sudden oak death info

**jo ellen meyers sharp h*@sbcglobal.net**

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Date: Thu, 31 Aug 2006 12:15:07 -0700
From: David Gilbert <degilbert@lbl.gov>
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Subject: DOE JGI, VBI describe disease mechanisms of sudden oak death, related
  soybean pathogens
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http://www.jgi.doe.gov/News/news_8_31_06.html
DOE JGI, VBI Describe Evolutionary Origin, Disease-Causing Mechanisms of
Sudden Oak Death, Related Soybean Disease Pathogens

WALNUT CREEK, CA-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-MORE-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. Additional 
information about DOE JGI can be found at: http://www.jgi.doe.gov/.

###

-- 
David E. Gilbert
Public Affairs Manager
DOE Joint Genome Institute
2800 Mitchell Drive
Walnut Creek, CA 94598
www.jgi.doe.gov
925-296-5643
-- 
Jo Ellen Meyers Sharp
Garden writer, author, photographer
Region III Director Garden Writers Association
Phone: (317) 251.3261
Fax: (317) 251.8545
E-mail: hoosiergardener@sbcglobal.net

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