New initiative with DOE JGI focuses on powdery mildew comparative genomics

PMB Professors Mary Wildermuth and Shauna Somerville lead effort with DOE Joint Genome Institute to unravel powdery mildew adaptation to diverse plant hosts

With resources from the U.S. Department of Energy Joint Genome Institute (DOE JGI), a DOE Office of Science user facility, UC Berkeley Plant and Microbial Biology Associate Professor Mary Wildermuth and Professor Shauna Somerville, also affiliated with the Energy Biosciences Institute, will lead a team of international researchers to obtain genome sequences for eleven powdery mildew fungi that are phylogenetically diverse and adapted to very different host plants.

Left unchecked, powdery mildews cause billions of dollars in agricultural damage each year – powdery mildew is the most significant disease affecting grapes. And bioenergy crops including eucalyptus, poplar, and camelina are also susceptible to powdery mildews. Growers combat powdery mildews with fungicides but this research should provide new strategies for limiting powdery mildews thereby reducing extensive chemical treatments.

Powdery mildew genomes of ~150 MB in size have challenged researchers trying to get complete genomes due to the unusual percent of their genome, as high as 90%, that is comprised of repeat elements. Currently, complete genomes exist only for Blumeria graminis that colonize cereals, like barley and wheat.

Wildermuth, Somerville, and collaborators will utilize the expertise and resources of the DOE JGI and its Fungal Genomes Program to study the comparative genomics of powdery mildews and associated plants through a recently selected Community Science Program proposal. This includes sequencing of powdery mildew genomes that infect eucalyptus, camelina, grape, tomato, lettuce, cucumber, hops, strawberry, and pepper.

Further efforts will investigate fungal and plant gene expression in tandem at three infection phases:

·      Germination of the powdery mildew spore

·      Formation of the fungal feeding structure in the host plant

·      Fungal surface growth and reproduction to form new spores.

Powdery mildews are “obligate biotrophs”, meaning that they can only grow and be cultivated on living plant tissue. These stealth pathogens manipulate the plant to provide resources while minimizing their detection and activation of plant defenses.

By comparing powdery mildew genomes adapted to different plants, the group can identify minimal gene sets required for obligate biotrophy. These minimal gene sets include those required to breakdown cell walls and redirect carbon metabolism – two items of great interest to the Department of Energy. Researchers can also figure out what determines the specific plants that a powdery mildew can colonize. For example, powdery mildews that infect pepper do not infect grapes.

All of the data obtained from this research will be publicly available and searchable at the DOE JGI MycoCosm website: http://jgi.doe.gov/fungi.

Powdery mildew project collaborators include: Dr. Yai Bai (Wageningen UR, Nederlands), Dr. Uwe Braun (Martin-Luther-Universitat, Halle, Germany), Dr. Rachel Brem (Buck Institute for Research on Aging, Novato, CA), Dr. Lance Cadle-Davison (USDA-ARS, Geneva, NY), Dr. Ian Dry (CSIRO, Urrbrae, Australia), Dr. David Gent (USDA-ARS, Corvallis, OR), Dr. Ralph Huckelhoven (Technische Universitat Munchen, Germany), Dr. Levente Kiss (Plant Protection Institute, Budapest, Hungary), James McCreight (USDA-ARS, Salinas, CA), Alejandro Perez Garcia (University of Malaga, Spain), and Dr. Susumu Takamatsu (Mie University, Tsu, Japan).