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Sudden Oak Death Microbe to Be Sequenced

17 October 2002 (All day)
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Sudden sequence. The microbe threatening California's oak trees is about to have its genome unraveled.

A new genome sequencing effort that takes aim at an important microbial foe of plants might help combat numerous agricultural diseases as well as the sudden oak death syndrome that is devastating California's oak trees.

Each of the 60 species of water mold in the protist genus Phytophthora attacks plants. The most famous species caused the 19th century potato crop failure that spurred immigration from Ireland to North America, but two other species are having a major impact today. Phytophthora sojae is responsible for soybean root rot, a crop disease costing $1 billion a year worldwide. P. ramorum, which causes sudden oak death syndrome, is gradually depleting the scenic oak woodlands of California and Oregon and could threaten other forests (ScienceNOW, 10 January).

Now three federal agencies (the Department of Energy, the National Science Foundation, and the Department of Agriculture) have awarded $4 million to sequence and analyze the full genomes of P. ramorum and P. sojae. Researchers under Jeffrey Boore at the Joint Genome Institute in Walnut Creek, California, will create and assemble draft sequences of the protists, and a team led by Brett Tyler at the Virginia Bioinformatics Institute in Blacksburg will identify genes and interpret their function by deciphering the data, which will be made public within a year. In a novel collaborative approach, Tyler says, Phytophthora experts will be encouraged to participate in refining the annotation via the World Wide Web.

The two Phytophthora genomes, when compared to each other and to those of similar organisms, might provide markers to rapidly identify the pathogen's presence in trees, and they could ultimately help pinpoint genes that determine virulence, says Boore. In addition, researchers potentially could track the disease by finding rapidly evolving portions of the Phytophthora genome and looking for minor differences among strains infecting woodlands.

Mapping the spread is especially important in the case of P. ramorum, says plant pathologist Matteo Garbelotto of the University of California, Berkeley. Although it's known that the pathogen needs an intermediate host between attacks on oaks, he says, "at this point we have no idea how far it can go" from one plant to another. He adds that although it might be a long time before the disease is stopped, the genomic information could help researchers screen oaks for resistance and understand what makes some trees more susceptible than others.

Related sites
Joint Genome Institute
Virginia Bioinformatics Institute
Sudden oak death
Soybean root rot
More about water molds

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