Gene Family Construction and Analysis in Phytozome

Phytozome (http://www.phytozome.net) is the JGI's genomics portal for plant genome data and analyses. As a key feature of Phytozome 12, we provide a set of automatically generated protein-coding gene families along with corresponding profiles, and ortholog and paralog assignments. Using family membership data, gene annotations from PFAM, KOG, KEGG, and PANTHER, and gene descriptions from highly curated plant genomes, we provide informative names for most of these families. We identify “core” sets of families from high-quality genome annotations, and construct profiles for these families that can be used to incorporate additional members as new annotations become available. In addition, we inventory sets of pan-angiosperm and pan-grass families with signatures broadly represented among Phytozome organisms, which can be used to expand and correct poorly-curated genome annotations.