Abstract
Clinopodium chinense (Benth.) O. Kuntze (C. chinense) is an important herb in traditional Chinese medicine. Triterpenoid saponins are a major class of active compounds in C. chinense with broad pharmacological activities and hemostatic, antitumor, and anti-hyperglycemic effects. To identify genes involved in triterpenoid saponin biosynthesis, transcriptomic analyses of leaves, stems, and roots from C. chinense were performed. A total of 135,968 unigenes were obtained by assembling the leaf, stem, and root transcripts, of which 102,154 were annotated in public databases. Differentially expressed genes were determined based on expression profile analysis and analyzed for differential expression of unique genes related to triterpenoid saponin biosynthesis. Multiple unigenes encoding crucial enzymes or transcription factors involved in triterpenoid saponin synthesis were identified and analyzed. The expression levels of unigenes encoding enzymes were experimentally validated using quantitative real-time PCR. This study greatly broadens the public transcriptome database for this species and provides a valuable resource for identifying candidate genes involved in the biosynthesis of triterpenoid saponins and other secondary metabolites.
Highlights
Total saponin content was higher in the aerial parts of C. chinense, but lower in roots (0.118%) (Supplementary Figure S1)
gene ontology (GO) enrichment analysis showed that 25,024 Differentially expressed genes (DEGs) derived from leaf versus root analysis in the “biological process” category were mainly mapped to “photosynthesis”, “cell wall organization or biogenesis”, “carbohydrate metabolic process”, and “cellular polysaccharide metabolic process” (Supplementary Table S5)
We performed the transcriptome analysis of leaf, stem and root tissues in C. chinense, and identified numerous genes related to triterpenoid saponin biosynthesis using RNA sequencing (RNA-seq) sequencing
Summary
Kuntze from the genus Clinopodium of the Lamiaceae family is recorded in the Chinese pharmacopoeia [1]. The aerial parts of C. chinense, as well as Clinopodium polycephalum, known as duanxueliu in China, are used as a traditional folk medicine for treating diseases such as hematuria, influenza, and allergic dermatitis [2]. Previous studies of the chemical constituents of C. chinense have indicated that triterpenoid saponins are the major chemical components of C. chinense [3]. Triterpenoid saponins exert important pharmacological effects including hemostatic [4], antitumor [5], and anti-hyperglycemic [6] activities. Triterpenoid saponin biosynthetic pathways have not been well characterized. Genome sequencing and transcriptome profiling studies of species such as C. chinense have the potential to significantly improve understanding of these pathways
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