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

Abstract

Coptis species are rich in protoberberine-type benzylisoquinoline alkaloids (BIAs). However, the differential BIA accumulation between Coptis chinensis and C. teeta, 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 C. chinensis versus C. teeta. Clearly, we observed significantly elevated BIA accumulation in C. chinensis rhizomes compared to C. teeta, in particular, the preferential BIA localization within the cortical tissues of C. chinensis 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 C. chinensis rhizomes, establishing their roles as speciation-associated regulators of medicinal quality divergence between C. chinensis and C. teeta. 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.

Acknowledgements

This work was supported by the Natural Science Foundation of Hubei Province of China (2024AFB956), the Chief Scientist Research Project of Hubei Shizhen Laboratory (HSL2024SX0006), and the Key Program of Hubei University of Chinese Medicine (2023ZDXM006).

Author contributions

D.L. and Y.L. conceived and supervised this study. X.T., S.W., W.L., G.L., S.Z., and J.W. carried out experiments. X.T. and S.Y. analyzed the data. X.T., S.Y., and S.W. wrote the manuscript with contributions from all authors. D.L. and Y.L. revised the manuscript. All authors approved the final version of the manuscript. X.T., S.Y., and S.W. contributed equally to this work.

Data availability

All data supporting the findings of this study are available within the paper and its supplementary data published online. Raw RNA-seq reads generated in this study have been deposited in the National Genomics Data Centre (https://ngdc.cncb.ac.cn/) under project no. PRJCA044774.

Conflicts of interest statement

The authors declare no competing interests.

Supplementary material

Supplementary material is available at Horticulture Research online.

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