Genomic data of three Gentianaceae species in the Qinling Mountains

Given alpine biome are particular sensitive to global warming, understanding how alpine plants react with climate fluctuation is crucial to evolution and conservation work. To explore this issue, we chose three alpine Gentianaceae species, Gentiana crassuloides, G. hexaphylla and Swertia bifolia, to present different life type and diverse genera and combined genomic and environmental data. For Gentiana crassuloides and Swertia bifolia, we employed genotype by sequencing (GBS) to obtain single nucleotide polymorphism (SNP) genotypes. For G. hexaphylla, restriction-site associated DNA sequencing (RAD-seq) data was retrieved from Fu et al. (2022a). The chromosome-level genome of Gentiana dahurica (GenBank no. PRJNA799480; Li et al., 2022) and Sinoswertia tetraptera (CNSA no. CNP0002339, https://db.cngb.org/cnsa/; Zhu et al., 2023) was used as the reference genome for Gentiana and Swertia samples, respectively. After filtering for minor allele frequency, missing data and linkage disequilibrium, the total number of unlinked SNPs obtained for G. crassuloides, G. hexaphylla and S. bifolia was 33,569, 185,133 and 33,317 respectively.