Mutation bias reflects natural selection in Arabidopsis thaliana

J. Grey Monroe (), Thanvi Srikant, Pablo Carbonell-Bejerano, Claude Becker, Mariele Lensink, Moises Exposito-Alonso, Marie Klein, Julia Hildebrandt, Manuela Neumann, Daniel Kliebenstein, Mao-Lun Weng, Eric Imbert, Jon Ågren, Matthew T. Rutter, Charles B. Fenster and Detlef Weigel ()
Additional contact information
J. Grey Monroe: Max Planck Institute for Biology Tübingen
Thanvi Srikant: Max Planck Institute for Biology Tübingen
Pablo Carbonell-Bejerano: Max Planck Institute for Biology Tübingen
Claude Becker: Max Planck Institute for Biology Tübingen
Mariele Lensink: University of California Davis
Moises Exposito-Alonso: Carnegie Institution for Science
Marie Klein: Max Planck Institute for Biology Tübingen
Julia Hildebrandt: Max Planck Institute for Biology Tübingen
Manuela Neumann: Max Planck Institute for Biology Tübingen
Daniel Kliebenstein: University of California Davis
Mao-Lun Weng: Westfield State University
Eric Imbert: ISEM, University of Montpellier
Jon Ågren: Uppsala University
Matthew T. Rutter: College of Charleston
Charles B. Fenster: South Dakota State University
Detlef Weigel: Max Planck Institute for Biology Tübingen

Nature, 2022, vol. 602, issue 7895, 101-105

Abstract: Abstract Since the first half of the twentieth century, evolutionary theory has been dominated by the idea that mutations occur randomly with respect to their consequences1. Here we test this assumption with large surveys of de novo mutations in the plant Arabidopsis thaliana. In contrast to expectations, we find that mutations occur less often in functionally constrained regions of the genome—mutation frequency is reduced by half inside gene bodies and by two-thirds in essential genes. With independent genomic mutation datasets, including from the largest Arabidopsis mutation accumulation experiment conducted to date, we demonstrate that epigenomic and physical features explain over 90% of variance in the genome-wide pattern of mutation bias surrounding genes. Observed mutation frequencies around genes in turn accurately predict patterns of genetic polymorphisms in natural Arabidopsis accessions (r = 0.96). That mutation bias is the primary force behind patterns of sequence evolution around genes in natural accessions is supported by analyses of allele frequencies. Finally, we find that genes subject to stronger purifying selection have a lower mutation rate. We conclude that epigenome-associated mutation bias2 reduces the occurrence of deleterious mutations in Arabidopsis, challenging the prevailing paradigm that mutation is a directionless force in evolution.

Date: 2022
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DOI: 10.1038/s41586-021-04269-6

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