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Integrated Data Reveal the Flavonoid Biosynthesis Metabolic Pathway in Semen Ziziphi Spinosae Using Transcriptomic and Metabolomic

Wei Tian1, Lingdi Liu1, Zhongxing Song2, Zhishu Tang2, Chunxiu Wen1, Tao Jiang1,*
1 Institute of Cash Crops, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, 050051, China
2 State Key Laboratory of Research & Development of Characteristic Qin Medicine Resources (Cultivation), Shaanxi University of Chinese Medicine, Xianyang, 712046, China
* Corresponding Author: Tao Jiang. Email:
(This article belongs to this Special Issue: Biotechnology of Plant Secondary Metabolites)

Phyton-International Journal of Experimental Botany 2023, 92(2), 369-382.

Received 14 April 2022; Accepted 26 May 2022; Issue published 12 October 2022


The extract from Semen Ziziphi Spinosae (SZS) contains many secondary metabolites (flavonoids, alkaloids, and terpenoids), widely reported for their high medicinal value. In order to know the number and type of flavonoids and the regulating mechanism of flavonoid biosynthesis during the growth and development of SZS, we identified and analyzed the flavonoid metabolites and genes in SZS using metabolomic and transcriptomic. A total of 13,232 differentially expressed genes and 83 flavonoid metabolites were identified at three different growth and development stages (T1, T2, and T3) of SZS. The main flavonoid metabolic components of SZS were catechin, L-epicatechin, (–)-epigallocatechin, (+)-gallocatechin, spinosin and its derivatives. A total of 53 unigenes encoding 15 enzymes were identified as candidate genes involved in flavonoid biosynthesis in SZS. Among, PAL, C4H, 4CL, CHS, CHI, FLS, FNS, ANS, ANR, LAR, and UFGT genes were all downregulated in T3 than in T1. The expression levels of these genes influence the accumulation of flavonoids in SZS. Our results should provide valuable information for flavonoid metabolites and candidate genes involved in flavonoid biosynthesis on SZS


Spinosin; secondary metabolites; transcriptomic; metabolomic; gene expression

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Cite This Article

Tian, W., Liu, L., Song, Z., Tang, Z., Wen, C. et al. (2023). Integrated Data Reveal the Flavonoid Biosynthesis Metabolic Pathway in Semen Ziziphi Spinosae Using Transcriptomic and Metabolomic. Phyton-International Journal of Experimental Botany, 92(2), 369–382.

This work is licensed under a Creative Commons Attribution 4.0 International License , which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
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