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New Genome Assembly and Analysis of Grape Pathogen Elucidate Virulence Mechanisms

Monday, December 12, 2016

A new publication from scientists at the University of California, Davis, and the USDA Agricultural Research Service presents important findings about a fungus that threatens global grape production. As part of the project, the team used SMRT Sequencing to generate a new assembly of the fungal genome, resulting in a more complete assembly than a previous short-read attempt.

Condition-dependent co-regulation of genomic clusters of virulence factors in the grapevine trunk pathogen Neofusicoccum parvum,” published in Molecular Plant Pathology, comes from lead author Mélanie Massonnet, senior author Dario Cantu, and collaborators. The team was eager to determine why the wood-infecting Neofusicoccum parvum has such pathogenicity and virulence.

The scientists had previously produced a genome assembly for the fungus using short-read data, but it was highly fragmented across more than 1,800 contigs. By contrast, the 43.7 Mb PacBio assembly they generated is represented in only 28 contigs, including one that fully covers the mitochondrial genome. More than half of the contigs had telomeric repeats at both ends, “suggesting that these contigs encompass complete chromosomes, telomere-to-telomere,” the authors write. An analysis found the assembly’s accuracy rate to be 99.99976%.

To understand the differences between the new long-read assembly and the existing short-read one, the team used nucmer and Assemblytics. These analyses showed that repeat reconstruction had been a problem in the short-read assembly, where these regions were consistently reported as shorter than they were revealed to be by PacBio log-read sequencing. More than 180 sites — for a total of 113 kb — were completely missing from the short-read assembly, and structural variation was less likely to be detected.

With this high-quality genome resource as a foundation, the scientists were able to delve into a detailed transcriptome analysis. “Co-expressed gene clusters were significantly enriched not only in genes associated with secondary metabolism, but also with cell wall degradation, suggesting that dynamic co-regulation of transcriptional networks contribute to multiple aspects of N. parvum virulence,” the scientists report. In the majority of these clusters, genes had common motifs in their promoter regions, suggesting that co-regulation is controlled by common transcription factors.

While these findings are important on their own, the scientists underscore the need for additional studies. “Understanding how functions that lead to colonization of certain cell types/tissues, and the corresponding fungal genes activated during subsequent degradation of such host tissues, may help us understand mechanism(s) of cultivar resistance and interactions within the trunk-pathogen community,” they conclude.

To hear more great research from plant and animal scientists using SMRT Sequencing, sign up to attend or receive the recording of our PAG 2017 workshop.

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