Plant & Animal Genomes XIII Conference

January 15-19, 2005
Town & Country Convention Center
San Diego, CA

Phytome: A Plant Comparative Genomics Resource

Stefanie Hartmann , Dihui Lu , Jason Phillips , Todd J Vision

  Department of Biology University of North Carolina Chapel Hill, NC 27599 USA

Phytome (www.phytome.org) is an internet database for plant comparative genomics. The current version enables phylogenetic and functional exploration of nearly three quarters of a million protein sequences from 39 species of land plants. The protein sequences (called Unpeptides) have been derived from the unigene assemblies of Expressed Sequence Tags (ESTs) and other DNA sequences generated by a number of third-party databases, including NCBI Unigene, the Plant Genome Network, PlantGDB, and TIGR Gene Indices.
Over half a million of the Unipeptides have been classified into appx. 26,000 protein families of size two or more. For each family, a multiple sequence alignment and phylogeny have been inferred. Subfamilies have also been determined based upon phylogenetic topology. Interpro and Gene Ontology assignments have been determined for one examplar from each subfamily.
In its current form, Phytome is a powerful tool for studies of functional diversification of gene families and taxonomic lineages. In addition, Phytome serves as a glue between otherwise disjoint plant unigene databases and between taxon-specific model organism databases. In the future, novel functionality will be enabled by inclusion of comparative mapping data and tools into the analysis pipeline.