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. 2021 Aug 19;5(10):1382–1393. doi: 10.1038/s41559-021-01523-y

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© The Author(s) 2021

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/.

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Fig. 3 — a, Chromosome features and methylation distributions. Notes in circos plots: (1) chromosomes, (2) gene and (3) TE density and (4) CG, (5) CHG and (6) CHH methylation levels using 100-kb windows in Ath (Ler4) or Aar, F₁, Allo733, Allo738 and A. suecica (in that order from outside to inside in each methylation context). Note that strain identity is omitted in naming T and A chromosomes. b,c, CG methylation levels in the gene body and flanking (2-kb) sequences of the A (b) and T (c) subgenomes in F₁, Allo733 (733), Allo738 (738) and A. suecica (Asu), relative to A. thaliana (Ath) and A. arenosa (Aar), respectively. d, Numbers of DMRs between T subgenome and Ath (Col) or A subgenome and Aar in F₁, 733, 738 and Asu, respectively. e, Expression ratio log₂TPM(Asu/(Aar or Ath)) of the genes flanking a 2-kb region of hypo- or hyper-DMRs between A. suecica (Asu) and A. arenosa (Aar) or A. thaliana (Ath, Ler4). Three asterisks indicate a statistical significance level of P < 0.001 (Mann–Whitney U-test). TPM, transcripts per kilobase per million.

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