From: Charles Plessy Date: Tue, 27 May 2025 05:17:55 +0000 (+0900) Subject: 咖啡 X-Git-Url: https://source.charles.plessy.org/?a=commitdiff_plain;h=95985fe88a5e5a3eff1ef982f444a51cebb8f7c6;p=source--%2F.git 咖啡 --- diff --git a/biblio/40347137.mdwn b/biblio/40347137.mdwn new file mode 100644 index 00000000..53f42962 --- /dev/null +++ b/biblio/40347137.mdwn @@ -0,0 +1,10 @@ +[[!meta title="Laboratory evolution of the bacterial genome structure through insertion sequence activation."]] +[[!tag variants]] + +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. + +[[!pmid 40347137 desc="“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”"]] diff --git a/tags/variants.mdwn b/tags/variants.mdwn index db4d006f..001511c6 100644 --- a/tags/variants.mdwn +++ b/tags/variants.mdwn @@ -23,6 +23,10 @@ vicinity. [[Donelly and coll., 2010|biblio/20116045]] gave a radically lower time estimate of 13,600 to 108,400 years, but an ancient origin was again supported by [[Steinberg and coll in 2012|biblio/22751100]]. +[[Kanai and coll., 2025|biblio/40347137]] engeneered _E. coli_ strains for high +transposon activity accumulated hundreds of rearrangements in 10 weeks, +including 54 inversions (range: 2.2 kbp–1.7 Mbp). + ### Between-species ~1100 small-scale inversions are estimated to have happened between _S.