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Article
Nature Genetics - 38, 1406 - 1412 (2006)
Published online: 5 November 2006; | doi:10.1038/ng1906

Comparative genome sequencing of Escherichia coli allows observation of bacterial evolution on a laboratory timescale

Christopher D Herring1, 6, 7, Anu Raghunathan1, 6, 7, Christiane Honisch2, 7, Trina Patel1, M Kenyon Applebee3, Andrew R Joyce2, Thomas J Albert4, Frederick R Blattner5, Dirk van den Boom2, Charles R Cantor2 & Bernhard Ø Palsson1

1  Department of Bioengineering, University of California, San Diego, California 92093, USA.

2  Bioinformatics Program, University of California, San Diego, California 92093, USA.

3  Department of Chemistry and Biochemistry, University of California, San Diego, California 92093, USA.

4  Nimblegen Systems, Inc., Madison, Wisconsin 53711, USA.

5  Laboratory of Genetics, University of Wisconsin, Madison, Wisconsin 53706, USA.

6  Current addresses: Mascoma Corporation, Lebanon, New Hampshire 03766, USA (C.D.H.); Division of Infectious Diseases, Mt. Sinai School of Medicine, New York, New York, 10029, USA (A.R.).

7  These authors contributed equally to this work.

Correspondence should be addressed to bpalsson@bioeng.ucsd.edu

We applied whole-genome resequencing of Escherichia coli to monitor the acquisition and fixation of mutations that conveyed a selective growth advantage during adaptation to a glycerol-based growth medium. We identified 13 different de novo mutations in five different E. coli strains and monitored their fixation over a 44-d period of adaptation. We obtained proof that the observed spontaneous mutations were responsible for improved fitness by creating single, double and triple site-directed mutants that had growth rates matching those of the evolved strains. The success of this new genome-scale approach indicates that real-time evolution studies will now be practical in a wide variety of contexts.

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Nature Genetics
ISSN: 1061-4036
EISSN: 1546-1718
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