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Phytophthora Genome Sequence Project Targets Soybean Wilt, Sudden Oak Death Pathogens

News Release

Scott Elliott, CSREES, (202) 720-7185
Sean Adams, ARS, (301) 504-1617
Randy Vines, NSF, (703) 292-7963
David Gilbert, DOE JGI, (925) 296-5643

WASHINGTON, Sept. 1, 2006 – An international team funded by USDA, the National Science Foundation (NSF) and the Department of Energy (DOE) published the first two genome sequences from a destructive group of pathogens called Phytophthora.

The two sequenced genomes belong to Phytophthora sojae and Phytophthora ramorum. P. sojae, an endemic pathogen of soybeans, and is responsible for $1 billion to $2 billion in losses worldwide each year. P. ramorum, a newly discovered species, is associated with sudden oak death, which has devastated the coastal live oak ecosystems and the nursery industry in California, Oregon and Washington.

“These results, which identify the DNA sequence of the two pathogens, arm scientists and practitioners to assist in the development of new Phytophthora disease control measures,” said Dr. Gale Buchanan, USDA under secretary for Research, Education and Economics. “Defeating these two pathogens could significantly reduce the billions of dollars lost to crop damage worldwide each year.”

The research appears in the Sept. 1, 2006, issue of Science, in the article “Phytophthora genome sequences uncover evolutionary origins and mechanisms of pathogenesis.”

The international team, led by Virginia Tech University’s Virginia Bioinformatics Institute (VBI), was supported by the Microbial Genome Sequencing Program, a joint program between the National Research Initiative of the USDA’s Cooperative State Research, Education and Extension Service (CSREES), NSF and DOE’s Joint Genome Institute (JGI). Grants worth nearly $2.5 million from CSREES and $1.5 million from NSF funded the project, and the sequencing was completed at JGI.

In addition, two of USDA’s Agricultural Research Service field units contributed to the project.  The Horticultural Crops Research Laboratory at Corvallis, Ore., mined the genomes for molecular markers, and the Vegetable Laboratory at Beltsville, Md., worked to identify the location of specific genes within a genetic sequence. The Horticultural Crops Research Laboratory also worked with the Ohio Agricultural Research and Development Center at Ohio State University to design a micro-array that enabled scientists to find the genes expressed in the pathogens during the early stages of infection.

There are more than 80 species of Phytophthora, which attack a broad range of plants of agricultural, ornamental and ecological importance. Phytophthora affects nearly all broad-leafed (dicotyledonous) plants. Phytophthora pathogens are oomycetes, fungal-like organisms that are closely related to marine algae such as diatoms and kelp.

The researchers found that these oomycete pathogens have nearly twice as many genes as fungal pathogens, and that more than 40 percent of the genes in the two species are undergoing rapid change. Many of the rapidly evolving genes encode toxins and other proteins that may act to weaken the plant. In particular, each Phytophthora species hosts more than 350 genes related to oomycete avirulence genes. In a sense, the avirulence genes work against the pathogen because they allow the plant to detect the presence of the pathogen and mount a defense response. Because avirulence genes are often necessary for pathogen survival, there is pressure on the pathogen to modify the avirulence genes so the plant can no longer recognize them.

“We speculate that the rapidly changing genes are being driven to evolve by pressure from the defense systems of the pathogens’ host plants,” said VBI Professor Brett Tyler, the project’s principal investigator.

The genome sequences suggest many new avenues for attempting to improve plants’ resistance to oomycete pathogens, according to Professor Jeffrey Boore of JGI.

The Microbial Genome Sequencing Program has more recently funded the genome sequencing of three additional oomycetes, the potato late blight pathogen P. infestans, the broad host range pathogen P. capsici, and the downy mildew pathogen of mustards, Hyaloperonospora parasitica. These additional sequences will further accelerate understanding of these highly successful pathogens.

CSREES advances knowledge for agriculture, the environment, human health and well-being, and communities by supporting research, education, and extension programs in the Land-Grant University System and other partner organizations. For more information, visit http://www.csrees.usda.gov. ARS is the chief in-house scientific research agency of USDA.  For more information, visit ARS’ Web site at http://www.ars.usda.gov.

NSF is an independent federal agency that supports fundamental research and education across all fields of science and engineering, with an annual budget of $5.58 billion. NSF funds reach all 50 states through grants to nearly 1,700 universities and institutions. For more information, visit http://www.nsf.gov.

The Joint Genome Institute, supported by the DOE Office of Science, unites the expertise of five national laboratories, Lawrence Berkeley, Lawrence Livermore, Los Alamos, Oak Ridge and Pacific Northwest, along with the Stanford Human Genome Center, to advance genomics in support of the DOE mission related to clean energy generation and environmental characterization and clean-up. For more information, visit http://www.jgi.doe.gov.