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Mutation bias reflects natural selection in Arabidopsis thaliana
Since the first half of the twentieth century, evolutionary theory has been dominated by the idea that mutations occur randomly with respect to their consequences(1). Here we test this assumption with large surveys of de novo mutations in the plant Arabidopsis thaliana. In contrast to expectations,...
Autores principales: | , , , , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Nature Publishing Group UK
2022
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8810380/ https://www.ncbi.nlm.nih.gov/pubmed/35022609 http://dx.doi.org/10.1038/s41586-021-04269-6 |
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author | Monroe, J. Grey Srikant, Thanvi Carbonell-Bejerano, Pablo Becker, Claude Lensink, Mariele Exposito-Alonso, Moises Klein, Marie Hildebrandt, Julia Neumann, Manuela Kliebenstein, Daniel Weng, Mao-Lun Imbert, Eric Ågren, Jon Rutter, Matthew T. Fenster, Charles B. Weigel, Detlef |
author_facet | Monroe, J. Grey Srikant, Thanvi Carbonell-Bejerano, Pablo Becker, Claude Lensink, Mariele Exposito-Alonso, Moises Klein, Marie Hildebrandt, Julia Neumann, Manuela Kliebenstein, Daniel Weng, Mao-Lun Imbert, Eric Ågren, Jon Rutter, Matthew T. Fenster, Charles B. Weigel, Detlef |
author_sort | Monroe, J. Grey |
collection | PubMed |
description | Since the first half of the twentieth century, evolutionary theory has been dominated by the idea that mutations occur randomly with respect to their consequences(1). 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 bias(2) reduces the occurrence of deleterious mutations in Arabidopsis, challenging the prevailing paradigm that mutation is a directionless force in evolution. |
format | Online Article Text |
id | pubmed-8810380 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | Nature Publishing Group UK |
record_format | MEDLINE/PubMed |
spelling | pubmed-88103802022-02-09 Mutation bias reflects natural selection in Arabidopsis thaliana Monroe, J. Grey Srikant, Thanvi Carbonell-Bejerano, Pablo Becker, Claude Lensink, Mariele Exposito-Alonso, Moises Klein, Marie Hildebrandt, Julia Neumann, Manuela Kliebenstein, Daniel Weng, Mao-Lun Imbert, Eric Ågren, Jon Rutter, Matthew T. Fenster, Charles B. Weigel, Detlef Nature Article Since the first half of the twentieth century, evolutionary theory has been dominated by the idea that mutations occur randomly with respect to their consequences(1). 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 bias(2) reduces the occurrence of deleterious mutations in Arabidopsis, challenging the prevailing paradigm that mutation is a directionless force in evolution. Nature Publishing Group UK 2022-01-12 2022 /pmc/articles/PMC8810380/ /pubmed/35022609 http://dx.doi.org/10.1038/s41586-021-04269-6 Text en © The Author(s) 2022, corrected publication 2023 https://creativecommons.org/licenses/by/4.0/Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . |
spellingShingle | Article Monroe, J. Grey Srikant, Thanvi Carbonell-Bejerano, Pablo Becker, Claude Lensink, Mariele Exposito-Alonso, Moises Klein, Marie Hildebrandt, Julia Neumann, Manuela Kliebenstein, Daniel Weng, Mao-Lun Imbert, Eric Ågren, Jon Rutter, Matthew T. Fenster, Charles B. Weigel, Detlef Mutation bias reflects natural selection in Arabidopsis thaliana |
title | Mutation bias reflects natural selection in Arabidopsis thaliana |
title_full | Mutation bias reflects natural selection in Arabidopsis thaliana |
title_fullStr | Mutation bias reflects natural selection in Arabidopsis thaliana |
title_full_unstemmed | Mutation bias reflects natural selection in Arabidopsis thaliana |
title_short | Mutation bias reflects natural selection in Arabidopsis thaliana |
title_sort | mutation bias reflects natural selection in arabidopsis thaliana |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8810380/ https://www.ncbi.nlm.nih.gov/pubmed/35022609 http://dx.doi.org/10.1038/s41586-021-04269-6 |
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