DNA methylation plays essential roles in gene regulation, chromatin structure stability, gene imprinting, X chromosome inactivation and embryonic development. However, the dynamics and functions of DNA methylation during the early stage of longan (Dimocarpus longan) somatic embryogenesis (SE) are still unclear. In this study, we carried out whole genome bisulphite sequencing (WGBS) and transcriptome sequencing analyses for embryogenic callus (EC), incomplete pro-embryogenic cultures (ICpEC) and globular embryos (GE) in an early SE system. At a global level, the DNA 5-methylcytosine (5mC) content in EC, ICpEC and GE was 24.59%, 19.65% and 19.74%, respectively, suggesting a global decrease in DNA methylation from EC to ICpEC and then a slight increase from ICpEC to GE. Differentially methylated region (DMR) analysis showed that hypomethylation mainly occurred in CHH contexts. Gene Ontology (GO) and KEGG analysis of hypomethylated (hypo)-CHH-DMR-associated genes revealed that zein biosynthesis, fatty acid biosynthesis, circadian rhythm and mitophagy pathways were involved in longan early SE. Expression patterns of DNA methyltransferase and demethylase genes during longan early SE suggested that the decrease in DNA methylation was probably regulated by DNA methyltransferase genes and the DNA demethylase gene REPRESSOR OF SILENCING 1 (ROS1). The correlation between DNA hypomethylation and gene expression revealed that decreased DNA methylation did not cause extensive changes in gene expression during early longan SE and that gene expression may be affected by methylation changes in gene and downstream regions. Inhibiting DNA methylation with 5-azacytidine (5-AzaC) treatment in EC promoted formation of GE and enhanced the capability of longan SE. Our results suggested that DNA demethylation has important roles in longan SE development.

中文翻译：

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全基因组研究的DNA甲基化动力学揭示了DNA脱甲基在Dimocarpus longan Lour早期体细胞胚发生过程中的关键作用。

DNA甲基化在基因调控，染色质结构稳定性，基因印迹，X染色体失活和胚胎发育中起着重要作用。然而，龙眼早期（Dimocarpus longan） DNA甲基化的动力学和功能）体细胞胚胎发生（SE）仍不清楚。在这项研究中，我们对早期SE系统中的胚性愈伤组织（EC），不完整的促胚培养物（ICpEC）和球状胚（GE）进行了全基因组亚硫酸氢盐测序（WGBS）和转录组测序分析。在全球范围内，EC，ICpEC和GE中DNA 5-甲基胞嘧啶（5mC）的含量分别为24.59％，19.65％和19.74％，这表明从EC到ICpEC的DNA甲基化总体下降，然后从ICpEC略有增加到GE。差异甲基化区域（DMR）分析表明，甲基化不足主要发生在CHH环境中。对低甲基化（hypo）-CHH-DMR相关基因的基因本体论（GO）和KEGG分析表明，龙眼早期SE与玉米蛋白的合成，脂肪酸的生物合成，昼夜节律和线粒体吞噬途径有关。SILENCING 1（ROS1）的阻遏物。DNA低甲基化与基因表达之间的相关性表明，DNA甲基化降低不会在龙眼SE早期引起基因表达的广泛变化，并且基因表达可能受到基因和下游区域甲基化变化的影响。在EC中用5-氮杂胞苷（5-AzaC）处理抑制DNA甲基化可促进GE的形成并增强龙眼SE的能力。我们的结果表明，DNA脱甲基在龙眼SE发育中具有重要作用。