Phytozome, the Plant Comparative Genomics portal of the Department of Energy's Joint Genome Institute, provides JGI users and the broader plant science community a hub for accessing, visualizing and analyzing JGI-sequenced plant genomes, as well as selected genomes and datasets that have been sequenced elsewhere.
As of release v12.1.6, Phytozome hosts 93 assembled and annotated genomes, from 82 Viridiplantae species. More than half of these genomes have been sequenced, assembled and/or annotated with JGI Plant Science program resources. By integrating this large collection of plant genomes into a single resource and performing comprehensive and uniform annotation and analyses, Phytozome facilitates accurate and insightful comparative genomics studies.
All gene sets in Phytozome have been annotated with KOG, KEGG, ENZYME, Pathway and the InterPro family of protein analysis tools. Inparanoid pairwise orthology and paralogy groups have been calculated across all Phytozome proteomes. Families of related genes representing the modern descendants of putative ancestral genes are constructed at key phylogenetic nodes. These families provide additional insight into clade-specific orthology/paralogy relationships as well as clade-specific novelties and expansions. Search and visualization tools let users quickly find and analyze genes or genomic regions of interest. Query-based data access is provided by Phytozome's InterMine and BioMart instances, while bulk data sets can be accessed via the JGI's Genome Portal. JBrowse genome browsers are available for all genomes.
The site is somewhat "clunky" and has an outdated appearance but there are help tutorials. An updated version (v13) is available as an alternative.