By comparing the complete genome sequences of two plant-killing pathogens and related organisms, researchers from the U.S. Department of Energy Joint Genome Institute (DOE JGI), in collaboration with the Virginia Bioinformatics Institute (VBI) and others, have uncovered crucial aspects of the disease-causing mechanisms of "Sudden Oak Death" (SOD) and soybean root rot disease. The research, the result of a four-year, $4 million multi-agency project supported by DOE, U.S. Department of Agriculture (USDA), and the National Science Foundation (NSF), appears in the Sept. 1, 2006, edition of Science (vol. 313, No. 5791).

"This project best exemplifies how the capabilities that were established at the DOE JGI for sequencing the human genome are now proving to be essential for addressing important environmental challenges," said Eddy Rubin, DOE JGI Director. "We are now capable of rapidly responding to the urgent needs of the nation's largest industry, agriculture, where genome sequence information can be brought to bear on characterizing such economically important microorganisms as those that cause sudden oak death and soybean root rot. For these pathogens, the genome sequence is the wiring diagram of the cellular processes that can be targeted for novel detection systems and for safe and effective means of control."

Phytophthora (pronounced "Fy-TOFF-thor-uh") species, the target pathogens, attack a wide variety of plants, including agricultural crops as well as trees and shrubs of native ecosystems and backyard gardens alike. Phytophthora ramorum ("ruh-MOOR-um") causes sudden oak death, and Phytophthora sojae ("SEW-jay") attacks primarily soybeans.

"Among the discoveries embedded in the DNA of Phytophthora ramorum is the presence of more than 13,000 diagnostically different single-letter changes that vary among strains of the disease," said Jeffrey Boore, senior author of the Science study and DOE JGI Evolutionary Genomics Program head. "These 'fingerprints' are already being used to track the movement and identity of these species as they progressively invade different regions. Knowing the pattern of the pathogen's spread may help researchers to design strategies for thwarting it.

"Another great benefit that has come from access to the genome sequence has been the design and production of technologies--now-available gene chips--that allow us to monitor the expression patterns of thousands of genes simultaneously as these change during the course of infection and other life stages of these organisms," Boore said. "Together, these advances promise to reveal processes that can be blocked by human intervention and thus prevent the devastating economic losses to soybean crops and the environmental destruction of woodlands."

The researchers observed that the pathogens, during the initial hours of infection, derive their nutrition from the living plant tissue, but after the infection has been established, they switch to fueling their growth from the killed plant tissue. They hypothesized that the two species produce gene products that enable them to evade or suppress the plant's defense responses during infection and later produce gene products that kill and destroy plant tissue.

"What is extraordinary about the Phytophthora genomes is that almost half of the genes contained in them show signs of rapid adaptation. 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 coordinator and lead author of the Science paper. "The unprecedented level of genetic flexibility in these organisms gives us insights into how these pathogens have become successful. At the same time it has helped us identify weak points in the organisms that can be targeted to control them."

"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 Undersecretary for Research, Education and Economics. "Defeating these two pathogens could significantly reduce the billions of dollars lost to crop damage worldwide each year."

Sudden oak death was first reported in 1995. The agent responsible for the disease was discovered by University of California scientists in 2000. The pathogen is known to be present in more than a dozen California counties and also in southern Oregon. It has also been detected at scores of nurseries across the nation, elevating concerns about the pathogen to an all-time high. Symptoms vary depending on the host. Infected oak trees exhibit oozing cankers on the trunk, and often succumb to the disease or to secondary infections as they are weakened by P. ramorum. In leaves, the pathogen reveals its presence through blight and twig dieback. In this manifestation, the disease can be transmitted by such plants as California bay laurel, camellia, and rhododendron.

The economic impact of Phytophthora sojae is far-reaching. The U.S. produces almost half the world's soybeans. Losses attributed to P. sojae infestation, soybean root rot, exceed $1 billion annually. Soybean, the world's most valuable legume crop, is of particular interest to DOE because it is the principal source of biodiesel, a renewable, alternative fuel. Biodiesel has the highest energy content of any alternative fuel and is significantly more environmentally friendly than comparable petroleum-based fuels, since it degrades rapidly in the environment. Earlier this year, DOE and USDA announced that they will share resources and coordinate the study of plant and microbial genomics, and as a result DOE JGI will tackle the sequencing of the soybean genome as the first project.

"The Phytophthoras, in addition to their great economic importance, are fascinating organisms with very distinct and interesting biology," said Maryanna Henkart, NSF's division director for Molecular and Cellular Biosciences. "These new genome sequences will contribute to our basic understanding of normal plant-microbe relationships as well as their roles in disease. Generating such fundamental knowledge is at the core of NSF's mission, and we are pleased to have played a role in promoting this important project."

DOE JGI, using the iterative whole-genome shotgun approach, generated nine-fold coverage of the 95 million nucleic acid bases, or units of the genetic code, of the P. sojae genome and seven-fold coverage of the 65-million-base P. ramorum genome.

The aptly named genus Phytophthora derives its moniker from the Greek words for "plant destroyer." Part of a fungus-like group of organisms known as oomycetes, or water molds, they are relatives of such aquatic algae as diatoms and kelp. The pathogens survive as thick-walled spores that can persist in soil for years. Of the 59 recognized Phytophthora species, it was P. infestans that was responsible for the mid-19th century Irish potato famine.

The Virginia Bioinformatics Institute (VBI) at Virginia Tech has a research platform centered on understanding the "disease triangle" of host-pathogen-environment interactions in plants, humans and other animals. By successfully channeling innovation into transdisciplinary approaches that combine information technology and biology, researchers at VBI are addressing some of today's key challenges in the biomedical, environmental and plant sciences.

The DOE 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. DOE JGI's Walnut Creek, Calif. Production Genomics Facility provides integrated high-throughput sequencing and computational analysis that enable systems-based scientific approaches to these challenges.

RELATED NEWS RELEASE

Blacksburg, Virginia
August 31, 2006

Sequences reveal benign origin of deadly plant pathogens

An international team of researchers has published the draft genome sequences of two deadly plant pathogens, Phytophthora ramorum and Phytophthora sojae. Phytophthora sojae causes severe damage in soybean crops and results in $1–2 million in annual losses for commercial farmers in the United States. Phytophthora ramorum, which causes sudden oak death, has attacked and killed tens of thousands of oak trees in California and Oregon. The sequences of both genomes, which are described in the September 1 issue of Science, reveal a recent, large expansion and diversification of many deadly genes involved in infection of the plant hosts of Phytophthora.

The sequence information shows how Phytophthora most likely evolved from a benign photosynthetic ancestor into a sophisticated, plant-killing machine. Phytophthora belongs to the kingdom Stramenopila, which also includes golden-brown algae, diatoms and kelp. Around 1300 million years ago, some or perhaps all stramenopiles acquired the ability to harness light for their energy needs by assimilating photosynthetically competent organisms. Today however, some stramenopiles, including Phytophthora, are non-photosynthetic. Did the kingdom arise from a photosynthetic or non-photosynthetic organism? A close look at the new sequence data shows as many as 800 genes with a potential photosynthetic origin, strongly supporting the hypothesis that the stramenopile ancestor was a photosynthetic organism, and that Phytophthora lost this capability as it became a parasite.

The genome sequences reveal that P. sojae and P. ramorum have a large number of genes compared to counterparts such as pathogenic fungi; 19 027 likely genes were identified in P. sojae and 15 743 in P. ramorum. The sequences also clearly indicate a recently acquired, large armory of proteins that enable the pathogens to attack their plant hosts.

Professor Brett Tyler of the Virginia Bioinformatics Institute, one of the leaders of the project, remarked: "The extraordinarily large and plastic array of pathogenicity genes that has been unveiled by the genome sequences provides us with a major insight into the basis for the success of this group of pathogens." A comparison of the genomes of the two Phytophthora species shows a rapid expansion and diversification of many protein families linked to plant infection, including toxins, protein inhibitors and enzymes that can break down cell walls. In particular, a group of genes encoding a large family of secreted proteins (the secretome) is evolving much more rapidly than other protein-coding genes. Secreted proteins are intimately involved in the mechanism of pathogenesis.

Professor Jeffrey Boore, a co-leader of the project from the US Department of Energy (DOE) Joint Genome Institute, remarked: "This has been a ground-breaking, large-scale, collaborative project. As a resource for the entire scientific community, it is already having an immediate impact on plant pathogen research. To take one example, the P. ramorum sequence has over 13 000 single nucleotide polymorphisms, which has already led to the development of genetic markers for population studies and for tracking the movement of different strains of P. ramorum. Further, this was the first case where researchers were able to infer gene function from actual evolutionary analyses based on the pipeline we have developed at http://PhIGs.org."

Professor Tyler added: "The sequences are a fundamental resource with wide-ranging applications for the Phytophthora community. We will be pursuing our investigations of the secreted proteins linked to damage of the plant host in the hope of developing much needed countermeasures against these deadly pathogens."

The project to sequence the genomes of P. ramorum and P. sojae started in 2002. The sequencing of P. ramorum represents the fastest sequencing of a newly emerged pathogen other than the Severe Acute Respiratory Syndrome (SARS) virus; P. ramorum was identified in 2000 and its draft sequence was complete by 2004. The work, which has been funded by the National Science Foundation, the United States Department of Agriculture's National Research Initiative and the Department of Energy, has been carried out by an international team of scientists led by the DOE Joint Genome Institute and the Virginia Bioinformatics Institute. The research appears in the September 1 issue of Science (vol. 313, no. 5791, 2006) in the article "Phytophthora genome sequences uncover evolutionary origins and mechanisms of pathogenesis."

The Virginia Bioinformatics Institute (VBI) at Virginia Tech has a research platform centered on understanding the "disease triangle" of host-pathogen-environment interactions in plants, humans and other animals. By successfully channeling innovation into transdisciplinary approaches that combine information technology and biology, researchers at VBI are addressing some of today's key challenges in the biomedical, environmental and plant sciences.

The DOE 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. DOE Joint Genome Institute's Walnut Creek, California, Production Genomics Facility provides integrated high-throughput sequencing and computational analysis that enable systems-based scientific approaches to these challenges. Additional information about DOE JGI can be found at: http://www.jgi.doe.gov/.