Genomic Approaches Soon to be Available for Understanding Sudden Oak Death
Jeffrey Boore1, Susan Lucas2, Paul Richardson2, Daniel Rokhsar2, Eddy Rubin2, and Brett Tyler3
The Joint Genome Institute (JGI) in Walnut Creek, CA, <http://www.jgi.doe.gov/> is a high throughput center for genome sequencing and analysis, with a capacity for producing nearly two billion nucleotides of DNA sequence per month and an extensive history of sequencing whole genomes. The JGI now intends to generate high depth draft sequence of the complete genomes of Phytophthora sojae and P. ramorum. Sequencing of P. sojae is already well underway and DNA is being isolated from P. ramorum. Both genomes are expected to be completed not later than June 2003. The JGI, along with collaborators at Virginia Bioinformatics Institute, will also perform deep annotation to identify all genes of P. ramorum as well as comparative sequence analyses of the two organisms. These sequences, along with gene annotations, etc. will be made available to all interested researchers via the web. We are in the process of setting up a genomic infrastructure for P. ramorum that will include both bioinformatics tools and laboratory reagents. The goal is to provide resources to enable JGI and other genome scientists to interact with the community of P. ramorum researchers to do such things as (1) Develop genomic markers with higher resolution for tracking the pattern and mode of infection; (2) Build a strategy for screening for early infection where treatment is most likely to be effective; (3) Select genes whose products are most likely to be effective targets for prevention or treatment of infection; (4) Screen compounds in vitro that might be effective for prevention or treatment. Further, the JGI hopes to offer opportunities for training of scientists interested in using genome technology to combat Phytophthora infections through our visiting scientists program and to provide a center for interaction of Phytophthora researchers, including those doing work in the field and at the whole organism level. We are describing this project here in its early stages in order to get researchers’ input on how we might best meet the needs of the community and to inform scientists of the resources soon to be available.
1DOE Joint Genome Institute and Lawrence Berkeley National Laboratory, 2800 Mitchell Drive, Walnut Creek, CA 94598; (925) 296-5691; jlboore@lbl.gov
2DOE Joint Genome Institute and Lawrence Berkeley National Laboratory, 2800 Mitchell Drive, Walnut Creek, CA 94598
3Virginia Bioinformatics Institute
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