Large Chromosomal Rearrangements during a Long-Term Evolution Experiment with Escherichia coli

ABSTRACT 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 popula-tions have been propagated in a glucose-limited environment for over 25 years. We used whole-genomemapping (optical map-ping) 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 in-versions, and 9 duplications, with lineages having between 5 and 20 events. In three populations, successive rearrangements im-pacted particular regions. In five populations, rearrangements affected over a third of the chromosome. Most rearrangement