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Core Genes Evolve Rapidly in the Long-term Evolution Experiment with Escherichia coli

View ORCID ProfileRohan Maddamsetti, Philip J. Hatcher, Barry L. Williams, View ORCID ProfileRichard E. Lenski
doi: https://doi.org/10.1101/042069
Rohan Maddamsetti
1Ecology, Evolutionary Biology, and Behavior Program, Michigan State University, East Lansing, MI 48824, USA.
2BEACON Center for the Study of Evolution in Action, Michigan State University, East Lansing, MI, 48824, USA.
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  • For correspondence: maddamse@msu.edu
Philip J. Hatcher
3Department of Computer Science, University of New Hampshire, Durham, NH 03824, USA
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Barry L. Williams
1Ecology, Evolutionary Biology, and Behavior Program, Michigan State University, East Lansing, MI 48824, USA.
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Richard E. Lenski
1Ecology, Evolutionary Biology, and Behavior Program, Michigan State University, East Lansing, MI 48824, USA.
2BEACON Center for the Study of Evolution in Action, Michigan State University, East Lansing, MI, 48824, USA.
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Abstract

Conserved genes evolve slowly in nature, by definition, but we find that some conserved genes are among the fastest-evolving genes in the long-term evolution experiment with Escherichia coli (LTEE). We identified the set of almost 2000 core genes shared among sixty clinical, environmental, and laboratory strains of E. coli. During the LTEE, these core genes accumulated significantly more nonsynonymous mutations than did flexible (i.e., noncore) genes after accounting for the mutational target size. Furthermore, the core genes under strongest positive selection in the LTEE are more conserved in nature than the average core gene based both on sequence diversity among E. coli strains and divergence between E. coli and Salmonella enterica. We conclude that the conditions of the LTEE are novel for E. coli, at least in relation to the long sweep of its evolution in nature. We suggest that what is most novel about the LTEE for the bacteria is the constancy of the environment, its biophysical simplicity, and the absence of microbial competitors, predators, and parasites.

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Posted March 01, 2016.
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Core Genes Evolve Rapidly in the Long-term Evolution Experiment with Escherichia coli
Rohan Maddamsetti, Philip J. Hatcher, Barry L. Williams, Richard E. Lenski
bioRxiv 042069; doi: https://doi.org/10.1101/042069
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Core Genes Evolve Rapidly in the Long-term Evolution Experiment with Escherichia coli
Rohan Maddamsetti, Philip J. Hatcher, Barry L. Williams, Richard E. Lenski
bioRxiv 042069; doi: https://doi.org/10.1101/042069

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