The Genetic Landscape of Structural Variants in Aspergillus flavus using ONT and PacBio Sequencing

Genetic rearrangement in the absence of selection is poorly understood. Long-read, high-depth sequencing has enabled analysis of the genetic landscape of spontaneous structural variants. We have applied PacBio Revio sequencing to identify the major classes of genetic alterations during long-term vegetative growth in Aspergillus flavus. These classes include a) precise deletions frequently associated with the flanking region of homology, b) clusters of short deletions that are heavily enriched within centromeric and subtelomeric regions that are typically 94% A+T, and c) deletions and expansions within a subset of homopolymer tracts. We find 70 homopolymer tracts longer than 44 bp, dispersed throughout the genome in noncoding regions and unassociated with transposable elements. A broader analysis of third-generation sequenced datasets from fungi found within the Phylum Ascomycota showed a high but variable prevalence of homopolymeric tracts across species. The adventitious identification of a putative flbA mutation, responsible for an altered conidial phenotype, by the Deep Variant AI system also demonstrates the power of this approach. These studies show that high-depth, long-read sequencing can probe SNPs, indels, homopolymeric tracts, and large-scale rearrangements in an unbiased fashion, and demonstrate that short deletions and homopolymer tract expansions arise spontaneously in A. flavus and other filamentous fungi.