Species in Phytozome v9.1

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Welcome to Phytozome!

Phytozome is a joint project of the Department of Energy's Joint Genome Institute and the Center for Integrative Genomics to facilitate comparative genomic studies amongst green plants. Famlies of orthologous and paralogous genes that represent the modern descendents of ancestral gene sets are constructed at key phylogenetic nodes. These families allow easy access to clade specific orthology/paralogy relationships as well as clade specific genes and gene expansions. As of release v9.1, Phytozome provides access to forty-one sequenced and annotated green plant genomes which have been clustered into gene families at 20 evolutionarily significant nodes. Where possible, each gene has been annotated with PFAM, KOG, KEGG, and PANTHER assignments, and publicly available annotations from RefSeq, UniProt, TAIR, JGI are hyper-linked and searchable.

Using Phytozome: video tutorials
Announcements
  • [03 May 2013]   v3.0 of Physcomitrella patens now available as early release.
  • [03 May 2013]   RNA-seq based expression data now available for Phaseolous and soybean.
  • [18 Mar 2013]   Phytozome v9.1, containing new gene families calculated at 20 internal nodes, is now available.
News
  • [03 May 2013]  v3.0 of Physcomitrella patens genome and annotation now available
    An early release of the Physcomitrella patens v3 assembly and annotation is now available.Go to the organism page for more information.
  • [03 May 2013]  Expression data now availabe for Phaseolus and soybean
    The GBrowse genome browsers for Phaseolus and soybean now incorporate three tracks related to RNA-seq gene expression analysis.RNA-Seq Read Coverage - Total RNA-Seq read coverage (counts of overlapping reads per base) from all samples in the study, on a log scale. Gene-level Expression - Gene locus expression FPKM values from RNA-Seq read alignment and cuffdiff analysis. Transcript-level expression - FPKM values resolved at the transcript level. The latter two tracks also provide mouse-overs where sample-resolved expression levels are displayed.
  • [18 Mar 2013]  New Gene Family set released
    Phytozome v9.1, containing gene families calculated at 20 internal nodes, is now available. In addition to the nodes available in Phytozome v9.0, gene families are now available at the following additional nodes: Malpighiales, Papilionoideae, Rosales-Cucurbitales, Arabidopsis, Brassicales-Malvales, Citrus, Asterid, Rosid, Panicoideae, Eudicot, Angiosperm, Tracheophyte, Embryophyte, Viridiplantae. Please note that, given the small modification to the clustering algorithm to prevent blow-up of very large families (see Release Notes), families were recomputed at all nodes, including those released in v9.0.
  • [07 Feb 2013]  GBrowse databases available from Bulk FTP
    Phytozome v9.0 GBrowse database snapshots and associated configuration files are now available from Bulk FTP. Please consult the associated readme file at that link for more information.
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Early release genomes
Info

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