Pan-chloroplast genome of Coptis species reveals genetic divergence and medicinal materials identification

Accurate identification of medicinal plants is fundamental to ensuring the efficacy, safety, and quality control of Traditional Chinese Medicine. Coptis species are the primary botanical sources of the important herbal medicine "Huanglian", which is officially derived from Coptis chinensis, Coptis deltoidea, and Coptis teeta. However, their high morphological similarity and the loss of distinguishing features in processed materials have led to long-standing species confusion in the medicinal materials market. Traditional identification methods have limitations, and commonly used universal DNA barcodes often lack sufficient resolution for distinguishing closely related species within the Coptis.

This study constructed the first genus-level pan-chloroplast genome for Asian Coptis. We sequenced, assembled, and annotated the chloroplast genomes of 172 individuals encompassing nine Asian Coptis species, including two species that were overlooked in previous studies. Through whole-genome alignment, variant analysis, phylogenetic reconstruction, and population genetic structure analysis, we systematically assessed the genetic diversity and divergence within the genus. Furthermore, we screened for hypervariable regions to develop specific molecular markers for authenticating commercially available medicinal materials and patent medicines containing Huanglian (Coptis spp.).

The chloroplast genomes of Coptis species were found to be highly conserved in size and structure, yet the distribution of variable sites (3589) was uneven. The inverted repeat regions were the most conserved, while some areas in the small single-copy region exhibited high mutation rates. Significant differences in intraspecific genetic diversity were observed; C. teeta had the highest number of variable sites, whereas no intraspecific variation was detected in species like C. deltoidea. Phylogenetic and population structure analyses clearly revealed the interspecific relationships. Sliding-window analysis identified four hypervariable regions, and the intergenic spacer ndhF-trnL was determined to be the specific DNA barcode for distinguishing Coptis species. Application of this marker successfully corrected misidentifications of commercial samples and identified the Coptis species within patent medicines.

The pan-chloroplast genome constructed in this study provides a valuable resource for understanding the genetics and evolution of Coptis. The identified ndhF-trnL marker serves as a reliable and efficient tool for the accurate authentication of Coptis medicinal materials, which is significant for ensuring quality, promoting sustainable resource utilization, and regulating the herbal market.