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Direct estimate of the spontaneous mutation rate uncovers the effects of drift and recombination in the Chlamydomonas reinhardtii plastid genome

Rob W. Ness, Susanne A. Kraemer, Nick Colegrave, Peter D. Keightley
doi: https://doi.org/10.1101/031898
Rob W. Ness
1Institute of Evolutionary Biology, University of Edinburgh Ashworth Laboratories, King’s Buildings, Charlotte Auerbach Road Edinburgh EH9 3FL, UK
2Department of Biology, University of Toronto Mississauga, William G. Davis Building, Mississauga, ON L5L 1C6, Cananda
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  • For correspondence: rob.ness@utoronto.ca
Susanne A. Kraemer
1Institute of Evolutionary Biology, University of Edinburgh Ashworth Laboratories, King’s Buildings, Charlotte Auerbach Road Edinburgh EH9 3FL, UK
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Nick Colegrave
1Institute of Evolutionary Biology, University of Edinburgh Ashworth Laboratories, King’s Buildings, Charlotte Auerbach Road Edinburgh EH9 3FL, UK
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Peter D. Keightley
1Institute of Evolutionary Biology, University of Edinburgh Ashworth Laboratories, King’s Buildings, Charlotte Auerbach Road Edinburgh EH9 3FL, UK
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Abstract

Plastids perform crucial cellular functions, including photosynthesis, across a wide variety of eukaryotes. Since endosymbiosis, plastids have maintained independent genomes that now display a wide diversity of gene content, genome structure, gene regulation mechanisms, and transmission modes. The evolution of plastid genomes depends on an input of de novo mutation, but our knowledge of mutation in the plastid is limited to indirect inference from patterns of DNA divergence between species. Here, we use a mutation accumulation experiment, where selection acting on mutations is rendered ineffective, combined with whole-plastid genome sequencing to directly characterize de novo mutation in Chlamydomonas reinhardtii. We show that the mutation rates of the plastid and nuclear genomes are similar, but that the base spectra of mutations differ significantly. We integrate our measure of the mutation rate with a population genomic dataset of 20 individuals, and show that the plastid genome is subject to substantially stronger genetic drift than the nuclear genome. We also show that high levels of linkage disequilibrium in the plastid genome are not due to restricted recombination, but are instead a consequence of increased genetic drift. One likely explanation for increased drift in the plastid genome is that there are stronger effects of genetic hitchhiking. The presence of recombination in the plastid is consistent with laboratory studies in C. reinhardtii and demonstrates that although the plastid genome is thought to be uniparentally inherited, it recombines in nature at a rate similar to the nuclear genome.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted November 16, 2015.
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Direct estimate of the spontaneous mutation rate uncovers the effects of drift and recombination in the Chlamydomonas reinhardtii plastid genome
Rob W. Ness, Susanne A. Kraemer, Nick Colegrave, Peter D. Keightley
bioRxiv 031898; doi: https://doi.org/10.1101/031898
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Direct estimate of the spontaneous mutation rate uncovers the effects of drift and recombination in the Chlamydomonas reinhardtii plastid genome
Rob W. Ness, Susanne A. Kraemer, Nick Colegrave, Peter D. Keightley
bioRxiv 031898; doi: https://doi.org/10.1101/031898

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