The Oömycete Genomes Project

Oömycetes ("water molds") is a group of organisms related to diatoms and brown algae. Many are important pathogens of plants, causing several billions of dollars in crop loss each year. Recently, the complete genome sequence has been determined for several members of this group and their relatives. Genome Project Solutions and the Virginia Microbial Database are collaborating on a major portion of the effort to better interpret and compare this extensive treasure trove of data.

The genomes listed below have been analyzed by the PHRINGE ("Phylogenetic Resources for the Interpretation of Genomes") pipeline. PHRINGE is part of our larger GATOR ("Genome Analysis Tools and Online Resources") system, currently in development. Briefly described, PHRINGE creates a graph with all inferred protein sequences as nodes, with edges formed from distance scores calculated from their full length alignments, then clusters these into gene families using a method that considers the evolutionary relationships among the organisms, then performs a phylogenetic analysis on each. This allows the most accurate possible assignment of orthologous and paralogous relationships, inference of retained gene function, and reconstruction of gene duplications and losses. Users can see the multiple sequence alignments and phylogenetic trees of all genes, compare intron-exon structures, and see the relative arrangements of homologs across all genomes. See a summary of the PHRINGE method, details of the PHRINGE pipeline, or an explanation of why it is important to use evolutionary analysis to find orthologs.

This project is funded by a grant (VAR-2007-04746) from the U.S. Department of Agriculture led by Professor Brett Tyler of the Virginia Bioinformatics Institute (part of Virginia Tech University) entitled “Phytophthora sojae: A High Quality Reference Sequence for the Oömycetes”. Credit for informatics work and database design and construction goes to Bob Stiles of Roundtrip Networks with assistance from Wayne Huang of Lawrence Berkeley National Laboratory.

There are two versions of this website, identical except that this version masks all of the Pythium ultimum gene models, since these have not yet been publicly released, and the other http://oomycetes.genomeprojectsolutions-databases.com includes these data, but with password protection. If you require that password, write to info@GenomeProjectSolutions.com.