Version 3 is now available of our evolutionary analysis of the complete genomes of oomycetes and diatoms. This now adds the genome of Pythium ultimum to that of the four previously included oomycete genomes (Phytophthora sojae, P. ramorum, P. infestans, and Hyaloperonospora arabidopsidis) and two diatoms (Thalassiosira pseudonana and Phaeodactylum tricornutum).
At this release, we are analyzing 109,682 total genes. We use a unique, graph-based method to cluster genes into families while considering the evolutionary relationships among the organisms, and then perform a true phylogenetic analysis on each set of genes. We assign all orthologous and paralogous relationships and determine when each gene duplication or loss occurred.
This is part of the PHRINGE (Phylogenetic Resources for the Interpretation of Genomes) method developed by Genome Project Solutions.
Learn more about the methods used here.
The initial development of PHRINGE was created as part of the project "Phytophthora sojae: A High Quality Reference Sequence for the Oomycetes", directed by Brett Tyler of the Virginia Bioinformatics Institute, and funded by the U.S. National Science Foundation / U.S. Department of Agriculture Microbial Genome Sequencing Program.