DNA methylation confers epigenetic regulation on gene expression and thereby on various biological processes. Tomato has emerged as an excellent system to study the function of DNA methylation in plant development. To date, regulation and function of DNA methylation maintenance remains unclear in tomato plants. Here, we report the critical function of tomato (Solanum lycopersicum) Methyltransferase 1 (SlMET1) in plant development and DNA methylome and transcriptome regulation. Using CRISPR‐Cas9 gene editing, we generated slmet1 mutants and observed severe developmental defects with a frame‐shift mutation, including small and curly leaves, defective inflorescence, and parthenocarpy. In leaf tissues, mutations in SlMET1 caused CG hypomethylation and CHH hypermethylation on a whole‐genome scale, leading to a disturbed transcriptome including ectopic expression of many RIN target genes such as ACC2 in leaf tissues, which are normally expressed in fruits. Neither the CG hypomethylation nor CHH hypermethylation in the slmet1 mutants is related to tissue culture. Meanwhile, tissue culture induces non‐CG hypomethylation, which occurs more frequently at gene regions than at TE regions. Our results depict SlMET1‐ and tissue culture‐dependent tomato DNA methylomes, and that SlMET1 is required for maintaining a normal transcriptome and normal development of tomato.

中文翻译：

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DNA甲基转移酶1在番茄发育以及DNA甲基化组和转录组调控中的关键功能。

DNA甲基化赋予基因表达以表观遗传调控，从而赋予其各种生物学过程。番茄已成为研究DNA甲基化在植物发育中的功能的出色系统。迄今为止，番茄植株中DNA甲基化维持的调控和功能尚不清楚。在这里，我们报告了番茄（Solanum lycopersicum）甲基转移酶1（SlMET1）在植物发育以及DNA甲基化和转录组调控中的关键功能。使用CRISPR‐Cas9基因编辑，我们生成了slmet1突变体，并观察到具有移码突变的严重发育缺陷，包括小而卷曲的叶子，花序缺陷和单性结实。在叶片组织中，SlMET1中的突变导致整个基因组规模上的CG低甲基化和CHH高甲基化，导致转录组混乱，包括许多RIN目标基因（如ACC2）在叶组织中的异位表达，而这些基因通常在果实中表达。slmet1突变体中的CG低甲基化或CHH高甲基化均与组织培养无关。同时，组织培养会诱导非CG低甲基化，这种现象在基因区域的发生频率要比TE区域的发生频率高。我们的结果描述了依赖于SlMET1和组织培养的番茄DNA甲基化组，而SlMET1是维持番茄正常转录组和正常发育所必需的。