Positive selective sweeps of epigenetic mutations regulating specialized metabolites in plants
- Kazumasa Shirai1,
- Mitsuhiko P. Sato2,
- Ranko Nishi3,
- Masahide Seki4,
- Yutaka Suzuki4 and
- Kousuke Hanada1
- 1Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, Fukuoka 820-8502, Japan;
- 2Kawatabi Field Science Center, Graduate School of Agricultural Science, Tohoku University, Miyagi 989-6711, Japan;
- 3RIKEN Center for Sustainable Resource Science, Kanagawa 230-0045, Japan;
- 4Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa 277-8562, Japan
Abstract
DNA methylation is an important factor regulating gene expression in organisms. However, whether DNA methylation plays a key role in adaptive evolution is unknown. Here, we show evidence of naturally selected DNA methylation in Arabidopsis thaliana. In comparison with single nucleotide polymorphisms, three types of methylation—methylated CGs (mCGs), mCHGs, and mCHHs—contributed highly to variable gene expression levels among an A. thaliana population. Such variably expressed genes largely affect a large variation of specialized metabolic quantities. Among the three types of methylations, only mCGs located in promoter regions of genes associated with specialized metabolites show a selective sweep signature in the A. thaliana population. Thus, naturally selected mCGs appear to be key mutations that cause the expressional diversity associated with specialized metabolites during plant evolution.
Footnotes
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[Supplemental material is available for this article.]
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Article published online before print. Article, supplemental material, and publication date are at https://www.genome.org/cgi/doi/10.1101/gr.271726.120.
- Received September 14, 2020.
- Accepted April 6, 2021.
This article is distributed exclusively by Cold Spring Harbor Laboratory Press for the first six months after the full-issue publication date (see https://genome.cshlp.org/site/misc/terms.xhtml). After six months, it is available under a Creative Commons License (Attribution-NonCommercial 4.0 International), as described at http://creativecommons.org/licenses/by-nc/4.0/.
