Li Hui, Yang Xingyu, Wang Qingfeng, Chen Jinming, Shi Tao
CAS Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China.
Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, China.
Mol Ecol. 2021 Jun;30(12):2831-2845. doi: 10.1111/mec.15933. Epub 2021 May 11.
DNA methylation is an epigenetic modification involved in phenotypic diversity, plant development, and environmental responses. However, the mechanisms of DNA methylation underpinning the adaption of lotus (Nelumbo nucifera) ecotypes to high and low latitudes remain unsolved, especially adaptive evolution of their storage organs. Tropical and temperate lotus ecotypes have thin and enlarged rhizomes which are adapted to low and high latitudes, respectively. Here, we investigated the DNA methylomes and transcriptomes of rhizomes of the temperate and tropical lotus to address this issue. Compared with that of the tropical lotus, the DNA of the temperate lotus was significantly more hypermethylated, indicating an increase in global DNA methylation in the lotus, with rhizome enlargement. Meanwhile, genes associated with differentially methylated regions in their promoters tended to be differentially expressed between the two ecotypes. Interestingly, the genes with their expression negatively correlated with methylation levels in their promoters and genomic regions displayed significantly higher transposon coverage, while the genes showing a significant positive correlation between expression and methylation showed lesser transposon coverage. Further, we identified that DNA methylation, especially in the promoter region, was significantly correlated with the expression of many starch-biosynthetic, gibberellin-, and brassinosteroid-signalling genes associated with rhizome differentiation. Overall, our study unveiled that distinct global and local methylation patterns between the two lotus ecotypes contribute to their expression differences and adaptive phenotypic divergence of their storage organs, highlighting the role of DNA methylation in shaping the ecotypic differentiation of lotus.
DNA甲基化是一种表观遗传修饰，参与表型多样性、植物发育和环境响应。然而，支撑莲（Nelumbo nucifera）生态型适应高纬度和低纬度的DNA甲基化机制仍未解决，尤其是其贮藏器官的适应性进化。热带和温带莲生态型分别具有适应低纬度和高纬度的细根茎和膨大根茎。在此，我们研究了温带和热带莲根茎的DNA甲基化组和转录组，以解决这一问题。与热带莲相比，温带莲的DNA甲基化程度显著更高，表明随着根茎膨大，莲的整体DNA甲基化增加。同时，两种生态型之间，其启动子中与差异甲基化区域相关的基因往往存在差异表达。有趣的是，启动子和基因组区域中表达与甲基化水平呈负相关的基因显示出显著更高的转座子覆盖率，而表达与甲基化呈显著正相关的基因显示出较低的转座子覆盖率。此外，我们发现DNA甲基化，尤其是在启动子区域，与许多与根茎分化相关的淀粉生物合成、赤霉素和油菜素内酯信号基因的表达显著相关。总体而言，我们的研究揭示了两种莲生态型之间不同的整体和局部甲基化模式导致了它们的表达差异和贮藏器官的适应性表型分化，突出了DNA甲基化在塑造莲生态型分化中的作用。
