Wheat is a powerful genetic model for studying polyploid evolution and crop domestication. Hexaploid bread wheat was formed by two rounds of interspecific hybridization and polyploidization, processes which are often accompanied by genetic and epigenetic changes, including DNA methylation. However, the extent and effect of such changes during wheat evolution, particularly from tetraploid-to-hexaploid wheat, are currently elusive. Here we report genome-wide DNA methylation landscapes in extracted tetraploid wheat (ETW, AABB), natural hexaploid wheat (NHW, AABBDD), resynthesized hexaploid wheat (RHW, AABBDD), natural tetraploid wheat (NTW, AABB), and diploid (DD). In the endosperm, levels of DNA methylation, especially in CHG (H=A, T, or C) context, were dramatically decreased in the ETW relative to natural hexaploid wheat; hypo-differentially methylated regions (DMRs) (850,832) were 24-fold more than hyper-DMRs (35,111). Interestingly, those demethylated regions in ETW were remethylated in the resynthesized hexaploid wheat after the addition of the D genome. In ETW, hypo-DMRs correlated with gene expression, and TEs were demethylated and activated, which could be silenced in the hexaploid wheat. In NHW, groups of TEs were dispersed in genic regions of three subgenomes, which may regulate the expression of TE-associated genes. Further, hypo-DMRs in ETW were associated with reduced H3K9me2 levels and increased expression of histone variant genes, suggesting concerted epigenetic changes after separation from the hexaploid. Genome merger and separation provoke dynamic and reversible changes in chromatin and DNA methylation. These changes correlate with altered gene expression and TE activity, which may provide insights into polyploid genome and wheat evolution.

中文翻译：

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多倍体小麦基因组分离和融合诱导的动态和可逆DNA甲基化变化

小麦是研究多倍体进化和农作物驯化的强大遗传模型。六倍体面包小麦是通过两轮种间杂交和多倍体化形成的，这些过程通常伴随着遗传和表观遗传变化，包括DNA甲基化。但是，目前在小麦进化过程中，尤其是从四倍体到六倍体小麦的进化过程中，这种变化的程度和影响尚不清楚。在这里，我们报告了四倍体小麦（ETW，AABB），天然六倍体小麦（NHW，AABBDD），再合成六倍体小麦（RHW，AABBDD），天然四倍体小麦（NTW，AABB）和二倍体（DD）的全基因组DNA甲基化景观）。在胚乳中，相对于天然六倍体小麦，ETW中的DNA甲基化水平，特别是在CHG（H = A，T或C）情况下显着降低。低差异甲基化区域（DMR）（850,832）比高DMR（35,111）高24倍。有趣的是，ETW中的那些去甲基区域在添加了D基因组之后在重新合成的六倍体小麦中被重新甲基化。在ETW中，hypo-DMR与基因表达相关，并且TE被去甲基化并被激活，可以在六倍体小麦中沉默。在NHW中，TEs群分散在三个亚基因组的基因区域中，这可能调节TE相关基因的表达。此外，ETW中的hypo-DMR与降低的H3K9me2水平和组蛋白变异基因表达增加相关，表明从六倍体分离后一致的表观遗传变化。基因组合并和分离引起染色质和DNA甲基化的动态和可逆变化。