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Background Viola philippica  Cav. is the only original plant for Violae Herba, as described in the Chinese Pharmacopoeia. The quality of this crude drug is affected by several adulterants from congeneric  Viola  species, and the authentic plant origin of Violae Herba is still controversial. Genome-based identification offers abundant genetic information and potential molecular markers that can be used for the authentication of closely related species. This study aims to investigate the certified origin of Violae Herba and to develop more effective markers for these easily confused species at the genetic level. Methods We compared the morphology and chemical composition of 18 batches of commercial samples and six widespread medicinal  Viola  plants used as Violae Herba or its substitutes by TLC and HPLC-Triple-TOF–MS/MS analyses. The complete chloroplast genomes of these species were sequenced and analyzed, including the general features, repeat sequences, mutational hotspots and phylogeny. The complete chloroplast genomes used as superbarcodes and some specific barcodes screened from mutational hotspots were tested for their ability to distinguish  Viola  species. Results A comparative study showed that Violae Herba is a multi-origin traditional Chinese medicine. Commercial decoction pieces and the standard reference drug were mainly derived from  V. prionantha , clashing with the record in the Chinese Pharmacopoeia. Chloroplast genome analyses of  V. philippica  and five adulterants indicated that sequence divergence was relatively low within  Viola  species. By tree-based approaches, the complete chloroplast genomes showed a better discrimination ability and phylogenetic resolution for each  Viola  species. These results indicate that the whole chloroplast genomes can be used as superbarcodes to differentiate  Viola  medicinal plants. More specific DNA barcodes could be further developed from the  Viola  chloroplast genomes for more efficient and rapid identification of commercial Violae Herba and its adulterants. Conclusions This study has implications for chloroplast genome-based phylogenetic analysis and the authentication of multiple  Viola  species used as Violae Herba. The legal origin recorded in the Chinese Pharmacopoeia should be further revised to  V. prionantha , in line with the commercial Violae Herba in the TCM markets.

chinese medicine

An integrated study of Violae Herba (Viola philippica) and five adulterants by morphology, chemical compositions and chloroplast genomes: insights into its certified plant origin