Momordica charantia, a medicinal and edible species of the Cucurbitaceae family, has been widely used as a vegetable around the world. Hundreds of pharmacological compounds isolated from the M. charantia have been reported. However, the mechanism of action of the secondary metabolites has not been fully elucidated. In this study, 118,590 unigenes were gained by de novo assembly based on the raw data from high-throughput sequencing of mRNA (RNA-Sequencing) upon systemic analysis, among which, 51,860 (43.73%) could be annotated to the public sequence databases such as Nr, GO, Swiss-Prot, KEGG and KOG. The transcriptomic changes of M. charantia seedlings treated with or without methyl jasmonate (MeJA) were analyzed to identify key genes involved in MeJA treatment. Additionally, 554 differentially expressed genes (DEGs), including 328 up-regulated ones and 226 down-regulated genes, have been identified. Most DEGs were associated with secondary metabolism and stress responses. Meanwhile, six DEGs were further confirmed by quantitative real-time RT-PCR (qRT-PCR) analysis, resulting in similar expression patterns as compared to those of RNA-Sequencing. Nine significantly enriched pathways including 11 DEGs were identified to be possibly involved in the MeJA-responsive biosynthesis of secondary metabolites based on the transcriptome sequencing analysis. Among them, 4 DEGs, encoding two peroxidases, one cinnamyl alcohol dehydrogenase and one hypothetical protein Csa, might play important roles in the process of phenylpropanoid biosynthesis. In addition, 9 transcription factors (TFs) were also detected as DEGs from 1899 unigenes. Most of them up-regulated by MeJA treatment might be potentially involved in regulating secondary metabolites biosynthesis. This work is the first research on the large-scale assessment of M. charantia transcriptomic resources and the analysis of DEGs and TFs in secondary metabolites biosynthesis of M. charantia seedings treated with or without MeJA, which will be conducive to the further applications of M. charantia.

苦瓜是葫芦科的一种药用和食用物种，已在世界范围内广泛用作蔬菜。已经报道了从苦瓜中分离出的数百种药理化合物。然而，次级代谢产物的作用机制尚未完全阐明。本研究基于mRNA高通量测序（RNA-Sequencing）的原始数据，通过系统分析，从头组装获得118,590条unigenes ，其中51,860条（43.73%）可注释到公共序列数据库，如如 Nr、GO、Swiss-Prot、KEGG 和 KOG。苦瓜的转录组学变化对用或不用茉莉酸甲酯 (MeJA) 处理的幼苗进行分析，以确定参与 MeJA 处理的关键基因。此外，已鉴定出 554 个差异表达基因 (DEG)，其中包括 328 个上调基因和 226 个下调基因。大多数DEGs与次生代谢和应激反应有关。同时，通过定量实时 RT-PCR (qRT-PCR) 分析进一步证实了六个 DEG，与 RNA 测序的表达模式相似。基于转录组测序分析，确定了包括 11 个 DEG 在内的 9 个显着富集的途径可能参与 MeJA 响应的次级代谢物生物合成。其中，4个DEGs，编码两种过氧化物酶、一种肉桂醇脱氢酶和一种假设蛋白Csa，可能在苯丙烷生物合成过程中发挥重要作用。此外，还检测到 9 个转录因子 (TF) 作为来自 1899 个 unigenes 的 DEG。其中大多数被 MeJA 处理上调可能潜在地参与调节次级代谢物的生物合成。这项工作是第一次对大规模评估的研究苦瓜转录组学资源及苦瓜种子经或不加MeJA处理的次生代谢产物生物合成中DEGs和TFs的分析，将有利于苦瓜的进一步应用。