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Pubmed ID :19165319
Publication Date : //

Organised genome dynamics in the Escherichia coli species results in highly diverse adaptive paths.


The Escherichia coli species represents one of the best-studied model organisms, but also encompasses a variety of commensal and pathogenic strains that diversify by high rates of genetic change. We uniformly (re-) annotated the genomes of 20 commensal and pathogenic E. coli strains and one strain of E. fergusonii (the closest E. coli related species), including seven that we sequenced to completion. Within the approximately 18,000 families of orthologous genes, we found approximately 2,000 common to all strains. Although recombination rates are much higher than mutation rates, we show, both theoretically and using phylogenetic inference, that this does not obscure the phylogenetic signal, which places the B2 phylogenetic group and one group D strain at the basal position. Based on this phylogeny, we inferred past evolutionary events of gain and loss of genes, identifying functional classes under opposite selection pressures. We found an important adaptive role for metabolism diversification within group B2 and Shigella strains, but identified few or no extraintestinal virulence-specific genes, which could render difficult the development of a vaccine against extraintestinal infections. Genome flux in E. coli is confined to a small number of conserved positions in the chromosome, which most often are not associated with integrases or tRNA genes. Core genes flanking some of these regions show higher rates of recombination, suggesting that a gene, once acquired by a strain, spreads within the species by homologous recombination at the flanking genes. Finally, the genome's long-scale structure of recombination indicates lower recombination rates, but not higher mutation rates, at the terminus of replication. The ensuing effect of background selection and biased gene conversion may thus explain why this region is A+T-rich and shows high sequence divergence but low sequence polymorphism. Overall, despite a very high gene flow, genes co-exist in an organised genome.

Authors : Touchon Marie , Hoede Claire , Tenaillon Olivier , Barbe Valérie , Baeriswyl Simon , Bidet Philippe , Bingen Edouard , Bonacorsi Stéphane , Bouchier Christiane , Bouvet Odile , Calteau Alexandra , Chiapello Hélène , Clermont Olivier , Cruveiller Stéphane , Danchin Antoine , Diard Médéric , Dossat Carole , Karoui Meriem El , Frapy Eric , Garry Louis , Ghigo Jean Marc , Gilles Anne Marie , Johnson James , Le Bouguénec Chantal , Lescat Mathilde , Mangenot Sophie , Martinez-Jéhanne Vanessa , Matic Ivan , Nassif Xavier , Oztas Sophie , Petit Marie Agnès , Pichon Christophe , Rouy Zoé , Ruf Claude Saint , Schneider Dominique , Tourret Jérôme , Vacherie Benoit , Vallenet David , Médigue Claudine , Rocha Eduardo P C , Denamur Erick ,

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