Authors
Idan Yelin, Roy Kishony
Published in
Nature microbiology. Jul 06, 2026. Epub Jul 06, 2026.
Abstract
Gene amplification, a common route to bacterial adaptation, often occurs through recombination between two copies of an insertion sequence (IS) element flanking a genomic region. Alternative non-canonical structures have also been proposed, in which a duplication is formed by a single IS element whose two ends join two distant chromosomal loci. However, the prevalence of such non-canonical structures and their role in bacterial adaptive evolution remain unclear. Here we developed AmpliFinder, a computational tool that uses short-read sequencing data to systematically identify pairs of IS-chromosome junctions that correspond to the two ends of the same IS element yet map to distant genomic loci flanking amplified regions. Applying AmpliFinder to 10,347 laboratory-evolved Escherichia coli and Acinetobacter baumannii isolates, we identified 113 distinct de novo IS-associated amplifications and found that non-canonical amplifications are the most abundant mode of amplification. We validated the inferred architectures using ultra-long-read sequencing and propose a model for non-canonical amplification formation supported by the observation of nested intermediate structures. Quantifying enrichment for antibiotic-resistance genes in amplicons, we find that non-canonical amplifications more effectively and narrowly amplify genes under selection. These results highlight the role of non-canonical IS-based amplifications in the adaptive evolution of bacteria.
PMID:
42410210
Bibliographic data and abstract were imported from PubMed on 07 Jul 2026.
Read full publication at:
Please sign in
to see all details.
Advertisement
Stats
- Recommendations n/a n/a positive of 0 vote(s)
- Views 6
- Comments 0