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Abstract The dried rhizomes of Coptis chinensis hold significance in Chinese medicine. Monocropping C. chinensis under the shade of a manmade scaffold, the primary planting mode, poses a threat to the ecological balance. In recent years, the practice of C. chinensis–Cunninghamia lanceolata understory cultivation has gained prevalence in southwest China. However, there is no evidence to suggest that understory cultivation enhances the viability, yield, or isoquinoline alkaloid content of C. chinensis. This study examined the physiological properties, yield indicators, and isoquinoline alkaloid content to investigate variations in C. chinensis in response to understory cultivation. Transcriptome analysis was conducted to elucidate potential mechanisms driving these alterations. The results indicate that understory cultivation significantly enhances the viability, yield, and levels of epiberberine, palmatine, and berberine in C. chinensis while reducing coptisine content. Transcriptomic analyses identified 2062 upregulated and 1853 downregulated genes in the understory cultivation system. Pathways such as “phenylpropanoid biosynthesis,” “zeatin biosynthesis,” “photosynthesis,” “tyrosine metabolism,” “isoquinoline alkaloid biosynthesis,” and “starch and sucrose metabolism” exhibited significant enrichment of differentially expressed genes (DEGs). DEGs involved in these pathways were thoroughly analyzed. INV, BGL-2, BGL-4, SPS-2, AMY-3, Psb B, Psb R, Psb S, Psa D, Psa E, Psa H, Psa O, Pet C, Pet H, deta, and b exhibited significant positive correlations with plant fresh weight, aboveground fresh weight, and underground fresh weight. 6-OMT-2 and COMT1-3 displayed significant positive correlations with coptisine content, but negative correlations with epiberberine, palmatine, and berberine content. ZOG-1, ZOG-3, TAT, PPO, POD-13 and UGT 73C5-1 showed noteworthy positive correlations with berberine content. Conversely, MIFH, POD-4, POD-5, and POD-8 displayed significant positive correlations with epiberberine, palmatine, and berberine content. POD-5, and POD-7 were significantly negatively correlated with coptisine content. Furthermore, gene expression levels determined by qRT–PCR aligned with the transcriptomic sequencing results, confirming the reliability of the transcriptomic findings. The results of this study contribute evidence elucidating potential mechanisms through which C. chinensis responds to understory cultivation. Graphical Abstract |
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