| Lamiophlomis rotata (Lamiaceae), an important medicine plant endemic to the Qinghai-Tibet Plateau, is widely spread over highlands of Tibet and sparsely distributed in certain areas of Qinghai, Gansu, Sichuan, and Yunnan. Its typical habitats are alpine meadow, rocky crevices, and alpine screes at an altitude of 3900-5100 m. In recent years, since the increasing clinical practices of L. rotata products have led to expansion in wildcrafting, natural resources have decreased remarkably. Therefore, the exploration and evaluation of genetic diversity and chemical components in natural populations of L. rotata is imperative to provide fundamental information for its sustainable use, domestication and efficient conservation. The phylogenetic and population genetic studies of L. rotata can also help us to obtain a better understanding of the factors that had influenced the evolutionary history of the flora in this region.The lipophilic extracts from flowers, leaves and roots of L. rotata from three regions in Qinghai-Tibetan Plateau were analyzed using GC-MS. A total of 67 compounds were identified: 59 of them were from flowers, 64 from leaves, and 48 from roots. In all the compounds we identified, 20 showed an average percentage higher than 4.00% and were considered as the major compound, in which linolenic acid methyl ester was the most abundant component (up to 26.6% in the roots of population X3 collected from the Tibetan Autonomous Region).To study the inter-population relationships, the results obtained from the GC-MS analyses of the lipophilic composition in flowers, leaves and roots of L. rotata from each population were used for a cluster analysis with Euclidean distances and UPGMA method. The results showed that the chemical variability of different part of L. rotata has association with geographical distribution.Based on rbcL sequences in 7 Phlomis species (14 individuals) and 8 individuals of L. rotata and combining rbcL sequences of partial species in Lamioideae retrieved from GenBank, we evaluated the relationships between the genera Phlomis and Lamiophlomis using phylogenetic analyses. All phylogenetic analyses indicated thatPhlomis and Lamiophlomis presented a close relationship in Lamioideae. L. rotata and P. younghusbandii were found to be sister taxon in Maximum likelihood (ML), Neighbor-joining (NJ), and Bayesian inference (BI) analyses, which further supported the hypothesis that the endemic plateau genera are closely related to and have originated from local or adjacently distributed genera. Based on a Bayesian relaxed molecular clock approach, the estimation of the divergence time between L. rotata and P. younghusbandii suggested that the third phase uplifting of the Qinghai-Tibetan Plateau could have led to the speciation of L. rotata.A total of 188 individuals from eight natural populations of L. rotata in Qinghai-Tibet Plateau (four from Tibet, two from Yunnan, and two from Qinghai) were also analyzed using ISSR and RAPD techniques, trnL-F and 5S-NTS fragments. Our results revealed that the level of genetic variation in L. rotata was relatively high with multiple algorithms and methodologies. The high levels of population genetic differentiation and three genetic groups (Tibet, Yunnan and Qinghai clusters) corresponding to the three geographic regions were detected, suggesting significant geographic structure in L. rotata. Our results suggested that the highly structured geographic pattern found in L. rotata might represent diverging evolutionary processes with the uplifting of the Qinghai-Tibet Plateau and the Quaternary climatic oscillations.These findings above-mentioned imply that as many populations as possible should be preserved in situ for the conservation, and Qinghai and Yunnan populations may constitute evolutionary significant units (ESUs) which should be assigned priority for conservation. Optimal harvesting strategies, domestication and tissue culture of the species should be developed as soon as possible for the sustainable use of L. rotata.
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