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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. 4 — a, CG methylation levels of homologues in A. thaliana (Ler4, T), A. arenosa (Aar, A), sT and sA subgenomes of A. suecica. b, Numbers of DMRs between T subgenome and Ath (Col) or A subgenome and Aar in F₁, 733, 738 and Asu, respectively. Note that Allo733 and Allo738 may be treated as biological replicates of resynthesized allotetraploids. c, Clustering analysis of CG hyper-DMRs (A-T) in Aar/Ath and their changes in F₁, Allo733 (733), Allo738 (738) and A. suecica (Asu), respectively. Dashed black box indicates 4,486 convergent DMRs where hyper-DMRs between A and T (Ler4) were conserved in newly formed allotetraploids and reduced to the sT subgenome level in Asu. Note that the upper portion (white dashed box) indicates the overlap group (1,875) with conserved DMRs (also see e). d, Clustering of CG hypo-DMRs in F₁ and their changes in 733, 738 and Asu relative to Aar/Ath. Black dashed boxes indicate hypo-DMRs between T subgenome and Ath (upper panel) and between A subgenome and Aar (lower panel) in F₁ were conserved in Allo733, Allo738 and Asu. e, Fraction of conserved CG hypo-DMRs in F₁, Allo733, Allo738 and all three lines and their inheritance in Asu relative to Aar, with the numbers (conserved/total) shown to the left of each column. f, Venn diagram of the genes that overlapped with convergent (blue) and conserved (red) CG hypo-DMRs in Asu relative to Aar. Absolute values of CG methylation change thresholds were 0.5 in c,d.

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