Upload
nina-wilson
View
14
Download
2
Embed Size (px)
Citation preview
Table S1. Chi-square tests for distributions of gene classes in Thaumarchaeota as compared to GII/III-
Euryarchaeota. HT-genes, horizontally transferred genes. *, only case for which the two distribution
patterns were not significantly similar.
COG KEGG
Thaumarchaeota vs. GII/III Euryarchaeota archaeal core 0.301596376 0.123338621
Thaumarchaeota vs. GII/III Euryarchaeota-specific core non HT-genes 0.097462121 0.196948972
Thaumarchaeota vs. GII/III Euryarchaeota-specific HT-genes (early transfers) 0.544409189 0.050684926
Thaumarchaeota vs. GII/III Euryarchaeota shell HT-genes (late transfers) 0.324156576 4.03236E-07*
Fig. S1. Number of 40 genes usually found in single copy in prokaryotic genomes (Creevey et al, 2011) present in genomes of deep-Mediterranean Thaumarchaeota an GII-Euryarchaeota.
Thaumarchaeota
Euryarchaeota
0.2
Thaumarchaeotal fosmid KM3-84-F03
Methanocella paludicola SANAE [YP_003356279]
Euryarchaeotal fosmid KM3-98-B01
Archaeoglobus fulgidus DSM 4304 [NP_070719]
Thaumarchaeotal fosmid KM3-15-F02
Haloferax volcanii DS2 [YP_003534431]
Candidatus Nitrososphaera gargensis Ga9.2 [YP_006863290]
Thaumarchaeotal fosmid SAT1000-40-A08
Uncultured marine archaeon SAT1000-21-C11 [ACF10069]
Aeropyrum pernix K1 [NP_147939]
Thaumarchaeotal fosmid KM3-47-C08
Candidatus Caldiarchaeum subterraneum [BAJ48749]
Thaumarchaeotal fosmid KM3-193-A03
Euryarchaeotal fosmid AD1000-53-H05
Candidatus Nitrosoarchaeum limnia SFB1 [ZP_08256590]
Thermoplasma acidophilum DSM 1728 [NP_393924]
Cenarchaeum symbiosum A [YP_875851]
Thaumarchaeotal fosmid KM3-67-E08
Thaumarchaeotal fosmid KM3-97-A02
Uncultured marine group II euryarchaeote [EHR76655]
Methanocaldococcus jannaschii DSM 2661 [NP_248042]
Picrophilus torridus DSM 9790 [YP_023195]
Thaumarchaeotal fosmid AD1000-71-A04
Euryarchaeotal fosmid SAT1000-18-B12
Uncultured Nitrosocaldus sp. [BAE95243]
Euryarchaeotal fosmid KM3-88-D11Euryarchaeotal fosmid AD1000-28-D03
Thermococcus gammatolerans EJ3 [YP_002959763]
Methanosarcina barkeri str. Fusaro [YP_307129]
Thaumarchaeotal fosmid KM3-15-A07
Thaumarchaeotal fosmid KM3-99-A02
Euryarchaeotal fosmid KM3-85-C06
Uncultured marine archaeon SAT1000-23-F7 [ACF09510]
Sulfolobus solfataricus P2 [NP_342235]
Methanothermus fervidus [YP_004004206]
Thermoproteus tenax Kra 1 [YP_004892221]
Uncultured marine archaeon KM3-34-D9 [ACF09590]
Natrialba magadii ATCC 43099 [YP_003480297]
Euryarchaeotal fosmid KM3-54-D07
Pyrococcus abyssi GE5 [NP_125969]
Uncultured marine archaeon AD1000-202-A2 [ACF09691]
Nitrosopumilus maritimus SCM1 [YP_001582082]
Uncultured marine archaeon AD1000-207-H3 [ACF09842]
Methanospirillum hungatei JF 1 [YP_504239]
Thaumarchaeotal fosmid KM3-73-E02
Euryarchaeotal fosmid KM3-51-E06
Thaumarchaeotal fosmid SAT1000-31-A02Thaumarchaeotal fosmid KM3-86-E11
Thaumarchaeotal fosmid SAT1000-12-D12
Thaumarchaeotal fosmid SAT1000-12-D12
Aciduliprofundum boonei T469 [YP_002577182]
100
99
100
100
92
100
100
99
81
56
100
100
73
100
89
100
100
100
58
70
87
100
100
100
95
81
100
97
100
52
9876
92
97
59
90
99
85
61
100
67
100
74
0.09
Thaumarchaeotal fosmid AD1000-41-B03Thaumarchaeotal fosmid KM3-199-D03
Methanospirillum hungatei JF 1 [YP_504303]
Aciduliprofundum boonei T469 [YP_002578452]
Thaumarchaeotal fosmid KM3-77-E10
Natrialba magadii ATCC 43099 [YP_003478580]
Euryarchaeotal fosmid KM3-162-H08
Thaumarchaeotal fosmid KM3-199-E03
Euryarchaeotal fosmid KM3-127-D04
Thaumarchaeotal fosmid SAT1000-18-G08
Picrophilus torridus DSM 9790 [YP_023295]
Thaumarchaeotal fosmid AD1000-60-A11
Methanosarcina barkeri str. Fusaro [YP_304962]
Haloferax volcanii DS2 [YP_003536788]
Methanocaldococcus jannaschii DSM 2661 [NP_247977]
Candidatus Caldiarchaeum subterraneum [BAJ47373]
Nitrosopumilus maritimus SCM1 [YP_001581650]Candidatus Nitrosoarchaeum limnia SFB1 [ZP_08257369]
Methanothermus fervidus [YP_004004453]
Thaumarchaeotal fosmid KM3-144-G01
Pyrococcus abyssi GE5 [NP_126228]
Candidatus Nitrososphaera gargensis Ga9.2 [YP_006861712]
Archaeoglobus fulgidus DSM 4304 [NP_069962]
Sulfolobus solfataricus P2 [NP_341638]
Uncultured marine group II euryarchaeote [EHR76040]
Euryarchaeotal fosmid KM3-69-F11
Euryarchaeotal fosmid KM3-13-C08
Euryarchaeotal fosmid AD1000-79-C02
Euryarchaeotal fosmid KM3-72-H01
Euryarchaeotal fosmid AD1000-53-H05Euryarchaeotal fosmid SAT1000-24-G08
Aeropyrum pernix K1 [NP_148143]
Methanocella paludicola SANAE [YP_003356696]
Thaumarchaeotal fosmid KM3-188-F10
Thaumarchaeotal fosmid KM3-160-B06
Thermoproteus tenax Kra 1 [YP_004893593]
Thermoplasma acidophilum DSM 1728 [NP_394646]
Thermococcus gammatolerans EJ3 [YP_002960325]
Thaumarchaeotal fosmid KM3-201-G04
Cenarchaeum symbiosum A [YP_876535]
Thaumarchaeotal fosmid KM3-81-E07
79
73
54
5178
100
6255
75
72
75
100
100
100
88
60
59
62
88
7983
80
76
100
100
78
83
53
93
53
80
57
95
100
EF2
rpS2
Fig. S2. Phylogenetic trees of elongation factor 2 (EF2) and ribosomal protein S2 genes present indeep-Mediterranean archaeal fosmids.
Thaum Eury
2331 1265
919 392
88 115
152 76
7 18
898 487
997 520
729 477
1 0
483 510
98 91
479 186
1595 1046
1107 624
13 0
1298 792
157 111
3 8
1242 470
17 5
541 231
54 45
78 102
636 349
1752 831
Translation, ribosomal structure and biogenesis
Transcription
Signal transduction mechanisms
Secondary metabolites biosynthesis, transport and catabolism
RNA processing and modification
Replication, recombination and repair
Posttranslational modification, protein turnover, chaperones
Nucleotide transport and metabolism
Nuclear structure
Lipid transport and metabolism
Intracellular trafficking, secretion, and vesicular transport
Inorganic ion transport and metabolism
General function prediction only
Function unknown
Extracellular structures
Energy production and conversion
Defense mechanisms
Cytoskeleton
Coenzyme transport and metabolism
Chromatin structure and dynamics
Cell wall/membrane/envelope biogenesis
Cell motility
Cell cycle control, cell division, chromosome partitioning
Carbohydrate transport and metabolism
Amino acid transport and metabolism
Fig. S3. Comparative distribution of genes in COG categories for the Thaumarchaeota (blue) and the Group II/III Euryarchaeota (red) in deep-Mediterranean archaeal fosmid metagenome sequence. Total gene counts are given on the right.
Thaumarchaeota
Euryarchaeota
Number of genes
Fig. S4. Comparative distribution of genes in KEGG classes for the Thaumarchaeota (blue) and the Group II/III Euryarchaeota (red) in deep-Mediterranean archaeal fosmid metagenome sequence. Total gene numbers are given on the right.
Thaumarchaeota
Euryarchaeota
Thaum Eury
33 40
18 9
1833 983
129 49
0 0
31 17
359 163
1053 655
1 2
0 0
170 75
94 39
1202 503
205 145
178 229
19 9
0 1
80 43
464 222
0 1
779 384
0 13
0 0
0 0
40 41
1114 485
1 4
67 18
1823 711
4515 2623
Number of genes
Fig. S5. Number of genes related to ammonium and urea metabolism in deep-Mediterranean Thaumarchaeotal genomes as compared to the number of typical single copy genes.
0
5
10
15
20
25
Gen
e co
un
t
Fig. S6. Synteny proxies per classes of gene origin in Thaumarchaeota (Thaum) and GII/III-Euryarchaeota (Eury) genomes. A, mean synteny block length per block origin. B, cluster of synteny blocks as a function of block bounds. A block is defined as an array of contiguous genes from same origin (class). 'Others' includes orphans plus non-HGT shell genes.
A
B
Mea
n b
lock
len
gth
Archaeal core in Thaum Archaeal core in Eury Eury_Shell_Late HTGs Thaum_Shell_Late HTGs Eury_Early HTGs Thaum_Early HTGs Thaum (others) Eury (others) Thaum-specific Eury-specific
Thaumarchaeota
Euryarchaeota O
the
r –
Oth
er
Oth
er –
Earl
y H
TGs
Oth
er –
Thau
m/E
yry-
spe
cifi
c
Oth
er –
Arc
hae
al c
ore
Oth
er –
She
ll /
late
HTG
s
Earl
y H
TGs –
Earl
y H
TGs
Earl
y H
TGs –
Thau
m/E
ury
-sp
eci
fic
Earl
y H
TGs –
Arc
hae
al C
ore
Earl
y H
TGs –
She
ll_La
te H
TGs
Thau
m/E
ury
-sp
eci
fic –
Thau
m/E
ury
-sp
eci
fic
Thau
m/E
ury
-sp
eci
fic –
Arc
hae
al c
ore
Thau
m/E
ury
-sp
eci
fic –
She
ll_LA
te H
TGs
Arc
hae
al c
ore
– A
rch
aeal
Co
re
Arc
hae
al c
ore
– S
he
ll_La
te H
TGs
She
ll_La
te H
TGs
- S
he
ll_la
te H
TGs
Archaeal core in Thaum Archaeal core in Eury Thaum-specific Eury-specific Eury_Shell_Late HTGs Thaum_Shell_Late HTGs Eury_Early HTGs Thaum_Early HTGs Thaum (others) Eury (others)
Fig. S7. Codon adaptation index (CAI) of different gene classes in deep-sea Thaumarchaeota and GII/III-Euryarchaeota as referred to the codon usage of thaumarchaeotal (Thaum) or GII/III-euryarchaeotal (Eury) ribosomal genes. Avg, average value; Std, standard deviation. HTG, horizontally transferred genes.
Reference: codon usage of Thaumarchaeotal ribosomal proteins
CA
I C
AI
Reference: codon usage of Euryarchaeotal ribosomal proteins
Fig. S8. Distribution of gene clusters of deep Mediterranean Thaumarchaeota in archaeal core, Thaumarchaeota-specific core, Thaumarchaeota early HTG and accessory (shell) HTG distributed in COG categories.
Thaum-specific core
Archaeal core
Thaum-specific core_early HTG
Thaum-shell_late HTG
Percentage of genes Number of genes
Fig. S9. Distribution of gene clusters of deep Mediterranean GII/III Euryarchaeota in archaeal core, Euryarchaeota-specific core, Euryarchaeota early HTG and accessory (shell) HTG distributed in COG categories.
Eury-specific core
Archaeal core
Eury-specific core_early HTG
Eury-shell_late HTG
Percentage of genes Number of genes
Fig. S10. Distribution of gene clusters (archaeal core, lineage-specific core, early HTG and accessory genes) distributed in KEGG pathways. Only pathways represented by more than 40 gene copies are included.
THAUMARCHAEOTA EURYARCHAEOTA
Eury-specific core
Archaeal core
Eury-specific core_early HTG
Eury-shell_late HTG
Thaum-specific core
Archaeal core
Thaum-specific core_early HTG
Thaum-shell_late HTG
Percentage of genes Number of genes Percentage of genes Number of genes