TIGRTIGRTIGRTIGR

TIGRTIGRTIGRTIGR

TIGRTIGRTIGRTIGR

Topics of Discussion• Introduction to genome sequencing and

analysis• Need for “phylogenomic” approaches• Phylogenomic examples

– Species evolution– Lateral vs. vertical evolution– Gene function– Gene duplications– Genome rearrangements

TIGRTIGRTIGRTIGR

The Institute for Genomic Research(TIGR)

• A not for profit institution, staff ~350

• Funded primarily by government grants

• Departments:– Research Departments– Bioinformatics– Sequencing Core

TIGRTIGRTIGRTIGR

Fleischmann et al. 1995

TIGRTIGRTIGRTIGR

Whole Genome Shotgun Sequencing

shotgunshotgun

sequencesequenceWarner Brothers, Inc.Warner Brothers, Inc.

TIGRTIGRTIGRTIGR

Assemble Fragments

sequencer sequencer outputoutput

assemble assemble fragmentsfragments

Closure &Closure &

AnnotationAnnotation

TIGRTIGRTIGRTIGR

General Steps in 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

TIGRTIGRTIGRTIGR

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

TIGRTIGRTIGRTIGR

Comparative Genomic Hybridizationof GroupB strep

TIGRTIGRTIGRTIGR

Chromosome Duplications in Arabidospsis

TIGRTIGRTIGRTIGR

100s of DNA Islands in O157:H7 vs. K12: Gene Loss or Transfer?

from Eisen (2001)

TIGRTIGRTIGRTIGRTIGRTIGRTIGRTIGR

“Nothing in biology makes senseexcept in the light of evolution.”

T. H. Dobzhansky (1973)

TIGRTIGRTIGRTIGR

Evolution and Genomics Overlap

• 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

TIGRTIGRTIGRTIGR

Phylogenomics?Evolutionary information improves genome analysis

-Classification of multigene families-Predicting functions-Origins of genes and pathways

Genomics information improves evolutionary reconstructions-More sequences of genes-Unbiased sampling-Presence/absence needed to infer certain events

Feedback loop between two types of analysis

TIGRTIGRTIGRTIGR

TIGRTIGRTIGRTIGR

TIGRTIGRTIGRTIGR

Why Completeness is Important• Improves characterization of genome features

– Gene order, replication origins

• Better comparative genomics– Genome duplications, inversions

• Determination of presence and absence of particular genes and features 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

TIGRTIGRTIGRTIGR

Uses of Phylogenomics

• Species evolution and systematics

• Lateral versus vertical evolution

• Gene function

• Gene and genome duplications

• Genome rearrangements

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.

Species Evolution I:

Selecting Genome Projects to Increase

PhylogeneticDiversity

TIGRTIGRTIGRTIGR

Species EvolutionI I:Major Evolutionary Transitions

• Analysis of S. pombe genome (Wood et al 2002)

• Compared the genomes of eukaryotes to those of prokaryotes

• Asked: “Are there genes in all eukaryotes with no obvious homologs in any prokaryote?”

• Found ~200 genes which included many with know major roles in “eukaryotic” features like the cytoskeleton and chromatin as well as many with no known function

TIGRTIGRTIGRTIGR

BacteriaArchaea

Eukaryotes

Giardia

Trichomonas

Naegleria

Trypanosoma

Euglena

Plasmodium

Tetrahymena

Phytophthora

Arabidopsis

Chlamydomonas

Dictyostelium

Humans

Fly

Worm

Encephalatozoon

S. cerevisiae

S. pombe

Evolutionary Scenario

TIGRTIGRTIGRTIGR

Evolutionary Transitions II:Single- vs. Multi-Cellularity

• Analysis of S. pombe genome (Wood et al. 2002)

• Compared multi-cellular vs. single-cellular species

• Asked “Are there genes in all multi-cellular and not in any single-cellular?”

• Found only 3

• Concluded that the multicellularity was likely the result of gene regulatory processes

TIGRTIGRTIGRTIGR

Plants

Giardia

Trichomonas Parabisalia

Diplomonads

Naegleria

Trypanosoma

Euglena

Plasmodium

Tetrahymena

Phytophthora

Arabidopsis

Chlamydomonas

Fungi

Animals

Dictyostelium

HumansFly

Worm

Encephalatozoon

S. cerevisiaeS. pombe

Microsporidia

Dictyostelia

HeterokontsCiliates

ApicomplexaKinetoplastids

EuglenasAcrasidae

Multiple Origins of Multicellularity

TIGRTIGRTIGRTIGR

Species Evolution III: Uncultured Microbes

• Vast majority of microbes have never been cultured

• Usually studied indirectly by cloning rRNA genes and using position within rRNA tree to predict biology

• These predictions are frequently inaccurate

TIGRTIGRTIGRTIGR

Genomics does not require initial culturing step.

• Isolate, by filtration, all bacteria in a water sample

• Extract total DNA in very large pieces

• Clone those pieces as BACs into E.coli to get enough.

• Sequence the BACs like a bacterial genome.

Natural Water

Filterconcentrate

ExtractDNA

CloneInto BACs

SequenceGeneList

TIGRTIGRTIGRTIGR

Phylogenetic Anchors

Beja et al. 2000

TIGRTIGRTIGRTIGR

Using a rRNA anchor allowed the

identification of a new form of phototrophy:

Proteorhodopsin

Beja et al. 2000

TIGRTIGRTIGRTIGR

Uses of Phylogenomics

• Species evolution and systematics

• Lateral versus vertical evolution

• Gene function

• Gene and genome duplications

• Genome rearrangements

TIGRTIGRTIGRTIGR

Vertical Inheritance

From C. Darwin, origin of species, via W. F. Doolittle

TIGRTIGRTIGRTIGR

Examples of Horizontal Transfers

• Antibiotic resistance genes

• Insertion sequences

• Agrobacterium Ti plasmid

• Toxin degradation genes on plasmids

• Virus and phage gene acquisition and transfer

• Organelle to nucleus transfers

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

TIGRTIGRTIGRTIGR

A Blast Search Does not Equal an Evolutionary Study

TIGRTIGRTIGRTIGR

• Claim– “Hundreds of human genes appear likely to have resulted from

horizontal transfer from bacteria at some point in the vertebrate lineage.”

• Evidence– Genes match bacteria but not non-vertebrate eukaryotes

– Or genes have stronger match to bacteria than to non-vertebrates

TIGRTIGRTIGRTIGR

Implied Model for BVTs

1

2

3-6

Non Verts Vertebrates Protists Bacteria

TIGRTIGRTIGRTIGR

Gene Loss?

Inverts Vertebrates Protists Bacteria

TIGRTIGRTIGRTIGR

Rate Variation?

Inverts

Vertebrates

Protists

Bacteria

TIGRTIGRTIGRTIGR

Implied Model for BVTs

1

2

3-6

Non Verts Vertebrates Protists Bacteria

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

Organellar to Nuclear Transfers in A. thaliana

TIGRTIGRTIGRTIGR

Organelle to Nucleus Transfer are Common

From W. F. Doolittle

TIGRTIGRTIGRTIGR

TIGRTIGRTIGRTIGR

Mitochondrial Genome Integration into A. thaliana chrII

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

Blast ≠ Phylogeny

231456

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

Uses of Phylogenomics

• Species evolution and systematics

• Lateral versus vertical evolution

• Gene function

• Gene and genome duplications

• Genome rearrangements

TIGRTIGRTIGRTIGR

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

TIGRTIGRTIGRTIGR

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

TIGRTIGRTIGRTIGR

TIGRTIGRTIGRTIGR

H. pylori and MutS• Prior to this genome, all species that

encoded a MutS homolog also encoded a MutL homolog

• Experimental studies have shown MutS and MutL always work together in mismatch repair

• Problem: what do we conclude about H. pylori mismatch repair

TIGRTIGRTIGRTIGR

Table 3. Presence of MutS Homologs in Complete Genomes Sequences

Species # of MutSHomologs

BacteriaEscherichia coli K12 1Haemophilus influenzae Rd KW20 1Neisseria gonorrhoeae 1Helicobacter pylori 26695 1Mycoplasma genitalium G-37 0Mycoplasma pneumoniae M129 0Bacillus subtilis 169 2Streptococcus pyogenes 2Synechocystis sp. PCC6803 2Treponema pallidum Nichols 1Borrelia burgdorferi B31 2Aquifex aeolicus 2Deinococcus radiodurans R1 2

ArchaeaArchaeoglobus fulgidus VC-16, DSM4304 0Methanococcus janasscii DSM 2661 0Methanobacterium thermoautotrophicum ΔH 1

EukaryotesSaccharomyces cerevisiae 6Homo sapiens 5

TIGRTIGRTIGRTIGR

MutS AlignmentEEDLKNRLCQKF.DA.HYNTIWMPTIQAISNIDCLLAITRTSEYLGAPSCDTSLKDCMRRLFCNFDKNHKDWQSAVECIAVLDVLLCLANYSQGGDGPMCCSAEWLDFLEK.FS..EHYHSLCKAVHHLATVDCIFSLAKV..AKQGDYCSELQYKEFLNK.IT..AEYTELRKITLNLAQYDCILSLAAT..SCNVNYVEYELYKELRER.VV..KELDKVGNNASAVAEVDFIQSLAQI..AYEKDWAEYELFTELREK.VK..QYIPRLQQLAKQMSELDALQCFATI..SENRHYTEYEIFTEVRAT.VA..EKAQPIRDVAKAVAAIDVLAGLAEV..AVYQGYCEQRVLKSITDE.IV..SHHKTLRSLANALDELDISTSLATL..AQEQDFVEANIIDLFKRK.FI..DRSNVVRQVATTLGYLDTLSSFAVL..ANERNLVQDAIVKEIVNI.SS..GYVEPMQTLNDVLAQLDAVVSFAHVSNGAPVPYVQSALVREIINI.TL..TYTPVFEKLSLVLAHLDVIASFAHTSSYAPIPYIEEERILRQLSDQVL..EVLLDLEHLLAIATRLDLATARVRY...SFWLGAEVRKVLQRITEYIG..DYAKELLESFEACVEVDFQQCKYRF..SKLVEGSEIERILRVLTEKTA..EYTEELFLDLQVLQTLDFIFAKARY..AKAVKATTYMIVCKLLSE.IY..EHIHCLYKLSDTVSMLDMLLSFAHA..CTLSDYVSEETVDELLDK.IA..THISELFMIAEAVAILDLVCSFTYN..LKENNYTETLLMYQLQCQ.VL..ARAAVLTRVLDLASRLDVLLALASA..ARDYGYSEIEILFSLQEQ.IL..RRKTQLTAYNILLSELEILLSFAQV..SAERNYARPTIVDEVDSKTNTQLNGFLKFKSLRHPCFNLGA...TTA.KDFIPNDIERPEIVLP..GEDTHP...FLEFKGSRHPCITKTF...FG..DDFIPNDILRPTVQEE......R....KIVIKNGRHPVIDVLL..GEQ..DQYVPNNTDRPTFVNG.....QQ....AIIAKNARNPIIESLD.......VHYVPNDIMKPQIHE......GY....ELIIEEGRHPVIEEF.....V..ENYVPNDTKKPEFSK......D.....EVEVIEGRHPVVEKVM...DS..QEYVPNNCMRPIMQM.....EPG....LIDIEAGRHPVVEQSL...GA..GFFVANDTQRPVVDD.....SH.....AHTVIQGRHPIVEKGL..SHKL.IPFTPNDCFCPKVDE.....SN.....KLEVVNGRHLMVEEGL..SARSLETFTANNCERPAILEK....GQG....RIILKASR...VEVQD....E..IAFIPNDVYRPKLHPM...DSER....RTHLISSRHPVLEMQD....D..ISFISNDVTHPPQWL...TPGDEK...PITLRQLRHPLLHWQA..EKEGGPAVVPITLTFPDFGE.....WVE.......LYEARHPVLVLVKED.....VVPVGILLKKPIMND.....TG.....FIRLKKARHPLLPP.........DQVVANDIERPEFTD............TLAIKQGWHPILEKIS....A..EKPIANNTYIPIFTN............NLLIRDSRHPLLEKVL.......KNFVPNTISRPRYSPQ....VL.....GVRIQNGRHPLMELCA.......RTFVPNSTEEPQLVE.....DEC....ILEIINGRHALYETFL.......DNYIPNSTMLGKE......QPR......IGCE...EEAEEHGKAY..LSED......SER......MSPE......NGK......LDRD......SF.......MGDN......RQ.......LGHD......HWHPD....VGNGNV....N........LAKD......N........FEKD......KQM......LESG......KGD......IDSQ......IR.......EKKG...............LGRD......FS.......VTE.......GSN......STKH......SSS......CGGD......KGR......IDGG..LFSELSWCEQNKG.LGLLTGANAAGKSTILRMACIAVIMAQMGC.CVLVTGPNMGGKSTLIRQAGLLAVMAQLGC.VMIITGPNMGGKSSYIKQVALITIMAQIGS.INIITGPNMGGKSSYIRQVALLTIMAQIGS.IHVITGPNMAGKSSYIRQVGVLTLLSHIGS.MLLITGPNMSGKSTYMRQIALISIMAQIGC.LVILTGPNASGKSCYLRQVGLIQLMAQTGS.IWLITGPNMAGKSTFLRQNAIISILAQIGS.LWVITGPNMGGKSTFLRQNAIIVILAQIGC.FHIITGPNMGGKSTYIRQTGVIVLMAQIGC.FLIITGPNMGGKSTYIRQVGVISLMAQIGC.VIAITGPNTGGKTVTLKTLGLVALMAKVGL..LILTGPNTGGKTVALKTLGLSVLMFQSAI.TIVITGPNTGGKTVTLKTLGLLTLMAQSGL.FLIITGPNMSGKSTYLKQIALCQIMAQIGS.LQIITGCNMSGKSVYLKQVALICIMAQMGS.VKVITGPNSSGKSIYLKQVGLITFMALVGSRIIVVTGANASGKSVYLTQNGLIVYLAQIGCYVPCESA.VLTPIDRIMTRLGANDNIMQGKSTFFVELAETKKILD.....YVPAEKC.RLTPVDRVFTRLGASDRIMSGESTFFVELSETASILR.....YVPAEEA.TIGIVDGIFTRMGAADNIYKGRSTFMEELTDTAEIIR.....FVPAEEI.RLSIFENVLTRIGAHDDIINGDSTFKVEMLDILHILK.....FIPARRA.KIPVVDALFTRIGSGDVLALGVSTFMNEMLEVSNILN.....FVPAKKA.VLPIFDQIFTRIGAADDLISGQSTFMVEMLEAKNAIV.....FIPAKTA.TLSICDRIFTRVGAVDDLATGQSTFMVEMNETANILN.....FVPASNA.RIGIVDQIFSRIGSADNLYQQKSTFMVEMMETSFILK.....FVPCSKA.RVGIVDKLFSRVGSADDLYNEMSTFMVEMIETSFILQ.....FVPCESA.EVSIVDCILARVGAGDSQLKGVSTFMAEMLETASILR.....FVPCEEA.EIAIVDAILCRVGAGDSQLKGVSTFMVEILETASILK.....YIPAKETVEMPWFAQILADIGDEQSLQQNLSTFSGHICRIIRILQALPSGPVPASPNSKLPLFEKVFTDIGDEQSIEQNLSTFSAHVKNMAEFLP.....HIPADEGSEAAVFEHVFADIGDEQSIEQSLSTFSSHMVNIVGILE.....YVPAEYS.SFRIAKQIFTRISTDDDIETNSSTFMKEMKEIAYILH.....GIPALYG.SFPVFKRLHARV.CNDSMELTSSNFGFEMKEMAYFLD.....FVPAEEA.EIGAVDAIFTRIHSCESISLGLSTFMIDLNQVAKAVN.....FVPAERA.RIGIADKILTRIRTQETVYKTQSSFLLDSQQMAKSLS.....CSAAASAAAAAAAGASL.............MATNRSLLVVDELGRGGSSSDGFAI.............HATAHSLVLVDELGRGTATFDGTAI.............KATSQSLVILDELGRGTSTHDGIAI.............NCNKRSLLLLDEVGRGTGTHDGIAI.............NATEKSLVILDEVGRGTSTYDGIAI.............NATKNSLILFDEIGRGTSTYDGMAL.............HATAKSLVLLDEIGRGTATFDGLAI.............NATRRSFVIMDEIGRGTTASDGIAI.............GATERSLAILDEIGRGTSGKEGISI.............SATKDSLIIIDELGRGTSTYDGFGL.............NASKNSLIIVDELGRGTSTYDGFGLVQDVLDPEIDSPNHPIFPSLVLLDEVGAGTDPTEGSAL.............KSDENTLVLIDELGAGTDPIEGSAL.............QVNENSLVLFDELGAGTDPQEGAAL.............NANDKSLILIDELGRGTNTEEGIGI.............DINTETLLILDELGRGSSIADGFCV.............NATAQSLVLIDEFGKGTNTVDGLAL.............LATEKSLILIDEYGKGTDILDGPSLFYESVLHHVATHISAVVKELAETIYATLEYFIRDVALIKYFSELSKAIVKYISEKLQAIIEYVHDHIWSVAEYLAGEIYGCLKYLSTINYATLKYLLENNWAISEYIATKIWAIAEHIASKIIALLRHLADQPIGILEYLKKKKMSILDDVHRTNYAVCEYLLSLKLAVTEHLLRTEAAVLRHWLARGGSIMLNMSKSE.QSLGF.FATHYGTLASSFKHHPQ.VRPLKMSIL...VDE.....A.....KCRTL.FSTHYHSLVEDYSKSVC.VRLGHMACM...VENECEDPS.....KSLTL.FVTHYPPVCELEKNYSHQVGNYHMGFL...VSEDESKLDPGAA.DCPLILFTTHFPMLGEIKSPL...IRNYHMDYV....EEQKTGED.....KAKTL.LATHFLEITELEGKIEG.VKNYHMEVE...........KT....GAKTL.FSTHYHELTVLEDKLPQ.LKNVHVRAE...........EY....QARTI.FATHYHELNELASLLEN.VANFQVTVK...........EL....HSRTL.FATHAHQLTNLTKSFKN.VECYCTNLS.....IDRD........QCRTL.FATHFGQELKQIIDNKC.SKGMSEKVK......FYQSGITDLG.GAFCM.FATHFHELTALANQIPT.VNNLHVTALT................GCFAL.FATHFHELTELSEKLPN.VKNMHVVAHI.....EKNLKEQKH...CLTV.ATTHYGELKALKYQDAR.FENASVEFD..................AWVF.VTTHHTPIKLYSTNSDY.YTPASVLFD..................ARVL.ATTHYPELKAYGYNREG.VMNASVEFD..................AFTL.FATHFLELCHIDALYPN.VENMHFEVQ........HVK...NT..ATVF.LSTHFQDIPKIMSKKPA.VSHLHMDAV........LLN.....PTCPHIFVATNFLSLVQLQLLPQGPLVQYLTMET.................KCPRIIACTHFHELFNENVLTENIKGIKHYCTDILISQKYNLLETAHVG....TRNVTFLYKMLEGQSEGSFGMHVASMCGISKEIIDNAQIAAD....QETITFLYKFIKGACPKSYGFNAARLANLPEEVIQKGHRKAREQV.PDFVTFLYQITRGIAARSYGLNVAKLADVPGEILKKAAHKSK....WMSVIFLYKLKKGLTYNSYGMNVAKLARLDKDIINRAFSISE....PEGIRFLYILKEGKAEGSFGIEVAKLAGLPEEVVEEARKILR....NGTVVFLHQIKEGAADKSYGIHVAQLAELPGDLIARAQDILK....PEEIIFLHQVTPGGADKSYGIEAGRLAGLPSSVITRARQVMA....DHTFSFDYKLKKGVNYQSHGLKVAEMAGIPKNVLLAAEEVLT....GNNFCYNHKLKPGICTKSDAIRVAELAGFPMEALKEAREILG...TEETLTMLYQVKKGVCDQSFGIHVAELANFPKHVIECAKQKAL...DDEDITLLYKVEPGISDQSFGIHVAEVVQFPEKIVKMAKRKAN....DQSLSPTYRLLWGIPGRSNALAIAQRLGLPLAIVEQAKDKLG....RETLKPLYKIAYNTVGESMAFYIAQKYGIPSEVIEIAKRHVG....IETLSPTYKLLIGVPGRSNAFEISKRLGLPDHIIGQAKSEMTSRNKEAILYTYKLSKGLTEEKNYGLKAAEVSSLPPSIVLDAKEITT....DNSVKMNYQLTQKSVAIENSGIRVVKKIFNPDIIAEAYNMDS...CEDGNDLVFFYQVCEGVAKASHASHTAAQAGLPDKLVARGKEVEDHESEGITFLFKVKEGISKQSFGIYCAKVCGLSRDIVERAEELSR----------------I-----------------------------II------------------------III------------------IV------MSH6__Yeast MSH6__Mouse MSH3__Human MSH3__Yeast MutS__Aquae MutS__Bacsu MutS__Synsp MSH1__Pombe MSH1__Yeast MSH2__Human MSH2__Yeast MutS2_Synsp MutS2_Aquae MutS2_Bacsu MSH4__Human MSH4__Yeast MSH5__Human MSH5__Yeast MSH6__Yeast MSH6__Mouse MSH3__Human MSH3__Yeast MutS__Aquae MutS__Bacsu MutS__Synsp MSH1__Pombe MSH1__Yeast MSH2__Human MSH2__Yeast MutS2_Synsp MutS2_Aquae MutS2_Bacsu MSH4__Human MSH4__Yeast MSH5__Human MSH5__Yeast MSH6__Yeast MSH6__Mouse MSH3__Human MSH3__Yeast MutS__Aquae MutS__Bacsu MutS__Synsp MSH1__Pombe MSH1__Yeast MSH2__Human MSH2__Yeast MutS2_Synsp MutS2_Aquae MutS2_Bacsu MSH4__Human MSH4__Yeast MSH5__Human MSH5__Yeast

TIGRTIGRTIGRTIGR

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

TIGRTIGRTIGRTIGR

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

TIGRTIGRTIGRTIGR

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

TIGRTIGRTIGRTIGR

TIGRTIGRTIGRTIGR

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

EvolutionaryMethod

PHYLOGENENETIC PREDICTION OF GENE FUNCTIONIDENTIFY HOMOLOGSOVERLAY KNOWNFUNCTIONS ONTO TREE

INFER LIKELY FUNCTIONOF GENE(S) OF INTEREST

1234563531A2A3A1B2B3B2A1B1A3A1B2B3BALIGN SEQUENCESCALCULATE GENE TREE1246CHOOSE GENE(S) OF INTEREST2A2A53Species 3Species 1Species 211222311A3A1A2A3A1A2A3A464564562B3B1B2B3B1B2B3B ACTUAL EVOLUTION(ASSUMED TO BE UNKNOWN)

Duplication?EXAMPLE AEXAMPLE BDuplication?Duplication?Duplication5 METHODAmbiguous

TIGRTIGRTIGRTIGR

rRNA and Uncultured Microbes

TIGRTIGRTIGRTIGR

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

Caution: Homology Based Predictions Have Many Flaws

• Not all orthologs have the same function

• Homology cannot be used to characterize novel pathways (e.g., D. radiodurans)

• Absence of genes can be important to phenotypes (e.g., pathogenicity)

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

TIGRTIGRTIGRTIGR

Recombination Genes in GenomesPathway |------------------------------Bacteria---------------------------| |---Archaea---| Euks

Protein Name(s)

Initiation

RecBCD pathwayRecB + + - - - - - - + + - + - - - - - - - -RecC + + - - - - - - + ±+ - ± - - - - - - - -RecD + + - - ± - - - + ±+ - ++ - ± ±+ - - - - -

RecF pathwayRecF + + + - + - - + + - + ± - - + - - ± ± ±RecJ + + + + + - - + - + + + + + + - - - - -RecO + + - - + - - + + - - - - - ± - - - - -RecR + + + ±+ + - - + + - + + - + + - - - - -RecN + + + + + - - + + - + - ± + + - - ± ± -RecQ + + - - + - - + - - + - - - + - - - - + ++

RecE pathwayRecE/ExoVIII + - - - - - - - - - - - - - - - - - - -RecT + - - - + - - - - - - - - - - - - - - -

SbcBCD pathwaySbcB/ExoI + + - - - - - - - - - - - - - - - - - -SbcC + - - - + - - + - + + - + + + ± ± ± ± ± ±SbcD + - - - + - - + - + + - + + + ± ± ± ± ± ±

AddAB PathwayAddA/RexA - - + - + - - - - - + + - ± - - - - - -AddB/RexB - - - - + - - - - - - - - - - - - - - -

Rad52 pathwayRad52, Rad59 - - - - - - - - - - - - - - - - - - - ++ +Mre11/Rad32 ± - - - ± - - ± - ± ± - ± ± ± + + + + + +Rad50 ± - - - ± - - ± - ± ± - ± ± ± + + + ± + +

RecombinaseRecA, Rad51 + + + + + + + + + + + + + + + + + + + ++ ++

Branch migrationRuvA + + + + + + + + + + + + + - + - - - - -RuvB + + + + + + + + + + + + + - + - - - - -

RecG + + + + + - - + + + + - + + + - - - - -

ResolvasesRuvC + + + + - - - + + - + + + - + - - - - -RecG + + + + + - - + + + + - + + + - - - - -Rus + - - - - - - - ±+ - - - - ±+ - - - - - -CCE1 - - - - - - - - - - - - - - - - - - - +

Other recombination proteinsRad54 - - - - - - - - - - - - - - - - - - - + +Rad55 - - - - - - - - - - - - - - - - - - - + +Rad57 - - - - - - - - - - - - - - - - - - - + +Xrs2 - - - - - - - - - - - - - - - - - - - +

TIGRTIGRTIGRTIGR

Unusual Features of D. radiodurans DNA Repair Genes

Process Genes

Nucleotide excision repair Two UvrAs

Base excision repair Four MutY-Nths

Recombination RecD but not RecBC

Replication Four Pol genes

dNTP pools Many MutTs, two RRases

Other UVDE

TIGRTIGRTIGRTIGR

Problem:

List of DNA repair gene homologs in D. radiodurans genome is not significantly different from other

bacterial genomes of the similar size

TIGRTIGRTIGRTIGR

Repair Studies in Different Species(determined by Medline searches as of 1998)

Humans 7028E. coli 3926S. cerevisiae 988Drosophila 387B. subtilits 284S. pombe 116Xenopus 56C. elegans 25A. thaliana 20Methanogens 16Haloferax 5Giardia 0

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

TIGRTIGRTIGRTIGR

Functional and Evolution III: Non-Homology Based Analysis

TIGRTIGRTIGRTIGR

Non Homology Based Functional Prediction: Phylogenetic Profiles

TIGRTIGRTIGRTIGR

TIGRTIGRTIGRTIGR

Phylogenetic Profile - E.coliFlagellar Genes

fhiAfliMfliPfliGflgGfliFflgIflhAflhBgcpE

Wu and Eisen, unpublished

TIGRTIGRTIGRTIGR

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

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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

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PG Profiling Works Better Using Orthology

Eisen and Wu 2002

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Uses of Phylogenomics

• Species evolution and systematics

• Lateral versus vertical evolution

• Gene function

• Gene and genome duplications

• Genome rearrangements

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Uses of Phylogenomics

• Species evolution and systematics• Lateral versus vertical evolution• Gene function• Gene and genome duplications• Genome rearrangements

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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

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Levels of Paralogy Within A Genome• All

– All members of a gene family are linked together

• Top matches– Only top matching pairs are linked together.

Therefore, if in a large gene family, only the pair from the most recent duplication event is included

• Recent– Operational definition based on comparison to other

species. Only pairs which are more similar to each other than to selected other species are included.

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C. pneumoniae Paralogs by Position

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C. pneumoniae Paralogs - Lineage Specific

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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)

Based on Read et al. submitted

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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

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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

TIGRTIGRTIGRTIGR

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

Superoxide Dismutase Duplication in D. radiodurans

D. radiodurans 2

D. radiodurans 1

V. choleraeE. coli

M. tuburculosis

B. subtilis

A. aeolicus 1

A. aeolicus 2

C. elegans

Yeast

see White et al. (1999)

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

Uses of Phylogenomics

• Species evolution and systematics

• Lateral versus vertical evolution

• Gene function

• Gene and genome duplications

• Genome rearrangements

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.

TIGRTIGRTIGRTIGR

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. coliTop Matches, Rotated

TIGRTIGRTIGRTIGR

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. coliBest Matching Proteins by Location

TIGRTIGRTIGRTIGR C. trachomatis MoPn

C. p

neu

mon

iae

AR

39Origin

Terminus

C. trachomatis vs C. pneumoniae Dot Plot

TIGRTIGRTIGRTIGR

M. leprae vs. M. tuberculosis Whole Genome Alignment

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

Acknowledgements• Outside TIGR

–A. Stoltzfus

–H. Ochman

–D. Bryant

–W. F. Doolittle

–M. Eisen

–M-I Benito

• $$$:

–NSF

–NIH

–ONR

–DOE

–NEB