The complete chloroplast genome and phylogentic results support the species position of Swertia banzragczii and Swertia marginata (Gentianaceae) in Mongolia

Background Swertia banzragczii and S. marginata are important medicinal species in Mongolia. However, their taxonomic positions and genetic backgrounds remain unknown. In this study, we explored the complete chloroplast genomes and DNA barcoding of these species and compared them with those of closely related species within the subgenus to determine their taxonomic positions and phylogenetic relationships. Result The chloroplast genomes of S. banzragczii and S. marginata encoded 114 genes, including 80 protein-coding genes, 30 tRNA genes, and 4 rRNA genes. Among them, 16 genes contained a single intron, and 2 genes had two introns. Closely related species had a conserved genome structure and gene content. Only differences in genome length were noticed, which were caused by the expansion and contraction of the inverted repeat (IR) region and loss of exons in some genes. The trn H-GUG– psb A and trn D-GUC– trn Y-GUA intergenic regions had high genetic diversity within Swertia plastomes. Overall, S. banzragczii and S. marginata are true species and belong to the subgenus Swertia . Conclusions These results provide valuable genetic and morphological information on rare and subendemic Swertia species in Mongolia, which can be used for further advanced studies on the Swertia genus.