A comparative plastomics approach reveals available molecular markers for the phylogeographic study of , an endangered orchid with extremely small populations.

Comparative plastomics approaches have been used to identify available molecular markers for different taxonomic level studies of orchid species. However, the adoption of such methods has been largely limited in phylogeographic studies. Therefore, in this study, , an endangered species with extremely small populations, was used as a model system to test whether the comparative plastomic approaches could screen available molecular markers for the phylogeographic study. We sequenced two more plastomes of . and compared them with our previously published one. A total of 27 mutational hotspot regions and six polymorphic cpSSRs have been screened for the phylogeographic studies of . . The cpDNA haplotype data revealed that the existence of haplotype distribution center was located in Dabieshan Mts. (Huoshan). The genetic diversity and phylogenetic analyses showed that the populations of . have been isolated and evolved independently for long period. On the contrary, based on cpSSR data, the genetic structure analysis revealed a mixed structure among the populations in Anhui and Jiangxi province, which suggested that the hybridization or introgression events have occurred among the populations of . These results indicated that human activities have played key roles in shaping the genetic diversity and distributional patterns of . According to our results, both two markers showed a high resolution for the phylogeographic studies of . . Therefore, we put forth that comparative plastomic approaches could revealed available molecular markers for phylogeographic study, especially for the species with extremely small populations.