{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"institution":[{"name":"bioRxiv"}],"indexed":{"date-parts":[[2026,4,11]],"date-time":"2026-04-11T05:44:04Z","timestamp":1775886244587,"version":"3.50.1"},"posted":{"date-parts":[[2025,1,19]]},"group-title":"Genetics","reference-count":62,"publisher":"openRxiv","license":[{"start":{"date-parts":[[2025,1,19]],"date-time":"2025-01-19T00:00:00Z","timestamp":1737244800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/www.biorxiv.org\/about\/FAQ#license"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"accepted":{"date-parts":[[2025,10,16]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n                <jats:p>The formation of inverted repeats frequently initiates rearrangements associated with gene amplification. Among these rearrangements are inverted triplications (TRP\/INVs) that are associated with multiple disease states in humans. 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 that these structures may function as sites of DNA resolution, strand transfer, and replicative stalling. These results are consistent with a replication-based model in which palindromes, under conditions of replication stress, facilitate the formation of TRP\/INV structures. These studies also represent, to our knowledge, the first characterization of spontaneous TRP\/INV formation, likely to underlie the complex rearrangements associated with higher eukaryotic genomic instability and disease states.<\/jats:p>\n                <jats:sec>\n                  <jats:title>AUTHOR SUMMARY<\/jats:title>\n                  <jats:p>Inverted triplications (TRP\/INVs), coupled with gene amplification, are sources of genetic instability. However, little is known about how these species arise spontaneously prior to selective pressures. We have established a fungal model system that uses long-read third-generation sequencing to identify low-abundance rearrangements in the absence of an intentional selection. We identified and characterized multiple classes of TRP\/INVs flanked by palindromic sequences. These rearrangements were concentrated in the AT-rich centromeric and subtelomeric regions, suggesting that these sites are regulated recombinational hotspots. Palindromes that are also associated with TRP\/INVs are also most prevalent in A+T-rich centromeric regions, suggesting that the abundance of palindromes, both as a source of DNA damage and fork stalling, is a driver of TRP\/INV formation. These studies provide the first evidence (to our knowledge) of the spontaneous formation of TRP\/INVs during DNA replication, which is likely to precede more complex sources of rearrangements associated with oncogenesis and other disease states in higher eukaryotes.<\/jats:p>\n                <\/jats:sec>","DOI":"10.1101\/2025.01.14.632981","type":"posted-content","created":{"date-parts":[[2025,1,19]],"date-time":"2025-01-19T10:35:13Z","timestamp":1737282913000},"source":"Crossref","is-referenced-by-count":0,"title":["Clustering of Inverted Triplications in Centromeric and Subtelomeric Chromosomal Regions of\n                  <i>Aspergillus flavus<\/i>"],"prefix":"10.64898","author":[{"given":"Jeffrey W.","family":"Cary","sequence":"first","affiliation":[{"name":"Food and Feed Safety Research Unit USDA\/ARS, Southern Regional Research Center New Orleans, LA 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