Medicinal plants are rich sources for treating various diseases due their bioactive secondary metabolites. Fenugreek (Trigonella foenum-graecum) is one of the medicinal plants traditionally used in human nutrition and medicine which contains an active substance, called diosgenin, with anticancer properties. Biosynthesis of this important anticancer compound in fenugreek can be enhanced using eliciting agents which involves in manipulation of metabolite and biochemical pathways stimulating defense responses. Methyl jasmonate elicitor was used to increase diosgenin biosynthesis in fenugreek plants. However, the molecular mechanism and gene expression profiles underlying diosgening accumulation remain unexplored. In the current study we performed an extensive analysis of publicly available RNA-sequencing datasets to elucidate the biosynthesis and expression profile of fenugreek plants treated with methyl jasmonate. For this purpose, seven read datasets of methyl jasmonate treated plants were obtained that were covering several post-treatment time points (6–120 h). Transcriptomics analysis revealed upregulation of several key genes involved in diosgenein biosynthetic pathway including Squalene synthase (SQS) as the first committed step in diosgenin biosynthesis as well as Squalene Epoxidase (SEP) and Cycloartenol Synthase (CAS) upon methyl jasmonate application. Bioinformatics analysis, including gene ontology enrichment and pathway analysis, further supported the involvement of these genes in diosgenin biosynthesis. The bioinformatics analysis led to a comprehensive validation, with expression profiling across three different fenugreek populations treated with the same methyl jasmonate application. Initially, key genes like SQS, SEP, and CAS showed upregulation, followed by later upregulation of Δ24, suggesting dynamic pathway regulation. Real-time PCR confirmed consistent upregulation of SQS and SEP, peaking at 72 h. Additionally, candidate genes Δ24 and SMT1 highlighted roles in directing metabolic flux towards diosgenin biosynthesis. This integrated approach validates the bioinformatics findings and elucidates fenugreek’s molecular response to methyl jasmonate elicitation, offering insights for enhancing diosgenin yield. The assembled transcripts and gene expression profiles are deposited in the Zenodo open repository at https://doi.org/10.5281/zenodo.8155183 .

中文翻译：

---

转录组数据揭示胡芦巴萜类生物合成途径的动态

药用植物因其具有生物活性的次生代谢物而成为治疗各种疾病的丰富来源。胡芦巴（Trigonella foenum-graecum）是传统上用于人类营养和医学的药用植物之一，含有一种称为薯蓣皂苷元的活性物质，具有抗癌特性。胡芦巴中这种重要抗癌化合物的生物合成可以使用引发剂来增强，引发剂涉及刺激防御反应的代谢物和生化途径的操纵。茉莉酸甲酯激发子用于增加胡芦巴植物中的薯蓣皂苷元生物合成。然而，薯蓣皂苷积累的分子机制和基因表达谱仍有待探索。在当前的研究中，我们对公开的 RNA 测序数据集进行了广泛的分析，以阐明用茉莉酸甲酯处理的胡芦巴植物的生物合成和表达谱。为此，获得了茉莉酸甲酯处理植物的七个读取数据集，涵盖多个处理后时间点（6-120 小时）。转录组学分析显示，参与薯蓣皂苷元生物合成途径的几个关键基因的上调，包括作为薯蓣皂苷元生物合成第一个关键步骤的角鲨烯合酶（SQS），以及茉莉酸甲酯应用后的角鲨烯环氧化酶（SEP）和环木犀烯醇合酶（CAS）。生物信息学分析，包括基因本体富集和通路分析，进一步支持这些基因参与薯蓣皂苷元生物合成。生物信息学分析导致​​了全面的验证，对使用相同茉莉酸甲酯处理的三个不同胡芦巴群体进行了表达谱分析。最初，SQS、SEP 和 CAS 等关键基因表现出上调，随后 Δ24 上调，表明存在动态通路调节。实时 PCR 证实 SQS 和 SEP 一致上调，在 72 小时达到峰值。此外，候选基因 Δ24 和 SMT1 强调了将代谢流引导至薯蓣皂苷元生物合成的作用。这种综合方法验证了生物信息学研究结果，并阐明了胡芦巴对茉莉酸甲酯诱导的分子反应，为提高薯蓣皂苷元产量提供了见解。组装的转录本和基因表达谱存放在 Zenodo 开放存储库中：https://doi.org/10.5281/zenodo.8155183。