Discovery of Horizontal Gene Transfer Events From Highly Accurate Long-Read Sequence Data

Horizontal gene transfer (HGT) plays an important role in the adaptive evolution of both prokaryotic and eukaryotic organisms. Here, we present FRAILEG (Fragmented Read Alignment for Identifying Laterally Exchanged Genes), a novel method for identifying HGT events through analysis of accurate long-read sequence data. FRAILEG builds on the general purpose long-read alignment program, minimap2, by fragmenting and realigning sequences that failed to map to a reference genome in their entirety. This method isolates foreign regions and differentiates between host and donor genetic material based on genomic differences. We validated the performance of our method with authentic sequence data of a mock microbial community and identified multiple potential HGT events. Accurate HGT detection and identification has significant implications for our understanding of evolutionary history, the development of many human-related diseases, and the spread of antibiotic resistance.