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Teams Use Genomic Strategies to Tackle Plant Pathogens

By a GenomeWeb staff reporter

NEW YORK (GenomeWeb News) – A quartet of studies appearing online today in Science is underscoring the value of genomic approaches for understanding plant pathogens adaptations to their hosts — and offering clues about strategies that these pathogens use to thwart plant defenses.

"These studies highlight the value of comparative genomics in identifying important virulence genes with host-specific functions," Commonwealth Scientific and Industrial Research Organisation plant researcher Peter Dodds wrote in an accompanying perspectives article. "The challenge now is to determine how the effector proteins that these genes encode turn the host cell to their own purposes."

In the first of the studies, researchers from the UK, the US, and Germany used comparative genomics to track the evolution of Phytophthora infestans — a water fungus that can infect potato, tomato, and related plants and is best known for its role in the Irish potato famine.

By looking at similarities and differences between the P. infestans genome and genome sequences from three related fungal species, the team found evidence that Phytophthora adaptation to particular hosts is a consequence of rapid evolution in repeat-rich bits of the genome. That, in turn, suggests that it may be possible to combat a range of related pathogens by focusing on parts of the genome that evolve more slowly and are shared between related pathogens.

"Our aim is to develop resistance to genes from the stable, slowly-evolving region of the pathogen's genome," senior author Sophien Kamoun, head of Norwich Research Park's Sainsbury Laboratory, said in a statement. "This should be more disruptive to the pathogen's ability to evolve new races."

The team re-sequenced the 240 million base genome of P. infestans, along with the genomes of three closely related species: P. ipomoeae, which infects morning glory plants, P. mirabilis, which infects four o' clocks, and P. phaseoli, which infects lima beans.

During their subsequent analyses of the genomes, the team found 747,744 non-redundant SNPs and nearly 4,000 copy number variants in the four genomes, along with 2,572 genes that appear to be under positive selection in at least one of the strains tested.

Consistent with past studies, the team detected expansions in repeat-rich parts of the genome that contain relatively few genes overall but tend to be enriched for disease effector genes.

The same repeat regions housed a higher proportion of the CNVs, gene gains or losses, and signals of positive selection than other areas of the genome, researchers explained, arguing that "gene-sparse, repeat-rich regions are highly enriched in genes induced in planta, therefore implicating host adaptation in genome evolution."

In a second Science study, an international research team led by investigators in Germany and the UK sequenced and analyzed the genome of the barley powdery mildew fungus, an obligate parasite that infects barley plants and relies on plant cells to grow and reproduce.

They tackled the 120 million base haploid genome of Blumeria gramis f. sp hordei, more commonly called Blumeria, using a combination of Sanger and high-throughput sequencing, generating sequence that covered the pathogen's genome about 140 times.

They then annotated the Blumeria genome and compared it with draft versions of two other powdery mildew genomes — the 151 million base genome of the pea pathogen Erysiphe pisi and the 160 million base genome of the Arabidopsis thaliana pathogen Golovinomyces orontii — each sequenced to about eight times coverage.

By looking for genes that are present in yeast and other fungi but absent in the powdery mildews, the team was able to get clues about which genes have been eliminated during powdery mildew specialization for life inside plants.

For instance, they found that while the powdery mildews had large genomes packed with retrotransposons, the obligate parasites were missing genes coding for some primary and secondary metabolic enzymes, as well as certain transporters and enzymes that help break down plant cell wall material.

Although predictions from the genome data suggest nearly 250 genes are involved in powdery mildew pathogenesis, only a handful of these are shared between all three of the genomes, fueling speculation that these powdery mildew effectors vary by species.

"Among the 248 candidate effectors of pathogenesis identified in the Blumeria genome, very few (less than 10) define a core set conserved in all three mildews, suggesting that most effectors represent species-specific adaptations," senior author Ralph Panstruga, a researcher with the Max Planck Institute for Plant Breeding Research, and co-authors wrote.

An international team led by investigators in the UK and US, meanwhile, focused on another obligate parasite: an Arabidopsis thaliana pathogen called Hyaloperonospora arabidopsidis, which causes downy mildew disease, sequencing the genome of the oomycete form of H. arabidopsis, or Hpa, to about 46 times coverage.

During their subsequent analysis of the genome, they found that Hpa is missing some effector coding genes found in Phytophthora species such as the potato blight pathogen, which are thought to share a common ancestor with Hpa. It also lacks some metabolic enzyme coding genes as well as genes for proteins involved in motility and other functions needed for life outside of plants.

Moreover, they found, Hpa seems to have jettisoned some genes that code for plant immune system-stimulating proteins, but appears to have built up an arsenal of other genes coding for proteins that help suppress plant immunity.

"This evolution towards stealth helps explain why this mildew and its relatives are widely distributed and cause diseases in many important crops," co-senior author John McDowell, a plant pathology, physiology, and weed science researcher at Virginia Tech, said in a statement.

Finally, by sequencing the genome of a maize-infecting fungus, Sporisorium reilianum, and comparing it the genome of the corn smut-causing fungal pathogen Ustilago maydis, German researchers found new clues about the different strategies that related pathogens use to infiltrate the same host species.

Their analysis of the newly sequenced S. reilianum genome turned up 6,648 predicted genes on 23 chromosomes — as well as extensive synteny with U. maydis.

Though both genomes contained genes coding for similar secreted effector proteins, the team detected dozens of effector gene-containing regions that had much less conservation than other parts of the genome, hinting that these genes are evolving especially quickly in the fungi.

Such patterns, combined with the team's subsequent U. maydis deletion and other experiments, indicate that even related pathogens that infect the same plant hosts can use distinct strategies to exploit these plants.

"[T]he U. maydis and S. reilianum genomes comprise conserved effector genes as expected for pathogens infecting the same host," senior author Regine Kahmann, a molecular phytopathology researcher at the Max Planck Institute for Terrestrial Microbiology, and co-authors wrote. "However, although the two pathogens are both recognized and challenged by the maize immune system, they also possess strongly differentiated effectors, suggesting that they are targeting different host molecules."