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

Understanding genetic rearrangement in the absence of selection presents complex challenges. However, long-read, high-depth sequencing, particularly through PacBio Revio, has made significant strides in analyzing the genetic landscape of spontaneous structural variants. This study focused on Aspergillus flavus, a type of filamentous fungus, during its long-term vegetative growth.

Several key classes of genetic alterations were identified, including a) precise deletions frequently linked to homology regions, b) clusters of short deletions heavily concentrated in centromeric and subtelomeric areas, typically rich in A+T nucleotides, and c) deletions and expansions within certain homopolymer tracts. The genome of Aspergillus flavus was found to contain 70 homopolymer tracts of more than 44 base pairs, scattered across noncoding regions without association with transposable elements.

A broader examination of third-generation sequenced datasets from fungi within the Phylum Ascomycota revealed a high but variable prevalence of homopolymeric tracts across different species. The opportunity to identify a putative flbA mutation, associated with a different conidial phenotype, using Deep Variant AI technology further highlights the efficacy of this sequencing approach.

These studies collectively demonstrate that high-depth, long-read sequencing can effectively analyze SNPs, indels, homopolymeric tracts, and large-scale rearrangements in an unbiased manner, proving that short deletions and homopolymer tract expansions emerge spontaneously in A. flavus and other filamentous fungi.