Advertisement
Research Article

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

  • Marie Touchon equal contributor,

    equal contributor Contributed equally to this work with: Marie Touchon, Claire Hoede, Olivier Tenaillon

    Affiliations: Atelier de BioInformatique, Université Pierre et Marie Curie - Paris 6 (UPMC), Paris, France, Microbial Evolutionary Genomics, Institut Pasteur, CNRS URA2171, Paris, France

    X
  • Claire Hoede equal contributor,

    equal contributor Contributed equally to this work with: Marie Touchon, Claire Hoede, Olivier Tenaillon

    Affiliation: Faculté de Médecine, Université Paris 7 Denis Diderot, INSERM U722, Site Xavier Bichat, Paris, France

    X
  • Olivier Tenaillon equal contributor,

    equal contributor Contributed equally to this work with: Marie Touchon, Claire Hoede, Olivier Tenaillon

    Affiliation: Faculté de Médecine, Université Paris 7 Denis Diderot, INSERM U722, Site Xavier Bichat, Paris, France

    X
  • Valérie Barbe,

    Affiliation: Génoscope, Institut de Génomique, CEA, Evry, France

    X
  • Simon Baeriswyl,

    Affiliation: Faculté de Médecine, Université Paris 5 René Descartes, INSERM U571, Paris, France

    X
  • Philippe Bidet,

    Affiliation: Université Paris 7 Denis Diderot, Hôpital Robert Debré (APHP), EA 3105, Paris, France

    X
  • Edouard Bingen,

    Affiliation: Université Paris 7 Denis Diderot, Hôpital Robert Debré (APHP), EA 3105, Paris, France

    X
  • Stéphane Bonacorsi,

    Affiliation: Université Paris 7 Denis Diderot, Hôpital Robert Debré (APHP), EA 3105, Paris, France

    X
  • Christiane Bouchier,

    Affiliation: Plate-Forme Génomique, Institut Pasteur, Paris, France

    X
  • Odile Bouvet,

    Affiliation: Faculté de Médecine, Université Paris 7 Denis Diderot, INSERM U722, Site Xavier Bichat, Paris, France

    X
  • Alexandra Calteau,

    Affiliation: Laboratoire de Génomique Comparative, CNRS UMR8030, Institut de Génomique, CEA, Génoscope, Evry, France

    X
  • Hélène Chiapello,

    Affiliation: UR1077 Mathématique, Informatique, et Génome, INRA, Jouy en Josas, France

    X
  • Olivier Clermont,

    Affiliation: Faculté de Médecine, Université Paris 7 Denis Diderot, INSERM U722, Site Xavier Bichat, Paris, France

    X
  • Stéphane Cruveiller,

    Affiliation: Laboratoire de Génomique Comparative, CNRS UMR8030, Institut de Génomique, CEA, Génoscope, Evry, France

    X
  • Antoine Danchin,

    Affiliation: Unité de Génétique des Génomes Bactériens, Institut Pasteur, CNRS URA2171, Paris, France

    X
  • Médéric Diard,

    Affiliation: Faculté de Médecine, Université Paris 5 René Descartes, INSERM U571, Paris, France

    X
  • Carole Dossat,

    Affiliation: Génoscope, Institut de Génomique, CEA, Evry, France

    X
  • Meriem El Karoui,

    Affiliation: UR888 Unité des Bactéries Lactiques et Pathogènes Opportunistes, INRA, Jouy en Josas, France

    X
  • Eric Frapy,

    Affiliation: Faculté de Médecine, Université Paris 5 René Descartes, INSERM U570, Paris, France

    X
  • Louis Garry,

    Affiliation: Faculté de Médecine, Université Paris 7 Denis Diderot, INSERM U722, Site Xavier Bichat, Paris, France

    X
  • Jean Marc Ghigo,

    Affiliation: Unité de Génétique des Biofilms, Institut Pasteur, CNRS URA2172, Paris, France

    X
  • Anne Marie Gilles,

    Affiliation: Unité de Génétique des Génomes Bactériens, Institut Pasteur, CNRS URA2171, Paris, France

    X
  • James Johnson,

    Affiliations: Veterans Affairs Medical Center, Minneapolis, Minnesota, United States of America, Department of Medicine, University of Minnesota, Minneapolis, Minnesota, United States of America

    X
  • Chantal Le Bouguénec,

    Affiliation: Pathogénie Bactérienne des Muqueuses, Institut Pasteur, Paris, France

    X
  • Mathilde Lescat,

    Affiliation: Faculté de Médecine, Université Paris 7 Denis Diderot, INSERM U722, Site Xavier Bichat, Paris, France

    X
  • Sophie Mangenot,

    Affiliation: Génoscope, Institut de Génomique, CEA, Evry, France

    X
  • Vanessa Martinez-Jéhanne,

    Affiliation: Pathogénie Bactérienne des Muqueuses, Institut Pasteur, Paris, France

    X
  • Ivan Matic,

    Affiliation: Faculté de Médecine, Université Paris 5 René Descartes, INSERM U571, Paris, France

    X
  • Xavier Nassif,

    Affiliation: Faculté de Médecine, Université Paris 5 René Descartes, INSERM U570, Paris, France

    X
  • Sophie Oztas,

    Affiliation: Génoscope, Institut de Génomique, CEA, Evry, France

    X
  • Marie Agnès Petit,

    Affiliation: UR888 Unité des Bactéries Lactiques et Pathogènes Opportunistes, INRA, Jouy en Josas, France

    X
  • Christophe Pichon,

    Affiliation: Pathogénie Bactérienne des Muqueuses, Institut Pasteur, Paris, France

    X
  • Zoé Rouy,

    Affiliation: Laboratoire de Génomique Comparative, CNRS UMR8030, Institut de Génomique, CEA, Génoscope, Evry, France

    X
  • Claude Saint Ruf,

    Affiliation: Faculté de Médecine, Université Paris 5 René Descartes, INSERM U571, Paris, France

    X
  • Dominique Schneider,

    Affiliation: Université Grenoble 1 Joseph Fourier, CNRS UMR 5163, Grenoble, France

    X
  • Jérôme Tourret,

    Affiliation: Faculté de Médecine, Université Paris 7 Denis Diderot, INSERM U722, Site Xavier Bichat, Paris, France

    X
  • Benoit Vacherie,

    Affiliation: Génoscope, Institut de Génomique, CEA, Evry, France

    X
  • David Vallenet,

    Affiliation: Laboratoire de Génomique Comparative, CNRS UMR8030, Institut de Génomique, CEA, Génoscope, Evry, France

    X
  • Claudine Médigue mail,

    cmedigue@genoscope.cns.fr (CM); erocha@pasteur.fr (EPCR); erick.denamur@inserm.fr (ED)

    Affiliation: Laboratoire de Génomique Comparative, CNRS UMR8030, Institut de Génomique, CEA, Génoscope, Evry, France

    X
  • Eduardo P. C. Rocha mail,

    cmedigue@genoscope.cns.fr (CM); erocha@pasteur.fr (EPCR); erick.denamur@inserm.fr (ED)

    Affiliations: Atelier de BioInformatique, Université Pierre et Marie Curie - Paris 6 (UPMC), Paris, France, Microbial Evolutionary Genomics, Institut Pasteur, CNRS URA2171, Paris, France

    X
  • Erick Denamur mail

    cmedigue@genoscope.cns.fr (CM); erocha@pasteur.fr (EPCR); erick.denamur@inserm.fr (ED)

    Affiliation: Faculté de Médecine, Université Paris 7 Denis Diderot, INSERM U722, Site Xavier Bichat, Paris, France

    X
  • Published: January 23, 2009
  • DOI: 10.1371/journal.pgen.1000344

Reader Comments (1)

Post a new comment on this article

Publisher's Note: Correction to Text

Posted by PLoS_Genetics on 27 Jan 2009 at 09:45 GMT

Our observations suggest that the intensity of diversifying selection acting on the rfb and leuX-fimH loci are under very strong selective pressure compared with the diversifying selection acting on the core LPS, the flagella or some of the porins. The fact that most hotspots of integration (117 among 133) do not result in hotspots of phylogenetic incongruence suggests that they carry neutral or deleterious genes. Conversely, it also suggests that some horizontally acquired genes can be highly beneficial (e.g., 11 hotspots of phylogenetic incongruence around the rfb or leuX-fimH locus) or moderately beneficial (e.g., 4 hotspots of integration associated with hotspots of phylogenetic incongruence) and that this results in different selection footprints in the neighbouring core genome.
http://plosgenetics.org/article/info:doi/10.1371/journal.pgen.1000344#article1.body1.sec2.sec9.p4

There were errors in the final three sentences of the last paragraph of the section 'Hotspots of Phylogenetic Incongruence'. The correct text can be found here: http://www.plosgenetics.org/corrections/pgen.1000344.cn.pdf