Comparative transcriptome analysis provides novel insights into the molecular mechanism of berberine biosynthesis in Coptis chinensis

Berberine is the primary medicinal component of Coptis chinensis, a perennial herb in Ranunculaceae. It has pharmacological effects, such as clearing away heat and dampness, purging fire and detoxifying, and resisting oxidation, and is widely used in clinical treatment. Anatomical analysis of the organs showed that berberine is mainly deposited in the xylem of the adventitious roots and rhizomes, as well as in thick-walled tissue layers containing vascular bundles in the leaves and petioles of C. chinensis. The content of total alkaloids in C. chinensis was highest in the rhizomes, among which berberine (54.44%) and coptisine (20.62%) were the main alkaloids. Furthermore, comparative transcriptome analysis of the leaves, petioles, rhizomes, and adventitious roots of C. chinensis was used to reveal the molecular regulation of alkaloid biosynthesis. A total 38 differentially expressed structural genes (DEGs) and 22 differentially expressed transcription factors were related to berberine biosynthesis in C. chinensis. Among these DEGs, the expression level of 13 genes was positively correlated with berberine content, including candidate structural genes (TYR, TYDC, TH, and PPO) and transcription factors (bHLH and WRKY), which may play key roles in berberine accumulation in C. chinensis. The results provide resources and technical support for improving the content of berberine in C. chinensis by genetic engineering, thus providing a theoretical foundation for enhancing the medicinal value of C. chinensis.