Clustering of Tandem Inverse Duplications in Centromeric and Subtelomeric Chromosomal Regions of Aspergillus flavus

Rearrangements associated with gene amplification are frequently initiated by the formation of inverted repeats. Among these rearrangements are breakage-fusion-bridge cycles and tandem inverted duplications (TIDs), both of which can be mediated through palindromic sequences. We have investigated spontaneous rearrangements within the genome of the filamentous fungus Aspergillus flavus by high-coverage third-generation sequencing of vegetatively cultured strains. Analysis of sequence data identified a class of rare and transient rearrangements having structures typical of TIDs. These putative TIDs (pTIDs) form both unprocessed and processed species and have a variably sized deletion at the junction between direct and inverted sequences. Most intact junctions contain the predicted palindromic sequences, supporting the TID model. However, palindrome-free junctions are also infrequently observed. pTIDs are highly enriched in heterochromatic centromeric and subtelomeric A+T rich regions, suggesting that this process is a source of genetic instability in these domains. Consistent with this finding, A+T rich regions contain elevated levels of direct, inverted, and perfect palindromic repeats. We propose a replication-based model in which palindromes and short inverted repeats, under condition of replication stress, are responsible for pTID structures.