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Why prokaryotes have pangenomes

Nature Microbiology volume 2, Article number: 17040 (2017) Cite this article

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The existence of large amounts of within-species genome content variability is puzzling. Population genetics tells us that fitness effects of new variants—either deleterious, neutral or advantageous—combined with the long-term effective population size of the species determines the likelihood of a new variant being removed, spreading to fixation or remaining polymorphic. Consequently, we expect that selection and drift will reduce genetic variation, which makes large amounts of gene content variation in some species so puzzling. Here, we amalgamate population genetic theory with models of horizontal gene transfer and assert that pangenomes most easily arise in organisms with large long-term effective population sizes, as a consequence of acquiring advantageous genes, and that the focal species has the ability to migrate to new niches. Therefore, we suggest that pangenomes are the result of adaptive, not neutral, evolution.

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Figure 1: Schematic representation of pangenomes as Venn diagrams.
Figure 2: Analysis of accessory gene functions in 228 E. coli ST131 genomes.

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Acknowledgements

We wish to thank J. Mallet for commenting on a draft of this manuscript. We would also like to thanks the anonymous reviewers. J.O.M. is funded by BBSRC grant no. BB/N018044/1 and the John Templeton Foundation.

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Authors and Affiliations

  1. Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, M13 9PL, UK

    James O. McInerney

  2. Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, B15 2TT, Birmingham, UK

    Alan McNally

  3. Computational and Molecular Evolutionary Biology Group, School of Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK

    Mary J. O'Connell

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  1. James O. McInerney
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  2. Alan McNally
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J.O.M., A.M. and M.J.O. collectively conceived and wrote this manuscript.

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Correspondence to James O. McInerney.

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McInerney, J., McNally, A. & O'Connell, M. Why prokaryotes have pangenomes. Nat Microbiol 2, 17040 (2017). https://doi.org/10.1038/nmicrobiol.2017.40

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