During the sexual reproduction of higher plants, DNA methylation and transcription are broadly changed to reshape a microspore into two sperm cells (SCs) and a vegetative cell (VC). However, when and how the DNA methylation of SCs is established remains not fully understood. Here we investigate the DNA methylation (5 mC) dynamics of SC lineage and the VC in tomato using whole‐genome bisulfite sequencing. We find the asymmetric division of the microspore gives its two daughter cells differential methylome. Compared with the generative cell (GC), the VC is hypomethylated at CG sites while hypermethylated at CHG and CHH sites, with the majority of differentially methylation regions targeted to transposable elements (TEs). SCs have a nearly identical DNA methylome to the GC, suggesting that the methylation landscape in SCs may be pre‐established following the asymmetric division or inherited from the GC. The random forest classifier for predicting gene and TE expression shows that methylation within the gene body is a more powerful predictor for gene expression. Among all tested samples, gene and TE expression in the microspore may be more predictable by DNA methylation. Our results depict an intact DNA methylome landscape of SC lineage in higher plants, and reveal that the impact of DNA methylation on transcription is variant in different cell types.

中文翻译：

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番茄精细胞谱系发育的DNA甲基化动力学

在高等植物的有性繁殖过程中，DNA甲基化和转录被广泛改变，以将小孢子重塑为两个精子细胞（SCs）和一个营养细胞（VC）。然而，何时以及如何建立SC的DNA甲基化仍未完全了解。在这里，我们使用全基因组亚硫酸氢盐测序研究了番茄中SC谱系和VC的DNA甲基化（5 mC）动态。我们发现小孢子的不对称分裂为其两个子细胞提供了不同的甲基化组。与生殖细胞（GC）相比，VC在CG位发生低甲基化，而在CHG和CHH位发生高甲基化，大部分差异甲基化区域靶向转座因子（TEs）。SC具有与GC几乎相同的DNA甲基基因组，提示SC中的甲基化态势可能是在不对称分裂后预先建立的，或者是从GC继承而来的。用于预测基因和TE表达的随机森林分类器显示，基因体内的甲基化是基因表达的更强大的预测因子。在所有测试样品中，小孢子中的基因和TE表达可能更容易通过DNA甲基化预测。我们的结果描述了高等植物中SC世系的完整DNA甲基化组景观，并揭示了DNA甲基化对转录的影响在不同细胞类型中是变异的。DNA甲基化可能更可预测小孢子中的基因和TE表达。我们的结果描述了高等植物中SC世系的完整DNA甲基组景观，并揭示了DNA甲基化对转录的影响在不同细胞类型中是变异的。DNA甲基化可能更可预测小孢子中的基因和TE表达。我们的结果描述了高等植物中SC世系的完整DNA甲基组景观，并揭示了DNA甲基化对转录的影响在不同细胞类型中是变异的。