Mutation Rate Inferred From Synonymous Substitutions in a Long-Term Evolution Experiment With Escherichia coli

G3: Genes, Genomes, Genetics

Béatrice Chane-Woon-Ming⁴  Olivier Tenaillon³  Stéphane Cruveiller⁴  Richard E. Lenski¹  Sébastien Wielgoss⁵  Claudine Médigue⁴  Jeffrey E. Barrick²  Dominique Schneider⁵ 

[1] Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan 48824Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan 48824Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan 48824;Chemistry and Biochemistry, Institute for Cell and Molecular Biology, University of Texas at Austin, Austin, TX 78712Chemistry and Biochemistry, Institute for Cell and Molecular Biology, University of Texas at Austin, Austin, TX 78712Chemistry and Biochemistry, Institute for Cell and Molecular Biology, University of Texas at Austin, Austin, TX 78712;Institut National de la Santé et de la Recherche Médicale, Unité Mixte de Recherche (INSERM, UMR) S 722, 75018 Paris, FranceUniversité Paris Diderot, Sorbonne Paris Cité, UMR-S 722, Faculté de Médecine, Site Xavier Bichat, 75018 Paris, FranceInstitut National de la Santé et de la Recherche Médicale, Unité Mixte de Recherche (INSERM, UMR) S 722, 75018 Paris, FranceInstitut National de la Santé et de la Recherche Médicale, Unité Mixte de Recherche (INSERM, UMR) S 722, 75018 Paris, FranceUniversité Paris Diderot, Sorbonne Paris Cité, UMR-S 722, Faculté de Médecine, Site Xavier Bichat, 75018 Paris, FranceUniversité Paris Diderot, Sorbonne Paris Cité, UMR-S 722, Faculté de Médecine, Site Xavier Bichat, 75018 Paris, FranceInstitut National de la Santé et de la Recherche Médicale, Unité Mixte de Recherche (INSERM, UMR) S 722, 75018 Paris, FranceUniversité Paris Diderot, Sorbonne Paris Cité, UMR-S 722, Faculté de Médecine, Site Xavier Bichat, 75018 Paris, France;CNRS-UMR 8030 and Commissariat à l'Energie Atomique CEA/DSV/IG/Genoscope LABGeM, 91057 Evry Cedex, FranceCNRS-UMR 8030 and Commissariat à l'Energie Atomique CEA/DSV/IG/Genoscope LABGeM, 91057 Evry Cedex, FranceCNRS-UMR 8030 and Commissariat à l'Energie Atomique CEA/DSV/IG/Genoscope LABGeM, 91057 Evry Cedex, France;Laboratoire Adaptation et Pathogénie des Micro-Organismes (LAPM), Université Joseph Fourier Grenoble 1, 38042 Grenoble Cedex 9, FranceCentre National de la Recherche Scientifique, Unité Mixte de Recherche (CNRS UMR) 5163, 38042 Grenoble Cedex 9, FranceLaboratoire Adaptation et Pathogénie des Micro-Organismes (LAPM), Université Joseph Fourier Grenoble 1, 38042 Grenoble Cedex 9, FranceLaboratoire Adaptation et Pathogénie des Micro-Organismes (LAPM), Université Joseph Fourier Grenoble 1, 38042 Grenoble Cedex 9, FranceCentre National de la Recherche Scientifique, Unité Mixte de Recherche (CNRS UMR) 5163, 38042 Grenoble Cedex 9, FranceCentre National de la Recherche Scientifique, Unité Mixte de Recherche (CNRS UMR) 5163, 38042 Grenoble Cedex 9, FranceLaboratoire Adaptation et Pathogénie des Micro-Organismes (LAPM), Université Joseph Fourier Grenoble 1, 38042 Grenoble Cedex 9, FranceCentre National de la Recherche Scientifique, Unité Mixte de Recherche (CNRS UMR) 5163, 38042 Grenoble Cedex 9, France

关键词: genomic base-substitution rate;    experimental evolution;    molecular evolution;    mutation pressure;    next-generation sequencing;   

DOI  :  10.1534/g3.111.000406

学科分类：生物科学（综合）

来源: Genetics Society of America

【 摘 要 】

The quantification of spontaneous mutation rates is crucial for a mechanistic understanding of the evolutionary process. In bacteria, traditional estimates using experimental or comparative genetic methods are prone to statistical uncertainty and consequently estimates vary by over one order of magnitude. With the advent of next-generation sequencing, more accurate estimates are now possible. We sequenced 19 Escherichia coli genomes from a 40,000-generation evolution experiment and directly inferred the point-mutation rate based on the accumulation of synonymous substitutions. The resulting estimate was 8.9 × 10^−11 per base-pair per generation, and there was a significant bias toward increased AT-content. We also compared our results with published genome sequence datasets for other bacterial evolution experiments. Given the power of our approach, our estimate represents the most accurate measure of bacterial base-substitution rates available to date.

【 授权许可】

Unknown