Objectives Gentiana dahurica was selected as the focal species to assemble and sequence analyze its chloroplast genome, investigate the phylogeographic structure of wild populations across China based on chloroplast gene sequences, assess genetic diversity and population genetic structure, explore the causes and correlations between the genetic characteristics and geographical distribution patterns of the G. dahurica population, and infer its glacial refugia and the dynamic history of the population. Methods A total of 27 wild populations of G. dahurica were collected from six provinces, including Qinghai, Gansu, Shaanxi, Inner Mongolia, ect. All individuals were subjected to DNA resequencing. Following genome assembly and annotation, the chloroplast genomes of all individuals were obtained for comparative genomic analyses, phylogenetic analysis, population dynamic history, and phylogeographic analyses. Results In total, 81 complete chloroplast genomes were generated, all exhibiting the typical quadripartite circular structure with lengths ranging from 148 792 to 149 000 bp. A total of 134 genes were annotated, including 85 protein-coding genes. The IR/SC boundaries of the chloroplast genomes of G. dahurica were conserved across populations. Variation in non-coding regions was markedly higher than in coding regions. G. dahurica exhibited high within-population genetic diversity (h_S = 0.632) and total genetic diversity (h_T = 0.923). Phylogenetic analyses assigned all populations into two genetic clades, but no significant correlation was detected between genetic distance and geographic location. Population size remained relatively stable over historical periods, with no evidence of strong population expansion. Based on the consensus of non-coding sequences of G. dahurica, 27 haplotypes were identified, Based on the consensus of non-coding sequences of G. dahurica, 27 haplotypes were identified. No clear phylogeographic structure was observed among populations. Dispersal corridor analyses suggested that the northeastern Qinghai-Tibet plateau-Qilian mountains-Liupan mountains-Lvliang mountains-Taihang mountains constituted an important historical migration pathway for G. dahurica. Conclusions The chloroplast genome of G. dahurica is highly conserved in structure and stable in gene content. Two mutation hotspots identified here may serve as candidate markers for molecular identification of germplasm resources. Wild G. dahurica likely originated on the Qinghai-Tibet plateau, and mountain chains such as the Qilian, Liupan, Lvliang, and Taihang ranges may have acted as historical migration corridors that facilitated genetic connectivity among populations. This study provides a theoretical foundation for germplasm conservation and development and utilization of this medicinal plant.

Gentiana dahurica Fischer  /  chloroplast genome  /  genetic diversity  /  phylogeography  /  migration corridor