Genetic Blueprint of Oak Disease Pathogen Mapped

Researchers have mapped the genetic blueprint of a widespread forest pathogen that is killing California oak trees on the Northern and Central coasts and attacking some common garden plants.

Breaking the genetic code of the fungus-like pathogen that causes sudden oak death should help fight the disease, which can infect dozens of types of plants.

“It gives us a look inside the armory of this thing, where we look at all of its weapons,” said Daniel Rokhsar, head of computational genomics at the U.S. Department of Energy’s Joint Genome Institute in the Bay Area city of Walnut Creek. “Now we can look for ways to interfere with its tool kit. How to play a good defense.”

During its work on the Human Genome Project, the institute learned how to perform genetic sequencing quickly and cheaply and has started decoding other organisms. On Thursday it announced that it had completed the mapping of Phytophthora ramorum, the pathogen that causes the oak disease, and a related organism, Phytophthora sojae, that causes a soybean disease.

Although there is a pesticide treatment for the forest disease that can be used on individual trees, there is no cure for sudden oak death. Confirmed in the wild in 13 counties from Humboldt south to Monterey, it has proved most lethal to coast live oak, California black oak and tanoak. It also infects a number of other common trees and shrubs, including manzanita, madrone and rhododendron. And in March it was found on camellias at a large Southern California nursery wholesaler that ships plants around the country.

UC Berkeley scientist Matteo Garbelotto, who helped identify the oak disease pathogen several years ago, said the genetic mapping had already helped his research. Using initial information from the sequencing, he and some colleagues analyzed American and European strains of the organism and found low levels of genetic diversity. That suggests it was recently introduced to both the United States and Europe from a third, as yet unknown, location.

“It’s really, really, really unlikely that it’s a native organism, which sets the tone for everything we do,” said Garbelotto, adding that greater urgency surrounds an exotic pathogen that native ecosystems haven’t adapted to. “It deserves all the attention and effort we can give it.”

Identifying the organism’s 15,000 genes should help develop techniques for detecting infection easily and quickly, which could help contain its spread.

“For a disease like this, rather than think about getting rid of it, we need to understand it -- how it functions -- to slow it down,” Garbelotto added. “Where is it? Where does it hide? What are the hosts?”

To map the two pathogens, researchers collected spore cells and pulled out the DNA. The genetic material was then broken into small pieces and read by machines in a series of 2 million experiments.

Spread over the last year, the actual decoding took about a month and cost about $4 million, partly funded by the U.S. Department of Agriculture and the National Science Foundation.

Since the discovery of the disease on plants at Monrovia Nursery in Los Angeles County, infected shipments have been traced to nurseries in Oregon and on the East Coast, prompting worries that sudden oak death could infect Eastern forests.

Quarantines were imposed on nursery shipments, and a number of states have banned importation of California nursery stock or plant species that can carry the disease.