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International Team Sequences, Compares Rust Fungi Genomes

By a GenomeWeb staff reporter

NEW YORK (GenomeWeb News) – An international team reported online this week in the Proceedings of the National Academy of Sciences that they have sequenced the genomes of two rust disease causing fungi: the poplar leaf rust fungus Melampsora larici-populina and Puccinia graminis, a fungus that causes wheat and barley stem rust.

By comparing the genomes to one another and to some previously sequenced fungal pathogens and symbionts, the researchers identified features in the rust fungi genomes that seem to coincide with their pathogenic lifestyles. For instance, they tracked down a slew of genes coding for so-called effectors — small, secreted proteins that help the fungi thwart plant defenses and set up shop in their hosts — along with other genetic clues about adaptations that have helped the fungi become specialized for life inside plants.

Those involved in the study say the findings are useful for understanding fungal biology and for finding ways to combat rust disease. That, in turn, may have implications for poplar-based bioenergy strategies, since infection by rust fungi can weaken the trees and check their growth.

"[S]equencing the rust fungus genome opens great perspectives to study the evolution of these candidate effectors and further define new resistances through breeding strategies in tree plantations," co-lead author Sébastien Duplessis, an ecogenomics researcher at the French National Institute for Agricultural Research (INRA), said in a statement.

"The precise analysis of these effectors, their localization and their targets in the host plant, and how they evolve to overcome plant resistances will contribute to the selection and management of sustainable resistances of poplar trees to the rust disease," he added.

Poplar leaf rust fungus and wheat and barley stem rust fungus are just two of the thousands of rust fungus species identified so far. These plant pathogens that are classified as obligate biotrophs, the researchers explained, since they can't grow independently from their host plants and rely on plant tissues for nutrients.

The team used Sanger whole-genome shotgun sequencing to sequence the 101.1 million base pair M. larici-populina genome as well as the 88.6 million base genome of Puccinia graminis f. sp. tritici.

The genome sequence for M. larici-populina, generated as part of a 2006 Community Sequencing Program spearheaded by the US Department of Energy's Joint Genome Institute, has been publicly available since 2008.

Analyses of the two rust fungi genomes indicate that the M. larici-populina genome houses an estimated 16,399 protein-coding sequences, while the smaller P. graminis f. sp. tritici genome contains 17,773 predicted protein-coding sequences.

Roughly 45 percent of each genome sequence is comprised of transposable elements, bulking up the genomes and making them larger than the sequenced genomes of other fungi from the same phylum, researchers explained.

This transposable element expansion, coupled with recombination of these elements, seems to have contributed to a lack of synteny between the two genomes, they found.

And while each of the newly sequenced rust genomes contained gene family expansions, including expansions of some membrane transport and enzyme gene families, some of the gene family expansions differed between the species, pointing to lineage-specific adaptations.

Compared to free-living fungi, the rust species seem to be less genetically equipped to assimilate nitrogen and sulfur, the researchers reported, though their repertoire of amino acid and oligopepetide transporter coding genes is enhanced. And consistent with their invasive lifestyle, gene expression experiments revealed an up tick in the levels of transcripts coding for small secreted proteins, hydrolytic enzymes, and transporters expected to aid in besting host defenses and nabbing nutrients from the plant host.

"The dramatic up-regulation of transcripts coding for small secreted proteins, secreted hydrolytic enzymes, and transporters in planta suggests that they play a role in host infection and nutrient acquisition," the team wrote.

By continuing to look at how these and other factors mediate fungal interactions with plants, they explained, researchers hope to garner genetic insights that might eventually help control rust fungi and other fungal pathogens with agricultural, economic, and ecological impacts.

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