Phytozome

Overview

Phytozome is a joint project of the Department of Energy's and the to facilitate comparative genomic studies amongst land plants. Clusters of orthologous and paralogous genes that represent the modern descendents of ancestral gene sets are constructed at key phylogenetic nodes. These clusters allow easy access to clade specific orthology/paralogy relationships as well as clade specific genes and gene expansions. As of version 2.0.4, Phytozome provides access to six sequenced and annotated land plant genomes, five of which have been clustered into gene families at six 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.

Included Organisms

The proteomes of the following organisms are clustered in release 2.0.4 of Phytozome:

Access is also provided to the sequence and annotation of soybean, though it is not yet included in Phytozome gene families.

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 and genome-wide duplication events:

Clustering Methodology

Clustering is performed hierarchically, from the crown nodes to the root. First, the recent whole genome duplications in poplar and Arabidopsis were analyzed. Next, poplar-Arabidopsis (Rosid) clusters were created as described above from poplar-Arabidopsis orthologs, while requiring that all previous intraspecies clusters remain together. The Grass node captures the rice-sorghum common ancestor. The Angiosperm (poplar-Arabidopsis-rice-sorghum) node was created from grass-Rosid orthologs, requiring all previous Rosid and grass clusters remain together. The final land plant node was created using mutual-best hits between the spike moss Physcomitrella patens and previously clustered plants as orthologs, as there is not a detectable syntenic signal left at this scale of evolutionary time.

Note that, by construction, every gene from an organism present at a particular node is in one and only one cluster at that node. Some clusters may contain only one extant gene (singletons). Singletons can come from "fast" evolution leading to so much sequence divergence that sequence-similarity based clustering is confounded, gene loss, or gene calling errors.

Clustering Statistics

Phytozome Team