Clustering of inverted triplications in centromeric and subtelomeric chromosomal regions of Aspergillus flavus

Authors: WOODS, ALEXIE - Tulane School Of Medicine; MALIK, AMNA - Tulane School Of Medicine; LUDECKE, ERILK - Tulane School Of Medicine; FLEMINGTON, ERIK - Tulane School Of Medicine; Cary, Jeffrey; LUSTIG, ARTHUR - Tulane School Of Medicine

Submitted to: Microbiology Spectrum
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/30/2026
Publication Date: 5/29/2026
Citation: Woods, A., Malik, A., Ludecke, E., Flemington, E., Cary, J.W., Lustig, A.J. 2026. Clustering of inverted triplications in centromeric and subtelomeric chromosomal regions of Aspergillus flavus. Microbiology Spectrum. https://doi.org/10.1128/spectrum.03473-25.
DOI: https://doi.org/10.1128/spectrum.03473-25

Interpretive Summary: Aspergillus flavus is a fungus that infects crops like corn and can produce dangerous toxins called aflatoxins, which are harmful to people. The genes that allow fungi to make toxins often occur in clusters, and these clusters can change quickly because fungi naturally gain and lose genes over time. Scientists want to understand how and why these genetic changes happen so they can find ways to keep harmful toxin-producing genes from appearing while preserving genes that are useful for safe biocontrol. In this study, researchers used advanced DNA sequencing to look for natural genetic rearrangements in A. flavus and discovered rare changes in parts of the genome that are already known to be unstable. These findings help pinpoint where genetic “hot spots” are located in the fungus and improve our understanding of how toxin-related genes can appear or disappear, ultimately providing new methods to keep toxins out of our food supply.

Technical Abstract: The formation of inverted repeats frequently initiates rearrangements associated with gene amplification and disease states. Among these rearrangements are inverted triplications (TRP/INVs). We have used the filamentous fungus Aspergillus flavus as a model system to analyze spontaneous DNA rearrangements using high-depth third-generation sequencing of DNA isolated from vegetatively cultured strains. Analysis of sequence data identified a class of infrequent and transient rearrangements having structures typical of TRP/INVs. These TRP/INVs form both unprocessed and processed species and have a variably sized deletion at the junction between direct and inverted sequences. We found that TRP/INVs are 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. Inverted junctions contain palindromic sequences that are typically associated with TRP/INVs. A closer examination of the class of genomic palindromes found at inverted junctions revealed a broad distribution, with the majority lying in AT-rich centromeric sequences. The distribution of TRP/INVs in centromeric and subtelomeric domains mirrors the frequency of palindromes, indicating that palindrome abundance is likely to be a driver of TRP/INVs. A further examination of predicted pairing patterns in palindrome-like structures suggests roles in strand transfer and replicative stalling. These results are predicted from a replication-based model in which palindromes, under conditions of replication stress, facilitate the formation of TRP/INV structures. These studies represent, to our knowledge, the first characterization of spontaneous TRP/INV formation.