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

Touchon, Marie and Hoede, Claire and Tenaillon, Olivier and Barbe, Valérie and Baeriswyl, Simon and Bidet, Philippe and Bingen, Edouard and Bonacorsi, Stéphane and Bouchier, Christiane and Bouvet, Odile and Calteau, Alexandra and Chiapello, Hélène and Clermont, Olivier and Cruveiller, Stéphane and Danchin, Antoine and Diard, Médéric and Dossat, Carole and Karoui, Meriem El and Frapy, Eric and Garry, Louis and Ghigo, Jean Marc and Gilles, Anne Marie and Johnson, James and Le Bouguénec, Chantal and Lescat, Mathilde and Mangenot, Sophie and Martinez-Jéhanne, Vanessa and Matic, Ivan and Nassif, Xavier and Oztas, Sophie and Petit, Marie Agnès and Pichon, Christophe and Rouy, Zoé and Ruf, Claude Saint and Schneider, Dominique and Tourret, Jérôme and Vacherie, Benoit and Vallenet, David and Médigue, Claudine and Rocha, Eduardo P. C. and Denamur, Erick. (2009) Organised genome dynamics in the Escherichia coli species results in highly diverse adaptive paths. PLoS Genetics, 5 (1). e1000344.

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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.
Faculties and Departments:05 Faculty of Science > Departement Biozentrum > Infection Biology > Pathogen Evolution (Diard)
UniBasel Contributors:Diard, Médéric
Item Type:Article, refereed
Article Subtype:Research Article
Publisher:Public Library of Science
Note:Publication type according to Uni Basel Research Database: Journal article
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Last Modified:02 Dec 2020 09:08
Deposited On:02 Dec 2020 09:08

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