News Release
For Immediate Release — September 9, 2009
Genetic Code of Infamous Potato Pathogen Deciphered
Findings suggest genomic strategy that “outwits” plant hosts
KNOXVILLE, Tenn. – A team of University of Tennessee plant pathologists contributed to a large international effort that decoded the genome of the notorious organism that triggered the Irish potato famine in the mid-19th century. That same organism, Phytophthora infestans, now threatens this season’s tomato and potato crops across much of the U.S.
Alon Savidor works in the lab on the UT agricultural campus in Knoxville. Download photo
Alon Savidor collects Phytophthora species from peppers and tomatoes (background) from an East Tennessee field in 2006. Download photo
Published in the September 9 online issue of the journal Nature, and scheduled to be the cover article for the September 17 print edition, the study reveals that the P. infestans organism boasts an unusually large genome size and an unusual genome structure. Together these characteristics appear to enable the rapid evolution of genes, particularly those involved in plant infection. These data expose an unusual mechanism that enables the pathogen to outsmart its plant hosts and may help researchers unlock new ways to control it.
“This pathogen has an exquisite ability to adapt and change, and that’s what makes it so dangerous,” said senior author Chad Nusbaum, co-director of the Genome Sequencing and Analysis Program at the Broad Institute of MIT and Harvard. “We now have a comprehensive view of its genome, revealing the unusual properties that drive its remarkable adaptability. Hopefully, this knowledge can foster novel approaches to diagnose and respond to outbreaks.”
“Our findings suggest a ‘two-speed’ genome, meaning that different parts of the genome are evolving at different rates,” said co-lead author Sophien Kamoun, a research leader at the Sainsbury Laboratory in Norwich, UK. “Future sequencing of additional strains and close relatives of this pathogen will help test this hypothesis and could transform our understanding of how it adapts to immune plants."
Dr. Kurt Lamour, an associate professor in the UT Department of Entomology and Plant Pathology and a core faculty member in the Genome Science and Technology graduate program, worked with his then graduate student Alon Savidor and Dr. W. Hayes McDonald at Oak Ridge National Laboratory to assist this effort by analyzing the organism’s proteins. Their experiments validated or refined many of the genes predicted in the genome. Savidor is now a postdoctoral researcher at Tel Aviv University in Israel and McDonald is now at Vanderbilt in Nashville.
P. infestans was responsible for the great potato famine that gripped Europe, particularly Ireland, in the mid 1800’s. Once considered a fungus, the organism is now known to be a member of the oomycetes or “water molds.” Oomycetes are more closely related to the malaria parasite than to fungi. P. infestans thrives in cool, wet weather, such as experienced for much of this growing season. The organism can infect potatoes and tomatoes, causing a “late blight” that can decimate entire fields in just a few days.
The pathogen can also adapt rapidly. It is known to quickly attack potato varieties that that have been bred to be genetically resistant to P. infestans infection. This rapid adaptability has long puzzled scientists.
To understand the genetic basis for the pathogen’s success, the researchers, led by scientists at the Broad Institute and the Sainsbury Laboratory, decoded the P. infestans genome. They produced a high-quality genome sequence and compared it to the genomes of two relatives: P. sojae, which infects soybeans, and P. ramorum, which prefers oak and other trees and causes a condition known as sudden oak death. Lamour and his lab have actively researched these other Phytophthora organisms as well.
A striking finding of the effort is the size of the P. infestans genetic blueprint. It is two and a half to four times the size of its relatives’ genomes. The source of the genome’s large size is a massive amount of repetitive DNA. This type of DNA, once considered “junk” DNA, accounts for about 75 percent of the entire P. infestans genome.
As part of his Ph.D. studies, Savidor, with input and co-mentoring from Lamour and McDonald, refined a protocol based on "shotgun proteomics" to measure a large number of proteins in the genome and helped check the quality of the predicted genes. Lamour says the effort generated useful proteomic data that supported the overall genome sequencing effort.
The overall findings suggest that P. infestans utilizes an unusual genomic strategy to support the rapid evolution of “effector” genes that disrupt the host plant’s normal physiology. “We think this could be a tactic that enables P. infestans to rapidly adapt to host plants,” said co-lead author Brian Haas, manager of genome annotation, outreach, bioinformatics, and analysis at the Broad Institute.
The researchers identified more than 700 previously unknown effector genes, many of which belong to two key groups known as RXLR genes and CRN genes. The team identified more than 500 RXLR genes and nearly 200 CRN genes, significantly more than are found in the pathogen’s relatives.
These findings not only expand the catalog of known P. infestans genes, they also highlight a critical subset of genes undergoing rapid evolution. Further studies of these genes will foster a deeper understanding of Phytophthora and other pathogens and help researchers identify potential means to defend against catastrophic infections that can decimate crops.
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Nature News article:
Potato blight's gene weaponry revealed
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Contacts:
Broad Institute of MIT and Harvard
Nicole M. Davis
617.714.7152
ndavis@broadinstitute.org
The Sainsbury Laboratory
Zoe Dunford
+44 (0) 1603 255111
zoe.dunford@bbsrc.ac.uk
The University of Tennessee Institute of Agriculture
Patricia McDaniels
615.835.4570
pmcdaniels@tennessee.edu
The Broad Institute of MIT and Harvard
The Eli and Edythe L. Broad Institute of MIT and Harvard was founded in 2003 to empower this generation of creative scientists to transform medicine with new genome-based knowledge. The Broad Institute seeks to describe all the molecular components of life and their connections; discover the molecular basis of major human diseases; develop effective new approaches to diagnostics and therapeutics; and disseminate discoveries, tools, methods and data openly to the entire scientific community.
Founded by MIT, Harvard and its affiliated hospitals, and the visionary Los Angeles philanthropists Eli and Edythe L. Broad, the Broad Institute includes faculty, professional staff and students from throughout the MIT and Harvard biomedical research communities and beyond, with collaborations spanning over a hundred private and public institutions in more than 40 countries worldwide. For further information about the Broad Institute, go to www.broadinstitute.org.
The Sainsbury Laboratory
The Sainsbury Laboratory (TSL) is a world-leading research centre focusing on making fundamental discoveries about plants and how they interact with microbes. TSL is evolving its scientific mission so that it not only provides fundamental biological insights into plant-pathogen interactions, but also delivers novel, genomics-based solutions, which will significantly reduce losses from major diseases of food crops, especially in developing countries. For further information about the Sainsbury Laboratory, go to www.tsl.ac.uk.
The University of Tennessee Institute of Agriculture
Dr. Lamour’s lab is housed in the Department of Entomology and Plant Pathology of the UT College of Agricultural Sciences and Natural Resources. CASNR is one of the UT Institute of Agriculture’s four units, which provides instruction, research and public service. The other units are the UT College of Veterinary Medicine; UT AgResearch, including its system of 10 research and education centers; and UT Extension with offices in every county in the state. For further information go to http://agriculture.tennessee.edu.