Integration of transcriptomics and metabolomics to identify key coumarin biosynthetic genes in Bupleurum chinense

Abstract

Bupleurum chinense DC. is a perennial herb plant belonging to the Umbelliferae family, genus Bupleurum, that is used as a traditional Chinese medicine. Coumarins are characteristic secondary metabolites of the Apiaceous family, which possess anti-inflammatory, anti-cancer and antiviral activities, among others. Few studies on the coumarin biosynthesis pathways in B. Chinese have been reported. In this study, we identified 89 differentially expressed genes belonging to 7 gene families involved in the synthesis of coumarins in B. chinense, using transcriptome and metabolomic data obtained by high-throughput RNA-sequencing data analysis, and liquid chromatography tandem mass spectrometry. Five coumarin compounds: esculetin (2), fraxetin (4), psoralen (5), parmesan (6) and angelicin (7) were identified through metabolomic analysis. A total of 39 unigenes belonging to five gene families: shikimate O-hydroxycinnamoyltransferase (HCT), caffeic acid ο-methyltransferase (COMT), 4-coumarate: coenzyme A ligase (4CL), feruloyl-CoA 6’-hydroxylase (F6’H) and psoralen synthase (PS), were identified by correlating coumarin content with transcriptional changes. According to correlation network analysis, PS genes (Bc09210, Bc12711), COMT genes (Bc14830, Bc17539, Bc28792, Bc32856) and HCT genes (Bc32814, Bc10245) may be important factors affecting coumarin biosynthesis.

Keywords:

• Bupleurum chinense DC
• coumarins
• key genes
• transcriptome
• metabolome

Disclosure statement

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Data availability statement

All data generated or analyzed during this study are included in this published article and its supplementary information files, further inquiries can be directed to the corresponding author.

Additional information

Funding

This work was supported by the China Agriculture Research System of MOF and MARA, the Young Elite Scientists Sponsorship Program by CACM (2019-QNRC2-C15), the CAMS Innovation Fund for Medical Sciences (CIFMS) under grant number 2016-I2M-2-003, the Crop and livestock Breeding Project in Sichuan (2021YFYZ0012), the Programs of Science and Technology Department of Sichuan Province (2019YFH0072), the Doctoral Research Funding of Southwest University of Science and Technology (19zx7117), China’s Ministry of Foreign Affairs 2017 Asia Regional Cooperation Special Fund Project under grant number [2016]318, and the Programs of Sichuan Provincial Administration of Traditional Chinese Medicine (A-2017N-18).