Investigating the origin of subtelomeric and centromeric AT-rich elements in Aspergillus flavus

An in silico study of Aspergillus flavus genome stability uncovered significant variations in both coding and non-coding regions. The non-coding insertions uniformly consisted of AT-rich sequences that are evolutionarily maintained, albeit distributed at widely different sites in an array of A. flavus strains. A survey of ≥ 2kb AT-rich elements (AT ≥ 70%; ATEs) uncovered three classes. The first class is composed of homologous insertions at ectopic, non-allelic sites that contain homology to transposable elements (TEs). Strains differed significantly in frequency, position, and TE type, but displayed a common enrichment in subtelomeric regions. The TEs were heavily mutated, with patterns consistent with the ancestral activity of repeat-induced point mutations (RIP). The second class consists of ∼100 kb regions at each centromere. Centromeric ATEs and TE clusters within these centromeres display a high level of sequence identity between strains. The third class consists of a conserved set of novel subtelomeric ATE repeats which lack discernible TEs and, unlike TEs, display a constant polarity relative to the telomere. Members of one of these classes are derivatives of a progenitor ATE that is predicted to have undergone extensive homologous recombination during evolution. These studies suggest that transposition and RIP are forces in the evolution of subtelomeric and centromeric structure and function.