Gene Family Construction and Analysis in Phytozome

Phytozome (http://www.phytozome.net) is a comparative hub for plant genome data and analysis. As a key feature of Phytozome 11, 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. In addition, we inventory sets of pan-angiosperm and pan-grass families with signatures broadly represented among Phytozome organisms, forming a “core” set of families that can be used to expand and improve upon poorly-curated genome annotations. We also investigate the origins of several lineage-specific genes and cases of lineage-specific family expansion and contraction in our set. Finally, we present search, visualization, and assignment tools available at Phytozome for working with plant gene families and homology data.