10.5061/DRYAD.283PP
Raeside, Colin
Grenoble Alpes University
Gaffé, Joël
Grenoble Alpes University
Deatherage, Daniel E.
The University of Texas at Austin
Tenaillon, Olivier
Inserm
Briska, Adam M.
OpGen (United States)
Ptashkin, Ryan N.
OpGen (United States)
Cruveiller, Stéphane
Genoscope
Médigue, Claudine
Genoscope
Lenski, Richard E.
Michigan State University
Barrick, Jeffrey E.
The University of Texas at Austin
Schneider, Dominique
Grenoble Alpes University
Data from: Large chromosomal rearrangements during a long-term evolution
experiment with Escherichia coli
Dryad
dataset
2015
DNA rearrangements
IS elements
2015-08-13T00:00:00Z
2015-08-13T00:00:00Z
en
https://doi.org/10.1128/mBio.01377-14
814 bytes
1
CC0 1.0 Universal (CC0 1.0) Public Domain Dedication
Large-scale rearrangements may be important in evolution because they can
alter chromosome organization and gene expression in ways not possible
through point mutations. In a long-term evolution experiment, twelve
Escherichia coli populations have been propagated in a glucose-limited
environment for over 25 years. We used whole-genome mapping (optical
mapping) combined with genome sequencing and PCR analysis to identify the
large-scale chromosomal rearrangements in clones from each population
after 40,000 generations. A total of 110 rearrangement events were
detected, including 82 deletions, 19 inversions, and 9 duplications, with
lineages having between 5 and 20 events. In three populations, successive
rearrangements impacted particular regions. In five populations,
rearrangements affected over a third of the chromosome. Most
rearrangements involved recombination between insertion sequence (IS)
elements, illustrating their importance in mediating genome plasticity.
Two lines of evidence suggest that at least some of these rearrangements
conferred higher fitness. First, parallel changes were observed across the
independent populations, with ~65% of the rearrangements affecting the
same loci in at least two populations. For example, the ribose-utilization
operon and the manB-cpsG region were deleted in 12 and 10 populations,
respectively, suggesting positive selection, and this inference was
previously confirmed for the former case. Second, optical maps from clones
sampled over time from one population showed that most rearrangements
occurred early in the experiment, when fitness was increasing most
rapidly. However, some rearrangements likely occur at high frequency and
may have simply hitchhiked to fixation. In any case, large-scale
rearrangements clearly influenced genomic evolution in these populations.
scriptA Python script to construct FASTA files containing reconstructed
genome sequences of evolved clones after DNA rearrangements.