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. 2020 May 27;11:2658. doi: 10.1038/s41467-020-16457-5

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© The Author(s) 2020

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. 6 — a Fraction of regions for each mark signal with significant differences based on pairwise comparison. Differential regions were identified using DESeq2 (using a q value cutoff of 10⁻² and a fold-change between individuals >1.5). b Number and percentage of histone marks that were differential in 20 rice varieties. c Distribution of core and distributed genes marked by different histone modifications in MH63. Core genes, present in more than 99% of 453 rice accessions; distributed genes, present in less than 99% of 453 rice accessions. The numbers in (b) and (c) indicate the sample sizes used in the analysis. d, f SNP (blue) density in H3K4me3 (d) and H3K9me2 (f) peak regions. e, g SNP enrichments upstream of H3K4me3-modified (e) and H3K9me2-modified (g) regions indicated by dotted boxes in 20 rice varieties. h The relative proportion of conserved chromatin state in the whole genome. i, j Nonmetric Multidimensional scaling (NMDS) plot of 20 rice varieties indicates their relationships based on similarity of five histone modification signal (i) and H3K9me2 signal (j). First two dimensions are shown as MDS1 versus MDS2. The five different subpopulations⁵² Xian/Indica, Aus, Geng/Japonica, aromatic and an intermediate group, are shown in different colors. k An example of a nonvariable and a variable region for chromatin state in 20 varieties. All epigenome datasets were mapped to the Nipponbare reference sequence MSU7.0⁵³. State colors are as in (g). l The pie chart of the relative frequency of CS from Xian/Indica to Geng/Japonica. Source Data underlying Fig. 6a, h–j, l are provided as a Source Data file.