Backed by nearly $4 million in funding from three Federal agencies, researchers in California and Virginia are joining forces to learn the genetic secrets of a notorious plant pathogen that causes billions of dollars a year in damage to forests and soybean crops.
Scientists at the U.S. Department of Energy’s Joint Genome Institute (JGI) in Walnut Creek and the Virginia Bioinformatics Institute (VBI) in Blacksburg will decode and study the genomes of two species of Phytophthora, which is Greek for “plant devourer.” Phytophthora is a fungus-like microbe responsible for sudden oak death syndrome, soybean root rot, and a wide variety of other destructive plant diseases, including the Irish potato famine in the 1840s.
By sequencing and comparing the DNA of the two Phytophthora genomes, the scientists hope to uncover clues to virulent diseases that are attacking 17 species of trees on the West Coast, including redwoods, big leaf maples, bay trees and Douglas fir, and causing serious damage to soybean crops in the Midwest and South.
“This is an ideal opportunity for genomics to make an important contribution to solving an enormous national problem,” said JGI Director Eddy Rubin. “By sequencing and studying the gene function of this pathogen, we can accelerate the diagnosis, prevention and treatment of the infections it causes.”
Phytophthora ramorum, the recently identified microbe responsible for sudden oak death, and P. sojae, which causes soybean root rot, resemble fungi but are actually Stramenopiles, a group of oomycetes or “water molds.” Phytophthora microbes resist treatment by conventional pesticides and other fungus control measures. Unless effective treatments are found, foresters are concerned that P. ramorum, which has already killed tens of thousands of trees in California and Oregon, could spread to northern red oak and pin oak forests in the Midwest and East despite quarantines restricting the movement of potentially infected trees (see http://www.na.fs.fed.us/sod/index.htm).
To attack the problem, DOE’s Office of Science has allocated $1.5 million to JGI to draft sequence the P. ramorum genome. In addition, the U.S. Department of Agriculture (USDA) and the National Science Foundation (NSF) have jointly awarded $2.3 million to JGI and VBI to draft sequence P. sojae, which causes more than a billion dollars a year in losses to the worldwide soybean crop.
Dr. Jeffrey Boore, who will lead the research for JGI, said the knowledge gained from sequencing the P. ramorum genome and comparing it with the DNA of P. sojae could lead to better techniques for diagnosing sudden oak death syndrome, such as kits that can be taken to the field that could quickly identify the microbe’s presence in tree samples.
“We can also identify rapidly changing parts of the genome that can be used to track the paths of infection through a forest,” Boore said. “We may also be able to identify specific genes that are necessary for infection and to develop treatments that attack the products of these genes and thus eliminate Phytophthora‘s ability to attack trees.”
P. sojae was chosen for the project because it has a compact genome, and because researchers have been studying its genetics for many years. Dr. Brett Tyler, Dr. Bruno Sobral, and their colleagues at the VBI 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 JGI.
The draft sequence data from both genomes will be made available to researchers around the world through a web-based bioinformatics annotation system. They will be the first publicly available Stramenopile pathogen genomes.
“Phytophthora pathogens are literally destroyers from a distant (biological) kingdom,” Tyler said. “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.”
According to the NSF, the research project is also intended to enhance the interaction between experimental and computational biology by training postdoctoral fellows, undergraduate students and visiting researchers from minority institutions in a multidisciplinary, team-oriented environment.
The NSF and USDA funds were made available through the agencies’ collaborative Microbial Genome Sequencing Program. The DOE funding was provided by the Office of Biological and Environmental Research in DOE’s Office of Science.
The JGI, one of the largest and most productive public genome sequencing centers in the world, is operated jointly by three DOE national laboratories managed by the University of California: Lawrence Berkeley and Lawrence Livermore in California, and Los Alamos in New Mexico. In addition to the Phytophthora projects, the JGI has whole genome sequencing programs that include vertebrates, fungi, plants, bacteria and other single-celled microbes. Additional information and progress reports on JGI projects, including daily updates of sequence information and assembly statistics, are available at www.jgi.doe.gov.
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. For more information regarding VBI, visit their website at www.vbi.vt.edu