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Talk by Jonathan Eisen for MBL Molecular Evolution course in 2004
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TIGRTIGRTIGRTIGR
TIGRTIGRTIGRTIGR
Phylogenomics and theAxis of Evol
orHow I Came to Love a Tree
Jonathan A. Eisen
The Institute for Genomic Research
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Topics of Discussion
• Introduction to evolution• Introduction to phylogenomics• Phylogenomic examples
– Species evolution
– Uncultured organisms
– Functional predictions
– Gene duplication
– Genome rearrangements
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Eisen Genome ProjectsExtremophiles, DNA repair models
Deinococcus radiodurans
Haloferax volcanii
Tetrahymena thermophila
Novel phylogenetic groups Tree of Life
Endosymbionts Wolbachia, Baumania, Chemosynthetic symbionts, Prochloron
Evolution of C1 metabolism Carboxydothermus, Methylococcus, Chlorobium, Acidothiobacillus
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Analysis of Complete Genomes
• Identification/prediction of genes
• Characterization of gene features
• Characterization of genome features
• Prediction of gene function
• Prediction of pathways
• Integration with known biological data
• Comparative genomics
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Comparative Genomics
• Comparison of genomes between species• Identify differences
– SNPs, Indels– Rearrangements– Presence/absence of genes, pathways, features
• Correlating with phenotypic differences• Can be used to improve on every step in
genome analysis
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DNA Islands in O157:H7 vs. K12:Gene Loss or Transfer?
Eisen (2001)
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GroupB Streptococcus CGH
Tettelin et al., 2002
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Segmented Duplications in Arabidospsis
AGI, 2000
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“Nothing in biology makes senseexcept in the light of evolution.”
T. H. Dobzhansky (1973)
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Evolutionary Perspective and Comparative Biology
• Comparative biology is the analysis of differences and similarities between species.
• An evolutionary perspective is useful in such studies because this allows one to focus not just on the levels and degrees of similarity or difference but on how and why similarities and differences came to be.
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Phylogenomics
• Genome sequences contain a record of the evolution of a species and all its genes
• Evolutionary analysis is the key to interpreting genome sequences and making the most use out of them
• There is a feedback loop between evolutionary and genome analysis such that they should be done together.
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Why Completeness is Important
• Improves characterization of genome features• Better comparative genomics• Presence/absence is less subjective• Missing sequence might be important (e.g.,
centromere)• Allows researchers to focus on biology not
sequencing• Facilitates large scale correlation studies• Controls for contamination
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Phylogenomics I:
Major Evolutionary Transitions
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• Analysis of S. pombe genome by Wood et al. 2002• Compared the predicted proteomes of all
completed genomes of eukaryotes to those of prokaryotes
• Asked: “Are there genes found in all eukaryotes with no obvious homologs in any prokaryote?”
Eukaryotes vs. Prokaryotes
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BacteriaArchaea
Eukaryotes
Giardia
Trichomonas
Naegleria
Trypanosoma
Euglena
Plasmodium
Tetrahymena
Phytophthora
Arabidopsis
Chlamydomonas
Dictyostelium
Humans
Fly
Worm
Encephalatozoon
S. cerevisiae
S. pombe
Evolutionary Scenario
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Eukaryotic Specific Genes
• >200 genes found including:– Cytoskeleton components: tubulin, ankyrin,
myosin– Protein degradation: ubiquitin, proteases– Chromatin and DNA packaging
• Of the 200 many had no known function: could encode novel eukaryotic wide processes
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Multi- vs. Single-Cellular Eukaryotes
• Further analysis of S. pombe genome• Compared multi-cellular vs. single-cellular
eukaryotes (animals and plants vs. yeast)• “Are there genes in all multi-cellular and not in
any single-cellular?”• Found only 3• Concluded that the genetic basis of multi-
cellularity was likely to be gene regulation and not invention of new genes
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Multiple Origins of Multicellularity
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Phylogenomics II:
Uncultured Organisms and Phylogenetic Anchors
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Selecting Genome Projects
• Economic importance• Relevance to human disease• Biochemical or physiological novelty• Ecological importance• Phylogenetic position
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Selecting Genome Projects
• If all else is (roughly) equal, select the most experimentally tractable organisms– Deinococcus radiodurans– Chlorobium tepidum– Tetrahymena thermophila
• Genome sequences are powerful tools for launching experimental studies for those organisms
• However, not all important organisms work nicely in the lab
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rRNA and Uncultured Microbes
Eisen et al. 1992
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Beyond rRNA I:Symbiont Genome Sequencing
shotgunshotgun
sequencesequence
Warner Brothers, Inc.Warner Brothers, Inc.
TIGRTIGRTIGRTIGR Wu et al., 2004
Wolbachia pipientis wMel
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Wolbachia Mobile/Repetitive DNA
RepeatClass
Size(Median)
Copies Protein motifs/families IS Family Possible Terminal Inverted Repeat Sequence
1 1512 3 Transposase IS4 5’ ATACGCGTCAAGTTAAG 3’2 360 12 - New 5’ GGCTTTGTTGCAT CGCTA 3’3 858 9 Transposase IS492/IS110 5’ GGCTTTGTTGCAT 3’4 1404.5 4 Conserved hypothetical,
phage terminaseNew 5’ ATACCGCGAWTSAWTCGCGGTAT 3’
5 1212 15 Transposase IS3 5’ TGACCTTACCCAGAAAAAGTGGAGAGAAAG 3’6 948 13 Transposase IS5 5’ AGAGGTTGTCCGGAAACAAGTAAA 3’7 2405.5 8 RT/maturase -8 468 45 - -9 817 3 conserved hypothetical,
transposaseISBt12
10 238 2 ExoD -11 225 2 RT/maturase -12 1263 4 Transposase ???13 572.5 2 Transposase ??? None detected14 433 2 Ankyrin -15 201 2 - -16 1400 6 RT/maturase -17 721 2 transposase IS63018 1191.5 2 EF-Tu -19 230 2 hypothetical -
Wu et al., 2004
TIGRTIGRTIGRTIGR Wu et al., 2004
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Selection Apparently Inefficient in wMel
• Likely not due to higher mutation rate– Full suite of DNA repair genes
• Likely not due to low amounts of homologous recombination– RecA present
– Population studies suggest homologous recombination occurs
• Wolbachia has multiple types of bottlenecks– Maternal transmission like obligate mutualists
– Infectious sweeps of cytoplasmic incompatibility like pathogens
Wu et al., 2004
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• Sap feeding insects
Glassy-winged Sharpshooter
• Carriers of Xylella fastidiosa that causes Pierce’s disease of grapevines
• There are >20000 sharpshooter species, within which intracellular symbiotic bacteria are wildspread
Baumannia cicadellinicola:1° symbionts of the Glassy-winged Sharpshooter
TIGRTIGRTIGRTIGR400,000
100,000
200,000
300,000
500,000
600,000
1
Baumania Genome Completed
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“Whole genome” tree of insect endosymbionts
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Bu_APS Bu_Bp Bu_Sg Wi_gl Ca_bl gebc recG&ruvABC(recombinate repa ir) - - - - - recG&ruvABC methy -direct DNA repair(correct T -G) mutSL mutSLH mutSL - - mutSLH 8-Oxo_ dGTP prevention(mutT, MutY||MutM ) mutTY mutY mutTY - mutTY mutTM uvrD(or homolog rep) rep rep rep uvrD - uvrD recA - - - recA - recA phrB(UV pyrimidine dimer) phrB phrB - phrB - - recBCD recBCD recBCD recBCD recBCD recBCD recBCD mutL(mismatch repair) mutL mutL mutL - - mutL recJ(rec based exision,methy -direct repair) - - - recJ - recJ transcription -repair coupling factor(mfd) mfd mfd - mfd - - uracil -DNA -glycosylase(remove U from DNA) ung ung - ung ung ung site -specific DNA inversion stimulation(fis) fis - fis - - - dna recombination protein rmuc (inversion) - - - - rmuc rmuc
DNA repair genes
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GlutamateArgA ArgB ArgC ArgD ArgE
OmithineAarAB ArgF ArgG ArgH
Arg
PyruvateIvHI IlvC IlvD IlvE
Val
Pyruvate+
Alpha-Ketobutyrate
ThreonineIle
IlvA
PEP +Erythrose 4-phosphate
AroH AroB AroD AroE AroK AroA AroCChorismate
PheA HisC Phe
TrpEG TrpD TrpC TrpABTrp
AspartateThrA Asd ThrA
HomoserineThrB ThrC
MetB MetC MetE
Thr
MetDapA DapB DapD DapC DapE DapF LysA Lys
PRPP+ATPHisG HisI HisA HisHF HisB HisC HisB HisD
His
Essential amino acid biosynthetic pathways
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9359 clones that are not included in the final assembly
Run_TA
7152 assembles (400 have been assembled)
<1kb 6996
1kb-2kb 125
2kb-3kb 18
3kb-4kb 6
4kb-5kb 3
5kb-6kb 2
6kb-7kb 1
7kb-8kb 1
Sequences from Another Symbiont
150 Bacteroides/Chlorobi (njtree/blast)
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AspartateThrA Asd
HomoserineThrB ThrC
MetB MetC MetE
Thr
MetDapA DapB DapD DapC DapE DapF LysA Lys
TIGRTIGRTIGRTIGR
TIGRTIGRTIGRTIGR
Beyond rRNA II: Metagenomics
• Isolate, by filtration, all microbes in a sample
• Extract total DNA in very large pieces
• Clone those pieces as BACs into E.coli to get enough.
• Identify which BAC contains phylogenetic marker of interest
• Sequence the BACs like a bacterial genome.
Sample
Filterconcentrate
ExtractDNA
CloneInto BACs
SequenceGeneList
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Using a rRNA anchor allowed the
identification of a new form of phototrophy:
Proteorhodopsin
Beja et al. 2000
TIGRTIGRTIGRTIGR Beja et al., 2001
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Phylogenetic Anchors
Beja et al., 2000
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Puf Operons vs. Cultured Species
Beja et al., 2002
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Beyond rRNA III:Shotgun Environmental Sequencing
shotgunshotgun
sequencesequence
Warner Brothers, Inc.Warner Brothers, Inc.
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Sargasso Sea
• High microbial diversity• Most of the abundant rRNA phylotypes have
never been cultured• Physiological processes of microbes largely
unknown• Well studied in terms of oceanographic parameters
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rRNA as a Phylogenetic Anchor
Venter et al., 2004
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Shotgun Sequencing Allows Use of Alternative Anchors (e.g., RecA)
Venter et al., 2004
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Shotgun Sequencing Detects More Diversity than PCR-methods
Venter et al., 2004
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Sargasso Phylotypes
0
0.05
0.1
0.15
0.2
0.25
0.3
0.35
0.4
0.45
0.5
AlphaproteobacteriaBetaproteobacteriaGammaproteobacteriaEpsilonproteobacteria
Deltaproteobacteria
CyanobacteriaFirmicutes
Actinobacteria
Chlorobi
CFB
ChloroflexiSpirochaetesFusobacteria
Deinococcus-Thermus
EuryarchaeotaCrenarchaeota
Major Phylogenetic Group
Weighted % of Clones
EFG
EFTu
HSP70
RecA
RpoB
rRNA
Venter et al., 2004
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Phylogenomics and Species Evolution II: Biased Sample of Genomes
• Of 40 bacterial phyla most genome sequences come from only 3 groups
Hugenholtz 2002
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# of Bacterial Phyla Sequenced
0
5
10
15
20
25
1995 1996 1997 1998 1999 2000 2001 2002 2003 2004 2005
Year
Total # of Bacterial Phyla with a Genome Sequenced
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# of Bacterial Phyla Sequenced
0
5
10
15
20
25
1995 1996 1997 1998 1999 2000 2001 2002 2003 2004 2005
Year
Total # of Bacterial Phyla with a Genome Sequenced
TIGRTIGRTIGRTIGR
0.1AcidobacteriaBacteroidesFibrobacteres GemmimonasVerrucomicrobia PlanctomycetesChloroflexiProteobacteriaChlorobi FirmicutesFusobacteria Actinobacteria Cyanobacteria Chlamydia Spriochaetes Deinococcus-Thermus AquificaeThermotogaeTM6OS-KTermite GroupOP8Marine GroupAWS3OP9NKB19OP3OP10TM7OP1OP11NitrospiraSynergistesDeferribacteresThermudesulfobacteriaChrysiogenetesThermomicrobiaDictyoglomusCoprothmermobacterThis projectPublishedIn progressUncultured lineageTree based on Hugenholtz (2002) with some modifications.
Solution:
Selecting Genome Projects
to IncreasePhylogenetic
Diversity
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Re-evaluating the Bacterial Tree
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Functional Diversity of Proteorhodopsins?
Venter et al., 2004
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Phylogenomics III:
Prediction of Function(s)
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Predicting Function• Identification of motifs
– Short regions of sequence similarity that are indicative of general activity
– e.g., ATP binding
• Homology/similarity based methods– Gene sequence is searched against a databases of other
sequences– If significant similar genes are found, their functional
information is used
• Problem– Genes frequently have similarity to hundreds of motifs
and multiple genes, not all with the same function
TIGRTIGRTIGRTIGR
TIGRTIGRTIGRTIGRTIGRTIGRTIGRTIGR
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Blast Search of H. pylori “MutS” Score E Sequences producing significant alignments: (bits) Value sp|P73625|MUTS_SYNY3 DNA MISMATCH REPAIR PROTEIN 117 3e-25 sp|P74926|MUTS_THEMA DNA MISMATCH REPAIR PROTEIN 69 1e-10 sp|P44834|MUTS_HAEIN DNA MISMATCH REPAIR PROTEIN 64 3e-09 sp|P10339|MUTS_SALTY DNA MISMATCH REPAIR PROTEIN 62 2e-08 sp|O66652|MUTS_AQUAE DNA MISMATCH REPAIR PROTEIN 57 4e-07 sp|P23909|MUTS_ECOLI DNA MISMATCH REPAIR PROTEIN 57 4e-07
• Blast search pulls up Syn. sp MutS#2 with much higher p value than other MutS homologs
Eisen, 1997
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Phylogenetic Tree of MutS Family
Aquae Trepa
FlyXenlaRatMouse
HumanYeast
NeucrArath
BorbuStrpy
BacsuSynsp
EcoliNeigo
ThemaTheaqDeira
Chltr
SpombeYeast
YeastSpombe
MouseHumanArath
YeastHumanMouseArath
StrpyBacsu
CelegHuman
YeastMetthBorbu
AquaeSynsp
Deira Helpy
mSaco
YeastCeleg
Human
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MutS Subfamilies
Aquae Trepa
FlyXenlaRatMouse
HumanYeast
NeucrArath
Borbu
StrpyBacsu
SynspEcoli
Neigo
ThemaTheaqDeira
Chltr
SpombeYeast
YeastSpombe
MouseHumanArath
YeastHumanMouseArath
StrpyBacsu
CelegHumanYeast
MetthBorbu
AquaeSynsp
Deira Helpy
mSaco
YeastCeleg
Human
MSH4
MSH5 MutS2
MutS1
MSH1
MSH3
MSH6
MSH2
TIGRTIGRTIGRTIGR
MutS Subfamilies
• MutS1 Bacterial MMR
• MSH1 Euk - mitochondrial MMR
• MSH2 Euk - all MMR in nucleus
• MSH3 Euk - loop MMR in nucleus
• MSH6 Euk - base:base MMR in nucleus
• MutS2 Bacterial - function unknown
• MSH4 Euk - meiotic crossing-over
• MSH5 Euk - meiotic crossing-over
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Overlaying Functions onto Tree
Aquae Trepa
Rat
FlyXenla
MouseHumanYeast
NeucrArath
Borbu
SynspNeigo
ThemaStrpy
Bacsu
Ecoli
TheaqDeiraChltr
SpombeYeast
YeastSpombe
MouseHuman
Arath
YeastHumanMouseArath
StrpyBacsu
HumanCeleg
YeastMetthBorbu
AquaeSynsp
Deira Helpy
mSaco
YeastCeleg
Human
MSH4
MSH5MutS2
MutS1
MSH1
MSH3
MSH6
MSH2
TIGRTIGRTIGRTIGR
Functional Prediction Using Tree
Aquae Trepa
FlyXenlaRatMouse
HumanYeast
NeucrArath
Borbu
StrpyBacsu
SynspEcoli
Neigo
ThemaTheaqDeira
Chltr
SpombeYeast
YeastSpombe
MouseHumanArath
YeastHumanMouseArath
MSH1MitochondrialRepair
MSH3 - Nuclear RepairOf Loops
MSH6 - Nuclear RepairOf Mismatches
MutS1 - Bacterial Mismatch and Loop Repair
StrpyBacsu
CelegHumanYeast
MetthBorbu
AquaeSynsp
Deira Helpy
mSaco
YeastCeleg
Human
MSH4 - Meiotic CrossingOver
MSH5 - Meiotic Crossing Over MutS2 - Unknown Functions
MSH2 - Eukaryotic NuclearMismatch and Loop Repair
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Table 3. Presence of MutS Homologs in Complete Genomes Sequences
Species # of MutSHomologs
WhichSubfamilies?
MutLHomologs
BacteriaEscherichia coli K12 1 MutS1 1Haemophilus influenzae Rd KW20 1 MutS1 1Neisseria gonorrhoeae 1 MutS1 1Helicobacter pylori 26695 1 MutS2 -Mycoplasma genitalium G-37 - - -Mycoplasma pneumoniae M129 - - -Bacillus subtilis 169 2 MutS1,MutS2 1Streptococcus pyogenes 2 MutS1,MutS2 1Mycobacterium tuberculosis - - -Synechocystis sp. PCC6803 2 MutS1,MutS2 1Treponema pallidum Nichols 1 MutS1 1Borrelia burgdorferi B31 2 MutS1,MutS2 1Aquifex aeolicus 2 MutS1,MutS2 1Deinococcus radiodurans R1 2 MutS1,MutS2 1
ArchaeaArchaeoglobus fulgidus VC-16, DSM4304 - - -Methanococcus janasscii DSM 2661 - - -Methanobacterium thermoautotrophicum ΔH 1 Mut 2S -
EukaryotesSaccharomyces cerevisiae 6 M 1-6SH 3+Homo sapiens 5 M 2-6SH 3+
TIGRTIGRTIGRTIGR
TIGRTIGRTIGRTIGR
rRNA and Uncultured Microbes
Eisen et al., 1992
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4 F17L22 170 Arabidopsis thali4455279 Arabidopsis thaliana1049068 Lycopersicon esculentuHomo sapiens5514652 Drosophila melanogasteDrosophila melanogaster2123725 Caenorhabditis elegans6606113 Capronia mansoniiRpoII.Yeast.YOR151C107346 Schizosaccharomyces pom151348 Euplotes octocarinatus265427 Euplotes octocarinatus3845258 Plasmodium falciparumRpoIII.DromeRpoIII.Drome.7303535EGAD 114464 Caenorhabditis eleRpoIII.Yeast.172383EGAD 145012 SchizosaccharomyceRpoIII.Neucr.7800864ARATH5 K18C1 1Aeropyrum pernixEGAD 8025 Sulfolobus acidocald5458046 Pyrococcus abyssiPH1546 Pyrococcus horikoshiiThermococcus celerEGAD 14667 Methanococcus vanniMJ1040 Methanococcus jannaschiAF1886 Archaeoglobus fulgidusHalobacterium halobiumThermoplasma acidophilumRPB2 Methanobacterium thermoauatmystery.BAB02021ARATH3 MRC8.7ARATH3 MYM9.126723961 Schizosaccharomyces poRpoI.Yeast.YPR010CRpoI.Neucr.3668171RPA2 Rattus norvegicusMus musculusRpoI.Drome.7296211Caenorhabditis elegans92131 Euplotes octocarinatusARATH1 T1P2.15ARATH1 F1N18.21492072Molluscum contagiosum v439046 Variola major virus1143635 Variola virus2772787 Vaccinia virus323395 Cowpox virus6578643 Rabbit fibroma virus6523969 Myxoma virus6682809 Yaba monkey tumor viru7271687 Fowlpox virus4049822 Melanoplus sanguinipes2887 Kluyveromyces lactisEGAD 151364 Sacch kluyveri1369760 Borrelia burgdorferiBB0389 Borrelia burgdorferiTP0241 Treponema pallidum6652714 Rickettsia massiliae6652723 Rickettsia sp. Bar296652720 Rickettsia conoriiRP140 Rickettsia prowazekii6960339 Salmonella typhimuriumEGAD 1084 Salmonella choleraesEC3987 Escherichia coliEGAD 23892 Buchnera aphidicolaHI0515 Haemophilus influenzaeEGAD 6020 Pseudomonas putidaRPOB Coxiella burnetii3549149 Legionella pneumophilaRPOB Neisseria meningitidisHP1198 Helicobacter pylori6967949 Campylobacter jejuniAA1339 Aquifex aeolicusBS0107 Bacillus subtilis4512396 Bacillus halodurans6002201 Listeria monocytogenesEGAD 32012 Staphylococcus aureEGAD 32011 Spiroplasma citriMG341 Mycoplasma genitaliumMP326 Mycoplasma pneumoniae6899151 Ureaplasma urealyticumRv0667 Mycobacterium tuberculoMycobacterium leprae7144498 Mycobacterium smegmatiEGAD 39063 Mycobacterium smegmGP 7331268 Amycolatopsis medit7248348 Streptomyces coelicolo7573273 Thermus aquaticusDR0912 Deinococcus radioduransTM0458 Thermotoga maritimaEGAD 74970 80693 Heterosigma cEGAD Odontella sinensisEGAD 60306 Spinacia oleraceaEGAD Nicotiana tabacum6723742 Oenothera elata5457427 Sinapis alba5881686 Arabidopsis thaliana4958867 Triticum aestivumEGAD 76270 Zea maysRPOB Oryza sativaEGAD Pinus thunbergiiEGAD Marchantia polymorpha7259525 Mesostigma viride5880717 Nephroselmis olivaceaRPOB Guillardia thetasll1787 Synechocystis PCC6803EGAD 75526 Porphyra purpurea6466433 Cyanidium caldariumEGAD 76712 Cyanophora paradoxaRPOB Chlorella vulgarisEGAD 76424 Euglena gracilis5231258 Toxoplasma gondii6492294 Neospora caninumEGAD 83446 Plasmodium falcipar
100
78
100
85
93
83
100
79
100
100
100100 100
100
94100
100
7499100
99100
100
99
9480
100
100
100
100
59
100
100
99
56100
100
100
10058 95100
9763
95100
100
10081
100
100
100
59
6099
100
10094
100100
69100
7710097
100
71
100
9958
83
100100
100
99100
98100
100
61
99
75100
73100
100
59
100
100
72
72
98
529859
100
100
a
Novel RNA Polymerase in A. thaliana
ArchaealIV
II
III
I
Viral
Bacterial - RpoB
Plastid- RpoBs
TIGRTIGRTIGRTIGR
Arabidopsis thalianaGP9651815gDrosophila melanogasterGP72929
Homo sapiensSPP49917DNL4 HUMANGallus gallusGP15778121dbjBAB6Xenopus laevisGP18029886gbAAL5
Candida albicansSPP52496DNLI CSaccharomyces cerevisiaeGP1151Schizosaccharomyces pombeGP700
Camelpox virusGP18483081gbAAL7Variola major virusGP439074gbA
Cowpox virusGP20153167gbAAM136Vaccinia virusGP2772802gbAAB96VIRUS vaccinia 9791118refNP 06Vaccinia virus strain Tian TanMonkeypox virusGP17529940gbAAL
Homo sapiensSPP49916DNL3 HUMANMus musculusGP1794221gbAAC5300
Xenopus laevisGP18029884gbAAL5lumpy skin disease virusGP1514
Swinepox virusGP18448623gbAAL6Myxoma virusGP6523988gbAAF1502Rabbit fibroma virusGP392838gb
Fowlpox virusGP453602embCAA828Drosophila melanogasterGP72996
Arabidopsis thalianaSPQ42572DNOryza sativaGP16905197gbAAL310
Crithidia fasciculataGP312384eCaenorhabditis elegansSPQ27474
Drosophila melanogasterGP72916Homo sapiensSPP18858DNL1 HUMANMus musculusSPP37913DNL1 MOUSERattus norvecusSPQ9JHY8DNL1 RAXenopus laevisSPP51892DNL1 XEN
Plasmodium falciparumGP1815859Schizosaccharomyces pombeSPP12Saccharomyces cerevisiaeSPP048
Aeropyrum pernixSPQ9YD18DNLI AAcidianus ambivalensSPQ02093DNSulfolobus solfataricusSPQ980TSulfolobus shibataeSPQ9P9K9DNLSulfolobus tokodaiiSPQ976G4DNLAquifex aeolicusGP2983805gbAACAquifex aeolicusSPO67398DNLI APyrobaculum aerophilumGP409906
uncultured crenarchaeote 74A4GThermoplasma acidophilumSPQ9HJThermoplasma volcaniumOMNINTL0
Methanosarcina acetivorans strArchaeoglobus fuldusSPO29632DN
A METAC 19916535gbAAM05952.1 DPyrococcus abyssiSPQ9V185DNLI Pyrococcus horikoshiiSPO59288DPyrococcus furiosusSPP56709DNLThermococcus kodakaraensisGP10Thermococcus fumicolansSPQ9HH0Methanopyrus kandleri AV19GP19
Methanococcus jannaschiiSPQ576Halobacterium sp.SPQ9HR35DNLI
Streptomyces coelicolorSPQ9FCBLymantria dispar nucleopolyhed
Ligase IV
Viral ligases
Ligase I
Archaeal Ligase
DNA Ligase Tree
TIGRTIGRTIGRTIGR
Problems with Similarity Based Functional Prediction
• Prone to database error propagation.• Cannot identify orthologous groups reliably.• Perform poorly in cases of evolutionary rate
variation and non-hierarchical trees (similarity will not reflect evolutionary relationships in these cases)
• May be misled by modular proteins or large insertion/deletion events.
• Are not set up to deal with expanding data sets.
TIGRTIGRTIGRTIGR
TIGRTIGRTIGRTIGR
Evolutionary Rate Variation
231456
TIGRTIGRTIGRTIGR
Rate Variation and DuplicationSpecies 3Species 1Species 21A2A3A1B2B3BDuplication
TIGRTIGRTIGRTIGR
AlkA Domain (O6-Me-G glycosylase)Ogt Domain (O6-Me-G alkyltransferase)Ada Domain (transcriptions regulator)Ada E. coliAda H. inflOgt E. coliOgt H. inflOgt Gram+Ogt D. radioAlkA Gram+AlkA E. coliMGMT Euks
Alkylation Repair Genes
TIGRTIGRTIGRTIGR
Clustering vs. Neighbor-joining
MutS2.SynsMutS2.BacsMutS2.HelpMutS2.DeirMutsl.MettMSH4.CelegMSH4.YeastMSH4.humanmMutS.SacoMSH3.yeastC23C11.SpoMSH1.YeastMSH3.HumanREP1.MouseGTBP.MouseGTBP.HumanMSH6.YeastMSH5.HumanMSH5.CelegMSH5.YeastMSH2.HumanMSH2.MouseMSH2.YeastMutS.EcoliMutS.SynspMutS.DeiraMutS.Bacsu
MutS.EcoliMutS.SynspMutS.BacsuMutS.DeiraMSH2.HumanMSH2.MouseMSH2.YeastMSH3.HumanREP1.MouseGTBP.MouseGTBP.HumanMSH6.YeastC23C11.SpoMSH1.YeastMSH3.yeastMSH4.CelegMSH4.humanMSH5.CelegMSH5.YeastmMutS.SacoMSH5.HumanMSH4.YeastMutS2.SynsMutS2.BacsMutS2.DeirMutS2.HelpMutsl.Mett
UPGMANeighbor-Joining
TIGRTIGRTIGRTIGR
Types of Molecular Homology
• Homologs: genes that are descended from a common ancestor (e.g., all globins)
• Orthologs: homologs that have diverged after speciation events (e.g., human and chimp -globins)
• Paralogs: homologs that have diverged after gene duplication events (e.g., and globin).
• Xenologs: homologs that have diverged after lateral transfer events
• Positional homology: common ancestry of specific amino acid or nucleotide positions in different genes
TIGRTIGRTIGRTIGR
Deinococcus radiodurans
TIGRTIGRTIGRTIGR
DNA Repair Genes in D. radiodurans Complete Genome
Process Genes in D. radiodurans
Nucleotide Excision Repair UvrABCD, UvrA2Base Excision Repair AlkA, Ung, Ung2, GT, MutM, MutY-Nths,
MPGAP Endonuclease XthMismatch Excision Repair MutS, MutLRecombination Initiation Recombinase Migration and resolution
RecFJNRQ, SbcCD, RecDRecARuvABC, RecG
Replication PolA, PolC, PolX, phage PolLigation DnlJdNTP pools, cleanup MutTs, RRaseOther LexA, RadA, HepA, UVDE, MutS2
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Problem:
List of DNA repair gene homologs in D. radiodurans genome is not significantly different from other
bacterial genomes of the similar size
TIGRTIGRTIGRTIGR
0.1
Acidobacteria
Bacteroides
Fibrobacteres
Gemmimonas
Verrucomicrobia
Planctomycetes
Chloroflexi
Proteobacteria
Chlorobi
FirmicutesFusobacteria Actinobacteria
Cyanobacteria
Chlamydia
Spriochaetes
Deinococcus-Thermus
Aquificae
Thermotogae
TM6OS-K
Termite GroupOP8
Marine GroupAWS3
OP9
NKB19
OP3
OP10
TM7
OP1OP11
Nitrospira
SynergistesDeferribacteres
Thermudesulfobacteria
Chrysiogenetes
Thermomicrobia
Dictyoglomus
Coprothmermobacter
Tree based on Hugenholtz (2002) with some modifications.
~40 Phyla of Bacteria
TIGRTIGRTIGRTIGR
0.1
Acidobacteria
Bacteroides
Fibrobacteres
Gemmimonas
Verrucomicrobia
Planctomycetes
Chloroflexi
Proteobacteria
Chlorobi
FirmicutesFusobacteria Actinobacteria
Cyanobacteria
Chlamydia
Spriochaetes
Deinococcus-Thermus
Aquificae
Thermotogae
TM6OS-K
Termite GroupOP8
Marine GroupAWS3
OP9
NKB19
OP3
OP10
TM7
OP1OP11
Nitrospira
SynergistesDeferribacteres
Thermudesulfobacteria
Chrysiogenetes
Thermomicrobia
Dictyoglomus
Coprothmermobacter
Tree based on Hugenholtz (2002) with some modifications.
Most DNA metabolism studies in two Phyla
TIGRTIGRTIGRTIGR
0.1
Acidobacteria
Bacteroides
Fibrobacteres
Gemmimonas
Verrucomicrobia
Planctomycetes
Chloroflexi
Proteobacteria
Chlorobi
FirmicutesFusobacteria Actinobacteria
Cyanobacteria
Chlamydia
Spriochaetes
Deinococcus-Thermus
Aquificae
Thermotogae
TM6OS-K
Termite GroupOP8
Marine GroupAWS3
OP9
NKB19
OP3
OP10
TM7
OP1OP11
Nitrospira
SynergistesDeferribacteres
Thermudesulfobacteria
Chrysiogenetes
Thermomicrobia
Dictyoglomus
Coprothmermobacter
Tree based on Hugenholtz (2002) with some modifications.
Deinococcus is very distant from well studied groups
TIGRTIGRTIGRTIGR
-Ogt-RecFRQN-RuvC-Dut-SMS
-PhrI-AlkA-Nfo-Vsr-SbcCD-LexA-UmuC
-PhrI-PhrII-AlkA-Fpg-Nfo-MutLS-RecFORQ-SbcCD-LexA-UmuC-TagI
-PhrI-Ogt-AlkA-Xth-MutLS-RecFJORQN-Mfd-SbcCD-RecG-Dut-PriA-LexA-SMS-MutT
-PhrI-PhrII?-AlkA-Fpg-Nfo-RecO-LexA-UmuC
-PhrI-Ung?-MutLS-RecQ?-Dut-UmuC
-PhrII-Ogg
-Ogt-AlkA-TagI-Nfo-Rec-SbcCD-LexA
-Ogt-AlkA-Nfo-RecQ-SbcD?-Lon-LexA
-AlkA-Xth-Rad25?
-AlkA-Rad25
-Nfo
-Ogt-Ung-Nfo-Dut-Lon
-Ung
-PhrII
-PhrI
Ecoli
Haein
Neig
o
Help
y
Bacsu
Str
py
Mycg
e
Mycp
n
Borb
u
Tre
pa
Syn
sp
Metj
n
Arc
fu
Mett
h
Hu
man
Yeast
BACTERIA ARCHAEA EUKARYOTES
from mitochondria
+Ada+MutH+SbcB
dPhr
+TagI?+Fpg
+UvrABCD+Mfd
+RecFJNOR+RuvABC
+RecG+LigI
+LexA+SSB
+PriA+Dut?
+Rus+UmuD
+Nei?+RecE
tRecT?
+Vsr+RecBCD?
+RFAs+TFIIH
+Rad4,10,14,16,23,26+CSA
+Rad52,53,54+DNA-PK, Ku
dSNF2dMutSdMutLdRecA
+Rad1+Rad2
+Rad25?+Ogg+LigII
+Ung?+SSB,
+Dut?
+PhrI, PhrII+Ogt
+Ung, AlkA, MutY-Nth+AlkA
+Xth, Nfo?+MutLS?
+SbcCD+RecA
+UmuC+MutT
+LondMutSI/MutSII
dRecA/SMSdPhrI/PhrII
+Sprt3MG
+Rad7+CCE1
+P53dRecQ
dRad23+MAG?
-PhrII-RuvC
tRad25
+TagI?
+RecT
tUvrABCD
tTagI ?
Gain and Loss of Repair Genes
TIGRTIGRTIGRTIGR Eisen and Hanawalt, 1999
TIGRTIGRTIGRTIGR
Non-Homology Prediction: Phylogenetic Profiles
• Step 1: Search all genes in organisms of interest against all other genomes
• Ask: Yes or No, is each gene found in each other species
• Cluster genes by distribution patterns (profiles)
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Phylogenetic Profile - E.coliFlagellar Genes
fhiAfliMfliPfliGflgGfliFflgIflhAflhBgcpE
Wu and Eisen, unpublished
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Chlorobium tepidum Strain TLS
C. tepidum mat in highly sulfidic “Travelodge Stream”, Rotorua, New Zealand
(from Castenholz and Pierson, 1995)
Phase contrast photomicrographof the 48-hours culture and electron
micrograph of thin cell section (from Wahlund et al, 1991)
TIGRTIGRTIGRTIGR
Phylogenetic Profile -C. tepidum Chlorophyll
Synthesis
Wu and Eisen, unpublished
5002_cobalamin biosynthesis protein CbiG/precorrin-4 C11-methyltransferase3939_precorrin-3B C17-methyltransferase/precorrin-8X methylmutase cbiJH882_cobyric acid synthase cbiP3160_dsrN protein dsrN862_cobyrinic acid a,c-diamide synthase cbiA-14010_cobN protein, putative2641_magnesium-protoporphyrin methyltransferase bchH-31498_magnesium-protoporphyrin methyltransferase bchH-14003_cobN protein, putative2636_magnesium-protoporphyrin methyltransferase bchH-24008_magnesium-chelatase, subunit I chlI-24007_magnesium-chelatase, subunit D/I family1504_magnesium-chelatase, subunit I chlI-1
TIGRTIGRTIGRTIGR
C. tepidum encodes a novel RbcLChlorobium tepidum ORF02314Pseudomonas hydrogenothermophi
Archaeoglobus fulgidus gi2648975Bacillus subtilis gi2633730Methanococcus jannaschiigi2129276Pyrococcus abysiigi|5458634Pyrococcus horikoshiigi|3257353Pyr ococcus karaensisgi3769302
Achaeoglobus fulgidusgi2648911
0.005 changesIVRhodobacter capsulatus2522275Rhodobacter sphaeroides1 15192Alcaligenes eutrophusRalstonia eutropha3377785Alcaligenes eutrophus 950106Xanthobacter flavus 48544Galdieria partita 4519903Galdieria partitaGaldieria sulphuraria 8925949Cyanidium caldariumCyanidioschyzon merolaeGephyrocapsa oceanicaEmiliania huxleyiPleurochrysis carteraePleurochrysis carterae 456606Calyptrosphaera sphaeroideaUmbilicosphaera sibogaeChrysochromulina hirtaPavlova salinaPorphyridium aerugineumGelidiella acerosaSpermothamnion repensEupogodon planusCeramium diaphanumAntithamnion sp.Sarcodia ceylanicaPterocladia lucidaGelidium sesquipedale 3581614Gelidium americanumGelidium elegans 7107687Gelidium pusillum 392980Capreolia implexaCallophyllis violaceaOnikusa japonicumYatabella hirsutaAcanthopeltis japonicaPterocladiella capillaceaPtilophora pinnatifidaPortieria japonicaGracilariopsis sp.Eucheuma isiforme 4323441Agardhiella ramosissimaMeristotheca papulosaEucheuma arnoldiiKappaphycus alvareziiBetaphycus philippinensisSolieria chordalisMastocarpus stellatusRhodogorgon carriebowensisHeringia mirabilisAhnfeltiopsis gigartinoidesCaulacanthus ustulatusAreschougia congestaCallophycus africanusErythroclonium angustatumHypnea charoidesRhabdonia clavigeraMastocarpus papillatus 450801Sarcothalia livida 5020070Gigartina skottsbergii 5020042Iridaea cordataIridaea cordata 5020044Mazzaella californicaChondrus nipponicus 5020030Chondrus pinnulatus 5020034Chondrus yendoi 5020036Chondrus canaliculatusTrematocarpus dichotomusTrematocarpus dichotomus 96154Chondracanthus chamissoi 50200Chondracanthus acicularisChondracanthus tenellus 502002Gigartina radula 5020040Amphiroa fragilissimaPorphyra purpurea cpst 1276692Cryptomonas cpst 3602978Aureoumbra lagunensisAureococcus anophagefferensOlisthodiscus luteus cpst 1192Tetrasporopsis fuscescens 6006Tetrasporopsis fuscescensPhaeothamnion confervicolaPhaeoschizochlamys mucosaTurbinaria ornataIsthmoplea sphaerophoraPogotrichum filiformeCoelocladia arcticaRosenvingea intricataHydroclathrus clathratusChnoospora implexaColpomenia sinuosaScytosiphon lomentariaPilayella littoralisDelamarea attenuataDictyosiphon foeniculaceusHecatonema sp.Elachista fucicolaPunctaria plantagineaPetalonia binghamiaeStictyosiphon soriferusStriaria attenuataLitosiphon pusillusLaminariocolax tomentosoidesMyriotrichia clavaeformisSorocarpus micromorusStreblonema tenuissimumMyrionema strangulansGiraudia sphacelarioidesHummia onustaMischococcus sphaerocephalusBotrydium stoloniferumXanthonema debileTribonema aequaleVaucheria bursataPleurochloridella botrydiopsisPseudopedinella elasticaPhaeodactylum tricornutumRhizosolenia setigeraDetonula confervaceaThalassiosira nordenskioeldiiOdontella sinensisUnidentified diatom endosymbioCylindrotheca sp.MnBradyrhizobium japonicum 41605
IIChlorellaChloromonas sp. ANT1Mesostigma viride 7259514AgmenellumProchlorothrix hollandic 45543Anabaena sp.Anabaena sp.Anabaena sp.142086Astasia longaEuglena gracilisSpirotaenia condensata 1145421Gonatozygon monotaeniumGenicularia spirotaeniaLycopodium clavatumLycopodiella alopecuroidesPhylloglossum drummondiiHuperzia campianaTrichomanes alatumSelaginella bombycinaSelaginella sp. 577150Botrypus strictusIsoetes melanopoda 577149Isoetes lacustrisAngiopteris lygodiifoliaElaphoglossum yoshinagaeBlechnum occidentaleAdiantum capillusvenerisMarsilea ancylopodaCyathea sp. Wolf 1994Hymenophyllopsis dejectaMatonia foxworthyiLophosoria quadripinnataOsmunda cinnamomeaDennstaedtia sp. Wolf 623Polypodium vulgareHypolepis sp. Wolf 628Polypodiodes formosanaGoniophlebium persicifoliumPhanerosorus majorSalvinia cucullata 515459Coleochaete nitellarumKlebsormidium sp. 552613Anthoceros formosae cp 1389564Lathyrus tuberosusCoronilla emerusPersicaria hydropiperAchlys triphyllaHibiscus punaluuensisMontinia caryophyllaceaHernandia albifloraAlangium chinenseCleome hasslerianaCitrus x paradisiFortunella japonicaStyrax japonicaWisteria sp.Ladenbergia pavoniiPolypremum procumbensBrodiaea coronariaDichelostemma multiflorumMedicago sativaPhiladelphus lewisiiAextoxicon punctatumPittosporum japonicumManglietia fordianaBerberis thunbergiiOphiocolea floribundaViburnum rhytidophyllumAucuba japonicaBulbinella caudafelisKniphofia uvariaAstelia banksiiCentrolepis strigosaEmpodium veratrifoliumCurculigo capitulataZingiber gramineumCalathea loeseneriStrelitzia nicolaiNephrophyllidium cristagalliAcicarpha tribuloidesKalanchoe daigremontianaOpercularia vaginataCalycophyllum candidissimumPhyllis noblaHippuris vulgarisDigitalis purpureaLathraea clandestinaAlectra orobanchoidesNemum spadiceumBulbostylis atrosanguineaFimbristylis complanatacyperus rigidifoliusKyllinga appendiculataPycreus flavescensLipocarpha microcephalaAscolepis capensisHarveya capensisCallitriche albomarginataMyriophyllum exalbescensPenthorum sedoidesTetracarpaea tasmanicaTetracarpaea tasmanica 7240484Geniostoma rupestreArceuthobium verticilliflorumGinalloa arnottianaConnarus conchocarpusPhysena sp.Apeiba tibourbouLasiopetalum sp. Chase 2195Didymosalpinx noraeTrigonia niveaMachaerium lunatumHolocalyx balansaeColona floribundaDalbergia hupeanaHugonia platysepalaMaackia amurensisCapparis hastataEuchresta horsfieldiiParkia roxburghiiGlycyrrhiza echinataCalpurnia aureaBolusanthus speciosusBrongniartia pacificaAteleia herbertsmithiiAdesmia exilisSarcocephalus latifoliusTrichocarya splendensCochlospermum intermediumReevesia thyrsoideaGonystylus macrophyllusMytilaria laosensisAdenium obesumNerium oleanderUvularia floridanaArthropodium cirratumElegia cuspidataCleistes divaricataChysis bractescensGyrocarpus sp. Chase 317Croomia heterosepalaHerreria montevidenseWitsenia mauraBarbacenia elegansAriopsis peltataComospermum yedoenseXanthosoma mafaffaNolina recurvataEichhornia azureaPontederia cordataPeltandra virginicaNeuwiedia veratrifoliaIsotria verticillataSymplocarpus foetidusEleutherine latifoliaClivia miniataThomasia solanaceaEriaxis rigidaQuisqualis indicaRauvolfia manniiTerminalia catappaRhexia virginicaAmpelocera hottleyiDissotis rotundifoliaStylogyne sp.Primula sieboldiiZanthoxylum monophyllumAbrus precatoriusCordyla africanaCeriops australisBauhinia candicansNauclea orientalisCasuarina cunninghaminaHillia trifloraSisyndite sparteaNeoluederitzia sericeocarpaThevetia peruvianaUlex europaeusCassia didymobotryaSalweenia wardiiDelonix regiaClitoria ternateaParkinsonia aculeataRhopalocarpus sp.Simarouba glaucaKelleronia revoiliiTribulus macropterusKallstroemia maximaTribulopis pentandraCeratonia siliquaPintoa chilensisSericodes greggiiRobinia pseudoacaciaGoethalsia meianthaDimocarpus longanRhizophora apiculataLeptonychia pallidaGuaiacum guatemalensePicralima nitidaBalanites maughamiiOpilia amentaceaDiegodendron humbertiiCadia purpureaLuetzelburgia sp. Pennington sHydrangea macrophyllaAugea capensisZygophyllum billardierei 66896Zygophyllum hirticaule 6689634Fagonia creticaEustoma russellianumZygophyllum albumMacrolobium acaciifoliumZygophyllum coccineum 6689622Pterospermum celebicum 4995777Pterospermum celebicumGymnocladus dioicaAcacia caveniaPorlieria chilensisGleditsia triacanthosGrewia occidentalisHeliocarpus americanusPavonia multifloraWrightia arboreaStephanostema stenocarpumHildegardia barteriSchoutenia glomerataCola nitidaPentaplaris doroteaeBerrya javanicaChorisia speciosaCecropia palmataMascarenhasia arborescensCalopogon tuberosusGloriosa superbaLarrea cuneifoliaThespesia populneaArgania spinosaDirachma socotranaSchlumbergera truncataSecuridaca diversifoliaAbroma angustaDionaea muscipulaStylidium calcaratumOreostylidium subulatumKeraudrenia hermanniifoliaSetchellanthus caeruleusHallea rubrostipulataSenna alataLeitneria floridanaLiparia splendensPachysandra procumbensTrema micranthaHelicteres baruensisSophora bhutanicaXanthocercis zambesiacaStrumpfia maritimaCyclopia genistoidesPodalyria bifloraHedysarum vicioidesCaesalpinia pulcherrimaCephalanthus natalensisBlepharocarya depauperataAndrosace spinuliferaChorizema cordatumViscainoa geniculataThottea tomentosaSimaba bidwilliiHovea ellipticaAcosmium dasycarpumTamarindus indicaTipularia discolorAntirhea lucidaSimmondsia chinensisLabordia tinifoliaEuclea natalensisTriplaris americanaTetraena mongolicaBulnesia arboreaTriplochiton zambesiacusLespedeza cuneataArachis hypogaeaBursera inaguensisCommiphora habessinicaAllamanda catharticaMimosa speggazziniiTimonius sp. Ridsdale 2204Eremocitrus glaucaSeverinia buxifoliaAtalantia ceylanicaMicrocos latistipulataPleiospermium alatumTachigali paniculataHumiria balsaminiferaBunchosia armeniacaChaetachme aristataMetternichia princepsGironniera subaequalisPeltophorum sp. 2343002Prostanthera niveaBerchemia discolorVitex agnuscastusBaphia massaiensisErythrophleum ivorensePericopsis moonianaMorkillia mexicanaBrucea mollisAmaroria soulameoidesStachys macranthaMarrubium incanumRuttya fruticosaCaryopteris bicolorThymus alsinoidesOriganum laevigatumSalvia aethiopisPerovskia abrotanoidesRosmarinus officinalisCuscuta reflexaMonarda didymaMentha longifoliaGlechoma hederaceaVigna radiataRhachicallis americanaBixa orellanaSaccifolium bandeiraeJusticia odoraDipteryx odorataCyclonema myricoidesSterculia apetalaLeucophyllum frutescensBruguiera gymnorhizaDiospyros whyteana 1834444Westringia rosmariniformisAgastache foeniculumTectona grandisPeltophorum peltatumLuxemburgia ciliosaCybistax donnellsmithiiCrypteronia paniculataJacaranda sparreiScutellaria alpinaGenipa americanaMouriri helleriMapouria umbrosaRutidea orientalisPouchetia gilletiiSimira viridifloraKraussia floribundaLeptactina platyphyllaAidia micranthaFeretia aeruginescensGlossostipula concinnaOxyanthus pyriformisTabernaemontana divaricataCydista aequinoctialisMassularia acuminataMitriostigma axillareCalochone redingiiPavetta abyssinicaCatesbaea spinosaBertiera brevifloraHymenocoleus hirsutusHirtella bicornisGardenia thunbergiaRamosmania rodriguesiiKailarsenia ochreataTarenna neurophyllaCasasia clusiifoliaCremaspora trifloraOchna serrulataPorterandia crosbyiMorinda citrifoliaNeurocalyx zeylanicusGlossocalyx longicuspisNemuaron vieillardiiBracteanthus glycycarpusSiparuna brasiliensisAdenia digitataSauvagesia calophyllumSanango sp. Bremer 3352Rapanea ferrugineaHalleria lucidaGomphostigma scoparioidesSeymeria pectinataPandorea jasminoidesTricalysia cryptocalyxCoffea arabicaParacoffea melanocarpaDichapetalum crassifoliumPalicourea lasiorrachisUsteria guineensisMacarisia emarginataCoptosapelta flavescensBonyunia minorAlstonia scholarisBlepharistemma membranifoliaVantanea guianensisMuntingia calaburaDichilus lebeckioidesOphiorrhiza mungosFagopyrum callianthumRumex acetosellaOxalis dilleniiSchwenckia laterifloraLinum perenneAngophora hispidaCalycanthus occidentalisBaeckea ramosissimaVahlia capensisRubia tinctorumCrucianella angustifoliaValantia muralisCruciata glabraAsperula laevigataPhopsis stylosaSherardia arvensisGalium elongatumStauntonia hexaphyllaSatyrium nepalenseSaruma henryiColeonema pulchellumImpatiens capensisCrassula marnieranaCanarium ovatumHaplomitrium hookeriDysosma versipellisBuddleja asiaticaRibes aureumSinopodophyllum hexandrumCornus alternifoliaAnthospermum herbaceumGratiola pilosaHumulus lupulusPodophyllum peltatumAdenandra unifloraDiphylleia cymosaDipteronia sinensisUlmus parvifoliaHemiptelea davidiiPinckneya pubensBongardia chrysogonumMelolobium microphyllumTorenia fournieriPteroceltis tatarinowiiTinnea zambesiacaIndigofera australisTapirira mexicanaAesculus paviaAcer saccharumCyrtocarpa proceraSpondias cythereaAbobra tenuifoliaChamaecrista fasciculataGlycine maxAstragalus sparsusPeriploca graecaHoya bellaAsclepias curassavicaApocynum cannabinumStapelia leendertziaeTylophora sylvaticaDicraspidia donnellsmithiiVitis aestivalisTephrosia grandifloraKummerowia stipulaceaZornia cantoniensisCampylotropis griffithiiSesbania sesbanPlocosperma buxifoliumPlocama pendulaPolygonum cuspidatumHedwigia ciliataFunaria hygrometricaUleastrum palmicolaOrthotrichum lyelliUlota obtusiusculaBryodixonia perichaetialisRhabdoweisia crenulataTayloria lingulataSplachnum sphaericumFelipponea esquiroliiClimacium dendroidesDozya japonicaPilotrichopsis dentataBartramia pomiformisLoeskeobryum cavifoliumAntitrichia formosanaDuthiella speciosissimaCtenidium molluscumPlatyhypnidium riparioides 623Platyhypnidium riparioidesRhynchostegium pallidifoliumTaiwanobryum speciosumIsopterygium vinealePterobryopsis orientalis var.Entodontopsis leucostegaStereophyllum radiculosumDesmotheca apiculataCardotiella quinquefariaDolichomitriopsis diversiformiEntodon myurusHerpetineuron toccoaeAnomodon abbreviatusHaplohymenium longinerveCyptodontopsis obtusifoliaOkamuraea hakoniensisRhytidiadelphus loreusPlagiothecium denticulatumHylocomium splendensRhytidiadelphus japonicus 9967Pleurozium schreberiPterobryon arbusculaPleuroziopsis ruthenicaTrachyloma indicumSciaromium tricostatumForsstroemia neckeroidesTomentypnum nitensDrepanocladus aduncusCalliergonella cuspidataHypnum lindbergii 6230584Hypnum lindbergiiBrachythecium rivulareHylocomiastrum pyrenaicumNeodolichomitra yunnanensisTaxiphyllum aomorienseMyuroclada maximowicziiWijkia hornschuchiiBrotherella henoniiHeterophyllium nematosumPylaisiadelpha tenuirostrisThuidium recognitumTrachypodopsis auriculataEumyurium sinicumLeucodon nipponicusCryphaea sinensisAbietinella abietinaPylaisiella intricataBoulaya mitteniiSchlotheimia tectaZygodon intermediusMiyabea fruticellaMacromitrium incurvifoliumMacrocoma tenuis subsp. sullivGroutiella apiculataVenturiella sinensisAulacopilum hodgkinsoniaePhyscomitrella patensPtychomitrium gardneriAmphidium lapponicumMnium cuspidatumSphagnum fallaxDrummondia prorepensEncalypta proceraPorella pinnataTolypella proliferaChara connivensLamprothamnium papulosumLychnothamnus barbatusJubula pennsylvanicaLeucobryum scabrumMetzgeria furcataCalypogeia muellerianaMakinoa crispataLophocolea heterophyllaHerbertus pensilisLepidozia reptansPetalophyllum ralfsiiFossombronia foveolataMonoclea gottscheiDumortiera hirsutaConocephalum conicumLunularia cruciataAsterella tenellaRicciocarpos natansMarchantia polymorphaSphaerocarpos texanusGeothallus tuberosaMougeotia sp.Mougeotia sp.Cylindrocystis sp. UTEX1925Bryopsis maximaChlorella ellipsoideaChlorella ellipsoidea cpst 285Synechococcus sp.SP P00880Synechococcus PCC6301 38927Synechococcus sp. 217137Synechocystis PCC6803Hydrogenovibrio marinus1 59956Acidithiobacillus ferrooxidansHalothiobacillus neapolitanusNitrobacter winogradskyi1 5230Nitrobacter winogradskyi2 5230Nitrobacter vulgaris 349304Thiobacillus intermedius K12 4Alvinoconcha hessleri sym 1546Chromatium vinosum1 516602Thiobacillus ferrooxidans2 297Thiobacillus denitrificans1Hydrogenophaga pseudoflavaHydrogenovibrio marinus2 59956Synechococcus sp. 1850939Chromatium vinosum2 804821Pisum sativum 3893097Pisum sativum cpstCeltis sinensis var. japonicaAphananthe asperaAilanthus altissimaRulingia sp. Chase 2196Koeberlinia spinosaRorippa amphibiaArabis stelleriCardamine flexuosaArmoracia rusticanaNasturtium officinaleReseda albaLepidium virginicumCapsella bursapastorisArabidopsis himalaicaNeobeckia aquaticaDistylium racemosumAnagyris foetidaAjuga chamaepitysIlex brevicuspisUncaria rhynchophyllaOnonis spinosaDaphniphyllum sp.Photinia fraseriMitchella repensIsopogon latifoliusTulipa kolpakowskianaCyanella hyacinthoidesWatsonia angustaFreesia albaPopulus deltoidesLepuropetalon spathulatumHamamelis mollisShaniodendron subaequaleTovaria pendulaLimnanthes douglasiiPiptanthus nepalensisDrosophyllum lusitanicumMillegrana radiolaPinguicula caeruleaErodium texanumOenothera elata subsp. hookeriSedum rubrotinctumJasminum suavissimumZelkova serrataCobaea scandensHeteropyxis natalensisParnassia fimbriataCamptotheca acuminataLeucadendron laureolumRhoiptelea chilianthaLuculia grandifoliaEschscholzia californicaEucryphia lucidaFouquieria columnarisCoris monspeliensisAltingia sp. RBGEViviania marifoliaPelargonium capitatumStylophorum diphyllumBeesia calthifoliaDicranostigma franchetianaAverrhoa carambolaAnopterus macleayanus 1922257Chrysolepis sempervirensDendromecon rigidumGrubbia tomentosaMacleaya cordataGlaucium flavumRhodoleia championiiSarcocaulon vanderietiaeGalax urceolataTicodendron incognitumHunnemannia fumariifoliaLambertia inermisDisanthus cercidifoliusAndrocymbium ciliolatumGunnera hamiltoniiCyclamen hederifoliumExbucklandia populneaCephalotus follicularisHeliamphora nutansRetzia capensisZaluzianskya katharinaeEmorya suaveolensHebenstretia dentataScrophularia sp. DePamphilis STozzia alpinaLloydia serotinaCycnium racemosumStriga asiaticaChelone obliquaCollinsia grandifloraHemiphragma heterophyllumCatharanthus roseusPlatystemon californicusTropaeolum majusMonsonia emarginataGeranium grandiflorumCliftonia monophyllaAmphianthus pusillusAlonsoa unilabiataNemesia strumosaAtherosperma moschatumSamolus valerandiDaucus carotaApium graveolensMorina coulteriana 2065207Levenhookia leptanthaForstera bidwilliiCortusa matthioliCortusa matthioli 1834405Hypecoum imberbeLogania vaginalisMitreola petiolataMitrasacme pilosaCastilleja linariifoliaAngelonia pubescensMalesherbia linearifoliaOrobanche corymbosaByblis linifloraKorthalsella lindsayiDendrophthora clavataPhoradendron serotinumRoridula gorgoniasVelleia paradoxaKopsia fruticosaKoelreuteria paniculataDonatia fascicularisCuttsia viburneaProtea repensPlacospermum coriaceumSarracenia flavaKingdonia unifloraDodecatheon meadiaSchoepfia schreberiDrypetes roxburghiiCasimiroa edulisLysimachia azoricaLunasia amaraDictamnus sp. M.W.Chase1820KCalodendrum capenseMelicope ternataPilocarpus pennatifoliusNotothixos subaureusBuxus sempervirensSarcomelicope simplicifoliaPhelline comosaClematepistephium smilacifoliuGovenia sp. Chase O146Erythrorchis altissimaStyppeiochloa gynoglossaCathaya argyrophyllaCarludovica palmataLasia spinosaPeliosanthes arisanensisApostasia stylidioidesZamioculcas zamiifoliaLiriope platyphyllaLudovia integrifoliaAnchomanes difformisIris ensataOphiopogon jaburanChlorophytum comosumLomandra longifoliaAnthurium scherzerianumTripladenia cunninghamiiPetermannia cirrosaSpathiphyllum clevelandiiTriphora trianthophoraScindapsus aureusBehnia reticulataTropidia sp. Chase O211Oubanguia alataMargaritaria tetracoccaEschweilera odoraLaurus nobilisCorythophora rimosaLecythis pranceiCareya arboreaPlanchonia validaCouratari tauariBertholletia excelsaAsteranthos brasiliensisCariniana legalisCouroupita guianensisBarringtonia asiaticaAllantoma lineataGustavia poeppigianaEcheandia sp.Vanilla africanaLitsea japonicaPogonia japonicaSelenipedium chicaMexipedium xerophyticumKibara rigidifoliaWilkiea huegelianaOuratea duparquetianaRipogonum elseyanumZygogynum sp. Qiu 90024Millettia japonicaBaloskion gracileDilomilis montanaPseudowintera colorataTasmannia insipidaCoelia tripteraTaxus chinensisNeocallitropsis araucarioidesMicrobiota decussataCupressus sempervirensZamia floridanaDiselma archeriWiddringtonia cedarbergensisPhyllocladus trichomanoidesMetasequoia glyptostroboidesLibocedrus plumosaCephalotaxus wilsonianaAmentotaxus argotaeniaThuja occidentalisJuniperus confertaChamaecyparis obtusaThujopsis dolabrataTetraclinis articulataCallitris rhomboideaPlatycladus orientalis flagellAraucaria angustifoliaAgathis moorei 1850530Agathis borneensisWollemia nobilisCedrus deodaraPseudolarix amabilisKeteleeria davidianaAbies fabriPinus balfourianaCalocedrus decurrensNyssa sylvaticaTaxodium distichumTsuga heterophyllaLarix deciduaPicea abiesDuckeodendron cestroidesMetroxylon vitienseViscum albumAlzatea verticillataSabia sp. Qiu 91025Magnolia grandifloraSpiraea x vanhoutteiPrunus emarginata533056Gladiolus guienziiAspidistra elatiorTricalistra ochreataTupistra albifloraOrthrosanthus polistachusVeratrum albumHymenanthera alpinaStewartia pseudocamelliaAkania bidwilliiDegeneria vitiensisBretschneidera sinensisRavenala madagascariensisRhynchocalyx lawsonioidesOncotheca balansaeGynotroches axillarisCapirona decorticansAndira inermisPellacalyx saccardiansSarcococca confusaBalanops vieillardiPotalia resiniferaGoetzia elegansPosoqueria latifoliaPouteria eerwahAngylocalyx brauniiManilkara zapotaBurckella oxycarpaMolongum laxumPicramnia polyanthaAcokanthera oblongifoliaMollinedia ovataMaesa myrsinoidesAegle marmelosEriostemon brevifoliusParaserianthes lophanthaGenista elataHardenbergia violaceaAlbizia julibrissinCercis canadensisExostema caribaeumCladrastis sikokianaGymnostoma webbianumRetama sphaerocarpaPithecellobium mexicanumNepenthes alataSpathelia excelsaIrvingbaileya sp. Plunkett 151Derris laxifloraApuleia leiocarpaCanavalia ensiformisGlycosmis pentaphyllaDiplolaena dampieriCalypso bulbosaEucommia ulmoidesThermopsis fabaceaChorilaena quercifoliaPhebalium woombyeOsbeckia stellataNymania capensisSwietenia macrophyllaLicania tomentosaBaptisia tinctoriaArgyrolobium harveyanumCaragana arborescensCipadessa bacciferaTambourissa tauTrichilia emeticaSchmardaea microphyllaAbrophyllum ornansClusia gundlachiiMauloutchia chapelieriPaphiopedilum bellatulumParinari sumatranaClausena excavataAmorpha fruticosaTheophrasta americanaMelastoma malabathricumTapura amazonicaHintonia latifloraPhragmipedium longifoliumNitraria retusaStemona japonicaAristea glaucaThysanotus spinigerLanaria lanataStreptopus lanceolatusChordifex amblycoleusSaropsis fastigiataGuringalia dimorphaAcion hookeriLepyrodia glaucaAlexgeorgea ganopodaLepidobolus chaetocephalusHarperia laterifloraDielsia stenostachyaMelanostachya ustulataCalorophus elongatusLoxocarya gigasTyrbastes glaucescensMeeboldina canaLeptocarpus tenaxKulinia eludensEmpodisma minusTaraxis grossaWinifredia solaChaetanthus aristatusTremulina tremulaEurychorda complanataSporadanthus tasmanicusDapsilanthus ramosusColeocarya gracilisDesmocladus castaneusBomarea hirtellaStawellia dimorphanthaSimethis mattiazziiPhormium tenaxStypandra glaucaNivenia corymbosaAmana edulisSparrmannia ricinocarpaProsartes lanuginosaXeronema callistemonRhodohypoxis milloidesSpirodela intermediaDisa tripetaloidesPersea americanaTorreya nuciferaHortonia floribundaIpheion dialystemonLeucocrinum montanumMedeola virginianaBorya septentrionalisWelwitschia mirabilisEphedra sinicaAloe bakeriHemerocallis fulvaJohnsonia pubescensAnemarrhena asphodeloidesBulbine succulentaPoellnitzia rubrifloraTrachyandra sp.Haworthia subfasciataLomatophyllum purpureumAstroloba foliosaEremurus himalaicusGasteria liliputianaAsphodeline luteaLimonium axillareSaharanthus ifniensisPsylliostachys suworowiiPlumbago auriculataLimoniastrum guyonianumArmeria splendensCeratolimon feeiDoryanthes excelsaIsophysis tasmanicaGeophila repensChassalia parvifloraVochysia hondurensisLachnocaulon ancepsOryza sativaHordeum jubatumPeridictyon sanctumLeymus chinensisEremium erianthumElytrophorus globularisAmphipogon strictusElymus glaucescensPseudoroegneria spicataZizania texanaAristida congesta subsp. barbiZea maysCyperochloa hirsutaBowiea volubilisAgapanthus africanusDasylirion serratifoliumCampylandra sp. Tamura and YamHuntleya heteroclitaCryptarrhena sp. Chase O307Dichaea riopalenquensisCalibanus hookeriTristagma bivalveMontrichardia arborescensPolianthes geminifloraKoellensteinia gramineaHosta rectifoliaTulbaghia violaceaXanthorrhoea hostilisMonochoria cyaneaZygopetalum intermediumPsychotria borucanaSchoenus nigricansFicinia gracilisBolboschoenus maritimusRhynchospora nervosaKyllingiella polyphyllaScirpus polystachyusCyperus dichroostachyusOxycaryum cubensePleurostachys sp. Kallunki etMesomelaena pseudostygiaGahnia javanicaSchoenoplectus articulatusAbildgaardia ovataFuirena ciliarisHellmuthia membranaceaTrichophorum caespitosumScirpoides burkeiIsolepis cernuaScleria distansCarex confertaOreobolus kuekenthaliiEleocharis atropurpureaCaustis dioicaBecquerelia cymosaColeochloa abyssinicaCladium jamaicenseLepironia articulataEriophorum vaginatumActinoscirpus grossusAmorphophallus rivieriAnomochloa marantoideaMapania cuspidataStenomesson pearceiLycoris sanguineaGalanthus plicatusLeucojum autumnaleDuckeella adolphiiHeteranthera dubiaAmaryllis belladonnaHemiphylacus latifoliaDressleria eburneaOrnithogalum longebracteatumEriocaulon microcephalusAllium altaicumTricoryne sp.Neofinetia falcataStellilabium pogonostalixOncidium excavatumGilliesia gramineaWashingtonia robustaParadisea liliastrumSolaria atropurpureaWhiteheadia bifoliaChlorogalum pomeridianumAnthericum liliagoLeucocoryne coquimbensisEriopsis bilobaPabellonia incrassataNothoscordum bivalvePatersonia glabrataSparattanthelium wonotoboenseGeorgeantha hexandraEcdeiocolea monostachyaCamassia leichtliniiArisaema triphyllumSmilacina hondoensisMaianthemum dilatatumAsphodelus aestivusSemele androgynaRuscus aculeatusDanae racemosaOxychloe andinaAlbuca shawiiPolygonatum cirrhifoliumCardiocrinum cordatumZantedeschia aethiopicaTofieldia pusillaAplectrum hyemaleXerophyllum tenaxOrontium aquaticumArundina graminifoliaLiparis lilifoliaMasdevallia infractaPeganum harmalaEarina autumnalisGinkgo bilobaStanhopea ecornutaBloomeria croceaPhyllanthus liebmannianusMaxillaria cucullataNeomoorea irrorataAngraecum sesquipedaleMuscari neglectumTapeinochilos ananassaePhilodendron oxycardiumHypolytrum bullatumOrchidantha fimbriataHypoxis glabellaPauridia longitubaMilla bifloraTriteleia bridgesiiMuilla maritimaNypa fruticansDaphnandra repandulaLaureliopsis philippianaKadsura japonicaAnomatheca laxaEriochilus cucullatusLapageria roseaLiriodendron chinenseEremothamnus marlothianusGagea luteaIxia latifoliaMonimia ovalifoliaLavatera acerifoliaLaurelia novaezelandiaeMalacocarpus crithmifoliusCephalanthera damasoniumParis tetraphyllaCyanea coriaceaCollospermum hastatumPhilesia buxifoliaPasithea coeruleaBulbophyllum lobbiiEria ferrugineaDaiswa fargesiiPalmorchis trilobulataDieffenbachia sp. Qiu 96007Anisoptera marginataCrispiloba dispermaPhyllonoma laticuspisSerissa foetidaPeperomia sp. Qiu 91047Combretocarpus rotundatusXerorchis amazonicaMalaxis spicataArgostemma hookeriTernstroemia stahliiPodochilus cultratusCoelogyne cristataCalanthe vestitaEpipactis helleborineArpophyllum giganteumPhreatia sp. Chase O203Illigera luzonensisDacrycarpus imbricatusThunia albaSobralia macranthaAnisophyllea corneriPleurothallis endotrachysCyrtopodium andersoniiGlomera sp. Chase O555Cymbidium ensifoliumDioscorea bulbiferaDiaphananthe rutilaCoryanthes verrucolineataNageia falcatusEncyclia sp. KMC1998Trichotosia feroxMonocostus uniflorusRohdea japonicaMaranta leuconeuraCryptocentrum peruvianumSpiranthes cernuaXylobium sp. KMC1998Phaius minorDisporum nantouenseAlstroemeria sp.Meiracyllium trinasutumCattleya dowianaCatasetum expansumDiceratostele gabonensisCorymborkis sp. Chase O542Monophyllorchis sp. Chase O435Sowerbaea junceaAnarthria polyphyllaHopkinsia adscendensLyginia barbataMayaca fluviatilisMyrsiphyllum asparagoidesIriartea deltoideaScilla bifloraGrammatophyllum speciosumAphyllanthes monspeliensisSansevieria cylindricaDracaena aubreyanaPetersianthus africanusAporusa frutescensGaertnera sp.Psilanthus manniiPodococcus barteriCorybas diemenicusHabenaria repensDiuris sulphureaCaladenia cf. caerulea Chase OGlossodia majorChloraea sp. Chase O551Platanthera ciliarisOrthoceras strictumPonthieva racemosaPlatythelys querceticolaMicrotis parvifloraChiloglottis trapeziformisLyperanthus nigricansThelymitra sp. Chase O489Cryptostylis subulataCalochilus robertsoniCranichis fertilisLasianthus pedunculatusMycetia malayanaClintonia borealisPterostylis nutansGoodyera pubescensCyrilla racemifloraDillenia indicaBrownea arizaAldina latifoliaMyrospermum sousanumOchroma pyramidaleAdansonia rubrostipaPhylloxylon perrieriMoringa oleiferaCastanospermum australeRoussea simplexPlumeria inodoraGeosiris sp.Epistephium cf. lucidum ChaseCouepia robustaEuphronia guianensisAcioa guianensisCalophyllum sp.Caryocar glabrumKinugasa japonicaGarrya ellipticaAptosimum sp. DePamphilis HWBGAlseis lugonisBacopa carolinianaAscarina sp. QiuM149Alnus incanaAlvaradoa amorphoidesBrachyloma daphnoidesMelichrus procumbensRhodothamnus chamaecistusRhododendron hippophaeoidesMonotoca scopariaLeucothoe racemosaSprengelia incarnataAndersonia sprengelioidesOligarrhena micranthaCraibiodendron yunnanenseAndromeda polifoliaLyonia ligustrinaPrionotes cerinthoidesVaccinium meridionaleSatyria warszewicziiDiplycosia acuminataCyathodes glaucaArcheria comberiBudawangia gnidioidesEpacris lanuginosaCosmelia rubraRupicola sprengelioidesWoollsia pungensSphenotoma dracophylloidesLeucopogon gibbosusTrochocarpa gunniiAstroloma humifusumLysinema ciliatumCorrea pulchellaTricyrtis affinisTetramerista sp.Danais xanthorrhoeaCarpinus carolinianaAphanopetalum resinosum 940979Corylopsis paucifloraBoehmeria niveaCrossostylis bifloraByrsonima crassifoliaPeltanthera floribundaSterigmapetalum guianense subsSymplocos costataMyrsine africanaBessera elegansAeranthes ramosaPhilydrum lanuginosumLycomormium squalidumAcineta chrysanthaLycaste cruentaKegeliella kupperiVerbena officinalisHeteropolygonatum pendulumEriospermum bayeriThymelaea hirsutaMyrica ceriferaSkimmia anquetiliaDovyalis rhamnoidesDesfontainia spinosaDrimys winteriCryptocarya obovataRothmannia longifloraCorokia cotoneasterIxerba brexioidesLonicera orientalisCurtisia dentataMorus albaMaclura pomiferaGoodia lotifoliaKandelia candelScyphiphora hydrophyllaceaDombeya sp. Chase 273Loeseneriella africanaErithalis fruticosaDriessenia glanduligeraAceratium ferrugineumSteganthera hirsutaMahonia bealeiHedera helixTeucridium parvifoliumShepherdia argenteaSaurauia nepaulensisClematoclethra lasiocladaActinidia chinensisTibouchina urvilleanaDiplectria divaricataSwartzia sp.Melissa officinalisOcimum basilicumHoffmannia refulgens X HoffmanAquilaria beccarianaMyrcianthes fragransChilocarpus suaveolensAmaracarpus sp. Parvis 680Declieuxia fruticosaDisporopsis arisanensisTrachelospermum jasminoidesCorynocarpus cribbianusLotus corniculatusHydnophytum formicarumMyrmecodia platyreaGravesia viscosaCubanola domingensisBuchanania latifoliaDeppea grandifloraMyroxylon balsamumCarallia brachiataArrabidaea pubescensOroxylum indicumHarpagophyton granidieriClavija eggersianaMeyna tetraphyllaKigelia africanaAntonia ovataChazaliella abruptaMacfadyena unguiscatiSukunia longipesCassipourea ceylanicaDactylopetalum ellipticifoliumRudgea lorentensisAlibertia edulisRandia aculeataCampsis radicansEuclinia longifloraPauridiantha paucinervisAmphitecna apiculataFaramea multifloraCrescentia portoricensisVangueria edulisEnterospermum coriaceumCanthium coromandelicumCollinsonia canadensisOrmosia emarginataTrichocladus crinitusLacunaria jenmaniiPachira aquaticaDryadodaphne sp. Gray 4853Touroulia guianensisElaeocarpus grandisLoropetalum chinenseBetula nigraNymphoides peltataDoryphora aromaticaAegiceras corniculatumPhellodendron amurensePassiflora quadrangularisPseudomonotes tropenbosiiPentace polyanthaTetraclea coulteriBrownlowia elataDiospyros kakiNelsonia campestrisMussaenda erythrophyllaIpomoea purpureaMimulus aurantiacusNeuburgia corynocarpumBaissea leonensisGeum chiloenseHolarrhena pubescensFuntumia elasticaSecamone afzeliiBeaumontia grandifloraMandevilla sanderiDictyophleba lucidaStrophanthus eminiiParsonsia heterophyllaParquetina nigrescensPrestonia quinquangularisPachypodium lamereiCeropegia woodiiBegonia boisianaHelmiopsiella madagascariensisEriolaena spectabilisCissampelos pareiraLantana camaraTuberaria guttataToisusu urbanianaChosenia arbutifoliaAdoxa moschatellinaCoprosma pumilaCladopus austroosumiensisOserya coulterianaMarathrum rubrumHydrobryum floribundumVanroyenella plumosaPodostemum ceratophyllumNertera granadensisSalix albaPremna microphyllaGuettarda uruguensisMarcgravia rectifloraReineckea carneaAsparagus officinalisBurchellia bubalinaTrochetiopsis erythroxylonRuizia cordataSeetzenia lanataQuiina pteridophyllaBurretiodendron esquiroliiHamelia cupreaChristiana africanaMatisia cordataParamelhania decaryanaAllocasuarina muellerianaDussia tessmanniiBrighamia insignisDelissea rhytidospermaRehderodendron macrocarpumHalesia carolinaSinojackia rehderianaSchinus molleToxicodendron radicansQuercus virginianaSargentodoxa cuneataElingamita johnsoniOsyris lanceolataOstryopsis davidianaSantalum albumLiquidambar styracifluaHoloptelea integrifoliaSideroxylon cinereumSchima superbaHeterocentron subtriplinerviumCorylus cornutaEubrachion ambiguumJeffersonia diphyllaSarcolaena oblongifoliaCarya glabraArgemone mexicanaGrevillea robustaFortunearia sinensisOstrya virginianaSanguinaria canadensisTrientalis europaeaGlaucidium palmatumHypseocharis sp.Listera smalliiBletilla striataConanthera campanulataHerpolirion novaezelandiaeAnemopsis californicaKunhardtia radiataOdontostomum hartwegiiHermannia erodioidesCypripedium irapeanumDais cotinifoliaGnetum parvifoliumLeonia glycycarpaPiptocalyx mooreiHennecartia omphalandraPetenaea cordataSpermadictyon suaveolensVirgilia divaricataRuta graveolensXymalos monosporaNicotiana debneyiChoisya mollisPhylica polifoliaWarszewiczia cordataArgophyllum sp.Trillium camtschatcensePalmeria scandensBurchardia umbellataErythronium japonicumLardizabala biternataJacquinia umbellataEmmenopterys henryiScabiosa sp. Albach 39Roupala macrophyllaPterostemon rotundifoliusIdesia polycarpaComptonia peregrinaCoopernookia strophiolataDiaspasis filifoliaKerria japonicaFagus crenataGoodenia ovataMyrothamnus flabellifoliusCaltha palustrisCondaminea corymbosaDrosera capensisPterocephalus lasiospermus 206Gaiadendron punctatumNesiota ellipticaSelliera radicansSaxifraga integrifoliaPlatytheca verticellataPeumus boldusItea virginicaPogonopus speciosusAlberta magnaRustia splendensRanzania japonicaSoldanella montanaLobelia cardinalisHeuchera micranthaPieris floribundaGaultheria miquelianaChimarrhis hookeriMelampyrum lineareOlea europaeaHedyosmum bonplandianumEuthystachys abbreviataStilbe vestitaLindenbergia philippinensisProboscidea louisianicaPhlox longifoliaStaphylea trifoliaAtuna racemosaColebrookea oppositifoliaPodranea ricasolianaTecoma stansRadermachera frondosaNectaroscordum siculumPrunella grandifloraOlinia ventosaCaulophyllum robustumMisodendron brachystachyumTrachelium caeruleumCalceolaria sp. dePamphilis 90Jovellana sp. DePamphilis 90 3Nothofagus alessandriiIva frutescensBaccharis halimifoliaHelianthus annuusBorrichia frutescensPentanopsis fragransConostomium quadrangulareKohautia caespitosaBouvardia glaberrimaSynaptantha tillaeaceaOldenlandia corymbosaPentodon pentandrusParapentas silvaticaCarphalea glaucescensPentanisia longitubaPlacopoda virgataHedyotis fruticosaSpermacoce tenuiorRichardia pilosaAmaranthus tricolorTheligonum cynocrambeHydrophyllum virginianumEriodictyon californicumBorago officinalis336406Eccremocarpus scaberLavandula angustifoliaSatureja hortensisHorminum pyrenaicumHyssopus officinalisDracocephalum grandiflorumLamium albumPedicularis foliosaHemimeris sabulosaNuxia sp. Hedberg 4731Peltoboykinia tellimoidesNotholirion thomsonianumMilligania densifloraCorydalis nobilisDarlingtonia californicaPlatanus occidentalisAntidaphne viscoideaDrosera regiaTiarella polyphyllaChrysosplenium albumDiervilla sessilifoliaLeptarrhena pyrolifoliaScoliopus bigeloviiTrochodendron aralioidesAsteropyrum cavalerieiLilium japonicumNomocharis pardanthinaAlania endlicheriFritillaria agrestisDecaisnea fargesiiNepeta tuberosaTeucrium chamaedrysTeline canariensisLaburnum anagyroidesArgyrocytisus battandieriChamaecytisus austriacusChamaespartium sagittaleAdenocarpus complicatusCalicotome villosaCytisus arboreusCytisophyllum sessilifoliumPetteria ramentaceaSpartocytisus supranubiusPolygala amaraSinapis albaRogiera suffrutescensHelianthemum grandiflorumOtholobium sericeumCistus revoliiErythrina cristagalliCajanus cajanBituminaria bituminosaNapoleonaea vogeliiGuarea glabraSpartium junceumLupinus albescensErinacea anthyllisLotononis galpinii
I
Eisen et al., 2002
TIGRTIGRTIGRTIGR
PG Profile of C. tepidum RbcL suggests link with Sulfur Metabolism
from Eisen et al., 2002and see Hanson and Tabita 2001
CT1893 sulfhydrogenase, delta subunit hydDCT1681 ABC transporter, permease proteinCT2206 polysaccharide efflux transporter, putativeCT1271 glycosyl transferaseCT1965 conserved hypothetical proteinCT2256 geranylgeranyl hydrogenase bchPCT0011 deoxyhypusine synthase, putativeCT1772 ribulose bisphosphate carboxylase, large subunit rbcLCT1894 sulhydrogenase, alpha subunit hydACT0472 conserved hypothetical proteinCT0274 carbon-nitrogen hydrolase family proteinCT1891 sulfhydrogenase, beta subunit hydB-1CT1892 sulfhydrogenase, gamma subunit hydG-1CT1250 sulfhydrogenase, gamma subunit hydG-2CT1249 sulfhydrogenase, beta subunit hydB-2
TIGRTIGRTIGRTIGR
Carboxydothermus hydrogenoformans
• Isolated in Yellowstone• Thermophile (grows at 80°C)• Anaerobic• Grows on CO (Carbon Monoxide)• Produces hydrogen gas• Low GC gram postive species• Many Archaeal-like genes
TIGRTIGRTIGRTIGR
QuickTime™ and aTIFF (LZW) decompressor
are needed to see this picture.
TIGRTIGRTIGRTIGR
PG Profiling Works Better Using Orthology
TIGRTIGRTIGRTIGR
Phylogenomics IV:
Duplications
TIGRTIGRTIGRTIGR
Why Duplications Are Useful to Identify
• Allows division into orthologs and paralogs
• Improves functional predictions
• Helps identify mechanisms of duplication
• Can be used to study mutation processes in different parts of a genome
• Lineage specific duplications may be indicative of species’ specific adaptations
TIGRTIGRTIGRTIGR
C. pneumoniae - All Paralogs
TIGRTIGRTIGRTIGR
C. pneumoniae Lineage-Specific Paralogs
TIGRTIGRTIGRTIGR
E. coli Paralogs - All
TIGRTIGRTIGRTIGR
E. coli Paralogs - Top
TIGRTIGRTIGRTIGR
E. coli Paralogs - Recent
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Expansion of MCP Family in V. choleraeE.coli gi1787690B.subtilis gi2633766Synechocystis sp. gi1001299Synechocystis sp. gi1001300Synechocystis sp. gi1652276Synechocystis sp. gi1652103H.pylori gi2313716H.pylori99 gi4155097C.jejuni Cj1190cC.jejuni Cj1110cA.fulgidus gi2649560A.fulgidus gi2649548B.subtilis gi2634254B.subtilis gi2632630B.subtilis gi2635607B.subtilis gi2635608B.subtilis gi2635609B.subtilis gi2635610B.subtilis gi2635882E.coli gi1788195E.coli gi2367378E.coli gi1788194E.coli gi1789453C.jejuni Cj0144C.jejuni Cj0262cH.pylori gi2313186H.pylori99 gi4154603C.jejuni Cj1564C.jejuni Cj1506cH.pylori gi2313163H.pylori99 gi4154575H.pylori gi2313179H.pylori99 gi4154599C.jejuni Cj0019cC.jejuni Cj0951cC.jejuni Cj0246cB.subtilis gi2633374T.maritima TM0014T.pallidum gi3322777T.pallidum gi3322939T.pallidum gi3322938B.burgdorferi gi2688522T.pallidum gi3322296B.burgdorferi gi2688521T.maritima TM0429T.maritima TM0918T.maritima TM0023T.maritima TM1428T.maritima TM1143T.maritima TM1146P.abyssi PAB1308P.horikoshii gi3256846P.abyssi PAB1336P.horikoshii gi3256896P.abyssi PAB2066P.horikoshii gi3258290P.abyssi PAB1026P.horikoshii gi3256884D.radiodurans DRA00354D.radiodurans DRA0353D.radiodurans DRA0352P.abyssi PAB1189P.horikoshii gi3258414B.burgdorferi gi2688621M.tuberculosis gi1666149V.cholerae VC0512V.cholerae VCA1034V.cholerae VCA0974V.cholerae VCA0068V.cholerae VC0825V.cholerae VC0282V.cholerae VCA0906V.cholerae VCA0979V.cholerae VCA1056V.cholerae VC1643V.cholerae VC2161V.cholerae VCA0923V.cholerae VC0514V.cholerae VC1868V.cholerae VCA0773V.cholerae VC1313V.cholerae VC1859V.cholerae VC1413V.cholerae VCA0268V.cholerae VCA0658V.cholerae VC1405V.cholerae VC1298V.cholerae VC1248V.cholerae VCA0864V.cholerae VCA0176V.cholerae VCA0220V.cholerae VC1289V.cholerae VCA1069V.cholerae VC2439V.cholerae VC1967V.cholerae VCA0031V.cholerae VC1898V.cholerae VCA0663V.cholerae VCA0988V.cholerae VC0216V.cholerae VC0449V.cholerae VCA0008V.cholerae VC1406V.cholerae VC1535V.cholerae VC0840V.cholerae VC0098V.cholerae VCA1092V.cholerae VC1403V.cholerae VCA1088V.cholerae VC1394V.cholerae VC0622NJ*******************************************************************************
Heidelberg et al. (2000)
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B. anthracis lineage specific duplications
ORF04205 molybdopterin biosynthesis protein MoeA (moeA)ORF05907 molybdopterin biosynthesis protein MoeA (moeA)ORF02636 molybdopterin biosynthesis protein MoeA (moeA)ORF04204 molybdopterin biosynthesis protein MoeB, putativeORF05908 molybdopterin biosynthesis protein MoeB, putativeORF02634 molybdopterin biosynthesis protein MoeB, putativeORF05904 molybdopterin converting factor, subunit 1 (moaD)ORF02639 molybdopterin converting factor, subunit 1 (moaD)ORF04206 molybdopterin converting factor, subunit 2 (moaE)ORF05905 molybdopterin converting factor, subunit 2 (moaE)ORF02638 molybdopterin converting factor, subunit 2 (moaE)
TIGRTIGRTIGRTIGR
S. aureus Lineage Specific Duplications
ORF02715 4-diphosphocytidyl-2C-methyl-D-erythritol synthase, putativeORF02712 alcohol dehydrogenase, zinc-containingORF00701 alpha-hemolysin precursor (2X)ORF00717 antibacterial proteinORF02597 capsular polysaccharide biosynthesis proteins CapABC (2X) ORF00804 cell wall hydrolase (3X)ORF00657 cell wall surface anchor family protein (2X)ORF00358 clumping factor (2X)ORF01758 deoxyribose-phosphate aldolase (deoC)ORF02579 purine nucleoside phosphorylase (deoD)ORF01031 drug transporter, putativeORF00805 endopeptidase resistance gene (eprH)ORF00706 exotoxin 1,3,4,5, unknown (2X)ORF02184 fibronectin(2X)ORF00097 glycosyl transferase, group 1 family protein (3X)ORF02086 IgG-binding protein (2X)ORF02431 integrase/recombinase, core domain family (3X)
Analysis done with S. Gill
TIGRTIGRTIGRTIGR
S. aureus Lineage Specific DuplicationsORF00137 conserved hypothetical proteinORF00138 conserved hypothetical proteinORF00139 conserved hypothetical proteinORF00140 conserved hypothetical proteinORF00141 conserved hypothetical proteinORF00142 conserved hypothetical proteinORF00143 conserved hypothetical proteinORF00144 conserved hypothetical proteinORF00145 conserved hypothetical proteinORF00146 conserved hypothetical proteinORF00148 conserved hypothetical proteinORF00667 conserved hypothetical proteinORF01251 conserved hypothetical proteinORF02160 conserved hypothetical proteinORF02166 conserved hypothetical proteinORF02170 conserved hypothetical proteinORF02171 conserved hypothetical proteinORF02507 conserved hypothetical proteinORF02745 conserved hypothetical proteinORF02760 conserved hypothetical proteinORF02762 conserved hypothetical proteinORF02763 conserved hypothetical proteinORF02766 conserved hypothetical proteinORF02768 conserved hypothetical proteinORF02769 conserved hypothetical proteinORF02770 conserved hypothetical proteinORF02771 conserved hypothetical proteinORF02772 conserved hypothetical proteinORF02773 conserved hypothetical proteinORF02774 conserved hypothetical proteinORF02896 conserved hypothetical proteinORF02974 conserved hypothetical proteinORF02711 conserved hypothetical protein UPF0007ORF02614 conserved hypothetical protein, authentic frameshift
ORF00286 hypothetical proteinORF00338 hypothetical proteinORF00361 hypothetical proteinORF00412 hypothetical proteinORF00415 hypothetical proteinORF00614 hypothetical proteinORF00697 hypothetical proteinORF00703 hypothetical proteinORF00705 hypothetical proteinORF00875 hypothetical proteinORF00876 hypothetical proteinORF00877 hypothetical proteinORF00879 hypothetical proteinORF00888 hypothetical proteinORF00889 hypothetical proteinORF01024 hypothetical proteinORF01041 hypothetical proteinORF01089 hypothetical proteinORF01091 hypothetical proteinORF01092 hypothetical proteinORF01093 hypothetical proteinORF01095 hypothetical proteinORF01446 hypothetical proteinORF01462 hypothetical proteinORF01918 hypothetical proteinORF02099 hypothetical proteinORF02102 hypothetical proteinORF02158 hypothetical proteinORF02159 hypothetical proteinORF02172 hypothetical proteinORF02430 hypothetical proteinORF02434 hypothetical proteinORF02530 hypothetical proteinORF02531 hypothetical proteinORF02532 hypothetical proteinORF02533 hypothetical proteinORF02534 hypothetical protein
Analysis done with S. Gill
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Lineage Specific Duplications in Wolbachia wMelAnnotationankyrin repeat domain proteinankyrin repeat domain proteinankyrin repeat domain proteinankyrin repeat domain proteinankyrin repeat domain proteinankyrin repeat domain proteinankyrin repeat domain proteinconserved domain proteinconserved domain proteinconserved domain proteinconserved domain proteinconserved hypothetical proteinconserved hypothetical proteinconserved hypothetical proteinconserved hypothetical proteinconserved hypothetical proteinconserved hypothetical proteinconserved hypothetical proteinconserved hypothetical proteinconserved hypothetical proteinconserved hypothetical proteinconserved hypothetical proteinconserved hypothetical proteinconserved hypothetical proteinconserved hypothetical proteinconserved hypothetical proteinconserved hypothetical proteinconserved hypothetical proteinconserved hypothetical proteinconserved hypothetical proteinconserved hypothetical proteinconserved hypothetical proteinconserved hypothetical proteinconserved hypothetical proteinconserved hypothetical proteinFRAMESHIFTconserved hypothetical proteinPOINT MUTATIONconserved hypothetical protein,degenerateconserved hypothetical protein,FRAMESHIFTconserved hypothetical protein,FRAMESHIFTconserved hypothetical protein,FRAMESHIFTconserved hypothetical protein,FRAMESHIFTconserved hypothetical protein,interruption-Cconserved hypothetical protein,POINT MUTATIONconserved hypothetical protein,POINT MUTATIONconserved hypothetical protein,truncatedconserved hypothetical protein,truncationDNA mismatch repair proteinMutL (mutL)DNA repair protein RadC,putativeDNA repair protein RadC,putative, truncationDNA repair protein RadC,truncationDnaJ domain proteinDnaJ domain proteinexopolysaccharide synthesisprotein ExoD-related proteinexopolysaccharide synthesisprotein ExoD-related proteinHNH endonuclease familyproteinHNH endonuclease familyproteinhypothetical proteinhypothetical proteinhypothetical proteinhypothetical proteinhypothetical proteinhypothetical proteinhypothetical proteinhypothetical proteinhypothetical proteinhypothetical proteinhypothetical proteinhypothetical proteinhypothetical proteinhypothetical proteinhypothetical proteinhypothetical protein
hypothetical proteinhypothetical proteinhypothetical proteinhypothetical proteinhypothetical proteinhypothetical proteinhypothetical proteinhypothetical proteinhypothetical proteinhypothetical proteinhypothetical proteinhypothetical proteinhypothetical proteinhypothetical proteinhypothetical proteinhypothetical proteinhypothetical proteinhypothetical proteinhypothetical proteinhypothetical proteinhypothetical proteinhypothetical proteinhypothetical proteinhypothetical proteinhypothetical proteinhypothetical proteinhypothetical proteinhypothetical proteinhypothetical proteinhypothetical proteinhypothetical proteinhypothetical proteinhypothetical proteinhypothetical proteinhypothetical proteinhypothetical proteinhypothetical proteinhypothetical proteinhypothetical proteinhypothetical proteinhypothetical proteinhypothetical proteinhypothetical proteinhypothetical proteinhypothetical proteinhypothetical proteinhypothetical proteinhypothetical proteinhypothetical proteinhypothetical proteinhypothetical proteinhypothetical proteinhypothetical proteinhypothetical proteinhypothetical proteinhypothetical proteinhypothetical proteinhypothetical proteinhypothetical proteinhypothetical proteinhypothetical proteinhypothetical proteinhypothetical proteinhypothetical proteinhypothetical proteinhypothetical proteinhypothetical proteinhypothetical proteinhypothetical proteinhypothetical proteinmajor facilitator familytransportermajor facilitator familytransportermajor facilitator familytransportermembrane protein, putativemembrane protein, putativemembrane protein, putativeMutL family proteinNa+/H+ antiporter family proteinNa+/H+ antiporter, putativepermease, putativeportal protein, FRAMESHIFTportal protein, FRAMESHIFTprophage LambdaW1, DNAmethylaseprophage LambdaW1, terminaselarge subunit, putativeprophage LambdaW2, ankyrinrepeat domain proteinprophage LambdaW2, ankyrinrepeat domain protein
prophage LambdaW2, baseplateassembly protein J, putativeprophage LambdaW2, baseplateassembly protein V, putativeFRAMESHIFTprophage LambdaW2, baseplateassembly protein V, putativeFRAMESHIFTprophage LambdaW2, baseplateassembly protein W, putativeprophage LambdaW2, minor tailprotein Z, putative,FRAMESHIFTprophage LambdaW2, site-specific recombinase, resolvasefamilyprophage LambdaW4, ankyrinrepeat domain proteinprophage LambdaW4, DNAmethylaseprophage LambdaW4, portalprotein, FRAMESHIFTprophage LambdaW4, portalprotein, FRAMESHIFTprophage LambdaW4, terminaselarge subunit, putativeprophage LambdaW5, ankyrinrepeat domain proteinprophage LambdaW5, ankyrinrepeat domain proteinprophage LambdaW5, ankyrinrepeat domain proteinprophage LambdaW5, baseplateassembly protein J, putative,FRAMESHIFTprophage LambdaW5, baseplateassembly protein V, putativeprophage LambdaW5, baseplateassembly protein W, putativeprophage LambdaW5, minor tailprotein Z, putative, degenerate,FRAMESHIFTprophage LambdaW5, site-specific recombinase, resolvasefamilyregulatory protein RepA, putativeregulatory protein RepA, putativereverse transcriptase, putativereverse transcriptase, putativereverse transcriptase, putativesodium/alanine symporter familyproteinsodium/alanine symporter familyproteinTenA/THI-4 family proteintranscriptional regulatortranscriptional regulatortranscriptional regulatortranscriptional regulatortranscriptional regulatortranscriptional regulatortranscriptional regulator, putativetranslation elongation factor Tu(tuf)translation elongation factor Tu(tuf)transposase, degeneratetransposase, IS4 familytransposase, IS4 familytransposase, IS4 familytransposase, IS5 family,interruption-Ntransposase, IS5 family,truncationtransposase, putative, degeneratetransposase, putative, degeneratetransposase, putative, degeneratetype IV secretion system proteinVirB4, putativeUDP-N-acetylglucosaminepyrophosphorylase-relatedprotein
TIGRTIGRTIGRTIGR
MutL Duplication in Wolbachia wMel
ORF01096 DNA mismatch repair protein MutL (mutL)ORF00446 MutL family protein
TIGRTIGRTIGRTIGR
MutL Duplication in Wolbachia wMel
TIGRTIGRTIGRTIGR
Archglbs fulgidus 2650206Archglbs profundus 3892197Desulfovibrio vulgaris 902747Dslfotomaculum thermocistern1Chlorobium tepdum CT0852Chlorobium tepdum CT2249Allochromatium vinosum 2576393Pyrobaculum islandicum 2459568Archglbs fulgidus 2650205Archglbs profundus 389219Dslfotomaculum thermocistern2Desulfovibrio vulgaris 902748Chlorobium tepdum CT0853Chlorobium tepdum CT2248Allochromatium vinosum 2576394Pyrobaculum islandicum 2459569Desulfovibrio vulgaris 1591554Methanobacterium thermoautotrophiucm coF420 2621331100901009510099100100989910010086100100DsrBDsrCDuplication of DsrBC
Recent Duplication of DsrBC in C. tepidum
TIGRTIGRTIGRTIGR0.1
Schizosaccharomyces pombeGP139
Neurospora crassaPIRS55262S552
Clostridium perfringensGP18145
Bacillus subtilisSPP45864YWJD
Bacillus cereusGP6759487embCAB
B BACAN 01914 UV endonuclease
Bacillus haloduransOMNINTL01BH
B BACAN 01459 UV endonuclease
Deinococcus radioduransGP61167
Nostoc sp. PCC 7120GP17130610d
Older Duplication of UVDE
TIGRTIGRTIGRTIGR
X-files
Eisen et al. 2000. Genome Biology 1(6): 11.1-11.9
Also see Tillier and Collins. 2000. Nature Genetics 26(2):195-7 and Suyama and Bork. 2001. Trends Genetics 17: 10-13.
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Phylogenomics V:
Genome Dynamics
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V. cholerae vs. E. coli All
TIGRTIGRTIGRTIGR
V. cholerae vs. E. coli Best
TIGRTIGRTIGRTIGR
V. cholerae vs. E. coli: if Top
TIGRTIGRTIGRTIGR
V. cholerae vs. E. coli: Top, Rotated
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Duplication and Gene Loss Model
A
B
CD
E
F
A
B
CD
E
F
A
B
CD
E
F
A
B
C
D
EF
A’
B’
C’
D’
E’F’
A
B
C
D
EF
A’
B’
C’
D’
E’F’
A
C
D
F
A’
B’
E’
E. coliE. coli
B
C
D
F
A’
B’
D’
E’
V. cholerae
A
B
C
D
EF
A’
B’
C’
D’
E’F’
TIGRTIGRTIGRTIGR
B1A1B2A2B3A3B3B22423222120191817161514131211109672582627282930123453132 B131326789101112131415161718192021222324252627282930123453132 B32423222120191817161514131211109672582627282933231304521 A131326789101112131415161718192021222324252627282930123453132 A231326789101112131918171615142021222324252627282930123453132 A32678910111213191817161514202122232425262754331302928132B2Inversion Around Terminus (*)
Inversion Around Terminus (*)
Inversion AroundOrigin (*)
Inversion AroundOrigin (*)
******** Common Ancestor of
A and B
31326789101112131415161718192021222324252627282930123453132A2A1A2A3B2B1
Symmetric Inversion Model
TIGRTIGRTIGRTIGR
V. cholerae vs. E. coli: Top
TIGRTIGRTIGRTIGR C. trachomatis MoPn
C. p
neu
mon
iae
AR
39Origin
Terminus
C. trachomatis vs C. pneumoniae
TIGRTIGRTIGRTIGR
M. leprae vs. M. tuberculosis
TIGRTIGRTIGRTIGR
B. subtilis vs. S. auerus
0
500
1000
1500
2000
2500
3000
2632200 2632700 2633200 2633700 2634200 2634700 2635200 2635700 2636200 2636700
analysis w/ S. Gill
TIGRTIGRTIGRTIGR
P. putida vs. P.aeruginosa Orthologs
9945700
9946700
9947700
9948700
9949700
9950700
9951700
0 2000 4000 6000 8000
Series1
analysis w/ K. Nelson
TIGRTIGRTIGRTIGR
StrpB vs. StrpA All
13621300
13621500
13621700
13621900
13622100
13622300
13622500
13622700
13622900
13623100
0 500 1000 1500 2000 2500
Series1
TIGRTIGRTIGRTIGR
StrpB vs. StrpA: Orthologs
13621300
13621500
13621700
13621900
13622100
13622300
13622500
13622700
13622900
13623100
0 500 1000 1500 2000 2500
Series1
TIGRTIGRTIGRTIGR
Why are Inversions Symmetrical Around Origin
• Genetic studies in Salmonella and E. coli suggest that there may be strong selection against other inversions
• See:– Mahan, Segall, Schmid and Roth– Liu and Sanderson– Rebollo, Francois, and, Louarn
TIGRTIGRTIGRTIGR
TIGRTIGR
Other peopleOther people
Mom and DadMom and Dad
H. OchmanH. Ochman
W. MartinW. Martin
F. RobbF. Robb
J. BattistaJ. Battista
E. OriasE. Orias
D. BryantD. BryantS. O’NeillS. O’Neill
M. EisenM. Eisen
N. MoranN. Moran
R. MyersR. Myers
C. M. CavanaughC. M. Cavanaugh
P. HanawaltP. Hanawalt
NSFNSF
J. HeidelbergJ. Heidelberg
T.ReadT.Read
N. WardN. Ward
M-I BenitoM-I Benito
J. C. VenterJ. C. Venter C. FraserC. Fraser
S. SalzbergS. Salzberg
O. WhiteO. White
I. PaulsenI. Paulsen
$$$$$$
ONRONR
DOEDOE
NIHNIHH. TettelinH. Tettelin
Eisen GroupEisen Group
Martin WuMartin WuDongying WuDongying WuJames SakwaJames SakwaJonathan BadgerJonathan Badger
TIGRTIGRTIGRTIGR
Vertical Inheritance
From C. Darwin, origin of species, via W. F. Doolittle
TIGRTIGRTIGRTIGR
Lateral Transfer
TIGRTIGRTIGRTIGR
Why Gene Transfers Are Useful to Identify
• Laterally transferred genes frequently involved in environmental adaptations and/or pathogenicity
• Identification of vectors of gene transfer (e.g., transposons, integrons, phage)
• Identify species associations in the environment (e.g., Thermotoga and Archaea, Nelson et al.)
• Identify organelle derived genomes in eukaryotic genomes
• Important for understanding of evolution
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Examples of Horizontal Transfers
• Antibiotic resistance genes on plasmids
• Toxin resistance genes on plasmids
• Insertion sequences
• Agrobacterium Ti plasmid
• Virus and phage gene acquisition and transfer
• Organelle to nucleus transfers
TIGRTIGRTIGRTIGR
Steps in Lateral Gene Transfer (LGT)
A B C D
1 Gene acquires host features
2
Transfer
6 Amelioration
3-5 Integration, selection, spread
TIGRTIGRTIGRTIGR
Inference of Gene Transfer Involves Identifying Unusual Genes
• Unusual distribution patterns
• High sequence similarity to supposedly distantly related species
• Unusual nucleotide composition
• Unusual patterns of evolutionary relatedness (gene vs. species)
TIGRTIGRTIGRTIGR
Alternative Explanations for Unusual Genes
• Gene loss• Evolutionary rate variation• Strong selection
– Purifying selection– Directional selection– Convergence
• Mistaken orthology assignment• Blast problems• Contamination
TIGRTIGRTIGRTIGR
“Hundreds of human genes appear likely to have resulted from horizontal transfer from bacteria at some point in
the vertebrate lineage.”
TIGRTIGRTIGRTIGR
IHGSC 2001
• Claim:– Lateral transfer from bacteria to vertebrates
• Evidence– Genes match bacteria but not non-vertebrate
eukaryotes– Or, genes have stronger match to bacteria than to
non-vertebrates– A set of ~120 of these genes are found in many
bacterial species
TIGRTIGRTIGRTIGR
Unusual Distribution Pattern
+ +
TIGRTIGRTIGRTIGR
Implied Model for BVTs
1
2
3-6
Inverts Vertebrates Protists Bacteria
TIGRTIGRTIGRTIGR
Gene Loss?
Inverts Vertebrates Protists Bacteria
TIGRTIGRTIGRTIGR
Rate Variation?
Inverts
Vertebrates
Protists
Bacteria
TIGRTIGRTIGRTIGR
Unusual Distribution -Incomplete Data
+ +
Gene present in ancestor
+/-+/-
TIGRTIGRTIGRTIGR
Number of pBVTs Dependson # of Genomes Analyzed
1 2 3 4 5 Other
0
200
400
600
800
1000
1200
1400
1600
1800
Number of protein sets
Fruit flyC. elegansArabidopsisYeastParasites
Salzberg et al. 2001
TIGRTIGRTIGRTIGR
Trees Don’t Support TransferParamecium bursaria Chlorella virus 1Homo sapiens HAS1Mus musculus HAS1Xenopus laevisXenopus laevis Danio rerio Homo sapiens Mus musculus Danio rerio Xenopus laevis Gallus gallus Bos taurus Homo sapiens Mus musculus Rattus norvegicus Bradyrhizobium sp SNU001Rhizobium leguminosarumRhizobium spRhizobium lotiRhizobium tropiciRhizobium sp. NodCMesorhizobium sp 7653RSinorhizobium melilotiRhizobium melilotiRhizobium leguminosarumRhizobium galegaeAzorhizobium caulinodansStigmatella aurantiacaStreptomyces coelicolorStreptococcus uberisStreptococcus equisimilisStreptococcus pyogenes HASAStreptococcus pneumoniae0.2BacteriaVertebratesVirusIIIIII
Salzberg et al. 2001
TIGRTIGRTIGRTIGR
Trees Don’t Support Transfer II
TIGRTIGRTIGRTIGR
Alternative explanations
• Gene loss from non-vertebrate eukaryotes• Rapid divergence in non-vertebrate
eukaryotes• Some non-vertebrate genomes are
incomplete• Bad annotation/gene finding• Contamination• Blast ≠ evolution
TIGRTIGRTIGRTIGR
Organellar to Nuclear Transfers in A. thaliana
TIGRTIGRTIGRTIGR
A. thaliana Nuclear Proteins:Best Matches to Complete Genomes
0
1000
2000
3000
4000
Bes
t M
atch
es
CH
LT
E
PO
RG
IB
AC
SUM
CY
TU
BB
UR
TR
EP
AC
HL
PN
EC
OL
IN
EIM
ER
ICP
RC
AU
CR
HE
LP
YSY
NSP
AQ
UA
ED
EIR
AT
HE
MA
AE
RP
EA
RC
FU
ME
TJA
ME
TT
HP
YR
AB
CE
LE
GY
EA
STD
RO
ME
B A E
TIGRTIGRTIGRTIGR
Best Matches vs. Prokaryotes
TIGRTIGRTIGRTIGR
Best Matches vs. Prokaryotes
TIGRTIGRTIGRTIGR
A. thaliana T1E2.8 is aChloroplast Derived HSP60ARATH -T1E2.8**********ECOLHAEINVIBCHVIBCHRICPR YEASTCHLPNCHLTRAQUAECAMJEHELPYBBURTREPATHEMA BACSUDEIRAMCYTU MCYTU SYNSPSYNSPODONT CPSTMYCGEMYCPNCHLPNCHLTRCHLPN CHLTR ARCFUARCFUMETJAPYRHOMETTH METTHYEAST YEASTYEASTYEAST CELEGYEASTYEASTYEASTCELEG YEAST YEAST CELEGYEASTCELEG CELEGEukaryaArchaeaBacteriaCyano/Cpst
TIGRTIGRTIGRTIGR
rRNA vs. Whole Genome Trees
Mycobacterium tuberculosisBacillus subtilisSynechocystis sp.Caenorhabditis elegansDrosophila melanogasterSaccharomyces cerevisiaeMethanobacterium thermoautotrophicumArchaeoglobus fulgidusPyrococcus horikoshiiMethanococcus jannaschiiAeropyrum pernixAquifex aeolicusThermotoga maritimaDeinococcus radioduransTreponema pallidumBorrelia burgdorferiHelicobacter pyloriCampylobacter jejuniNeisseria meningitidisEscherichia coliVibrio choleraeHaemophilus influenzaeRickettsia prowazekiiMycoplasma pneumoniaeMycoplasma genitaliumChlamydia trachomatisChlamydia pneumoniae0.05 changesArchaeaBacteriaEukarya
