title: 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 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.
  
  
  OBJECTIVE
  Bacterial chromosomes are dynamic structures shaped by long histories of evolution. Among genomic changes, large-scale DNA rearrangements can have important effects on the presence, order, and expression of genes. Whole-genome sequencing that relies on short DNA reads cannot identify all large-scale rearrangements. Therefore, deciphering changes in the overall organization of genomes requires alternative methods, such as optical mapping. We analyzed the longest-running microbial evolution experiment (more than 25 years of evolution in the laboratory) by optical mapping, genome sequencing, and PCR analyses. We found multiple large genome rearrangements in all 12 independently evolving populations. In most cases, it is unclear whether these changes were beneficial themselves or, alternatively, hitchhiked to fixation with other beneficial mutations. In any case, many genome rearrangements accumulated over decades of evolution, providing these populations with genetic plasticity reminiscent of that observed in some pathogenic bacteria.
authors.forename: Colin
authors.initials: C
authors.lastname: Raeside
authors.forename: Joël
authors.initials: J
authors.lastname: Gaffé
authors.affiliation: Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, Texas, USA.
authors.forename: Daniel E
authors.initials: DE
authors.lastname: Deatherage
authors.forename: Olivier
authors.initials: O
authors.lastname: Tenaillon
authors.affiliation: OpGen, Inc., Gaithersburg, Maryland, USA.
authors.forename: Adam M
authors.initials: AM
authors.lastname: Briska
authors.affiliation: OpGen, Inc., Gaithersburg, Maryland, USA.
authors.forename: Ryan N
authors.initials: RN
authors.lastname: Ptashkin
authors.forename: Stéphane
authors.initials: S
authors.lastname: Cruveiller
authors.forename: Claudine
authors.initials: C
authors.lastname: Médigue
authors.forename: Richard E
authors.initials: RE
authors.lastname: Lenski
authors.forename: Jeffrey E
authors.initials: JE
authors.lastname: Barrick
authors.affiliation: dominique.schneider@ujf-grenoble.fr.
authors.forename: Dominique
authors.initials: D
authors.lastname: Schneider
mesh_terms: D007446:Chromosome Inversion; D002874:Chromosome Mapping; D002876:Chromosomes, Bacterial / Q000235:genetics*; D004251:DNA Transposable Elements; D004269:DNA, Bacterial / Q000235:genetics; D004926:Escherichia coli / Q000235:genetics; D019143:Evolution, Molecular; D017353:Gene Deletion; D015321:Gene Rearrangement; D016680:Genome, Bacterial; D023281:Genomics; D017422:Sequence Analysis, DNA
chemical_list: D004251:DNA Transposable Elements; D004269:DNA, Bacterial