目的 以小秦艽Gentiana dahurica为研究对象，对其叶绿体基因组进行组装和序列分析，基于叶绿体基因序列对我国不同地区野生小秦艽进行谱系地理学研究，分析其遗传多样性及群体遗传结构，探讨小秦艽居群遗传特征及地理分布格局间的成因及关联，推测其冰期避难所及群体动态历史。方法 收集来自青海、甘肃、陕西和内蒙古等6个省份共27个野生小秦艽居群样本进行DNA重测序，经组装及注释后获取所有个体叶绿体基因组，并以此开展比较叶绿体基因组分析、系统发育分析、种群动态历史及谱系地理学分析。结果 共获得81个小秦艽叶绿体基因组，均为典型环状四分体结构，全长148 792～149 000 bp，注释得到134个基因（85个蛋白编码基因），不同居群小秦艽叶绿体基因组IR/SC边界保守。叶绿体基因组非编码区变异明显高于编码区。小秦艽居群遗传多样性（h_S＝0.632）和总遗传多样性（h_T＝0.923）较高。系统发育分析结果表明小秦艽所有居群分为2个遗传分支，但遗传距离与地理位置间无明显相关性。历史上小秦艽的群体规模总体较为恒定，未出现明显的种群扩张现象。基于小秦艽非编码序列共识别到27种单倍型，居群不存在明显的谱系地理结构。扩散廊道分析结果显示，青藏高原东北边缘-祁连山-六盘山-吕梁山-太行山为小秦艽历史迁移的重要通道。结论 小秦艽叶绿体基因组结构高度保守，基因数量稳定，发现的2个突变热点可作为小秦艽特定区域种质资源分子鉴定的候选标记。野生小秦艽可能起源于青藏高原地区，并以祁连山-六盘山-吕梁山-太行山等山脉作为潜在迁移廊道并维持了其不同居群的遗传连接度。将为药用植物小秦艽种质保护和资源开发利用提供理论基础。

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.

国家自然科学基金面上项目（32270386）；陕西省重点研发计划（2025SF-YBXM-501）