Sequencing and comparative analysis of chloroplast genomes of three medicinal plants: Gentiana manshurica, G. scabra and G. triflora

Three species of Gentiana (Gentiana manshurica kitag., Gentiana scabra bunge., and Gentiana triflora pall.) were the main source for an important traditional Chinese medicine, "Longdan", which was first mentioned in " Shennong materia medica Sutra " 2000 years ago. Until recently, there were very few reports on taxonomic classification of these three traditional medicinal Gentiana species. In the current study, chloroplast genomes of the three Gentiana species were sequenced and the phylogenetic analyses were performed in combination with 31 NCBI downloaded Gentiana species sequences and two species of Swertia as outgroup. Based on the phylogenetic results, a new taxonomic classification for Gentiana was proposed, including 4 independent clades with 6 subdivisions (Group 1–Group 6). All the general features, SSR characteristics and gene composition of Gentiana chloroplast genomes strongly supported such a new classification system for Gentiana, which could lay a theoretical foundation for Gentiana in the molecular evolutionary research. Finally, phylogenetic analyisis also demonstrated that the three examined species from Gentiana could cluster together into one group (Group 6), which was far away from the evolutionary position of the medicinal species, Gentiana rigescens Franch, which was consistent with the traditional classification in traditional medicinal uses and taxonomy.