Genome Project Solutions

Version 2 is now available of our evolutionary analysis of the complete genomes of four oomycetes (Phytophthora sojae, P. ramorum, P. infestans, and Hyaloperonospora arabidopsidis) and their diatom outgroups (Thalassiosira pseudonana and Phaeodactylum tricornutum).

Users can see the multiple sequence alignments and phylogenetic trees of all genes, compare intron-exon structures, and see maps of the relative arrangements of homologous genes across all genomes.
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 at http://genomeprojectsolutions.com/PHRINGE_project.html.

Results can be seen at http://oomycetes.genomeprojectsolutions-databases.com/.

At this release, we are analyzing greater than 90,000 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 maximum likelihood phylogenetic analysis on each set of genes. We assign all orthologous and paralogous relationships and determine when each gene duplication or loss occurred.

This work is a sizable portion of the $2,130,000 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.

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