Resumo PHYTOZOME

• Included Organisms• The proteomes of the following organisms are clustered in release v9.1 of Phytozome:• Organismcommon nameSourceAquilegia coeruleaColorado blue columbineJGI 8X assembly v1.0, annotation v1.2aArabidopsis lyrataLyre-leaved rock cressJGI release v1.0Arabidopsis thaliana

Thale cressTAIR release 10 acquired from TAIRBrachypodium distachyonPurple false bromeJGI 8x assembly release v1.0 of strain Bd21 with JGI/MIPS PASA annotation v1.2Brassica rapaNapa cabbageAnnotation v1.2 on assembly v1.1 from brassicadb.orgCapsella rubellaRed shepherd's purseJGI annotation v1.0 on assembly v1Carica papayaPapayaASGPB release of 2007Chlamydomonas reinhardtiiGreen algaeJGI v5.0 assembly, annot v5.3.1 based on Augustus u11.6Citrus clementinaClementineJGI v1 assembly and v1.0 annotationCitrus sinensisSweet orangeJGI v1.1 annotation on v1 assemblyCoccomyxa subellipsoidea C-169Coccomyxa C-169JGI v2.0 assembly and annotationCucumis sativusCucumberRoche 454-XLR assembly and JGI v1.0 annotationEucalyptus grandisEucalyptusJGI assembly v1.0, annotation v1.1Fragaria vescaStrawberryv1.1 assembly and v1.0 annotation from Shulaev et. al., hosted at GDRGlycine maxSoybeanJGI Glyma1.1 annotation of the chromosome-based Glyma1 assemblyGossypium raimondiiCottonJGI annotation v2.1 on assembly v2.0Linum usitatissimumFlaxBGI v1.0 on assembly v1.0Malus domesticaAppleGDR prediction v1.0 on Malus x domestica assembly v1.0Manihot esculentaCassavaAssembly version 4, JGI annotation v4.1Medicago truncatulaBarrel medicMt3.5v4 on assembly MedtrA17_3.5 from the Medicago Genome Sequence ConsortiumMicromonas pusilla CCMP1545Micromonas CCMP1545JGI v3.0 assembly and annotationMicromonas pusilla CCMP1545Micromonas RCC299JGI v3.0 assembly and annotationMimulus guttatusMonkey flowerJGI 7x assembly release v1.0 of strain IM62, annotation v1.1Oryza sativaRiceMSU Release 7.0 of the Rice Genome AnnotationOstreococcus lucimarinusJGI v2.0 assembly and annotationPanicum virgatumSwitchgrassJGI v0.0 annotation on assembly v0Phaseolus vulgarisCommon beanJGI annotation v1.0 on assembly v1.0 using published ESTs, and JGI RNAseqPhyscomitrella patensMossJGI assembly release v1.1 and COSMOSS annotation v1.6Populus trichocarpaPoplarJGI assembly release v3.0, annotation v3.0Prunus persicaPeachJGI release v1.0Ricinus communisCastor beanTIGR release 0.1Selaginella moellendorffiiSpikemossJGI v1.0 assembly and annotationSetaria italicaFoxtail milletJGI 8.3X chromosome-scale assembly release 2.0, annotation version 2.1Solanum lycopersicumTomatoSGNTomato Genome Project ITAG2.3Solanum tuberosumPotatoDM1-3 516R44 (CIP801092) Genome Annotation v3.4 mapped to pseudomolecule sequenceSorghum bicolorSweet SorghumSbi1.4 models from MIPS/PASA on v1.0 assemblyThellungiella halophilaSalt cressJGI annotation v1.0 on assembly v1Theombroma cacaoCocoa beanD. Gilbert public gene set 8 Mar 2012 on assembly v1.1Vitis viniferaGrapeMarch 2010 12X assembly and annotation from GenoscopeVolvox carteriVolvoxJGI annotation 2.0 on assembly v2Zea maysMaize5b.60 annotation (filtered set) of the maize "B73" genome v2 produced by the Maize Genome Project

• Nodes• Clustering is used to group extant genes into sets representing the ancestral genes that existed just prior to various significant evolutionary events (nodes). Extant genes have been clustered at

nodes representing the following speciation events:

• Viridiplantae (~475 Mya):Genes representing the most recent common ancestor of Embryophytes and chlorophytes.Chlorophyte (~50-200 Mya):Genes representing the most recent common ancestor of Chlamydomonas and Ostreococcus.Embryophyte (~450 Mya):Genes representing the most recent common ancestor of Tracheophytes and Bryophyta (represented by Physcomitrella).Tracheophyte (~420 Mya):Genes representing the most recent common ancestor of Selaginella and the angiosperms.Angiosperm(~160 Mya):Genes representing the most recent common ancestor of grasses and eudicots.Eudicot(~115 Mya)Genes representing the most recent common ancestor of the rosids and asterids.AsteridGenes representing the most recent common ancestor of the mimulus and tomato.CitrusGenes representing the most recent common ancestor of the C.sinensis and C. clementina.Brassicales-MalvalesGenes representing the most recent common ancestor of the cotton and the Brassicales.Arabidopsis(~10 Mya)Genes representing the most recent common ancestor of the rosids and asterids.Rosid (~1 Mya)Genes representing the most recent common ancestor of the Fabidae and the Malvidae cladesFabid(~107 Mya):Genes representing the most recent common ancestor the nitrogen-fixing and Malpighiales clades.Malvid(~95 Mya):Genes representing the most recent common ancestor of Eucalyptus and the Brassicales-Malvales clade.Brassicaceae(~90 Mya):Genes representing the most recent common ancestor of arabidopsis and cabbage.Nitrogen-fixing(~90 Mya):Genes representing the most recent common ancestor of the Rosales-Cucurbitales and Papilionoideae clades.Rosales-Cucurbitales(~90 Mya):Genes representing the most recent common ancestor of the cucumber and the stone fruits.Papilionoideae:Genes representing the most recent common ancestor of the common bean and soybean. A subfamily of the leguemes, with distinctive butterfly-like flowers.Malpighiales:Genes representing the most recent common ancestor of the cassava and poplar.Panicoideae:Genes representing the most recent common ancestor of Maiz and foxtail millet.Grass (~70 Mya):Genes representing the most recent common ancestor of Sorghum, Maize, foxtail millet and the BEP clade.

Arabidopsis lariata

Laguncularia racemosa

Café

Eucalipto e laguncularia

Arabidopsis e mamão

soja

Sorgo, cana e setaria