM_1[KOG0122]scl-Selaginella moellendorfii@jgi_Selmo1_8401_gw1_62_42_1_RRM_1[KOG4207]

scl-Physcomitrella patens@jgi_Phypa1_1_141868_RRM_1scl-Physcomitrella patens@jgi_Phypa1_1_108464_RRM_1

scl-Selaginella moellendorfii@jgi_Selmo1_8339_gw1_49_32_1_RRM_1[KOG4207]scl-Selaginella moellendorfii@jgi_Selmo1_102070_e_gw1_25_62_1_RRM_1[KOG0148]scl-Selaginella moellendorfii@jgi_Selmo1_79810_e_gw1_3_146_1_RRM_1[KOG4207]

scl-Sorghum bicolor_BTx623@jgi_Sorbi1_5049384_Sb01g034590_RRM_1[KOG0127]scl-Oryza sativa_japonica_cultivar_group@NP_001050168_RRM_1

scl-Populus trichocarpa@jgi_Poptr1_1_814124_estExt_fgenesh4_kg___RRM_1scl-Populus trichocarpa@jgi_Poptr1_1_420699_gw1_VIII_2127_1_RRM_1[SR|SCL28]

scl-Arabidopsis thaliana@NP_197382_RRM_1[SR|SCL28][KOG0127]scl-Populus trichocarpa@jgi_Poptr1_1_547618_eugene3_00010059_RRM_1

scl-Arabidopsis thaliana@NP_187966_RRM_1[SR|SCL30a]scl-Arabidopsis thaliana@NP_564685_RRM_1[SR|SR33/SCL33][KOG0110]scl-Arabidopsis thaliana@NP_001031195_RRM_1[SR|SR33/SCL33][KOG0110]

scl-Populus trichocarpa@jgi_Poptr1_1_256035_gw1_XVI_1974_1_RRM_1[SR|SCL25][KOG0111]scl-Sorghum bicolor_BTx623@jgi_Sorbi1_5049360_Sb01g034200_RRM_1

scl-Oryza sativa_japonica_cultivar_group@NP_001050213_RRM_1[KOG4207]scl-Sorghum bicolor_BTx623@jgi_Sorbi1_5052097_Sb02g040350_RRM_1[SR|SCL25]scl-Oryza sativa_japonica_cultivar_group@NP_001060372_RRM_1[SR|SCL25]

rs2z-Sorghum bicolor_BTx623@jgi_Sorbi1_5052652_Sb03g005500_RRM_1[KOG0109]rs2z-Oryza sativa_japonica_cultivar_group@NP_001042066_RRM_1[SR|RSZ37a][KOG0109]


rs2z-Sorghum bicolor_BTx623@jgi_Sorbi1_5045949_Sb09g004685_RRM_1[KOG0106]rs2z-Oryza sativa_japonica_cultivar_group@NP_001054731_RRM_1[SR|RSZ39]


rs2z-Sorghum bicolor_BTx623@jgi_Sorbi1_5060000_Sb09g001920_RRM_1[SR|RSZ36][KOG0106]rs2z-Sorghum bicolor_BTx623@jgi_Sorbi1_5059999_Sb09g001910_RRM_1[SR|RSZ36][KOG0109]



srp457-Caenorhabditis elegans@T28D9_2a_RRM_1[SR|CeSC35-2/rsp-5][KOG0106]srp457-Caenorhabditis elegans@T28D9_2d_RRM_1[SR|CeSC35-2/rsp-5][KOG0106]srp457-Caenorhabditis elegans@T28D9_2b_RRM_1[SR|CeSC35-2/rsp-5][KOG0106]

srp457-Homo sapiens@ENSP00000342294_RRM_1[SR|SRp40][KOG0106]srp457-Homo sapiens@ENSP00000377892_RRM_1[SR|SRp40][KOG0105]srp457-Mus musculus@ENSMUSP00000021562_RRM_1[SR|SRp40][KOG0106]srp457-Mus musculus@ENSMUSP00000105985_RRM_1[SR|SRp40][KOG0106]srp457-Mus musculus@ENSMUSP00000105983_RRM_1[SR|SRp40][KOG0106]

srp457-Mus musculus@ENSMUSP00000061474_RRM_1[SR|SRp75][KOG0105]srp457-Homo sapiens@ENSP00000362900_RRM_1[SR|SRp75][KOG0105]

srp457-Mus musculus@ENSMUSP00000017065_RRM_1[SR|SRp55][KOG0105]srp457-Homo sapiens@ENSP00000244020_RRM_1[SR|SRp55][KOG0105]srp457-Homo sapiens@ENSP00000362251_RRM_1[SR|SRp55][KOG0106]

srp457-Caenorhabditis elegans@W02B12_2_RRM_1[SR|CeSRp40/rsp-2][KOG0106]srp457-Caenorhabditis elegans@W02B12_3a_RRM_1[SR|CeSRp75/rsp-1][KOG0106]srp457-Caenorhabditis elegans@W02B12_3c_RRM_1[SR|CeSRp75/rsp-1][KOG0106]srp457-Caenorhabditis elegans@W02B12_3b_RRM_1[SR|CeSRp75/rsp-1][KOG0106]

srp457-Drosophila melanogaster@CG10851_PF_RRM_1[SR|Hrp45][KOG0106]srp457-Drosophila melanogaster@CG10851_PB_RRM_1[SR|SRp55][KOG0106]srp457-Drosophila melanogaster@CG10851_PC_RRM_1[SR|SRp55][KOG0105]srp457-Drosophila melanogaster@CG10851_PE_RRM_1[SR|SRp55][KOG0105]srp457-Drosophila melanogaster@CG10851_PD_RRM_1[SR|Hrp45][KOG0106]

9g8-Drosophila melanogaster@CG5655_PA_RRM_1[KOG0107]srp20-Drosophila melanogaster@CG10203_PA_RRM_1[SR|9G8][KOG0107]

9g8-Drosophila melanogaster@CG1987_PA_RRM_1[KOG0107]9g8-Drosophila melanogaster@CG17136_PC_RRM_1[KOG0107]9g8-Drosophila melanogaster@CG17136_PD_RRM_1[KOG0107]9g8-Drosophila melanogaster@CG17136_PB_RRM_1[KOG0107]

srp20-Mus musculus@ENSMUSP00000100538_RRM_1[SR|SRp20][KOG0107]srp20-Mus musculus@ENSMUSP00000049025_RRM_1[SR|SRp20][KOG0107]srp20-Mus musculus@ENSMUSP00000110365_RRM_1[SR|SRp20][KOG0107]srp20-Homo sapiens@ENSP00000344762_RRM_1[SR|SRp20][KOG0107]srp20-Homo sapiens@ENSP00000362820_RRM_1[SR|SRp20][KOG0107]

9g8-Mus musculus@ENSMUSP00000066393_RRM_1[SR|9G8][KOG0107]9g8-Mus musculus@ENSMUSP00000070983_RRM_1[SR|9G8][KOG0107]9g8-Mus musculus@ENSMUSP00000108040_RRM_1[SR|9G8][KOG0107]9g8-Homo sapiens@ENSP00000368146_RRM_1[SR|9G8][KOG0107]9g8-Homo sapiens@ENSP00000325905_RRM_1[SR|9G8]9g8-Homo sapiens@ENSP00000368134_RRM_1[SR|9G8][KOG0107]

9g8-Caenorhabditis elegans@C33H5_12a_2_RRM_1[SR|CeSRp20/rsp-6][KOG0116]9g8-Caenorhabditis elegans@C33H5_12c_RRM_1[SR|CeSRp20/rsp-6][KOG0107]9g8-Caenorhabditis elegans@C33H5_12b_1_RRM_1[SR|CeSRp20/rsp-6][KOG0107]

rsz-Chlorella sp._NC64A@jgi_ChlNC64A_1_139931_IGS_gm_27_00109_RRM_1[KOG0107]rsz-Chlamydomonas reinhardtii@jgi_Chlre3_132362_RRM_1[KOG0107]

rsz-Volvox carteri@jgi_Volca1_121301_RRM_1[KOG0107]rsz-Chlamydomonas reinhardtii@jgi_Chlre3_192053_RRM_1[KOG0107]

rsz-Chlorella sp._NC64A@jgi_ChlNC64A_1_135849_IGS_gm_14_00382_RRM_1rsz-Populus trichocarpa@jgi_Poptr1_1_248500_gw1_XIX_900_1_RRM_1[SR|SRZ21/RSZ21][KOG0107]


rsz-Arabidopsis thaliana@NP_564208_RRM_1[SR|SRZ21/RSZ21]rsz-Arabidopsis thaliana@NP_180035_RRM_1[SR|RSZ22a]

rsz-Arabidopsis thaliana@NP_194886_RRM_1[SR|SRZ22/RSZ22][KOG0107]rsz-Selaginella moellendorfii@jgi_Selmo1_68846_gw1_3_1555_1_RRM_1[KOG0107]rsz-Selaginella moellendorfii@jgi_Selmo1_172361_estExt_Genewise1Plus____RRM_1

rsz-Physcomitrella patens@jgi_Phypa1_1_151194_RRM_1[KOG0107]rsz-Physcomitrella patens@jgi_Phypa1_1_143810_RRM_1[KOG0107]



rsz-Oryza sativa_japonica_cultivar_group@NP_001048352_RRM_1[SR|RSZp21b]asflkpl-Chlamydomonas reinhardtii@jgi_Chlre3_120469_RRM_1[KOG0105]

asflkpl-Volvox carteri@jgi_Volca1_72532_RRM_1[KOG0105]asflkan-Caenorhabditis elegans@Y111B2A_18_3_RRM_1[SR|CeSF2/ASF/rsp-3][KOG0105]

asflkpl-Volvox carteri@jgi_Volca1_45192_RRM_1[KOG0105]asflkpl-Chlamydomonas reinhardtii@jgi_Chlre3_129159_RRM_1[KOG0105]

asflkpl-Chlorella sp._NC64A@jgi_ChlNC64A_1_36976_estExt_Genewise1Plus____RRM_1asflkan-Mus musculus@ENSMUSP00000031513_RRM_1[SR|SRp30c][KOG0105]asflkan-Homo sapiens@ENSP00000229390_RRM_1[SR|SRp30c][KOG0105]

asflkan-Drosophila melanogaster@CG6987_PA_RRM_1[KOG0105]asflkan-Mus musculus@ENSMUSP00000103553_RRM_1[SR|ASF/SF2][KOG0105]asflkan-Mus musculus@ENSMUSP00000078792_RRM_1[SR|ASF/SF2][KOG0105]asflkan-Homo sapiens@ENSP00000258962_RRM_1[SR|ASF/SF2][KOG0105]

asflkpl-Oryza sativa_japonica_cultivar_group@NP_001060608_RRM_1[SR|SRp33a][KOG0105]asflkpl Populus trichocarpa@jgi_Poptr1_1_421685_gw1_XII_145_1_RRM_1[SR|SRp34a][KOG0105]

RSZ

"plant"

9G8SRp20

ASF-like

"animal"

SRp40

SRp55

SRp75

RS2Z

"plant"

SCL

N3

N4

N6Fig. S27

179

0.16

83

93100

57

76

100

73

100

98 64

74

83

96

90

82

100

97 77

59

55

66 99

58

94

84

77

68

99

55

57

89

100

62

93

51

100

64

rnps1-Caenorhabditis elegans@K02F3_11_1_RRM_1[KOG4209]rnps1-Drosophila melanogaster@CG16788_PA_RRM_1

rnps1-Drosophila melanogaster@CG41105_PC_RRM_1rnps1-Mus musculus@ENSMUSP00000057332_RRM_1[KOG4209]

rnps1-Mus musculus@ENSMUSP00000111025_RRM_1[RNPS1|RNPS1][KOG4209]rnps1-Mus musculus@ENSMUSP00000111028_RRM_1[RNPS1|RNPS1][KOG4209]rnps1-Homo sapiens@ENSP00000380275_RRM_1[RNPS1|RNPS1][KOG4209]

sr45-Volvox carteri@jgi_Volca1_105177_RRM_1[KOG0462]sr45-Chlorella sp._NC64A@jgi_ChlNC64A_1_138910_IGS_gm_22_00151_RRM_1

sr45-Micromonas pusilla_CCMP1545@jgi_MicpuC2_9037_gw1_7_479_1_RRM_1sr45-Micromonas pusilla_RCC299@jgi_MicpuN3_63440_EuGene_1300010090_RRM_1

sr45-Selaginella moellendorfii@jgi_Selmo1_446044_estExt_fgenesh2_pg____RRM_1sr45-Selaginella moellendorfii@jgi_Selmo1_424875_fgenesh2_pg____RRM_1



sr45-Oryza sativa_japonica_cultivar_group@NP_001054414_RRM_1[KOG0117]sr45-Sorghum bicolor_BTx623@jgi_Sorbi1_5054420_Sb03g046480_RRM_1

sr45-Oryza sativa_japonica_cultivar_group@NP_001045458_RRM_1sc35-Ostreococcus lucimarinus@jgi_Ost9901_3_8174_RRM_1[KOG4207]

sc35-Ostreococcus sp._RCC809@jgi_OstRCC809_1_16908_gw1_5_1114_1_RRM_1[KOG4207]sc35-Micromonas pusilla_CCMP1545@jgi_MicpuC2_9129_gw1_3_931_1_RRM_1[KOG4207]

sc35-Micromonas pusilla_RCC299@jgi_MicpuN3_91839_estExt_Genewise2____RRM_1sc35-Drosophila melanogaster@CG5442_PB_RRM_1[SR|SC35][KOG4207]

sc35-Caenorhabditis elegans@EEED8_7b_RRM_1[SR|CeSC35/rsp-4][KOG4207]sc35-Caenorhabditis elegans@EEED8_7a_RRM_1[SR|CeSC35/rsp-4]


sc35-Mus musculus@ENSMUSP00000072182_RRM_1[SR|SC35][KOG4207]sc35-Homo sapiens@ENSP00000293233_RRM_1[SR|SC35][KOG4368]sc35-Mus musculus@ENSMUSP00000090059_RRM_1[SR|SC35][KOG4368]sc35-Homo sapiens@ENSP00000353089_RRM_1[SR|SC35][KOG4368]

scl-Ostreococcus sp._RCC809@jgi_OstRCC809_1_16959_gw1_4_1177_1_RRM_1[KOG0108]scl-Ostreococcus lucimarinus@jgi_Ost9901_3_9858_RRM_1[KOG0108]

scl-Ostreococcus tauri@jgi_Ostta4_7793_RRM_1[KOG0108]sc35-Cyanidioschyzon merolae@gnl_CMER_CML202C_RRM_1

sc35-Oryza sativa_japonica_cultivar_group@NP_001060322_RRM_1[SR|SC35b][KOG4207]sc35-Sorghum bicolor_BTx623@jgi_Sorbi1_5029845_Sb01g033710_RRM_1[KOG4207]

sc35-Oryza sativa_japonica_cultivar_group@NP_001050263_RRM_1[SR|SC35c][KOG4207]sc35-Populus trichocarpa@jgi_Poptr1_1_709848_estExt_Genewise1___RRM_1[KOG4207]sc35-Populus trichocarpa@jgi_Poptr1_1_559112_eugene3_00050727_RRM_1[SR|SC35a][KOG4207]

sc35-Arabidopsis thaliana@NP_851261_RRM_1[SR|SC35][KOG4207]sc35-Populus trichocarpa@jgi_Poptr1_1_672394_grail3_1445000102_RRM_1[SR|SC35a][KOG4207]sc35-Populus trichocarpa@jgi_Poptr1_1_645719_grail3_0067008905_RRM_1[SR|SC35b][KOG4207]

sc35-Selaginella moellendorfii@jgi_Selmo1_134332_e_gw1_124_43_1_RRM_1[SR|SC35a][KOG4207]sc35-Sorghum bicolor_BTx623@jgi_Sorbi1_5059167_Sb07g029000_RRM_1[KOG0147]

sc35-Oryza sativa_japonica_cultivar_group@NP_001062094_RRM_1[SR|SC35a][KOG0415]sc35-Selaginella moellendorfii@jgi_Selmo1_7952_gw1_7_122_1_RRM_1[SR|SC35a][KOG4207]


scl-Micromonas pusilla_CCMP1545@jgi_MicpuC2_11901_gw1_8_619_1_RRM_1[KOG4207]scl-Micromonas pusilla_RCC299@jgi_MicpuN3_74643_gw2_11_587_1_RRM_1[KOG0107]

scl-Chlorella sp._NC64A@jgi_ChlNC64A_1_135593_IGS_gm_14_00126_RRM_1[KOG4207]srrp-Mus musculus@ENSMUSP00000103794_RRM_1[SRrp|SRrp35][KOG0111]

srrp-Homo sapiens@ENSP00000358479_RRM_1[SRrp|SRrp35]srrp-Mus musculus@ENSMUSP00000095455_RRM_1[SRrp|SRp38]srrp-Mus musculus@ENSMUSP00000030437_RRM_1[SRrp|SRp38][KOG0415]srrp-Mus musculus@ENSMUSP00000101479_RRM_1[SRrp|SRp38][KOG0415]srrp-Mus musculus@ENSMUSP00000099603_RRM_1[SRrp|SRp38][KOG0111]srrp-Mus musculus@ENSMUSP00000030438_RRM_1[SRrp|SRp38][KOG0111]srrp-Homo sapiens@ENSP00000342913_RRM_1[SRrp|SRp38][KOG0111]srrp-Homo sapiens@ENSP00000340764_RRM_1[SRrp|SRp38][KOG0111]srrp-Homo sapiens@ENSP00000363577_RRM_1[SRrp|SRp38][KOG0111]srrp-Homo sapiens@ENSP00000363576_RRM_1[SRrp|SRp38][KOG0111]srrp-Homo sapiens@ENSP00000363573_RRM_1[SRrp|SRp38][KOG0415]srrp-Homo sapiens@ENSP00000345293_RRM_1[SRrp|SRp38]

scl-Chlorella sp._NC64A@jgi_ChlNC64A_1_17896_gw1_13_295_1_RRM_1scl-Volvox carteri@jgi_Volca1_120666_RRM_1scl-Chlamydomonas reinhardtii@jgi_Chlre3_188086_RRM_1


scl-Volvox carteri@jgi_Volca1_121229_RRM_1[KOG0415]scl Chlamydomonas reinhardtii@jgi_Chlre3_116256_RRM_1

SRrp

SC35

RNPS1

SR45

N1

N2

Fig. S27

180

95

100

100

100 84

97

95

79

95

100 62

94

92 88

99 86

100

95

100

100

99

100 74

64

100

100 62

78

69

93

100 92

60

srp457-Homo sapiens@ENSP00000362251 RRM 1[SR|SRp55][KOG0106]srp457-Homo sapiens@ENSP00000244020_RRM_1[SR|SRp55][KOG0105]

srp457-Drosophila melanogaster@CG10851_PE_RRM_1[SR|SRp55][KOG0105]srp457-Drosophila melanogaster@CG10851_PC_RRM_1[SR|SRp55][KOG0105]srp457-Drosophila melanogaster@CG10851_PF_RRM_1[SR|Hrp45][KOG0106]srp457-Drosophila melanogaster@CG10851_PD_RRM_1[SR|Hrp45][KOG0106]srp457-Drosophila melanogaster@CG10851_PB_RRM_1[SR|SRp55][KOG0106]

srp457-Caenorhabditis elegans@T28D9_2b_RRM_1[SR|CeSC35-2/rsp-5][KOG0106]srp457-Caenorhabditis elegans@T28D9_2a_RRM_1[SR|CeSC35-2/rsp-5][KOG0106]srp457-Caenorhabditis elegans@T28D9_2d_RRM_1[SR|CeSC35-2/rsp-5][KOG0106]

srp457-Caenorhabditis elegans@W02B12_2_RRM_1[SR|CeSRp40/rsp-2][KOG0106]srp457-Caenorhabditis elegans@W02B12_3c_RRM_1[SR|CeSRp75/rsp-1][KOG0106]srp457-Caenorhabditis elegans@W02B12_3b_RRM_1[SR|CeSRp75/rsp-1][KOG0106]srp457-Caenorhabditis elegans@W02B12_3a_RRM_1[SR|CeSRp75/rsp-1][KOG0106]

asflkpl-Ostreococcus lucimarinus@jgi_Ost9901_3_8794_RRM_1[KOG0105]asflkpl-Ostreococcus sp._RCC809@jgi_OstRCC809_1_16551_gw1_5_1077_1_RRM_1[KOG0105]

rs-Chlorella sp._NC64A@jgi_ChlNC64A_1_25380_e_gw1_15_148_1_RRM_1[KOG0106]rs-Cyanidioschyzon merolae@gnl_CMER_CMO009C_RRM_1


rs-Populus trichocarpa@jgi_Poptr1_1_245070_gw1_XIV_1813_1_RRM_1[KOG0106]rs-Populus trichocarpa@jgi_Poptr1_1_552308_eugene3_00021623_RRM_1[KOG0106]

rs-Oryza sativa_japonica_cultivar_group@NP_001052061_RRM_1[SR|RSp29][KOG0106]rs-Sorghum bicolor_BTx623@jgi_Sorbi1_5056945_Sb06g001100_RRM_1[SR|RSp29][KOG0106]

rs-Arabidopsis thaliana@NP_567120_RRM_1[SR|RSp31][KOG0106]rs-Sorghum bicolor_BTx623@jgi_Sorbi1_5030607_Sb01g049590_RRM_1[KOG0106]

rs-Arabidopsis thaliana@NP_182184_RRM_1[SR|RSp31a][KOG0106]rs-Physcomitrella patens@jgi_Phypa1_1_167387_RRM_1[KOG0106]

rs-Selaginella moellendorfii@jgi_Selmo1_124209_e_gw1_74_375_1_RRM_1[KOG0106]rs-Selaginella moellendorfii@jgi_Selmo1_82477_e_gw1_5_1267_1_RRM_1[KOG0106]

rs-Populus trichocarpa@jgi_Poptr1_1_423171_gw1_XII_1631_1_RRM_1[KOG0106]rs-Populus trichocarpa@jgi_Poptr1_1_253698_gw1_XV_3134_1_RRM_1[KOG0106]


rs-Oryza sativa_japonica_cultivar_group@NP_001045729_RRM_1[SR|RSp33][KOG0106]rs-Sorghum bicolor_BTx623@jgi_Sorbi1_5054582_Sb04g001910_RRM_1[KOG0106]

rs-Populus trichocarpa@jgi_Poptr1_1_244286_gw1_XIV_1029_1_RRM_1[KOG0106]rs-Populus trichocarpa@jgi_Poptr1_1_411608_gw1_II_2943_1_RRM_1[SR|RSp33][KOG0106]rs-Populus trichocarpa@jgi_Poptr1_1_644386_grail3_0033034501_RRM_1[SR|RSp33][KOG0106]


asflkan-Caenorhabditis elegans@Y111B2A_18_3_RRM_1[SR|CeSF2/ASF/rsp-3][KOG0105]asflkpl-Chlamydomonas reinhardtii@jgi_Chlre3_129159_RRM_1[KOG0105]

asflkpl-Volvox carteri@jgi_Volca1_45192_RRM_1[KOG0105]asflkpl-Chlorella sp._NC64A@jgi_ChlNC64A_1_36976_estExt_Genewise1Plus____RRM_1

asflkpl-Oryza sativa_japonica_cultivar_group@NP_001060608_RRM_1[SR|SRp33a][KOG0105]asflkpl-Selaginella moellendorfii@jgi_Selmo1_97566_e_gw1_19_485_1_RRM_1[KOG0105]asflkpl-Selaginella moellendorfii@jgi_Selmo1_119951_e_gw1_61_278_1_RRM_1[KOG0105]

asflkpl-Sorghum bicolor_BTx623@jgi_Sorbi1_5035702_Sb03g013010_RRM_1[SR|SR20][KOG0105]asflkpl-Oryza sativa_japonica_cultivar_group@NP_001055323_RRM_1[SR|SRp33b][KOG0105]

asflkpl-Arabidopsis thaliana@NP_683288_RRM_1[SR|SRp30][KOG0105]asflkpl-Arabidopsis thaliana@NP_172386_RRM_1[SR|SRp30][KOG0105]

asflkan-Homo sapiens@ENSP00000229390_RRM_1[SR|SRp30c][KOG0105]asflkan-Mus musculus@ENSMUSP00000031513_RRM_1[SR|SRp30c][KOG0105]

asflkan-Drosophila melanogaster@CG6987_PA_RRM_1[KOG0105]asflkan-Mus musculus@ENSMUSP00000103553_RRM_1[SR|ASF/SF2][KOG0105]asflkan-Mus musculus@ENSMUSP00000078792_RRM_1[SR|ASF/SF2][KOG0105]asflkan-Homo sapiens@ENSP00000258962_RRM_1[SR|ASF/SF2][KOG0105]

asflkpl-Arabidopsis thaliana@NP_849537_RRM_1[SR|SRp34b][KOG0105]asflkpl-Arabidopsis thaliana@NP_567235_RRM_1[SR|SRp34b][KOG0105]

asflkpl-Arabidopsis thaliana@NP_850934_RRM_1[SR|SR1/SRp34][KOG0105]asflkpl-Arabidopsis thaliana@NP_850933_RRM_1[SR|SR1/SRp34][KOG0105]

asflkpl-Populus trichocarpa@jgi_Poptr1_1_409414_gw1_II_749_1_RRM_1[KOG0105]asflkpl-Populus trichocarpa@jgi_Poptr1_1_664446_grail3_0061020502_RRM_1[SR|SRp33a][KOG0105]

asflkpl-Populus trichocarpa@jgi_Poptr1_1_773626_fgenesh4_pg___RRM_1[SR|SRp30][KOG0105]asflkpl-Populus trichocarpa@jgi_Poptr1_1_811208_fgenesh4_pm____RRM_1




asflkpl-Selaginella moellendorfii@jgi_Selmo1_36388_gw1_41_236_1_RRM_1[KOG0105]asflkpl-Physcomitrella patens@jgi_Phypa1_1_205547_RRM_1[KOG0105]


ASF-like

"plant"ASF-like

"animal"

RRM1

RS "plant"

SRp40

SRp55

SRp75

N5

N6

Fig. S28

181

67 83

73

100

67

52

91

61

55 52

57

71

81

98

100

95 69 52

55

68

86

96

97

100100

90

73

71 67

99

88 70

100

90

87 84

100 88

57

64

100

75

62

87

52 83

100

100

95 86

67 55

srp20-Drosophila melanogaster@CG10203 PA RRM 1[SR|9G8][KOG0107]srp20-Mus musculus@ENSMUSP00000100538_RRM_1[SR|SRp20][KOG0107]

srp20-Mus musculus@ENSMUSP00000049025_RRM_1[SR|SRp20][KOG0107]srp20-Homo sapiens@ENSP00000344762_RRM_1[SR|SRp20][KOG0107]srp20-Homo sapiens@ENSP00000362820_RRM_1[SR|SRp20][KOG0107]srp20-Mus musculus@ENSMUSP00000110365_RRM_1[SR|SRp20][KOG0107]

9g8-Mus musculus@ENSMUSP00000070983_RRM_1[SR|9G8][KOG0107]9g8-Mus musculus@ENSMUSP00000108040_RRM_1[SR|9G8][KOG0107]9g8-Homo sapiens@ENSP00000325905_RRM_1[SR|9G8]9g8-Homo sapiens@ENSP00000368134_RRM_1[SR|9G8][KOG0107]9g8-Homo sapiens@ENSP00000368146_RRM_1[SR|9G8][KOG0107]9g8-Mus musculus@ENSMUSP00000066393_RRM_1[SR|9G8][KOG0107]

scl-Micromonas pusilla_RCC299@jgi_MicpuN3_74643_gw2_11_587_1_RRM_1[KOG0107]scl-Micromonas pusilla_CCMP1545@jgi_MicpuC2_11901_gw1_8_619_1_RRM_1[KOG4207]

sc35-Cyanidioschyzon merolae@gnl_CMER_CML202C_RRM_1sc35-Oryza sativa_japonica_cultivar_group@NP_001060322_RRM_1[SR|SC35b][KOG4207]

sc35-Populus trichocarpa@jgi_Poptr1_1_559112_eugene3_00050727_RRM_1[SR|SC35a][KOG4207]sc35-Populus trichocarpa@jgi_Poptr1_1_709848_estExt_Genewise1___RRM_1[KOG4207]

sc35-Arabidopsis thaliana@NP_851261_RRM_1[SR|SC35][KOG4207]sc35-Populus trichocarpa@jgi_Poptr1_1_645719_grail3_0067008905_RRM_1[SR|SC35b][KOG4207]sc35-Populus trichocarpa@jgi_Poptr1_1_672394_grail3_1445000102_RRM_1[SR|SC35a][KOG4207]

sc35-Oryza sativa_japonica_cultivar_group@NP_001062094_RRM_1[SR|SC35a][KOG0415]sc35-Sorghum bicolor_BTx623@jgi_Sorbi1_5029845_Sb01g033710_RRM_1[KOG4207]

sc35-Oryza sativa_japonica_cultivar_group@NP_001050263_RRM_1[SR|SC35c][KOG4207]sc35-Sorghum bicolor_BTx623@jgi_Sorbi1_5059167_Sb07g029000_RRM_1[KOG0147]

sc35-Selaginella moellendorfii@jgi_Selmo1_134332_e_gw1_124_43_1_RRM_1[SR|SC35a][KOG4207]sc35-Selaginella moellendorfii@jgi_Selmo1_7952_gw1_7_122_1_RRM_1[SR|SC35a][KOG4207]


sc35-Micromonas pusilla_CCMP1545@jgi_MicpuC2_9129_gw1_3_931_1_RRM_1[KOG4207]sc35-Micromonas pusilla_RCC299@jgi_MicpuN3_91839_estExt_Genewise2____RRM_1

sc35-Ostreococcus sp._RCC809@jgi_OstRCC809_1_16908_gw1_5_1114_1_RRM_1[KOG4207]sc35-Ostreococcus lucimarinus@jgi_Ost9901_3_8174_RRM_1[KOG4207]

scl-Ostreococcus tauri@jgi_Ostta4_7793_RRM_1[KOG0108]scl-Ostreococcus sp._RCC809@jgi_OstRCC809_1_16959_gw1_4_1177_1_RRM_1[KOG0108]

scl-Ostreococcus lucimarinus@jgi_Ost9901_3_9858_RRM_1[KOG0108]sc35-Drosophila melanogaster@CG5442_PB_RRM_1[SR|SC35][KOG4207]

sc35-Caenorhabditis elegans@EEED8_7b_RRM_1[SR|CeSC35/rsp-4][KOG4207]sc35-Caenorhabditis elegans@EEED8_7a_RRM_1[SR|CeSC35/rsp-4]


sc35-Mus musculus@ENSMUSP00000090059_RRM_1[SR|SC35][KOG4368]sc35-Homo sapiens@ENSP00000353089_RRM_1[SR|SC35][KOG4368]sc35-Homo sapiens@ENSP00000293233_RRM_1[SR|SC35][KOG4368]sc35-Mus musculus@ENSMUSP00000072182_RRM_1[SR|SC35][KOG4207]

scl-Chlamydomonas reinhardtii@jgi_Chlre3_188086_RRM_1scl-Volvox carteri@jgi_Volca1_120666_RRM_1


scl-Chlorella sp._NC64A@jgi_ChlNC64A_1_135593_IGS_gm_14_00126_RRM_1[KOG4207]scl-Volvox carteri@jgi_Volca1_121229_RRM_1[KOG0415]scl-Chlamydomonas reinhardtii@jgi_Chlre3_116256_RRM_1scl-Chlorella sp._NC64A@jgi_ChlNC64A_1_17896_gw1_13_295_1_RRM_1

srrp-Mus musculus@ENSMUSP00000103794_RRM_1[SRrp|SRrp35][KOG0111]srrp-Homo sapiens@ENSP00000358479_RRM_1[SRrp|SRrp35]

srrp-Mus musculus@ENSMUSP00000101479_RRM_1[SRrp|SRp38][KOG0415]srrp-Homo sapiens@ENSP00000363573_RRM_1[SRrp|SRp38][KOG0415]srrp-Homo sapiens@ENSP00000342913_RRM_1[SRrp|SRp38][KOG0111]srrp-Homo sapiens@ENSP00000345293_RRM_1[SRrp|SRp38]srrp-Mus musculus@ENSMUSP00000095455_RRM_1[SRrp|SRp38]srrp-Homo sapiens@ENSP00000340764_RRM_1[SRrp|SRp38][KOG0111]srrp-Mus musculus@ENSMUSP00000099603_RRM_1[SRrp|SRp38][KOG0111]srrp-Mus musculus@ENSMUSP00000030437_RRM_1[SRrp|SRp38][KOG0415]srrp-Mus musculus@ENSMUSP00000030438_RRM_1[SRrp|SRp38][KOG0111]srrp-Homo sapiens@ENSP00000363577_RRM_1[SRrp|SRp38][KOG0111]srrp-Homo sapiens@ENSP00000363576_RRM_1[SRrp|SRp38][KOG0111]

scl-Selaginella moellendorfii@jgi_Selmo1_8401_gw1_62_42_1_RRM_1[KOG4207]scl-Physcomitrella patens@jgi_Phypa1_1_141868_RRM_1scl-Physcomitrella patens@jgi_Phypa1_1_108464_RRM_1

scl-Populus trichocarpa@jgi_Poptr1_1_227475_gw1_X_2172_1_RRM_1[KOG0127]scl-Populus trichocarpa@jgi_Poptr1_1_656109_grail3_0049021701_RRM_1[KOG0122]

scl-Sorghum bicolor_BTx623@jgi_Sorbi1_5047478_Sb0514s002010_RRM_1[KOG0110]scl-Oryza sativa_japonica_cultivar_group@NP_001046448_RRM_1[SR|SCL30a]scl-Oryza sativa_japonica_cultivar_group@NP_001067091_RRM_1[SR|SCL30b]

scl-Arabidopsis thaliana@NP_567021_RRM_1[SR|SCL30][KOG0122]scl-Sorghum bicolor_BTx623@jgi_Sorbi1_5056881_Sb05g027700_RRM_1

scl-Oryza sativa_japonica_cultivar_group@NP_001068546_RRM_1[KOG0127]scl-Selaginella moellendorfii@jgi_Selmo1_8339_gw1_49_32_1_RRM_1[KOG4207]

scl-Sorghum bicolor_BTx623@jgi_Sorbi1_5049384_Sb01g034590_RRM_1[KOG0127]scl-Oryza sativa_japonica_cultivar_group@NP_001050168_RRM_1

scl-Populus trichocarpa@jgi_Poptr1_1_814124_estExt_fgenesh4_kg___RRM_1scl-Populus trichocarpa@jgi_Poptr1_1_420699_gw1_VIII_2127_1_RRM_1[SR|SCL28]

scl-Arabidopsis thaliana@NP_197382_RRM_1[SR|SCL28][KOG0127]scl-Selaginella moellendorfii@jgi_Selmo1_102070_e_gw1_25_62_1_RRM_1[KOG0148]scl-Selaginella moellendorfii@jgi_Selmo1_79810_e_gw1_3_146_1_RRM_1[KOG4207]

scl-Populus trichocarpa@jgi_Poptr1_1_256035_gw1_XVI_1974_1_RRM_1[SR|SCL25][KOG0111]scl-Sorghum bicolor_BTx623@jgi_Sorbi1_5052097_Sb02g040350_RRM_1[SR|SCL25]scl-Oryza sativa_japonica_cultivar_group@NP_001060372_RRM_1[SR|SCL25]

scl-Oryza sativa_japonica_cultivar_group@NP_001050213_RRM_1[KOG4207]scl-Sorghum bicolor_BTx623@jgi_Sorbi1_5049360_Sb01g034200_RRM_1

scl-Populus trichocarpa@jgi_Poptr1_1_547618_eugene3_00010059_RRM_1scl-Arabidopsis thaliana@NP_187966_RRM_1[SR|SCL30a]scl-Arabidopsis thaliana@NP_001031195_RRM_1[SR|SR33/SCL33][KOG0110]scl-Arabidopsis thaliana@NP_564685_RRM_1[SR|SR33/SCL33][KOG0110]



rs2z-Sorghum bicolor_BTx623@jgi_Sorbi1_5045949_Sb09g004685_RRM_1[KOG0106]rs2z-Oryza sativa_japonica_cultivar_group@NP_001054731_RRM_1[SR|RSZ39]

rs2z-Populus trichocarpa@jgi_Poptr1_1_667717_grail3_0004036801_RRM_1[SR|RSZ37b][KOG0107]rs2z-Populus trichocarpa@jgi_Poptr1_1_653760_grail3_0013007302_RRM_1[SR|RSZ37b][KOG0107]rs2z-Arabidopsis thaliana@NP_190918_RRM_1[SR|RSZ32][KOG0107]

rs2z-Arabidopsis thaliana@NP_850280_RRM_1[SR|RSZ33][KOG0107]rs2z-Oryza sativa_japonica_cultivar_group@NP_001042066_RRM_1[SR|RSZ37a][KOG0109]

rs2z-Sorghum bicolor_BTx623@jgi_Sorbi1_5052652_Sb03g005500_RRM_1[KOG0109]rs2z-Sorghum bicolor_BTx623@jgi_Sorbi1_5059999_Sb09g001910_RRM_1[SR|RSZ36][KOG0109]rs2z-Sorghum bicolor_BTx623@jgi_Sorbi1_5060000_Sb09g001920_RRM_1[SR|RSZ36][KOG0106]


srp457-Mus musculus@ENSMUSP00000105983_RRM_1[SR|SRp40][KOG0106]srp457-Mus musculus@ENSMUSP00000021562_RRM_1[SR|SRp40][KOG0106]srp457-Homo sapiens@ENSP00000377892_RRM_1[SR|SRp40][KOG0105]srp457-Mus musculus@ENSMUSP00000105985_RRM_1[SR|SRp40][KOG0106]srp457-Homo sapiens@ENSP00000342294_RRM_1[SR|SRp40][KOG0106]

srp457-Homo sapiens@ENSP00000362900_RRM_1[SR|SRp75][KOG0105]srp457-Mus musculus@ENSMUSP00000061474_RRM_1[SR|SRp75][KOG0105]

srp457-Mus musculus@ENSMUSP00000017065_RRM_1[SR|SRp55][KOG0105]p p _ _ [ p ][ ] SRp75

RS2Z

"plant"

SCL

SRrp

SC35

9G8SRp20

N1

N2

Fig. S28

182

0.17

71

99 94

52

63

100

72

100

94 87

52

85

78

82 50

100 60

98

95

97 98

93

89

100

100

64

77

100 53

100

100

57

54

58

56 82

74

62

100 85

sr45-Volvox carteri@jgi_Volca1_105177_RRM_1[KOG0462]rnps1-Caenorhabditis elegans@K02F3_11_1_RRM_1[KOG4209]

rnps1-Drosophila melanogaster@CG41105_PC_RRM_1rnps1-Drosophila melanogaster@CG16788_PA_RRM_1rnps1-Mus musculus@ENSMUSP00000057332_RRM_1[KOG4209]

rnps1-Homo sapiens@ENSP00000380275_RRM_1[RNPS1|RNPS1][KOG4209]rnps1-Mus musculus@ENSMUSP00000111025_RRM_1[RNPS1|RNPS1][KOG4209]rnps1-Mus musculus@ENSMUSP00000111028_RRM_1[RNPS1|RNPS1][KOG4209]

sr45-Chlorella sp._NC64A@jgi_ChlNC64A_1_138910_IGS_gm_22_00151_RRM_1sr45-Micromonas pusilla_CCMP1545@jgi_MicpuC2_9037_gw1_7_479_1_RRM_1

sr45-Micromonas pusilla_RCC299@jgi_MicpuN3_63440_EuGene_1300010090_RRM_1sr45-Selaginella moellendorfii@jgi_Selmo1_424875_fgenesh2_pg____RRM_1sr45-Selaginella moellendorfii@jgi_Selmo1_446044_estExt_fgenesh2_pg____RRM_1



sr45-Oryza sativa_japonica_cultivar_group@NP_001054414_RRM_1[KOG0117]sr45-Sorghum bicolor_BTx623@jgi_Sorbi1_5054420_Sb03g046480_RRM_1

sr45-Oryza sativa_japonica_cultivar_group@NP_001045458_RRM_12rs-Cyanidioschyzon merolae@gnl_CMER_CMO009C_RRM_2

2rs-Chlorella sp._NC64A@jgi_ChlNC64A_1_25380_e_gw1_15_148_1_RRM_22rs-Chlamydomonas reinhardtii@jgi_Chlre3_120019_RRM_2[KOG0106]

2rs-Volvox carteri@jgi_Volca1_80657_RRM_12rs-Chlamydomonas reinhardtii@jgi_Chlre3_80366_RRM_2[KOG0106]


2rs-Populus trichocarpa@jgi_Poptr1_1_423171_gw1_XII_1631_1_RRM_22rs-Populus trichocarpa@jgi_Poptr1_1_253698_gw1_XV_3134_1_RRM_22rs-Arabidopsis thaliana@NP_200017_RRM_22rs-Arabidopsis thaliana@NP_851174_RRM_2



2rs-Populus trichocarpa@jgi_Poptr1_1_411608_gw1_II_2943_1_RRM_22rs-Populus trichocarpa@jgi_Poptr1_1_244286_gw1_XIV_1029_1_RRM_2


2rs-Populus trichocarpa@jgi_Poptr1_1_245070_gw1_XIV_1813_1_RRM_22rs-Populus trichocarpa@jgi_Poptr1_1_552308_eugene3_00021623_RRM_2

2rs-Arabidopsis thaliana@NP_973702_RRM_12rs-Arabidopsis thaliana@NP_182184_RRM_22rs-Arabidopsis thaliana@NP_567120_RRM_2

2rs-Sorghum bicolor_BTx623@jgi_Sorbi1_5030607_Sb01g049590_RRM_29g8-Drosophila melanogaster@CG5655_PA_RRM_1[KOG0107]

rsz-Chlorella sp._NC64A@jgi_ChlNC64A_1_135849_IGS_gm_14_00382_RRM_1rsz-Chlamydomonas reinhardtii@jgi_Chlre3_132362_RRM_1[KOG0107]

rsz-Volvox carteri@jgi_Volca1_121301_RRM_1[KOG0107]rsz-Chlamydomonas reinhardtii@jgi_Chlre3_192053_RRM_1[KOG0107]

rsz-Chlorella sp._NC64A@jgi_ChlNC64A_1_139931_IGS_gm_27_00109_RRM_1[KOG0107]rsz-Selaginella moellendorfii@jgi_Selmo1_68846_gw1_3_1555_1_RRM_1[KOG0107]rsz-Selaginella moellendorfii@jgi_Selmo1_172361_estExt_Genewise1Plus____RRM_1

rsz-Physcomitrella patens@jgi_Phypa1_1_151194_RRM_1[KOG0107]rsz-Physcomitrella patens@jgi_Phypa1_1_143810_RRM_1[KOG0107]

rsz-Arabidopsis thaliana@NP_564208_RRM_1[SR|SRZ21/RSZ21]rsz-Populus trichocarpa@jgi_Poptr1_1_248500_gw1_XIX_900_1_RRM_1[SR|SRZ21/RSZ21][KOG0107]



rsz-Oryza sativa_japonica_cultivar_group@NP_001048352_RRM_1[SR|RSZp21b]rsz-Arabidopsis thaliana@NP_180035_RRM_1[SR|RSZ22a]rsz-Arabidopsis thaliana@NP_194886_RRM_1[SR|SRZ22/RSZ22][KOG0107]


9g8-Drosophila melanogaster@CG1987_PA_RRM_1[KOG0107]9g8-Drosophila melanogaster@CG17136_PC_RRM_1[KOG0107]9g8-Drosophila melanogaster@CG17136_PB_RRM_1[KOG0107]9g8-Drosophila melanogaster@CG17136_PD_RRM_1[KOG0107]

p p g _ _ _ [ ][ ]

RSZ

"plant"

RRM2

RS

"plant"

SR45

RNPS1

N4Fig. S28

183

8894

99

70 96

100

70 68

60

100

100100

62

99

71

96 95

98

92 88

99

100 86

95 58

57

99

60

99

99

100

64

82

94

90

94 57

100

99 99

52

66

88

53

52

62

68

56

99

58

75

asflkpl-Arabidopsis thaliana@NP_850934_RRM_1[SR|SR1/SRp34][KOG0105]asflkpl-Arabidopsis thaliana@NP_567235_RRM_1[SR|SRp34b][KOG0105]asflkpl-Arabidopsis thaliana@NP_849537_RRM_1[SR|SRp34b][KOG0105]

asflkpl-Oryza sativa_japonica_cultivar_group@NP_001050082_RRM_1[SR|SRp32][KOG0105]asflkpl-Sorghum bicolor_BTx623@jgi_Sorbi1_5049442_Sb01g035680_RRM_1[SR|SRp32][KOG0105]

asflkpl-Populus trichocarpa@jgi_Poptr1_1_664446_grail3_0061020502_RRM_1[SR|SRp33a][KOG0105]asflkpl-Populus trichocarpa@jgi_Poptr1_1_409414_gw1_II_749_1_RRM_1[KOG0105]

asflkpl-Populus trichocarpa@jgi_Poptr1_1_773626_fgenesh4_pg___RRM_1[SR|SRp30][KOG0105]asflkpl-Populus trichocarpa@jgi_Poptr1_1_811208_fgenesh4_pm____RRM_1



asflkpl-Physcomitrella patens@jgi_Phypa1_1_113630_RRM_1[KOG0105]asflkpl-Physcomitrella patens@jgi_Phypa1_1_140978_RRM_1[KOG0105]asflkpl-Physcomitrella patens@jgi_Phypa1_1_205547_RRM_1[KOG0105]

asflkpl-Selaginella moellendorfii@jgi_Selmo1_36388_gw1_41_236_1_RRM_1[KOG0105]asflkpl-Arabidopsis thaliana@NP_001078264_RRM_1[SR|SRp34a][KOG0105]asflkpl-Arabidopsis thaliana@NP_190512_RRM_1[SR|SRp34a][KOG0105]


asflkan-Caenorhabditis elegans@Y111B2A_18_3_RRM_1[SR|CeSF2/ASF/rsp-3][KOG0105]asflkpl-Ostreococcus lucimarinus@jgi_Ost9901_3_8794_RRM_1[KOG0105]asflkpl-Ostreococcus sp._RCC809@jgi_OstRCC809_1_16551_gw1_5_1077_1_RRM_1[KOG0105]

asflkpl-Chlamydomonas reinhardtii@jgi_Chlre3_129159_RRM_1[KOG0105]asflkpl-Volvox carteri@jgi_Volca1_45192_RRM_1[KOG0105]

rs-Sorghum bicolor_BTx623@jgi_Sorbi1_5054582_Sb04g001910_RRM_1[KOG0106]rs-Oryza sativa_japonica_cultivar_group@NP_001045729_RRM_1[SR|RSp33][KOG0106]

rs-Populus trichocarpa@jgi_Poptr1_1_244286_gw1_XIV_1029_1_RRM_1[KOG0106]rs-Populus trichocarpa@jgi_Poptr1_1_411608_gw1_II_2943_1_RRM_1[SR|RSp33][KOG0106]rs-Populus trichocarpa@jgi_Poptr1_1_644386_grail3_0033034501_RRM_1[SR|RSp33][KOG0106]rs-Populus trichocarpa@jgi_Poptr1_1_253698_gw1_XV_3134_1_RRM_1[KOG0106]rs-Populus trichocarpa@jgi_Poptr1_1_423171_gw1_XII_1631_1_RRM_1[KOG0106]rs-Arabidopsis thaliana@NP_194280_RRM_1[SR|RSp40/SRp35][KOG0106]rs-Arabidopsis thaliana@NP_200017_RRM_1[SR|RSp41][KOG0106]rs-Arabidopsis thaliana@NP_851174_RRM_1[SR|RSp41][KOG0106]

rs-Cyanidioschyzon merolae@gnl_CMER_CMO009C_RRM_1rs-Chlorella sp._NC64A@jgi_ChlNC64A_1_25380_e_gw1_15_148_1_RRM_1[KOG0106]


rs-Physcomitrella patens@jgi_Phypa1_1_167387_RRM_1[KOG0106]rs-Selaginella moellendorfii@jgi_Selmo1_82477_e_gw1_5_1267_1_RRM_1[KOG0106]rs-Selaginella moellendorfii@jgi_Selmo1_124209_e_gw1_74_375_1_RRM_1[KOG0106]

rs-Arabidopsis thaliana@NP_567120_RRM_1[SR|RSp31][KOG0106]rs-Populus trichocarpa@jgi_Poptr1_1_552308_eugene3_00021623_RRM_1[KOG0106]rs-Populus trichocarpa@jgi_Poptr1_1_245070_gw1_XIV_1813_1_RRM_1[KOG0106]rs-Arabidopsis thaliana@NP_182184_RRM_1[SR|RSp31a][KOG0106]

rs-Sorghum bicolor_BTx623@jgi_Sorbi1_5030607_Sb01g049590_RRM_1[KOG0106]rs-Oryza sativa_japonica_cultivar_group@NP_001052061_RRM_1[SR|RSp29][KOG0106]

rs-Sorghum bicolor_BTx623@jgi_Sorbi1_5056945_Sb06g001100_RRM_1[SR|RSp29][KOG0106]2rs-Chlamydomonas reinhardtii@jgi_Chlre3_120019_RRM_2[KOG0106]


2rs-Chlorella sp._NC64A@jgi_ChlNC64A_1_25380_e_gw1_15_148_1_RRM_22rs-Cyanidioschyzon merolae@gnl_CMER_CMO009C_RRM_2

2rs-Selaginella moellendorfii@jgi_Selmo1_124209_e_gw1_74_375_1_RRM_22rs-Selaginella moellendorfii@jgi_Selmo1_82477_e_gw1_5_1267_1_RRM_2

2rs-Physcomitrella patens@jgi_Phypa1_1_167387_RRM_22rs-Oryza sativa_japonica_cultivar_group@NP_001052061_RRM_2

2rs-Sorghum bicolor_BTx623@jgi_Sorbi1_5056945_Sb06g001100_RRM_22rs-Populus trichocarpa@jgi_Poptr1_1_552308_eugene3_00021623_RRM_22rs-Populus trichocarpa@jgi_Poptr1_1_245070_gw1_XIV_1813_1_RRM_22rs-Arabidopsis thaliana@NP_973702_RRM_12rs-Arabidopsis thaliana@NP_182184_RRM_22rs-Arabidopsis thaliana@NP_567120_RRM_2


2rs-Sorghum bicolor_BTx623@jgi_Sorbi1_5054582_Sb04g001910_RRM_22rs-Populus trichocarpa@jgi_Poptr1_1_411608_gw1_II_2943_1_RRM_2

2rs-Populus trichocarpa@jgi_Poptr1_1_244286_gw1_XIV_1029_1_RRM_22rs-Populus trichocarpa@jgi_Poptr1_1_423171_gw1_XII_1631_1_RRM_22rs-Populus trichocarpa@jgi_Poptr1_1_253698_gw1_XV_3134_1_RRM_22rs-Arabidopsis thaliana@NP_200017_RRM_22rs-Arabidopsis thaliana@NP_851174_RRM_2


RRM2

RS "plant"

RRM1

RS "plant"

ASF-like

"plant"

Fig. S29

184

54 82

56

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100

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71

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83

64

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100

50 51

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100

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57

scl-Volvox carteri@jgi_Volca1_121229_RRM_1[KOG0415]scl-Arabidopsis thaliana@NP_567021_RRM_1[SR|SCL30][KOG0122]

scl-Sorghum bicolor_BTx623@jgi_Sorbi1_5056881_Sb05g027700_RRM_1scl-Oryza sativa_japonica_cultivar_group@NP_001068546_RRM_1[KOG0127]

scl-Sorghum bicolor_BTx623@jgi_Sorbi1_5047478_Sb0514s002010_RRM_1[KOG0110]scl-Oryza sativa_japonica_cultivar_group@NP_001046448_RRM_1[SR|SCL30a]scl-Oryza sativa_japonica_cultivar_group@NP_001067091_RRM_1[SR|SCL30b]

scl-Populus trichocarpa@jgi_Poptr1_1_656109_grail3_0049021701_RRM_1[KOG0122]scl-Populus trichocarpa@jgi_Poptr1_1_227475_gw1_X_2172_1_RRM_1[KOG0127]

scl-Selaginella moellendorfii@jgi_Selmo1_8401_gw1_62_42_1_RRM_1[KOG4207]scl-Physcomitrella patens@jgi_Phypa1_1_108464_RRM_1scl-Physcomitrella patens@jgi_Phypa1_1_141868_RRM_1scl-Selaginella moellendorfii@jgi_Selmo1_8339_gw1_49_32_1_RRM_1[KOG4207]

scl-Oryza sativa_japonica_cultivar_group@NP_001050168_RRM_1scl-Sorghum bicolor_BTx623@jgi_Sorbi1_5049384_Sb01g034590_RRM_1[KOG0127]scl-Populus trichocarpa@jgi_Poptr1_1_814124_estExt_fgenesh4_kg___RRM_1

scl-Arabidopsis thaliana@NP_197382_RRM_1[SR|SCL28][KOG0127]scl-Populus trichocarpa@jgi_Poptr1_1_420699_gw1_VIII_2127_1_RRM_1[SR|SCL28]

scl-Selaginella moellendorfii@jgi_Selmo1_79810_e_gw1_3_146_1_RRM_1[KOG4207]scl-Selaginella moellendorfii@jgi_Selmo1_102070_e_gw1_25_62_1_RRM_1[KOG0148]

scl-Populus trichocarpa@jgi_Poptr1_1_256035_gw1_XVI_1974_1_RRM_1[SR|SCL25][KOG0111]scl-Populus trichocarpa@jgi_Poptr1_1_547618_eugene3_00010059_RRM_1scl-Arabidopsis thaliana@NP_187966_RRM_1[SR|SCL30a]scl-Arabidopsis thaliana@NP_001031195_RRM_1[SR|SR33/SCL33][KOG0110]scl-Arabidopsis thaliana@NP_564685_RRM_1[SR|SR33/SCL33][KOG0110]scl-Oryza sativa_japonica_cultivar_group@NP_001060372_RRM_1[SR|SCL25]scl-Sorghum bicolor_BTx623@jgi_Sorbi1_5052097_Sb02g040350_RRM_1[SR|SCL25]scl-Oryza sativa_japonica_cultivar_group@NP_001050213_RRM_1[KOG4207]

scl-Sorghum bicolor_BTx623@jgi_Sorbi1_5049360_Sb01g034200_RRM_1srrp-Homo sapiens@ENSP00000358479_RRM_1[SRrp|SRrp35]

srrp-Mus musculus@ENSMUSP00000103794_RRM_1[SRrp|SRrp35][KOG0111]srrp-Homo sapiens@ENSP00000345293_RRM_1[SRrp|SRp38]srrp-Mus musculus@ENSMUSP00000030437_RRM_1[SRrp|SRp38][KOG0415]srrp-Homo sapiens@ENSP00000363576_RRM_1[SRrp|SRp38][KOG0111]srrp-Mus musculus@ENSMUSP00000099603_RRM_1[SRrp|SRp38][KOG0111]srrp-Homo sapiens@ENSP00000363577_RRM_1[SRrp|SRp38][KOG0111]srrp-Homo sapiens@ENSP00000340764_RRM_1[SRrp|SRp38][KOG0111]srrp-Homo sapiens@ENSP00000342913_RRM_1[SRrp|SRp38][KOG0111]srrp-Homo sapiens@ENSP00000363573_RRM_1[SRrp|SRp38][KOG0415]srrp-Mus musculus@ENSMUSP00000095455_RRM_1[SRrp|SRp38]srrp-Mus musculus@ENSMUSP00000101479_RRM_1[SRrp|SRp38][KOG0415]srrp-Mus musculus@ENSMUSP00000030438_RRM_1[SRrp|SRp38][KOG0111]

sc35-Micromonas pusilla_RCC299@jgi_MicpuN3_91839_estExt_Genewise2____RRM_1sc35-Micromonas pusilla_CCMP1545@jgi_MicpuC2_9129_gw1_3_931_1_RRM_1[KOG4207]sc35-Ostreococcus sp._RCC809@jgi_OstRCC809_1_16908_gw1_5_1114_1_RRM_1[KOG4207]

sc35-Ostreococcus lucimarinus@jgi_Ost9901_3_8174_RRM_1[KOG4207]sc35-Drosophila melanogaster@CG5442_PB_RRM_1[SR|SC35][KOG4207]

sc35-Caenorhabditis elegans@EEED8_7a_RRM_1[SR|CeSC35/rsp-4]sc35-Caenorhabditis elegans@EEED8_7b_RRM_1[SR|CeSC35/rsp-4][KOG4207]


sc35-Homo sapiens@ENSP00000353089_RRM_1[SR|SC35][KOG4368]sc35-Mus musculus@ENSMUSP00000072182_RRM_1[SR|SC35][KOG4207]sc35-Homo sapiens@ENSP00000293233_RRM_1[SR|SC35][KOG4368]sc35-Mus musculus@ENSMUSP00000090059_RRM_1[SR|SC35][KOG4368]

sc35-Oryza sativa_japonica_cultivar_group@NP_001060322_RRM_1[SR|SC35b][KOG4207]sc35-Oryza sativa_japonica_cultivar_group@NP_001050263_RRM_1[SR|SC35c][KOG4207]

sc35-Sorghum bicolor_BTx623@jgi_Sorbi1_5029845_Sb01g033710_RRM_1[KOG4207]sc35-Arabidopsis thaliana@NP_851261_RRM_1[SR|SC35][KOG4207]

sc35-Populus trichocarpa@jgi_Poptr1_1_645719_grail3_0067008905_RRM_1[SR|SC35b][KOG4207]sc35-Populus trichocarpa@jgi_Poptr1_1_672394_grail3_1445000102_RRM_1[SR|SC35a][KOG4207]sc35-Populus trichocarpa@jgi_Poptr1_1_559112_eugene3_00050727_RRM_1[SR|SC35a][KOG4207]sc35-Populus trichocarpa@jgi_Poptr1_1_709848_estExt_Genewise1___RRM_1[KOG4207]

sc35-Oryza sativa_japonica_cultivar_group@NP_001062094_RRM_1[SR|SC35a][KOG0415]sc35-Selaginella moellendorfii@jgi_Selmo1_7952_gw1_7_122_1_RRM_1[SR|SC35a][KOG4207]sc35-Physcomitrella patens@jgi_Phypa1_1_172957_RRM_1[KOG0415]

sc35-Physcomitrella patens@jgi_Phypa1_1_122960_RRM_1[KOG4207]sc35-Selaginella moellendorfii@jgi_Selmo1_134332_e_gw1_124_43_1_RRM_1[SR|SC35a][KOG4207]

sc35-Cyanidioschyzon merolae@gnl_CMER_CML202C_RRM_1sc35-Sorghum bicolor_BTx623@jgi_Sorbi1_5059167_Sb07g029000_RRM_1[KOG0147]


rs2z-Oryza sativa_japonica_cultivar_group@NP_001054731_RRM_1[SR|RSZ39]rs2z-Sorghum bicolor_BTx623@jgi_Sorbi1_5045949_Sb09g004685_RRM_1[KOG0106]

rs2z-Sorghum bicolor_BTx623@jgi_Sorbi1_5060000_Sb09g001920_RRM_1[SR|RSZ36][KOG0106]rs2z-Oryza sativa_japonica_cultivar_group@NP_001054489_RRM_1[SR|RSZ36][KOG0109]rs2z-Oryza sativa_japonica_cultivar_group@NP_001049771_RRM_1[SR|RSZ37b][KOG0109]

rs2z-Sorghum bicolor_BTx623@jgi_Sorbi1_5059999_Sb09g001910_RRM_1[SR|RSZ36][KOG0109]rs2z-Oryza sativa_japonica_cultivar_group@NP_001042066_RRM_1[SR|RSZ37a][KOG0109]rs2z-Sorghum bicolor_BTx623@jgi_Sorbi1_5052652_Sb03g005500_RRM_1[KOG0109]



srp457-Homo sapiens@ENSP00000377892_RRM_1[SR|SRp40][KOG0105]srp457-Homo sapiens@ENSP00000342294_RRM_1[SR|SRp40][KOG0106]srp457-Mus musculus@ENSMUSP00000105985_RRM_1[SR|SRp40][KOG0106]srp457-Mus musculus@ENSMUSP00000105983_RRM_1[SR|SRp40][KOG0106]srp457-Mus musculus@ENSMUSP00000021562_RRM_1[SR|SRp40][KOG0106]srp457-Homo sapiens@ENSP00000362900_RRM_1[SR|SRp75][KOG0105]srp457-Mus musculus@ENSMUSP00000061474_RRM_1[SR|SRp75][KOG0105]

srp457-Mus musculus@ENSMUSP00000017065_RRM_1[SR|SRp55][KOG0105]srp457-Homo sapiens@ENSP00000362251_RRM_1[SR|SRp55][KOG0106]srp457-Homo sapiens@ENSP00000244020_RRM_1[SR|SRp55][KOG0105]srp457-Drosophila melanogaster@CG10851_PE_RRM_1[SR|SRp55][KOG0105]srp457-Drosophila melanogaster@CG10851_PD_RRM_1[SR|Hrp45][KOG0106]srp457-Drosophila melanogaster@CG10851_PC_RRM_1[SR|SRp55][KOG0105]srp457-Drosophila melanogaster@CG10851_PB_RRM_1[SR|SRp55][KOG0106]srp457-Drosophila melanogaster@CG10851_PF_RRM_1[SR|Hrp45][KOG0106]

srp457-Caenorhabditis elegans@T28D9_2a_RRM_1[SR|CeSC35-2/rsp-5][KOG0106]srp457-Caenorhabditis elegans@T28D9_2b_RRM_1[SR|CeSC35-2/rsp-5][KOG0106]srp457-Caenorhabditis elegans@T28D9_2d_RRM_1[SR|CeSC35-2/rsp-5][KOG0106]

srp457-Caenorhabditis elegans@W02B12_2_RRM_1[SR|CeSRp40/rsp-2][KOG0106]srp457-Caenorhabditis elegans@W02B12_3b_RRM_1[SR|CeSRp75/rsp-1][KOG0106]srp457-Caenorhabditis elegans@W02B12_3a_RRM_1[SR|CeSRp75/rsp-1][KOG0106]srp457-Caenorhabditis elegans@W02B12_3c_RRM_1[SR|CeSRp75/rsp-1][KOG0106]

asflkpl-Chlorella sp._NC64A@jgi_ChlNC64A_1_36976_estExt_Genewise1Plus____RRM_1asflkpl-Oryza sativa_japonica_cultivar_group@NP_001060608_RRM_1[SR|SRp33a][KOG0105]

asflkpl-Sorghum bicolor_BTx623@jgi_Sorbi1_5035702_Sb03g013010_RRM_1[SR|SR20][KOG0105]asflkan-Homo sapiens@ENSP00000229390_RRM_1[SR|SRp30c][KOG0105]asflkan-Mus musculus@ENSMUSP00000031513_RRM_1[SR|SRp30c][KOG0105]

asflkan-Drosophila melanogaster@CG6987_PA_RRM_1[KOG0105]asflkan-Mus musculus@ENSMUSP00000103553_RRM_1[SR|ASF/SF2][KOG0105]asflkan-Homo sapiens@ENSP00000258962_RRM_1[SR|ASF/SF2][KOG0105]asflkan-Mus musculus@ENSMUSP00000078792_RRM_1[SR|ASF/SF2][KOG0105]

asflkpl-Oryza sativa_japonica_cultivar_group@NP_001055323_RRM_1[SR|SRp33b][KOG0105]asflkpl-Arabidopsis thaliana@NP_172386_RRM_1[SR|SRp30][KOG0105]asflkpl-Arabidopsis thaliana@NP_683288_RRM_1[SR|SRp30][KOG0105]

asflkpl-Arabidopsis thaliana@NP_850933_RRM_1[SR|SR1/SRp34][KOG0105]p p p

ASF-like

"animal"

SRp40

SRp55

SRp75

RS2Z

"plant"

SC35

SRrp

SCL

N1

N5

N6

Fig. S29

185

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sr45-Chlorella sp._NC64A@jgi_ChlNC64A_1_138910_IGS_gm_22_00151_RRM_1sr45-Volvox carteri@jgi_Volca1_105177_RRM_1[KOG0462]

rnps1-Caenorhabditis elegans@K02F3_11_1_RRM_1[KOG4209]rnps1-Drosophila melanogaster@CG41105_PC_RRM_1

rnps1-Drosophila melanogaster@CG16788_PA_RRM_1rnps1-Homo sapiens@ENSP00000380275_RRM_1[RNPS1|RNPS1][KOG4209]rnps1-Mus musculus@ENSMUSP00000111028_RRM_1[RNPS1|RNPS1][KOG4209]

rnps1-Mus musculus@ENSMUSP00000057332_RRM_1[KOG4209]rnps1-Mus musculus@ENSMUSP00000111025_RRM_1[RNPS1|RNPS1][KOG4209]

sr45-Micromonas pusilla_RCC299@jgi_MicpuN3_63440_EuGene_1300010090_RRM_1sr45-Micromonas pusilla_CCMP1545@jgi_MicpuC2_9037_gw1_7_479_1_RRM_1


sr45-Populus trichocarpa@jgi_Poptr1_1_823076_estExt_fgenesh4_pg___RRM_1sr45-Oryza sativa_japonica_cultivar_group@NP_001054414_RRM_1[KOG0117]

sr45-Oryza sativa_japonica_cultivar_group@NP_001045458_RRM_1sr45-Sorghum bicolor_BTx623@jgi_Sorbi1_5054420_Sb03g046480_RRM_1

sr45-Arabidopsis thaliana@NP_973844_RRM_1[SR|SR45]sr45-Arabidopsis thaliana@NP_173107_RRM_1[SR|SR45]

sr45-Selaginella moellendorfii@jgi_Selmo1_424875_fgenesh2_pg____RRM_1sr45-Selaginella moellendorfii@jgi_Selmo1_446044_estExt_fgenesh2_pg____RRM_1

9g8-Drosophila melanogaster@CG5655_PA_RRM_1[KOG0107]9g8-Homo sapiens@ENSP00000368134_RRM_1[SR|9G8][KOG0107]9g8-Homo sapiens@ENSP00000368146_RRM_1[SR|9G8][KOG0107]9g8-Homo sapiens@ENSP00000325905_RRM_1[SR|9G8]9g8-Mus musculus@ENSMUSP00000070983_RRM_1[SR|9G8][KOG0107]9g8-Mus musculus@ENSMUSP00000108040_RRM_1[SR|9G8][KOG0107]9g8-Mus musculus@ENSMUSP00000066393_RRM_1[SR|9G8][KOG0107]

srp20-Drosophila melanogaster@CG10203_PA_RRM_1[SR|9G8][KOG0107]srp20-Mus musculus@ENSMUSP00000110365_RRM_1[SR|SRp20][KOG0107]srp20-Homo sapiens@ENSP00000362820_RRM_1[SR|SRp20][KOG0107]srp20-Mus musculus@ENSMUSP00000100538_RRM_1[SR|SRp20][KOG0107]srp20-Homo sapiens@ENSP00000344762_RRM_1[SR|SRp20][KOG0107]srp20-Mus musculus@ENSMUSP00000049025_RRM_1[SR|SRp20][KOG0107]9g8-Drosophila melanogaster@CG1987_PA_RRM_1[KOG0107]9g8-Drosophila melanogaster@CG17136_PB_RRM_1[KOG0107]9g8-Drosophila melanogaster@CG17136_PD_RRM_1[KOG0107]9g8-Drosophila melanogaster@CG17136_PC_RRM_1[KOG0107]


rsz-Chlamydomonas reinhardtii@jgi_Chlre3_132362_RRM_1[KOG0107]rsz-Chlorella sp._NC64A@jgi_ChlNC64A_1_139931_IGS_gm_27_00109_RRM_1[KOG0107]rsz-Chlamydomonas reinhardtii@jgi_Chlre3_192053_RRM_1[KOG0107]rsz-Volvox carteri@jgi_Volca1_121301_RRM_1[KOG0107]

rsz-Chlorella sp._NC64A@jgi_ChlNC64A_1_135849_IGS_gm_14_00382_RRM_1rsz-Populus trichocarpa@jgi_Poptr1_1_248500_gw1_XIX_900_1_RRM_1[SR|SRZ21/RSZ21][KOG0107]

rsz-Physcomitrella patens@jgi_Phypa1_1_143810_RRM_1[KOG0107]rsz-Physcomitrella patens@jgi_Phypa1_1_151194_RRM_1[KOG0107]rsz-Selaginella moellendorfii@jgi_Selmo1_172361_estExt_Genewise1Plus____RRM_1rsz-Selaginella moellendorfii@jgi_Selmo1_68846_gw1_3_1555_1_RRM_1[KOG0107]

rsz-Arabidopsis thaliana@NP_564208_RRM_1[SR|SRZ21/RSZ21]rsz-Arabidopsis thaliana@NP_194886_RRM_1[SR|SRZ22/RSZ22][KOG0107]

rsz-Arabidopsis thaliana@NP_180035_RRM_1[SR|RSZ22a]rsz-Populus trichocarpa@jgi_Poptr1_1_261622_gw1_XVIII_2163_1_RRM_1[KOG0116]rsz-Populus trichocarpa@jgi_Poptr1_1_583122_eugene3_01470007_RRM_1[SR|RSZp21a][KOG0107]rsz-Populus trichocarpa@jgi_Poptr1_1_583120_eugene3_01470005_RRM_1[SR|RSZ22a]

rsz-Oryza sativa_japonica_cultivar_group@NP_001057018_RRM_1[SR|RSZp21a]rsz-Oryza sativa_japonica_cultivar_group@NP_001047400_RRM_1[SR|RSZp23][KOG0107]rsz-Sorghum bicolor_BTx623@jgi_Sorbi1_5061430_Sb10g005960_RRM_1[SR|RSZp21a]

rsz-Oryza sativa_japonica_cultivar_group@NP_001048352_RRM_1[SR|RSZp21b]rsz-Sorghum bicolor_BTx623@jgi_Sorbi1_5056021_Sb04g035540_RRM_1[SR|RSZp21b]

scl-Micromonas pusilla_RCC299@jgi_MicpuN3_74643_gw2_11_587_1_RRM_1[KOG0107]scl-Micromonas pusilla_CCMP1545@jgi_MicpuC2_11901_gw1_8_619_1_RRM_1[KOG4207]

scl-Ostreococcus sp._RCC809@jgi_OstRCC809_1_16959_gw1_4_1177_1_RRM_1[KOG0108]scl-Ostreococcus tauri@jgi_Ostta4_7793_RRM_1[KOG0108]

scl-Ostreococcus lucimarinus@jgi_Ost9901_3_9858_RRM_1[KOG0108]scl-Chlorella sp._NC64A@jgi_ChlNC64A_1_135593_IGS_gm_14_00126_RRM_1[KOG4207]scl-Chlamydomonas reinhardtii@jgi_Chlre3_188086_RRM_1scl-Volvox carteri@jgi_Volca1_120666_RRM_1

scl-Chlamydomonas reinhardtii@jgi_Chlre3_113900_RRM_1[KOG4207]scl-Volvox carteri@jgi_Volca1_73973_RRM_1[KOG4207]scl-Chlorella sp._NC64A@jgi_ChlNC64A_1_17896_gw1_13_295_1_RRM_1

scl-Chlamydomonas reinhardtii@jgi_Chlre3_116256_RRM_1jg

SRp20 9G8

RSZ

"plant"

SR45

RNPS1

N1

Fig. S29

186

Documents

Supplemental Data A single ancient origin for …...Supplemental Data A single ancient origin for prototypical SR splicing factors Sophie Califice, Denis Baurain , Marc Hanikenne and