Quantifying evolutionary dynamics of E. coli strains
Sergei Maslov, Brookhaven Nat. Lab., USA.
Building on our previous work (F William Studier, Patrick Daegelen, Richard E Lenski, Sergei Maslov, and Jihyun F Kim (2009) J Mol Biol 394:653) we developed reliable methods for deriving the basic genome - the consensus genomic sequence of a bacterial species - and tested it on a compendium of 32 independently isolated E. coli strains. Basic genomes will have broad utility for analyzing and annotating rapidly expanding collection of known genomes of bacterial strains. When a new strain is sequenced one can rapidly infer its strain-specific insertions, deletions and inversions simply by aligning the newly assembled genome against the basic genome of the entire species or more narrowly defined phylogenetic clades (such as e.g. A, B1, and B2 groups of E. coli).
We also analyzed the distribution of Single-Nucleotide Polymorphisms (SNP) along the basic genome. For closely related pairs of strains we found a patchwork of long (10s to 100s kb) horizontally transferred genomic segments interspersed among clonally inherited ones results. Our analysis shows that as a pair of strains evolutionary diverges, clonally inherited segments are rapidly lost so that almost none of them are left when average DNA divergence exceeds ~1.25%. For example, only 35 of the 496 possible pairs of the 32 strains used in our study appear to share a significant fraction of clonally inherited genomic sequences. Furthermore, horizontally transferred regions contribute about ten-fold more genomic diversity than de novo mutations in clonal regions. This puts to rest the notion of nearly asexual nature of bacterial evolution. A simple neutral evolutionary model that simulates evolution of a bacterial population by mutations and random horizontal exchange of genomic segments generates SNP distributions very similar to those we observe between pairs of basic genomes.
The combination of our results and previous knowledge suggest that E. coli, and likely many other bacterial species, are shaped by co-evolving populations of bacteria and phages responsible for horizontal transfer of genomic segments between strains. Bacterial species are thus defined by phage-bacterial infection networks, various defense mechanisms such as RM or CRISPR, and last but not least by the detailed biophysical mechanisms of homologous recombination.