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. 2020 Aug 14;21:560. doi: 10.1186/s12864-020-06975-3

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© The Author(s) 2020

Open AccessThis 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 licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence 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 licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.

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Fig. 1 — Overview of the methylation analysis workflow (a) and cytosine variation induced by high nighttime temperatures (b). WGBS, whole-genome bisulfite sequencing; HNT, high nighttime temperature; mC, methylated cytosine; DMC, a cytosine differentially methylated between the heat-tolerant and heat-sensitive coisogenic rice strains after exposure to HNTs; DMR, a DNA region < 100 bp long with a GC content of > 30%, where > 60% of all cytosines in the region were DMCs and at least 15 successive DMCs exhibited identical patterns of consistent methylation or demethylation; DMG, a differentially methylated gene adjacent to a DMR. Type I DMCs were methylated by HNTs in the heat-tolerant rice strain XN0437T, but the corresponding cytosine in the heat-sensitive rice strain XN0437S was either unchanged or demethylated after HNT. Type II DMCs were demethylated by HNTs in XN0437T, but the corresponding cytosine in XN0437S was either unchanged or methylated after HNT. Type III DMCs were unchanged by HNT in XN0437T, but the corresponding cytosine in XN0437S was either methylated or demethylated after HNT