title: Organised genome dynamics in the Escherichia coli species results in highly diverse adaptive paths.
abstract: 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.affiliation: Atelier de BioInformatique, Université Pierre et Marie Curie--Paris 6, Paris, France.
authors.forename: Marie
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authors.lastname: Touchon
authors.forename: Claire
authors.initials: C
authors.lastname: Hoede
authors.forename: Olivier
authors.initials: O
authors.lastname: Tenaillon
authors.forename: Valérie
authors.initials: V
authors.lastname: Barbe
authors.forename: Simon
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authors.lastname: Baeriswyl
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authors.lastname: Bidet
authors.forename: Edouard
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authors.lastname: Bingen
authors.forename: Stéphane
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authors.forename: Alexandra
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authors.lastname: Calteau
authors.forename: Hélène
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authors.lastname: Chiapello
authors.forename: Olivier
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authors.lastname: Clermont
authors.forename: Stéphane
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authors.lastname: Cruveiller
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authors.lastname: Danchin
authors.forename: Médéric
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authors.lastname: Diard
authors.forename: Carole
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authors.lastname: Dossat
authors.forename: Meriem El
authors.initials: ME
authors.lastname: Karoui
authors.forename: Eric
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authors.lastname: Frapy
authors.forename: Louis
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authors.lastname: Garry
authors.forename: Jean Marc
authors.initials: JM
authors.lastname: Ghigo
authors.forename: Anne Marie
authors.initials: AM
authors.lastname: Gilles
authors.forename: James
authors.initials: J
authors.lastname: Johnson
authors.forename: Chantal
authors.initials: C
authors.lastname: Le Bouguénec
authors.forename: Mathilde
authors.initials: M
authors.lastname: Lescat
authors.forename: Sophie
authors.initials: S
authors.lastname: Mangenot
authors.forename: Vanessa
authors.initials: V
authors.lastname: Martinez-Jéhanne
authors.forename: Ivan
authors.initials: I
authors.lastname: Matic
authors.forename: Xavier
authors.initials: X
authors.lastname: Nassif
authors.forename: Sophie
authors.initials: S
authors.lastname: Oztas
authors.forename: Marie Agnès
authors.initials: MA
authors.lastname: Petit
authors.forename: Christophe
authors.initials: C
authors.lastname: Pichon
authors.forename: Zoé
authors.initials: Z
authors.lastname: Rouy
authors.forename: Claude Saint
authors.initials: CS
authors.lastname: Ruf
authors.forename: Dominique
authors.initials: D
authors.lastname: Schneider
authors.forename: Jérôme
authors.initials: J
authors.lastname: Tourret
authors.forename: Benoit
authors.initials: B
authors.lastname: Vacherie
authors.forename: David
authors.initials: D
authors.lastname: Vallenet
authors.forename: Claudine
authors.initials: C
authors.lastname: Médigue
authors.forename: Eduardo P C
authors.initials: EP
authors.lastname: Rocha
authors.forename: Erick
authors.initials: E
authors.lastname: Denamur
mesh_terms: D004251:DNA Transposable Elements; D004926:Escherichia coli / Q000235:genetics*; D019143:Evolution, Molecular; D005823:Genetics; D016678:Genome; D016680:Genome, Bacterial; D023281:Genomics; D016013:Likelihood Functions; D008954:Models, Biological; D008957:Models, Genetic; D010802:Phylogeny; D011110:Polymorphism, Genetic; D011995:Recombination, Genetic
chemical_list: D004251:DNA Transposable Elements