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    Oomycete Genomes Project, in collaboration with VBI Microbial Database  
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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.

Genomes Currently Being Presented
Organism Details Group
Sequenced by Genome URL Publication
Hyaloperonospora arabidopsidis 1 Oomycete
WUGSC Genome home Baxter et al. (2010) Science 330: 1486-1487.
Phytophthora infestans 2 Oomycete
Broad Institute Genome database In preparation.
Phytophthora ramorum 3 Oomycete
DOE JGI Genome browser Tyler BM (51 others) & Boore JL (2006) Science 313:1261.
Phytophthora sojae 4 Oomycete
DOE JGI Genome browser Tyler BM (51 others) & Boore JL (2006) Science 313:1261.
Phaeodactylum tricornutum 5 Diatom
DOE JGI Genome browser Bowler C et al. (2008) Nature 456:239.
Pythium ultimum 6 Oomycete
Buell lab Genome browser Lévesque et al. (2010) Genome Biol. 11: R73.
Thalassiosira pseudonana 7 Diatom
DOE JGI Genome browser Ambrust EV et al. (2004) Science 306:79.
For the Detail Page of a particular gene, enter one of these identifiers
PHRINGE Gene or Protein ID
or VMD Gene ID
Maximum distance to show
Maximum matches per taxon to show
"Detail Pages" contain information on a particular gene, including its position, length, and intron-exon structure, most similar sequences with links, and the clusters (at various phylogenetic depths) to which it has been assigned by PHRINGE. Find a Detail Page either by the query above or by clicking on any particular gene box on a Synteny Page. The cluster ID is linked to the corresponding "Cluster and Compare Page".

"Cluster and Compare Pages" contain information on a particular PHRINGE cluster, including the multiple sequence alignment, comparison of intron-exon structures, and the phylogeny of the member genes. Find a Cluster and Compare Page from the cluster IDs on a corresponding Detail Page.

"Synteny Pages" show an overview of the relative physical arrangements of homologous genes for specified portions of specified genomes. Connecting lines are red if there has been an inversion. Mouse over gene boxes for more information.

For the Synteny Page of relative gene arrangements
Query genome
Scaffold (or chromosome) #
First gene position #
Last gene position #
Max Gene Distance
Min Auto-flip Distance
(to maximize the portions in the same orientation)
Specify the display size:
Genomes to compare Hyaloperonospora arabidopsidis
Phytophthora infestans
Phytophthora ramorum
Phytophthora sojae
Phaeodactylum tricornutum
Pythium ultimum
Thalassiosira pseudonana