Wintergreen oil is a folk medicine widely used in foods, pesticides, cosmetics and drugs. In China, nine out of 47 species within Gaultheria (Ericaceae) are traditionally used as Chinese medicinal wintergreens; however, phylogenetic approaches currently used to discriminating these species remain unsatisfactory. In this study, we sequenced and characterized plastomes from nine Chinese wintergreen species and identified candidate DNA barcoding regions for Gaultheria. Each Gaultheria plastome contained 110 unique genes (76 protein-coding, 30 tRNA, and four rRNA genes). Duplication of trnfM, rps14, and rpl23 genes were detected, while all plastomes lacked ycf1 and ycf2 genes. Gaultheria plastomes shared substantially contracted SSC regions that contained only the ndhF gene. Moreover, plastomes of Gaultheria leucocarpa var. yunnanensis contained an inversion in the LSC region and an IR expansion to cover the ndhF gene. Multiple rearrangement events apparently occurred between the Gaultheria plastomes and those from several previously reported families in Ericales. Our phylogenetic reconstruction using 42 plastomes revealed well-supported relationships within all nine Gaultheria species. Additionally, seven mutational hotspot regions were identified as potential DNA barcodes for Chinese medicinal wintergreens. Our study is the first to generate complete plastomes and describe the structural variations of the complicated genus Gaultheria. In addition, our findings provide important resources for identification of Chinese medicinal wintergreens.

Species diversity is high in the Himalaya-Hengduan Mountains, particularly at the edges characterized by deep ravines and “sky islands”. Studies focused on sky-island species are sparse and the patterns observed in response to both geographic and climatic factors are inconsistent. Here phylogeographic and phylogenetic analyses of Gaultheria nummularioides, a species originating in the late Pliocene with its main distribution in the Himalaya-Hengduan Mountains, were conducted to reveal the pattern of genetic dynamics in response to physical geography, glacial fluctuations, and monsoons. We found that in this species genetic variation is higher among populations than within populations, with a significant phylogeographic boundary between the central Himalaya and the eastern Himalaya and the Hengduan Mountains. We also found a high incidence of private alleles, possibly associated with strong habitat isolation. The phylogeographic pattern recovered is consistent with populations in glacial refugia that have experienced expansion after glaciation. The divergence times of most haplotypes coincide with the time of the weakening of the Asian monsoon in these regions. Models of geographic range size showed a significant decrease from the Last Interglacial through the Last Glacial Maximum to the Current, and a predicted increase from the Current to the year 2070. Our study provides insights for understanding speciation among sky islands in this region.

Gaultheria griffithiana is an evergreen shrub in the family Ericaceae. It is used as a source of the Chinese traditional medicine, Tougucao, with distribution of the junction of eastern Himalaya and Hengduan Mountain. The chloroplast genome of G. griffithiana is 175,649 bp in length with 135 genes, including eight rRNA genes, 39 tRNA genes, and 85 protein-coding genes. Phylogenetic analysis has converged on the placement of G. griffithiana as sister to G. praticola, G. nummularioides, and G. hookeri within the Leucothoides clade of Gaultheria in this study.