Phytozome

Overview

Phytozome is a joint project of the U.S. Department of Energy's Joint Genome Institute and the University of California to facilitate comparative genomic studies among land plants. Clusters of orthologous and paralogous genes that represent the modern descendants of ancestral gene sets are constructed at key phylogenetic nodes. These clusters allow easy access to clade specific orthology and 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, and JGI are hyperlinked and searchable.

Included organisms

The proteomes of the following organisms are clustered in release 2.0.4 of Phytozome. Several organism names link to the current Phytozome record for that species.

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, called nodes. Extant genes have been clustered at nodes representing the following speciation and genome wide duplication events.

Land Plants node, about 450 Mya

Genes representing the most recent common ancestor of Tracheophyta, represented by angiosperms, and bryophyta, represented by the moss Physcomitrella.

Angiosperms node, about 120 Mya

Genes representing the most recent common ancestor of grasses (Sorghum and Rice) and Rosids (Arabidopsis and Poplar).

Grasses, about 68 Mya

Genes representing the most recent common ancestor of Sorghum and Rice.

Rosids, about 110 Mya

Genes representing the most recent common ancestor of Arabidopsis and Poplar.

Poplar duplication, about 60 Mya

Genes representing the ancestral gene set just prior to the post speciation genome wide duplication in poplar.

Arabidopsis duplication, about 60 Mya

Genes representing the ancestral gene set just prior to the post speciation genome wide duplication in Arabidopsis.

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 and Arabidopsis (Rosid) clusters were created as described above from poplar and Arabidopsis orthologs, while requiring that all previous intraspecies clusters remain together.

The Grass node captures the rice and sorghum common ancestor. The Angiosperm node, covering poplar, Arabidopsis, rice, and sorghum, was created from grass and Rosid orthologs, requiring all previous Rosid and grass clusters to 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.

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, called a singleton. Singletons can come from fast evolution leading to so much sequence divergence that sequence similarity based clustering is confounded, from gene loss, or from gene calling errors.

Clustering statistics

Phytozome team