Ohio State University plant pathologist Sophien Kamoun likes to know his enemies. And as the key player in two recently funded, $6.7 million projects aimed at sequencing the genome of two devastating crop killers, he will get to know all 20,000 genes of them.

A scientist with the university’s Ohio Agricultural Research and Development Center (OARDC) in Wooster, Kamoun is the only investigator who is part of both research teams sequencing the genome of Phytophthora infestans and Phytophthora capsici -- fungus-like oomycetes (pronounced o-o-my-seats) that cause serious diseases in popular vegetables such as potatoes, tomatoes and peppers, and which have the potential to threaten food security in many developing countries.

Funding this research are the National Science Foundation (NSF) and the U.S. Department of Agriculture’s Cooperative Research, Education and Extension Service (both projects), as well as the U.S. Department of Energy’s (DOE) Community Sequencing Program (P. capsici project).

Once thought to be fungi because of their physical resemblance, Phytophthora pathogens are actually more closely related to brown algae at the molecular level. As a result, they function and infect plants differently, posing chemical control challenges and generating new questions as to how they exactly interact with plant hosts.

Answering those questions is the goal of Kamoun, a global leader in oomycete molecular genetics and genomics who has opened up new research territory for many other scientists.

“When dealing with plant diseases, the most important step is to know your enemy, and obtaining the genome sequence of these pathogens is key to learning more about them,” said Kamoun, an associate professor in the Department of Plant Pathology, part of Ohio State’s College of Food, Agricultural, and Environmental Sciences. “For example, there are some 20,000 genes in P. infestans and we have to find the subset of those genes that is important for triggering disease symptoms. Once we identify those genes, we would be able to manipulate them or target them with chemicals. This data would also allow us to identify the corresponding resistance gene in the plant.”

The first project, with funding totaling over $3.7 million, is the third phase of an ongoing effort to complete the genome sequence of P. infestans -- the pathogen that causes late blight of potato and tomato and was responsible for the Irish potato famine. Kamoun and his colleagues had previously received a four-year, $1.9 million grant from NSF to begin their quest to crack down the genetic code of this pathogen.

P. infestans has re-emerged as a pervasive enemy of potato and tomato production, with worldwide losses exceeding $5 billion a year -- making it the single greatest pathogenic threat to global food security, as potatoes are the staple food in many countries and the most important non-cereal crop in the world. Recent widespread occurrence of new fungicide-resistant strains of this pathogen is another reason to take P. infestans seriously, even in countries where farmers can afford to treat their crops with fungicides.

“The reality is that you can’t grow potatoes without spraying for late blight,” Kamoun pointed out. “It’s a manageable disease, but an expensive one. However, in many parts of the world, farmers don’t have the means to apply chemicals; there, this disease could cause food shortages and hunger.”

Collaborators in this project include the Massachusetts Institute of Technology (MIT), Cornell University, the University of California Riverside and North Carolina State University.

The second project, funded at approximately $3 million, seeks to map the genome of P. capsici employing a novel DNA-sequencing method developed by Branford, Conn.-based 454 Life Sciences. This will be the first instance in which a eukaryotic (non-viral or non-bacterial) microorganism is sequenced from scratch using 454’s technology since it was introduced in 2003 -- marking the first time a new way to sequence whole genomes became available in over 20 years.

P. capsici affects crops such as peppers, cucumbers, squash, pumpkins and tomatoes. It has become a disease of national economic importance, spreading widely since 1922 when it was first reported in the United States on New Mexico chili peppers. However, research on this pathogen has been negligible.

“P. capsici is the one of the most genetically diverse Phytophthora species,” Kamoun said, “so there was interest in using this pathogen to test this new technology, which makes it possible to quickly sequence and compare the genome of multiple pathogen strains that infect different vegetable crops and differ in virulence and resistance to fungicides.”

Collaborators in this project include the National Center for Genome Resources, DOE’s Joint Genome Institute, 454 Life Sciences and the University of Tennessee.

As the link between both research teams, Kamoun sees great promise in having the unprecedented chance to compare the genomes of two major Phytophthora pathogens. “We will be able to compare the two species, see what their differences are at the molecular level, and learn what makes one infect one crop and not the other,” he explained. “This will open up many possibilities for research and ultimately new management options for growers.”

Writer: Mauricio Espinoza
Source: Sophien Kamoun, Plant Pathology