Genomic signatures of sub-lethal fungicide stress in Sclerotinia sclerotiorum
Nikita Gambhir: University of Nebraska
<div>Cellular stress from exposure to sub-lethal doses of antifungals is known to cause genomic instability in human pathogens, which may confer antifungal resistance or other adaptive traits, yet little is known about similar genomic stress on fungal plant pathogens. In a previous study, we exposed five isolates of <em>Sclerotinia sclerotiorum</em> to sub-lethal doses of four commercially formulated fungicides with different modes of action (iprodione, dicarboximide; thiophanate-methyl, MBC; boscalid, SDHI; azoxystrobin, QoI) for twelve consecutive generations with experimental replication. In the present study, we sequenced the genomes of pre- and post-exposure individuals (55 in total). Obtained were 115 GB of 150bp paired-end reads that were aligned to the reference genome and used to call variants, which were filtered for read depth (>5X), mapping quality(>Q41), and loci that mutated in controls. From the first experiment, identified were 297 variants, 42% were SNPs and 22% variants were in a putative coding region. From the repeated experiment, results were similar: 294 variants, 50% SNPs and 25% variants in the coding region. This is the first study to characterize genomic alterations of a plant pathogen after exposure to sub-lethal fungicides. Further analysis will characterize duplications, chromosomal rearrangements and mutated genes under positive selection.</div>
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