Melissa officinalis (lemon balm) is a well-known pharmaceutical plant in traditional medicine around the world because of the high-value secondary metabolites. Nowadays, advances in computational biology and bioinformatics have opened new avenues to plant-based natural product drug discovery. Despite the pharmacological importance, there is low information about the genes encoding the important biosynthetic pathways related to the secondary metabolite in M. officinalis. In this study, the main genes related to the rosmarinic acid (RA) and terpenoid biosynthesis pathways were detected using transcriptome analysis. Furthermore, we isolated and characterized a novel M. officinalis Hydroxyphenylpyruvate reductase (HPPR) gene involved in RA biosynthesis pathway. An effective pipeline was used to generate 37,055 unigenes by evaluating 42,837,601 Illumina paired-end reads. Functional annotation of the unigenes revealed that 27,363 (73.84%) and 35,822 (96.67%) unigenes had significant similarity to identified proteins in the SwissProt and NR databases, respectively. Also, 10,062 (36.83%) out of 37,055 unigenes were assigned to 399 KEGG pathways. Since terpenes and RA are two prominent metabolites in this plant, the attention of this study has been on the pathways related to them. A total of 149 unigenes were found that are related to the terpenoids biosynthesis, including 75 unigenes involved in the methyl-erythritol phosphate and mevalonate pathway, terpenoid backbone biosynthesis genes, and 74 unigenes related to the terpene synthase. We also identified 144 and 30 unigenes that were associated with the biosynthesis of phenylpropanoid and the rosmarinic acid pathway. Consequently, this investigation can be a comprehensive and accurate transcriptome basis for further investigation in the metabolic engineering and detection of new genes and pathways in M. officinalis.

香蜂草（柠檬香蜂草）因其次生代谢产物的高价值而成为世界各地传统医学中著名的药用植物。如今，计算生物学和生物信息学的进步为基于植物的天然产物药物发现开辟了新途径。尽管具有药理学重要性，但有关编码与药用次级代谢产物相关的重要生物合成途径的基因的信息很少。在本研究中，利用转录组分析检测了与迷迭香酸（RA）和萜类生物合成途径相关的主要基因。此外，我们分离并表征了一种参与 RA 生物合成途径的新型M. officinalis羟苯丙酮酸还原酶 (HPPR) 基因。通过评估 42,837,601 个 Illumina 双端读数，使用有效的流程生成了 37,055 个 unigene。 Unigenes 的功能注释显示，分别有 27,363 个 (73.84%) 和 35,822 个 (96.67%) unigenes 与 SwissProt 和 NR 数据库中已识别的蛋白质具有显着相似性。此外，37,055 个 unigene 中有 10,062 个 (36.83%) 被分配到 399 个 KEGG 通路。由于萜烯和 RA 是该植物中两种重要的代谢物，因此本研究的注意力集中在与它们相关的途径上。共发现149个与萜类生物合成相关的unigenes，其中75个涉及甲基赤藓糖醇磷酸和甲羟戊酸途径的unigenes、萜类骨架生物合成基因和74个与萜烯合酶相关的unigenes。我们还鉴定了 144 个和 30 个与苯丙素生物合成和迷迭香酸途径相关的 unigenes。 因此，本研究可为进一步研究药用植物的代谢工程和新基因及途径的检测提供全面、准确的转录组基础。