Researchers are closer now to thwarting two related plant pathogens, one causing "Sudden Oak Death" (SOD) and another Phytophthora sojae (P. sojae) responsible for a devastating soybean disease, thanks to DNA sequence information. SOD has been detected at 125 nurseries across the nation, elevating concerns about the pathogen to an all-time high. Losses attributed to P. sojae infestation, known as Phytophthora root rot of soybean or damping-off disease, exceeded $1 billion in 2003.
The U.S. Department of Energy (DOE) Joint Genome Institute (JGI), Walnut Creek, Calif. produced the breakthrough. JGI worked in collaboration with the Virginia Bioinformatics Institute (VBI). The projects received nearly $4 million in support from the U.S. Department of Agriculture (USDA), the National Science Foundation (NSF), and the DOE in this multi-agency effort.
"The ability to use large-scale multi-agency collaborations to rapidly characterize such economically important microorganisms is the cornerstone of the resource that we have established at the Joint Genome Institute," says Raymond L. Orbach, director of the DOE Office of Science, which funds operations of the JGI. "For both these pathogens, the genome sequence information will enable the identification of cellular processes that can be targeted for novel detection systems and for safe and effective means of chemical or biological control."
"The genome sequences for these two Phytophthora [pronounced Fy-TOFF-thor-uh] species provide a framework for understanding how these plant pathogens cause disease and what can be done to control them," says Joseph Jen, USDAâ€™s Undersecretary for Research, Education, and Economics. "USDA is pleased to be working with the Department of Energy and the National Science Foundation to jointly support the genome sequencing of these microorganisms."
"Phytophthora species attack a wide variety of plants, including agricultural crops as well as trees and shrubs of native ecosystems," explains Mary Clutter, NSF Assistant Director for the Biological Sciences. The projects to sequence the genomes of Phytophthora sojae and Phytophthora ramorum, "will contribute great value in combating these devastating diseases, and the success of these projects clearly demonstrates the value of agencies working together to address major scientific challenges," Clutter adds.
Sudden Oak Death was first reported in 1995 and University of California scientists discovered the agent responsible for the disease in 2000. The pathogen is known to be present in 13 California counties and also in Southern Oregon. It has also been detected at 125 nurseries across the nation. Symptoms vary depending on the host. Infected oak trees exhibit bleeding cankers on the trunk, and often succumb to the disease or to secondary infections as they are weakened by P. ramorum. In foliar hosts, the pathogen reveals its presence through leaf blight and twig dieback. Foliar hosts serve as a vector for the disease, and include such plants as California bay laurel, camellia, and rhododendron.
The economic impact of Phytophthora sojae has been far-reaching. The U.S. produces almost half the worldâ€™s soybeans. Losses attributed to P. sojae infestation, known as Phytophthora root rot of soybean, a post-emergence disease of the field, exceeded $1 billion in 2003.
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 sequencing of the P. ramorum genome represents the fastest tracking from identification of a new plant pathogen to the completion of its genome," says Brett Tyler of VBI. Tylerâ€™s research group provided a genetic map of the P. sojae genome from which JGI was able to assemble the raw DNA sequence data. "Sequencing P. sojae will enable the past 15 years of advances in understanding the genetics of Phytophthora pathogens to be rapidly transferred to P. ramorum, in effect serving as the Rosetta Stone for sudden oak death.
"The genome sequence of P. ramorum will help researchers to track the spread of SOD much more accurately by enabling them to develop more detailed genetic fingerprints," says Tyler. "Based on experience with developing fingerprints for other organisms, including humans, researchers know what kinds of sequences to look for in the genome sequenceâ€”for example, simple sequence repeats. Accurate tracking of P. ramorum will help determine the routes of spread, and to answer the question more accurately as to whether P. ramorum can spread from nursery plants into the forest."
"Thus far, over 30,000 genes have been identified in these pathogens," says JGI director Eddy Rubin. The USDA is sponsoring additional applied research at the JGI that will exploit the sequence information for the development of rapid, more effective field detection systems for SOD. "This second-generation detection method relies on distinguishing traces of DNA sequences, or aptamers, to home in on substances released by the pathogen during infection," Rubin says. Aptamers are single-stranded DNA molecules that fold into three-dimensional structures and bind other molecules with high affinity and specificity.
A public biotechnology company, Affymetrix, headquartered in Santa Clara, Calif., has utilized the publicly available sequence generated by JGI and VBI to develop a GeneChip Microarray containing probes to detect DNA transcripts of Phytophthora sojae for soybean gene expression research. The power of Affymetrix technology to package the entire expressed genomes of multiple organisms on a single arrayâ€”host and pathogens in this caseâ€”affords scientists the unique ability to ask new biological questions. For example, gene expression in both soybean and Phytophthera can be measured during the pathogenic process. This would help identify genes from both organisms specifically involved in pathogenic mechanisms and host defense.
Phytophthora ramorum, with a genome size of some 65 million nucleic acid bases, or letters of the genetic code, was sequenced by JGI seven times to assure the quality of the data. Phytophthora sojae, at approximately 95 megabases, was sequenced nine times over. The sequences of these organisms can be found on the JGI portal at http://genome.jgi-psf.org/ramorum/ and at http://genome.jgi-psf.org/sojae/.