Development of Specific-Barcode Based on Chloroplast Genome and Its Application in Metabarcoding Molecular Identification of Chinese Patent Medicines Berberidis Radix

Abstract

Abstract Background Berberidis Radix (Sankezhen), a typical multi-origin Chinese medicinal material, originates from the dried roots of the Berberis genus plants. Previous studies have shown that there were significant differences in chemical compositions in different Berberis species. Therefore, it was exceedingly important to accurately identify different species of Berberis. Results In this study, for the first time, we systematically compared the complete chloroplast genome sequences of the six Berberis species (B. julianae, B. tsienii, B. pruinose, B. thunbergii, B. poiretii and B. wilsoniae), which commonly were used as medicinal herb Berberidis Radix. The ndhD-ccsA as highly divergent region was found and taken as a potential marker for species identification. Subsequently, the barcode was applied to the Chinese patent medicines containing Berberidis Radix (Sankezhen) combined with DNA metabarcoding technology. The results showed that the six complete chloroplast genomes exhibited a typical quadripartite structure which ranging from 165,934 to 168,828 bp in length. A total of 147 unique genes were identified in each chloroplast genome, comprising 101 protein-coding genes, 38 tRNA genes, and 8 rRNA genes. Comparative genome analysis demonstrated that the six chloroplast genomes were highly conserved in genome size, gene organization and GC contents. The phylogenetic relationships of six Berberis plants were revealed and the results showed that Mahonia was supported as separate clade in the Berberis genera tree, which was coincident with previous studies. The nucleotide diversity analysis revealed seven variable loci in protein coding regions, and four variable loci in gene spacer regions, respectively. The primer pair 1508F-1864R on ndhD-ccsA region was proven to precisely discriminate the six studied Berberis species and recovered the biodiversity of Berberis species in Chinese patent medicines. Conclusions In general, this study provides meaningful genetic information for Berberis plants, and establishes a method to realize the identification of Berberidis Radix as multi-origin Chinese medicinal materials, which can be applied to Chinese patent medicines containing Berberidis Radix.