Transcriptome analysis of azacitidine (5-AzaC)-treatment affecting the development of early somatic embryogenesis in longan

DNA methylation plays key roles in regulating genes which control somatic embryogenesis (SE) in plant. 5-Azacytidine (5-AzaC) was considered as a common inhibitor of DNA methylation. Longan (<i>Dimocarpus longan</i> Lour.) SE has been established and used as model system for studying mechanism of SE in woody plants. However, effects of 5-AzaC on longan EC and the underlying mechanism at molecular level are rarely understood. In this study, RNA-seq was performed for transcriptome analysis of longan EC treated with or without 5-AzaC were analysed. A total of 29,232 expressed genes were obtained by aligned to longan reference genome and 1,617 differentially expressed genes (DEGs) were got in the pairwise comparisons of CK_<i>vs</i>_T. Integrating the KEGG enrichment pathway analysis showed that ‘butanoate metabolism’, ‘C5-branched dibasic acid metabolism’, ‘sulphur metabolism’, ‘selenocompound metabolism’, ‘pantothenate and CoA biosynthesis’, ‘phagosome’, and ‘plant hormone signal transduction’ were significantly enriched pathways, while the analysis of DEGs revealed that 5-AzaC-treatment could alter genes expression which related to the SE to adjust the complicated metabolic pathways. Therefore, these results indicated that 5-AzaC-treatment positively impact the development of early SE from longan and a decrease in the global DNA methylation level during early SE in longan.

DNA甲基化在调控控制植物体细胞胚发生（somatic embryogenesis, SE）的基因中发挥关键作用。5-氮杂胞苷（5-Azacytidine, 5-AzaC）是一类常用的DNA甲基化抑制剂。龙眼（Dimocarpus longan Lour.）体细胞胚发生体系已被成功建立，并作为木本植物体细胞胚发生机制研究的模式体系。然而，目前关于5-AzaC对龙眼胚性愈伤组织（embryogenic callus, EC）的影响及其分子层面的潜在调控机制仍鲜为人知。本研究通过RNA测序（RNA-seq）对经5-AzaC处理与未处理的龙眼胚性愈伤组织开展转录组分析。通过比对龙眼参考基因组，共鉴定得到29232个表达基因；在CK与T的两两对照比较组中，共获得1617个差异表达基因（differentially expressed genes, DEGs）。整合KEGG富集通路分析结果显示，丁酸代谢（butanoate metabolism）、C5支链二元酸代谢（C5-branched dibasic acid metabolism）、硫代谢（sulphur metabolism）、硒化合物代谢（selenocompound metabolism）、泛酸与辅酶A生物合成（pantothenate and CoA biosynthesis）、吞噬体（phagosome）以及植物激素信号转导（plant hormone signal transduction）为显著富集通路；差异表达基因分析进一步揭示，5-AzaC处理可通过改变与体细胞胚发生相关的基因表达，调控复杂的代谢通路。综上，本研究结果表明，5-AzaC处理可正向促进龙眼早期体细胞胚的发育，并降低龙眼早期体细胞胚发生过程中的全基因组DNA甲基化水平。