Kanai Y, Shibai A, Yokoi N, Tsuru S, Furusawa C.

Nucleic Acids Res. 2025 May 10;53(9):gkaf331. doi:10.1093/nar/gkaf331

Laboratory evolution of the bacterial genome structure through insertion sequence activation.

“we developed an E. coli strain with high IS activity and demonstrated rapid IS-mediated genome evolution under relaxed selection in the laboratory, simulating the natural evolution of symbionts and pathogens. In just ten weeks, we observed numerous IS insertions, IS-mediated duplications, and deletions, contributing to at most −4.4% to 9.2% genome size changes (Fig. 4).” “We detected a total of 457 large-scale rearrangements, including 54 inversions, 363 deletions, and 40 duplications. [...] The median size of inversions was 84 kbp (range: 2.2 kbp–1.7 Mbp). All three inversions exceeding 1 Mbp were nearly symmetric to the ori-ter axis, consistent with observations of large inversions in nature. [...] Deletions ranged from 102 bp to 163 kbp (Fig. 3C), with the largest deletion being a deletion of a duplicated region. [...] Duplications had a median size of 40 kbp (range: 4830 bp–372 kbp). Surprisingly, the majority of the duplications resulted from transpositions of composite transposons with a copy of IS at each end (25/40), rather than tandem duplications. [...] The rearrangements led to genome size changes ranging from 174 kbp reduction to 369 kbp increase or −4.4% to 9.2%. However, overall, deletions were offset by the genome size increase from duplications and IS insertions, resulting in negligible changes in the median genome sizes”