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International Team Sequences Blackleg Fungus Genome

By a GenomeWeb staff reporter

NEW YORK (GenomeWeb News) – An international research group led by researchers in Australia and France reported in Nature Communications online today that they have sequenced the draft genome of a fungus known for damaging canola crops.

Their sequencing and analyses of the Blackleg fungus, Leptosphaeria maculans, genome indicate that the fungus' genome sequence oscillates between cytosine and guanine nucleotide-rich compartments packed with genes and adenine and thymine nucleotide-rich regions that contain fewer predicted genes overall but are enriched for genes involved in pathogenicity.

"Such a feature has not been seen previously in a fungal genome," senior author Barbara Howlett, a botany researcher at the University of Melbourne, said in a statement. "These gene-poor regions have few active genes but those that are present play important roles in the disease."

Blackleg fungus is a genetically diverse fungal pathogen that can infect and cause severe damage to canola and related plants.

In an effort to understand the genetic underpinnings of this pathogen and its plant infection strategies, Howlett and her co-workers used whole-genome shotgun sequencing to sequence the 45 million base haploid genome of an L. maculans 'brassicae' isolate known as v23.1.3.

In the process, they identified 12,469 predicted protein-coding genes. Of these, the team noted, some 95 percent are found in GC-rich parts of the genome, while just five percent turned up in AT-rich stretches of sequence.

Nevertheless, the researchers reported, pathogenicity-related genes tend to be over-represented in these gene-poor, AT-rich blocks of the fungal genome. For instance, they found that roughly 20 percent of genes in these regions apparently code for small, secreted proteins contributing to plant infection.

Moreover, the team's analyses suggest that AT-heavy chunks of the L. maculans genome contain more transposable elements than the gene-rich, GC-nucleotide loaded regions, fueling speculation that the repeats may have helped shape AT-rich chunks of the genome.

"What our study revealed is that it is the location of the disease-related genes within the junk DNA which allows the genes to be readily mutated, lost or gained," Howlett said in a statement. "This enables the blackleg fungus to cause disease outbreaks on canola varieties with particular resistant genes."

Although they noted that additional research on the fungus is needed, included sequencing studies of related fungal species and sub-species, those involved in the study say information from the L. maculans genome may have applications for those trying to come up with strategies for battling the pathogen and for producers looking to select the most resistant crop plants.

"We have known for a long time that this fungus can evolve to become virulent and cause disease very quickly," Howlett said.

"Now we are much better placed to tell farmers which canola varieties they should sow to maximize their yield," she added. "If an epidemic is predicted then farmers can plant a different canola variety, which will not readily succumb to disease."

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