Integrated transcriptomics and metabolomics reveal cadmium uptake and stress response mechanisms in Coptis chinensis Franch

Introduction Coptis chinensis Franch. is a medicinally important plant of global significance. However, its clinical application safety is undermined by excessive cadmium (Cd) accumulation. Methods In this study, we determined Cd levels in different tissues of C. chinensis and integrated metabolomic and transcriptomic approaches to elucidate the mechanisms underlying Cd uptake and stress response. Results That roots act as the primary organ for Cd uptake and accumulation. Metabolomic analysis revealed that Cd stress disrupted flavonoid biosynthesis, cofactor biosynthesis, and DNA-related metabolic pathways. Transcriptomic profiling identified a large set of differentially expressed genes (DEGs), which were predominantly enriched in biological processes including metal ion transport, Cd2 + chelation, cell wall metabolism, antioxidant activity, and signal transduction. Integrated multi-omics analysis further confirmed that amino acid biosynthesis pathways are involved in the Cd stress response, with the phenylalanine and lysine biosynthesis pathways being particularly prominent. Notably, two novel genes, novel.5228 and novel.14850 , which directly regulate pyruvate synthesis, were found to play critical roles in these regulatory mechanisms. Discussion This study provides novel insights into the molecular mechanisms governing Cd uptake and stress adaptation in C. chinensis , laying a solid foundation for the breeding of low-Cd-accumulating varieties of this medicinal plant.