Organised Genome Dynamics in the Escherichia coli Species Results in Highly Diverse Adaptive Paths Export

@article{citeulike:4001539, 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 \~{}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.}, author = {Touchon, Marie and Hoede, Claire and Tenaillon, Olivier and Barbe, Val\'{e}rie and Baeriswyl, Simon and Bidet, Philippe and Bingen, Edouard and Bonacorsi, St\'{e}phane and Bouchier, Christiane and Bouvet, Odile and Calteau, Alexandra and Chiapello, H\'{e}l\`{e}ne and Clermont, Olivier and Cruveiller, St\'{e}phane and Danchin, Antoine and Diard, M\'{e}d\'{e}ric and Dossat, Carole and Karoui, Meriem E. and Frapy, Eric and Garry, Louis and Ghigo, Jean M. and Gilles, Anne M. and Johnson, James and Le Bougu\'{e}nec, Chantal and Lescat, Mathilde and Mangenot, Sophie and Martinez-J\'{e}hanne, Vanessa and Matic, Ivan and Nassif, Xavier and Oztas, Sophie and Petit, Marie A. and Pichon, Christophe and Rouy, Zo\'{e} and Ruf, Claude S. and Schneider, Dominique and Tourret, J\'{e}r\^{o}me and Vacherie, Benoit and Vallenet, David and M\'{e}digue, Claudine and Rocha, Eduardo P. C. and Denamur, Erick}, citeulike-article-id = {4001539}, citeulike-linkout-0 = {http://dx.doi.org/10.1371/journal.pgen.1000344}, day = {23}, doi = {10.1371/journal.pgen.1000344}, journal = {PLoS Genet}, keywords = {chromosome, duplication, evolution, microbes, selection}, month = {January}, number = {1}, pages = {e1000344+}, posted-at = {2009-02-05 17:55:51}, priority = {2}, publisher = {Public Library of Science}, title = {Organised Genome Dynamics in the Escherichia coli Species Results in Highly Diverse Adaptive Paths}, url = {http://dx.doi.org/10.1371/journal.pgen.1000344}, volume = {5}, year = {2009} }

TY - JOUR ID - citeulike:4001539 L3 - citeulike-article-id:4001539 N2 - 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. IS - 1 JF - PLoS Genet TI - Organised Genome Dynamics in the Escherichia coli Species Results in Highly Diverse Adaptive Paths PB - Public Library of Science VL - 5 SP - e1000344 KW - chromosome KW - duplication KW - evolution KW - microbes KW - selection AU - Touchon, Marie AU - Hoede, Claire AU - Tenaillon, Olivier AU - Barbe, Valérie AU - Baeriswyl, Simon AU - Bidet, Philippe AU - Bingen, Edouard AU - Bonacorsi, Stéphane AU - Bouchier, Christiane AU - Bouvet, Odile AU - Calteau, Alexandra AU - Chiapello, Hélène AU - Clermont, Olivier AU - Cruveiller, Stéphane AU - Danchin, Antoine AU - Diard, Médéric AU - Dossat, Carole AU - Karoui, Meriem AU - Frapy, Eric AU - Garry, Louis AU - Ghigo, Jean AU - Gilles, Anne AU - Johnson, James AU - Le Bouguénec, Chantal AU - Lescat, Mathilde AU - Mangenot, Sophie AU - Martinez-Jéhanne, Vanessa AU - Matic, Ivan AU - Nassif, Xavier AU - Oztas, Sophie AU - Petit, Marie AU - Pichon, Christophe AU - Rouy, Zoé AU - Ruf, Claude AU - Schneider, Dominique AU - Tourret, Jérôme AU - Vacherie, Benoit AU - Vallenet, David AU - Médigue, Claudine AU - Rocha, Eduardo AU - Denamur, Erick PY - 2009/01/23/ UR - http://dx.doi.org/10.1371/journal.pgen.1000344 ER -