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Pathogen-infected Arabidopsis plant

Stealthy Pathogen’s Genome Provides Plant Disease Clues

An international team of scientists has sequenced the genome of a plant disease-causing organism, revealing that it acts like a "stealth bomber of plant pathogens."

The research, published in the journal Science, has uncovered the tactics used by the organism to sneak past the plant's immune defenses. This same discovery also provides tools for researchers to identify the components of the plant immune system and devise new ways to prevent disease.

The research looked at Hyaloperonospora arabidopsidis, a downy mildew classified as an oomycete, a fungal-like organism that has evolved from marine algae. It is also an obligate biotroph, a type of plant pathogen that has adapted so exquisitely to its host that it extracts nutrients only from living plant tissue and cannot grow away from the plant. While the organism may once have been able to exist by itself, it has now evolved in such a way that it cannot survive without a specific type of host plant.

“Some plant pathogens like H. arabidopsidis must keep their host alive throughout the infection cycle in order to survive,” said Dr. Brett Tyler, professor at the Virginia Bioinformatics Institute at Virginia Tech and one of the lead authors of the study. “Other pathogen species that destroy soybean and potato crops as well as oak tree forests, keep plants alive for part of the time before killing and devouring the plant tissue.”

H. arabidopsidis can only survive on its host plant Arabidopsis, the model of the plant science world. Close relatives cause disease and damage on many crops including broccoli, maize, grapes and lettuce. The researchers found that this particular plant pathogen has evolved a highly successful strategy that allows it to present a very small genetic profile to its host plant. By losing, or never acquiring in the first place, many abilities found in other pathogens, H. arabidopsidis is able to minimize the number of genetic markers it carries that could be picked up by a plant's defenses and seen as a threat.

Plant Pathogen 'Stealth Bomber'

Hyaloperonospora arabidopsidis is one of the stealth bombers of the world of plant pathogens. We can see much of how it has actually slimmed down some key elements of its genetic material in order to get around the plant's natural defenses - essentially by stealth,” said Dr. Jim Beynon, a lead researcher from the University of Warwick's School of Life Sciences.

In the paper, the sequence of H. arabidopsidis is compared with other fully sequenced genomes of destructive plant pathogens to shed light on the differences in the ways microbes interact with their host and how those differences evolve. The availability of multiple genome sequences for these types of pathogens is an important step in allowing scientists to determine how both the host plant and its pathogen carry out this evolutionary ‘arms race.’ “Sequencing a model pathogen like H. arabidopsis is key to understanding what parts of this organism’s genome makes it so destructive to its plant host,” said author Dr. Sandra Clifton, the former Assistant Director of Genomics at Washington University’s Genome Institute.

Using this genomic data, the researchers discovered that this plant pathogen mounts its sneak assault on a plant host through the ‘RXLR effector’ proteins. Such pathogens use a large armory of ‘RXLR effectors’ to suppress the mechanisms used by plants to detect and then block pathogens. Despite its slimmed down stealth genetic profile, H. arabidopsidis still maintains an amazing 134 RXLR effectors in its armory. Understanding the role of these effectors will be the key direction of future research in the field.

This pared-down genetic approach may help H. arabidopsidis in its stealth attack but it also opens up a major opportunity for researchers to gain insights across a vast range of plant pathogens. Not only does H. arabidopsidis infect the ideal plant model (Arabidopsis) used by plant researchers the world over for decades – it also attacks that model plant with a bare bones set of weapons that greatly simplifies a researcher's task in figuring out how those weapons work. Any insights gained can then be directly applied to the understanding of how those same weapons work in much more complicated pathogens.

Dr. Beynon added: “This research provides a new window into how Hyaloperonospora arabidopsidis has slimmed down key elements of its genetic material to avoid the plant's natural defenses. Despite this reduction, amazingly, it still sends over 100 proteins into plant cells to suppress the immune responses. Understanding how these proteins suppress plant immunity will enable us to select disease resistant crop plants and combat plant disease such as potato blight and sudden oak death.”

Food Crop Losses

“Losses to disease in food crops can be very significant. And to feed a growing population set to reach 9 billion by 2050 we need to increase food production. Reducing losses because of disease will be an important part of this.”

The project was a collaboration involving scientists at The Genome Institute at Washington University, United States; the College of Agriculture and Life Sciences at Virginia Tech, United States; The Sainsbury Laboratory, United Kingdom; the Sequencing Centre at the Wellcome Trust Sanger Institute, United Kingdom; the University of Warwick, United Kingdom; and the Virginia Bioinformatics Institute at Virginia Tech, United States. The work was supported by funds from the Agriculture and Food Research Initiative of the United States Department of Agriculture’s National Institute of Food and Agriculture, and by the Emerging Frontiers program of the National Science Foundation.