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.

中文翻译：

---

不同的甲基化模式有助于开花植物（圣莲）贮藏器官生长的生态型分化

DNA甲基化是一种涉及表型多样性、植物发育和环境反应的表观遗传修饰。然而，支撑莲花适应的DNA甲基化机制（Nelumbo nucifera) 高低纬度的生态型仍未解决，尤其是其储存器官的适应性进化。热带和温带莲花生态型的根茎细而粗，分别适应低纬度和高纬度地区。在这里，我们研究了温带和热带莲花根茎的 DNA 甲基化组和转录组以解决这个问题。与热带莲相比，温带莲的DNA甲基化程度明显更高，表明莲的整体DNA甲基化增加，根茎增大。同时，与启动子中差异甲基化区域相关的基因往往在两种生态型之间差异表达。有趣的是，表达与其启动子和基因组区域的甲基化水平呈负相关的基因显示出显着更高的转座子覆盖率，而在表达和甲基化之间显示显着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、赤霉素和油菜素类固醇信号基因的表达显着相关。总的来说，我们的研究揭示了两种莲花生态型之间不同的全局和局部甲基化模式导致它们的表达差异和它们储存器官的适应性表型差异，突出了 DNA 甲基化在塑造莲花生态型分化中的作用。