Resumo phytozome
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Resumo PHYTOZOME PowerPoint PPT Presentation

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Resumo PHYTOZOME. Included Organisms The proteomes of the following organisms are clustered in release v9.1 of Phytozome :

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Resumo phytozome


Resumo phytozome

  • IncludedOrganisms

  • The proteomes of thefollowingorganisms are clustered in release v9.1 of Phytozome:

  • OrganismcommonnameSourceAquilegiacoeruleaColoradobluecolumbineJGI 8X assembly v1.0, annotation v1.2aArabidopsis lyrataLyre-leaved rock cressJGI release v1.0Arabidopsis thalianaThalecressTAIR release 10 acquiredfromTAIRBrachypodiumdistachyonPurplefalsebromeJGI 8x assembly release v1.0 of strain Bd21 with JGI/MIPS PASA annotation v1.2Brassica rapaNapacabbageAnnotation v1.2 onassembly v1.1 frombrassicadb.orgCapsellarubellaRedshepherd'spurseJGIannotation v1.0 onassembly v1Carica papayaPapayaASGPB release of 2007Chlamydomonas reinhardtiiGreenalgaeJGI v5.0 assembly, annot v5.3.1 basedon Augustus u11.6Citrus clementinaClementineJGI v1 assembly and v1.0 annotationCitrussinensisSweetorangeJGI v1.1 annotationon v1 assemblyCoccomyxasubellipsoideaC-169CoccomyxaC-169JGI v2.0 assembly and annotationCucumissativusCucumberRoche 454-XLR assembly and JGI v1.0 annotationEucalyptusgrandisEucalyptusJGIassembly v1.0, annotation v1.1Fragaria vescaStrawberryv1.1 assembly and v1.0 annotationfromShulaev et. al., hostedatGDRGlycinemaxSoybeanJGI Glyma1.1 annotation of thechromosome-based Glyma1 assemblyGossypiumraimondiiCottonJGIannotation v2.1 onassembly v2.0Linum usitatissimumFlaxBGI v1.0 onassembly v1.0Malus domesticaAppleGDRprediction v1.0 onMalus x domestica assembly v1.0Manihot esculentaCassavaAssembly version 4, JGI annotation v4.1Medicago truncatulaBarrel medicMt3.5v4 onassembly MedtrA17_3.5 fromtheMedicago Genome SequenceConsortiumMicromonaspusilla CCMP1545Micromonas CCMP1545JGI v3.0 assembly and annotationMicromonaspusilla CCMP1545Micromonas RCC299JGI v3.0 assembly and annotationMimulusguttatusMonkeyflowerJGI 7x assembly release v1.0 of strain IM62, annotation v1.1Oryza sativaRiceMSU Release 7.0 of the Rice Genome AnnotationOstreococcuslucimarinusJGI v2.0 assembly and annotationPanicumvirgatumSwitchgrassJGI v0.0 annotationonassembly v0Phaseolus vulgarisCommonbeanJGIannotation v1.0 onassembly v1.0 usingpublishedESTs, and JGI RNAseqPhyscomitrellapatensMossJGIassembly release v1.1 and COSMOSS annotation v1.6Populus trichocarpaPoplarJGIassembly release v3.0, annotation v3.0Prunus persicaPeachJGI release v1.0Ricinus communisCastorbeanTIGR release 0.1SelaginellamoellendorffiiSpikemossJGI v1.0 assembly and annotationSetariaitalicaFoxtailmilletJGI 8.3X chromosome-scaleassembly release 2.0, annotation version 2.1SolanumlycopersicumTomatoSGNTomato Genome Project ITAG2.3Solanum tuberosumPotatoDM1-3 516R44 (CIP801092) Genome Annotation v3.4 mapped to pseudomoleculesequenceSorghumbicolorSweet SorghumSbi1.4modelsfrom MIPS/PASA on v1.0 assemblyThellungiellahalophilaSaltcressJGIannotation v1.0 onassembly v1Theombroma cacaoCocoabeanD. Gilbert public gene set 8 Mar 2012 onassembly v1.1Vitis viniferaGrapeMarch 2010 12X assembly and annotationfromGenoscopeVolvoxcarteriVolvoxJGIannotation 2.0 onassembly v2Zea maysMaize5b.60 annotation (filtered set) of themaize "B73" genome v2 producedbytheMaize Genome Project

  • Nodes

  • Clustering is used to groupextant genes into sets representingthe ancestral genes thatexistedjust prior to varioussignificantevolutionaryevents (nodes). Extant genes havebeenclusteredatnodesrepresentingthefollowingspeciationevents: 

  • Viridiplantae (~475 Mya):Genes representingthemostrecentcommonancestor of Embryophytes and chlorophytes.Chlorophyte (~50-200 Mya):Genes representingthemostrecentcommonancestor of Chlamydomonas and Ostreococcus.Embryophyte (~450 Mya):Genes representingthemostrecentcommonancestor of Tracheophytes and Bryophyta (representedbyPhyscomitrella).Tracheophyte (~420 Mya):Genes representingthemostrecentcommonancestor of Selaginella and theangiosperms.Angiosperm(~160 Mya):Genes representingthemostrecentcommonancestor of grasses and eudicots.Eudicot(~115 Mya)Genes representingthemostrecentcommonancestor of therosids and asterids.AsteridGenesrepresentingthemostrecentcommonancestor of themimulus and tomato.CitrusGenesrepresentingthemostrecentcommonancestor of theC.sinensis and C. clementina.Brassicales-MalvalesGenesrepresentingthemostrecentcommonancestor of thecotton and theBrassicales.Arabidopsis(~10 Mya)Genes representingthemostrecentcommonancestor of therosids and asterids.Rosid (~1 Mya)Genes representingthemostrecentcommonancestor of theFabidae and theMalvidaecladesFabid(~107 Mya):Genes representingthemostrecentcommonancestorthenitrogen-fixing and Malpighialesclades.Malvid(~95 Mya):Genes representingthemostrecentcommonancestor of Eucalyptus and theBrassicales-Malvalesclade.Brassicaceae(~90 Mya):Genes representingthemostrecentcommonancestor of arabidopsis and cabbage.Nitrogen-fixing(~90 Mya):Genes representingthemostrecentcommonancestor of theRosales-Cucurbitales and Papilionoideaeclades.Rosales-Cucurbitales(~90 Mya):Genes representingthemostrecentcommonancestor of thecucumber and thestonefruits.Papilionoideae:Genes representingthemostrecentcommonancestor of thecommonbean and soybean. A subfamily of theleguemes, withdistinctivebutterfly-likeflowers.Malpighiales:Genes representingthemostrecentcommonancestor of the cassava and poplar.Panicoideae:Genes representingthemostrecentcommonancestor of Maiz and foxtailmillet.Grass (~70 Mya):Genes representingthemostrecentcommonancestor of Sorghum, Maize, foxtailmillet and the BEP clade.

Resumo phytozome

Arabidopsis lariata

Laguncularia racemosa


Resumo phytozome

Sorgo, cana e setaria


Arabidopsis e mamão

Eucalipto e laguncularia


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