BLACKSBURG, Va., Oct. 17, 2002 - The US Department of Agriculture (USDA) and National Science Foundation (NSF) have jointly awarded $2.3 million to Virginia Bioinformatics Institute (VBI) researchers at Virginia Tech. Combined with $1.5 million from the Department of Energy (DOE) Office of Science, these funds will enable sequencing of the genomes of two species of Phytophthora, a plant pathogen whose name means "plant devourer."
Phytophthora species and their relatives, called oomycetes or "water molds," are fungus-like organisms that are close cousins of kelp and diatoms. Attacking a vast number of plants including soybean, cacao, potatoes, and forest trees, Phytophthora costs agriculture, forestry and nursery industries hundreds of billions of dollars each year.
This joint award will enable VBI's Brett Tyler and his collaborators to sequence the genomes of two Phytophthora species. One of the two species to be sequenced, P. sojae, causes over a billion dollars of losses to the worldwide soybean crop. P. sojae was chosen for this project because researchers have been studying its genetics for many years, and because it has a relatively compact genome. The other species to be sequenced, P. ramorum, is responsible for a disease called Sudden Oak Death Syndrome that is destroying California's coast oak ecosystems. It also threatens redwood and Douglas fir forests on the West coast, and red and pin oak forests in the East.
Dr. Tyler's research group will provide a genetic map of the P. sojae genome that will be used to assemble the raw DNA sequence data to be produced at the DOE Joint Genome Institute (JGI). The VBI team will then create a Web-based bioinformatics annotation system that will enable Phytophthora experts from around the world to log in and interpret the DNA sequence. The annotation system will be adapted from a software program called ASAP developed at the University of Wisconsin by Dr. Nicole Perna. ASAP will also enable the sequence from P.ramorum to be compared directly to the P. sojae sequence. The P. sojae roadmap will be essential to interpreting the P. ramorum sequence, since this forest pathogen has only recently emerged and its genetics are presently a mystery.
Phytophthora pathogens are especially difficult to control because they come from an entirely different kingdom of life than most other pathogens and are impervious to most pesticides. Another Phytophthora species, P. infestans, caused the Irish potato famine in the nineteenth century. This project will help researchers understand how Phytophthora operates and how best to inhibit it from infecting crops and forests.
According to Tyler, "Phytophthora pathogens are literally destroyers from a distant kingdom. The genome sequences of these two species will for the first time enable us to identify and target their vulnerabilities in order to control them." Sequences of Phytophthora will further aid scientists in decoding the genomes of diatoms, important marine species. The research activities will also train postdoctoral fellows and undergraduate students in a multidisciplinary, team-oriented environment. Bruno Sobral from the Virginia Bioinformatics Institute and Jeffrey Boore from the DOE JGI will collaborate with Tyler on this project. USDA and NSF funding was provided by those agencies’ collaborative Microbial Genome Sequencing Program. DOE funds are from its Office of Science.
VBI at Virginia Tech is a Commonwealth of Virginia shared resource. In two years, the Institute has combined platforms in biological sciences and information technology to secure more than $25 million in bioinformatics grants and contracts. VBI plays a significant role in understanding host-pathogen-disease interactions from a systems biology perspective.
Established in 1997, JGI is a consortium of scientists, engineers and support staff from the U.S. Department of Energy's Lawrence Berkeley, Lawrence Livermore, and Los Alamos National Laboratories. JGI has played a significant role in the effort to determine the genetic text that makes up the human genome. For more information about JGI, visit their website at www.jgi.doe.gov
October 16, 2002