Impermanence of bacterial clones

Abstract

Bacteria reproduce asexually and pass on a single genome copied from the parent, a reproductive mode that assures the clonal descent of progeny; however, a truly clonal bacterial species is extremely rare. The signal of clonality can be interrupted by gene uptake and exchange, initiating homologous recombination that results in the unique sequence of one clone being incorporated into another. Because recombination occurs sporadically and on local scales, these events are often difficult to recognize, even when considering large samples of completely sequenced genomes. Moreover, several processes can produce the appearance of clonality in populations that undergo frequent recombination. The rates and consequences of recombination have been studied in Escherichia coli for over 40 y, and, during this time, there have been several shifting views of its clonal status, population structure, and rates of gene exchange. We reexamine the studies and retrace the evolution of the methods that have assessed the extent of DNA flux, largely focusing on its impact on the E. coli genome.

Keywords: E. coli; clonality; genome evolution; homologous exchange; recombination.

Fig. 1.

Recombinational landscape of E. coli. Genomic features and recombination parameters were calculated for the entire core genome of concatenated orthologs shared by 19 fully sequenced strains of E. coli. (A) Proportion of homoplasic sites, inferred by a distance metric that uses fixed branch lengths (see How to Best Assess the Impact of Recombination on E. coli Evolution) in nonoverlapping 10-kb windows spanning the core genome. (B) Proportion of homoplasic sites, inferred by a phylogenetic topology method (implemented in recHMM) (54), in nonoverlapping 10-kb windows spanning the core genome. (C) Proportion of the total variation (polymorphism) present in nonoverlapping 10-kb windows (gray) that is attributable to homoplasic sites (red). (D) Relative impact of recombination (π_r) and mutation (π_m) on the polymorphism in nonoverlapping 10-kb windows spanning the core genome based on the r/m (π_r/π_m) statistic. (Polymorphisms identified with the distance metric, as in A.) (E) Detecting recombination within core fragments (orthologous gene contigs) spanning the core genome with PHI (10,000 permutations; P < 0.001) (57). Because this method detects recombination on a gene-by-gene (not site-by-site) scale, results are presented for 50-kb sliding windows with 10-kb steps. (F) G+C contents in nonoverlapping 10-kb windows spanning the core genome.