Crassulacean acid metabolism (CAM) photosynthesis is an important carbon fixation pathway especially in arid environments because it leads to higher water-use efficiency compared to C3 and C4 plants. However, the role of DNA methylation in regulation CAM photosynthesis is not fully understood. Here, we performed temporal DNA methylome and transcriptome analysis of non-photosynthetic (white base) and photosynthetic (green tip) tissues of pineapple leaf. The DNA methylation patterns and levels in these two tissues were generally similar for the CG and CHG cytosine sequence contexts. However, CHH methylation was reduced in white base leaf tissue compared with green tip tissue across diel time course in both gene and transposon regions. We identified thousands of local differentially methylated regions (DMRs) between green tip and white base at different diel periods. We also showed that thousands of genes that overlapped with DMRs were differentially expressed between white base and green tip leaf tissue across diel time course, including several important CAM pathway-related genes, such as beta-CA, PEPC, PPCK, and MDH. Together, these detailed DNA methylome and transcriptome maps provide insight into DNA methylation changes and enhance our understanding of the relationships between DNA methylation and CAM photosynthesis.

中文翻译：

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DNA甲基化组和转录组的综合分析揭示了菠萝CAM光合作用的表观遗传调控

景天酸代谢 (CAM) 光合作用是重要的碳固定途径，尤其是在干旱环境中，因为与 C3 和 C4 植物相比，它导致更高的水分利用效率。然而，DNA 甲基化在调节 CAM 光合作用中的作用尚不完全清楚。在这里，我们对菠萝叶的非光合（白底）和光合（绿尖）组织进行了时间 DNA 甲基化和转录组分析。对于 CG 和 CHG 胞嘧啶序列背景，这两种组织中的 DNA 甲基化模式和水平通常相似。然而，在基因和转座子区域的生长时间过程中，与绿色尖端组织相比，白色基部叶组织中的 CHH 甲基化减少。我们在不同的生长周期确定了绿色尖端和白色碱基之间的数千个局部差异甲基化区域 (DMR)。我们还表明，与 DMR 重叠的数千个基因在白基和绿尖叶组织之间在整个生长时间过程中差异表达，包括几个重要的 CAM 通路相关基因，如 beta-CA、PEPC、PPCK 和 MDH。这些详细的 DNA 甲基化组和转录组图谱共同提供了对 DNA 甲基化变化的洞察，并增强了我们对 DNA 甲基化与 CAM 光合作用之间关系的理解。PPCK 和 MDH。这些详细的 DNA 甲基化组和转录组图谱共同提供了对 DNA 甲基化变化的洞察，并增强了我们对 DNA 甲基化与 CAM 光合作用之间关系的理解。PPCK 和 MDH。这些详细的 DNA 甲基化组和转录组图谱共同提供了对 DNA 甲基化变化的洞察，并增强了我们对 DNA 甲基化与 CAM 光合作用之间关系的理解。