Whole-genome sequencing analysis of Microhomology-Mediated Tandem Duplications across microbial species

Microhomology-mediated tandem duplications (MTDs) are a specific class of genomic structural variations that involve the duplication of single-copy DNA segments flanked by microhomologous sequences. While initially identified in Schizosaccharomyces pombe, their presence and evolutionary significance across other organisms remain underexplored. In this study, we performed whole-genome deep sequencing (WGS) on a diverse collection of microbial species, encompassing prokaryotic, eukaryotic, archaeal, and viral genomes, to systematically identify and characterize MTDs. We further analyzed reference genomes from 2,245 species, along with large-scale population genomic datasets from 103 microbial species, to investigate the prevalence and evolutionary dynamics of MTDs. Additionally, we sequenced Saccharomyces cerevisiae mutants with deletions in key replication-associated genes, particularly rad27?, which resulted in a significant increase in MTD formation. Our results link MTD formation to Rad27-mediated Okazaki fragment processing, a conserved mechanism in DNA replication. The dataset includes several hundred gigabases of sequencing data from microbial species, as well as whole-genome sequencing data from mutagenized S. cerevisiae strains. These datasets provide a valuable resource for studying the role of MTDs in genome evolution, mutation dynamics, and their functional implications in microbial adaptation and human disease-associated genetic variations.