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author 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
author_facet 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
author_sort Touchon, Marie
collection PubMed
description 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 ∼18,000 families of orthologous genes, we found ∼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.
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spelling pubmed-26177822009-01-23 Organised Genome Dynamics in the Escherichia coli Species Results in Highly Diverse Adaptive Paths 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 PLoS Genet Research Article 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 ∼18,000 families of orthologous genes, we found ∼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. Public Library of Science 2009-01-23 /pmc/articles/PMC2617782/ /pubmed/19165319 http://dx.doi.org/10.1371/journal.pgen.1000344 Text en Touchon et al. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.
spellingShingle Research Article
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
Organised Genome Dynamics in the Escherichia coli Species Results in Highly Diverse Adaptive Paths
title Organised Genome Dynamics in the Escherichia coli Species Results in Highly Diverse Adaptive Paths
title_full Organised Genome Dynamics in the Escherichia coli Species Results in Highly Diverse Adaptive Paths
title_fullStr Organised Genome Dynamics in the Escherichia coli Species Results in Highly Diverse Adaptive Paths
title_full_unstemmed Organised Genome Dynamics in the Escherichia coli Species Results in Highly Diverse Adaptive Paths
title_short Organised Genome Dynamics in the Escherichia coli Species Results in Highly Diverse Adaptive Paths
title_sort organised genome dynamics in the escherichia coli species results in highly diverse adaptive paths
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2617782/
https://www.ncbi.nlm.nih.gov/pubmed/19165319
http://dx.doi.org/10.1371/journal.pgen.1000344
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