An international team of researchers, which includes scientists from the Virginia Bioinformatics Institute at Virginia Tech, 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 Sept. 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”

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. For additional information visit the DOE JGI website.

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