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Chloroplast haplotypes and main haplotypes of nrITS clones of Gentiana crassicaulis

Citation

Ni, Lianghong et al. (2023), Chloroplast haplotypes and main haplotypes of nrITS clones of Gentiana crassicaulis, Dryad, Dataset, https://doi.org/10.5061/dryad.z8w9ghxf1

Abstract

The Himalaya-Hengduan Mountain region is one of the hotspots of biodiversity research. The uplift of the Qinghai-Tibetan Plateau (QTP) and the Quaternary glaciation caused great environmental changes in this region, and the responses of many species in the QTP to the Quaternary climate are still largely unknown. The genetic structure and phylogeographical history of Gentiana crassicaulis Duthie ex Burk, an endemic Chinese alpine species in this area, were investigated based on four chloroplast fragments and internal transcribed spacer region of the nuclear ribosomal DNA (nrITS) sequences of 11 populations. The populations with highly diverse chloroplast haplotypes were mainly found at the edge of the QTP. There were two main haplotypes of nrITS clones, one shared by the Yunnan and Guizhou populations, and the other by the remaining populations. The population with the highest diversity was the Gansu population, located at the edge of the plateau. Based on molecular dating, the diversification of G. crassicaulis at the edge of the plateau occurred before the Last Glacial Maximum (LGM), and the species may have completed its expansion from the edge to the platform. Ecological Niche Models were conducted to predict the distributional ranges of G. crassicaulis at present, during the LGM, and during the last interglacial (LIG) period. The results demonstrated that G. crassicaulis survived on the QTP platform and at the edge during the LGM but afterward retreated from the platform to the southern edge, followed by expansion to the platform.

Methods

Total genomic DNA was extracted from the silica-gel–dried leaves.

Four chloroplast fragments were amplified and sequenced, including rpl33, rpl33-rps18, rpl16 intron, and trnC-GCA-petN. The four fragments were concatenated, and a total of 6 haplotypes (H1–H6) were identified from 113 individuals of Gentiana crassicaulis.

The ITS region was amplified and the PCR products were cloned using the pUCm-T Vector PCR Products Cloning Kit (Sangon, Shanghai, China), and 10 clones per individual were sequenced. From 11 populations of Gentiana crassicaulis, 330 ITS cloning sequences were obtained. The haplotypes shared among the populations were S1 and S2, which accounted for 44.8% (148/330) and 11.2% (37/330) of all the cloning sequences, respectively.

Funding

National Natural Science Foundation of China, Award: 82073959

National Natural Science Foundation of China, Award: 81173654

Collaborative Innovation Center for Tibetan Medicines, Award: 2018XTCX005