Multi-omics analysis reveals structural and transcriptional regulation specificity underlying differential benzylisoquinoline alkaloid accumulation in <i>Coptis</i>

<i>Coptis</i> species are rich in protoberberine-type benzylisoquinoline alkaloids (BIAs). However, the differential BIA accumulation between <i>Coptis chinensis</i> and <i>C. teeta</i>, two primary botanical sources of traditional Chinese medicine 'Huanglian', remains mechanistically poorly understood. Here, we combined widely targeted metabolomics, matrix-assisted laser desorption/ionization mass spectrometry imaging, histological characterization, and transcriptomic analyses to investigate the mechanisms underlying the specialized BIA accumulation in <i>C. chinensis</i> versus <i>C. teeta</i>. Clearly, we observed significantly elevated BIA accumulation in <i>C. chinensis</i> rhizomes compared to <i>C. teeta</i>, in particular, the preferential BIA localization within the cortical tissues of <i>C. chinensis</i> rhizomes, consistent with the anatomically expanded cortical and xylem regions. This structural specialization facilitates BIA compartmental distribution patterns. Integrated transcriptomic-metabolomic analysis further constructed a BIA biosynthetic regulatory network, identifying key transcription factors that synergistically promote BIA accumulation in <i>C. chinensis</i> rhizomes, establishing their roles as speciation-associated regulators of medicinal quality divergence between <i>C. chinensis</i> and <i>C. teeta</i>. Overall, this study provides the first integrated anatomical and transcriptional framework explaining interspecies differences in BIA accumulation, enabling the development of quality improvement strategies for medicinal plants.