GBS results of Cornus kousa subsp. chinensis
Data files
Jun 15, 2026 version files 39.18 MB
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GBS_results_of_Cornus_kousa_subsp._chinensis.vcf
39.17 MB
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README.md
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Abstract
This dataset encompasses a solitary VCF file featuring single-nucleotide polymorphisms (SNPs) obtained through genotyping-by-sequencing (GBS) for 348 specimens of Cornus kousa subsp. chinensis. These specimens were gathered from 25 natural populations spanning the provinces of Jiangxi, Hubei, and Hunan in China.
The file “GBS results of Cornus kousa subsp. chinensis.vcf” comprises 5,939 high-calibre single-nucleotide polymorphisms (SNPs) subsequent to filtering. The filtering criteria were as follows: a missing rate of less than 20%, a minor allele frequency greater than 0.05, a quality depth (QD) less than 2.0, a mapping quality (MQ) less than 40.0, a Fisher strand (FS) greater than 60.0, and a strand odds ratio (SOR) greater than 3.0. This VCF file contains genotype calls for all 348 samples. The population codes and geographic coordinates for each sample are presented in the accompanying manuscript (Table S1).
Reuse potential:
This single-nucleotide polymorphism (SNP) dataset holds the potential for reuse in a diverse array of research domains. In the realm of population genetics, it can be employed to conduct in-depth analyses encompassing genetic diversity, population structure, and gene flow. For landscape genomics, it serves as a valuable resource for exploring genotype-environment associations, thereby facilitating the identification of climate-adaptive loci. Moreover, this dataset is well-suited for applications in conservation genetics, as well as for comparative studies within the Cornaceae family.
Dataset identifier:
Dryad DOI: https://doi.org/10.5061/dryad.hdr7sqvx6
Associated manuscript: Li et al., "Climate-induced Genomic Selection: Genetic Structure Variation of Cornus kousa subsp. chinensis and Its Adaptive Reaction to Future Climate Change".
Contact information:
Corresponding author: Bicai Guan (guanbicai@ncu.edu.cn).
Data submitter: Junru Li (Junr2025@163.com).
Overview:
This dataset encompasses a solitary VCF file that harbors 5,939 single-nucleotide polymorphism (SNP) loci. These loci are derived from 348 individuals of Cornus kousa subsp. chinensis, which were sampled from 25 natural populations across China. The data were utilized to evaluate genetic diversity, delineate population structure, and investigate climate-associated selection.
File description:
File name: GBS_results_of_Cornus_kousa_subsp._chinensis.vcf
Format: Variant Call Format (VCF) version 4.2.
Number of samples: 348.
Number of SNP loci: 5,939.
Reference genome: Cornus florida (NCBI assembly not provided, but SNPs were called using BWA alignment to C. florida genome).
Quality filtering criteria were applied using VCFtools as follows: For the Quality Depth (QD), values less than 2.0 were excluded; regarding the Mapping Quality (MQ), those below 40.0 were filtered out. In the case of the Fisher Strand (FS), data with values exceeding 60.0 were removed, and for the Strand Odds Ratio (SOR), values greater than 3.0 were discarded. The missing rate per single-nucleotide polymorphism (SNP) was set to be less than 20%, and the Minor Allele Frequency (MAF) was required to be greater than 0.05. With respect to missing data, missing genotypes were coded as ./.
Header information: The VCF header contains contig information, FILTER definitions, FORMAT fields (GT, DP, GQ), and sample IDs.
Sample metadata:
The population codes and geographical coordinates (longitude, latitude, and altitude) for each of the 348 samples are presented in Table S1 of the accompanying manuscript. The sample identifiers within the VCF file are consistent with those specified in the manuscript.
Software requirements:
To access and conduct an in - depth analysis of the VCF file, the following tools and software are requisite:
VCFtools: filtering, conversion, summary statistics.
PLINK: binary conversion, PCA.
R Programming Environment: packages vcfR, adegenet, hierfstat, LEA, vegan.
STRUCTURE: requires conversion via PGDSpider or vcf2str.
BayeScan: requires conversion to BayeScan input format.
Reuse instructions:
The VCF file can be analyzed using standard population genomics software:
Load in R: Use the vcfR package to read the VCF file.
Convert to PLINK: Use PLINK with the --vcf and --make-bed options.
Convert to STRUCTURE: Use PGDSpider or a custom conversion script.
Population genetics: Compute observed/expected heterozygosity, FST, AMOVA, PCA using GenAlEx, PLINK, or R packages.
Genotype-environment association: Combine with 19 bioclimatic variables (WorldClim) and run LFMM (using the LEA package in R) or BayeScan.
For detailed analysis steps, please refer to the Methods section of the associated manuscript (Li et al., accepted).
Ethical and legal information:
Samples were procured in accordance with permits obtained from the local forestry authorities in the provinces of Jiangxi, Hubei, and Hunan. None of the species included in the sampling were classified as protected or endangered.
The dataset is being made available under the terms of the CC0 1.0 Universal license (https://creativecommons.org/publicdomain/zero/1.0/). It is earnestly requested that users cite the corresponding manuscript when utilizing these data, thereby acknowledging the origin and contributing to the proper dissemination of scientific knowledge.
Version history:
2025.10: Initial submission to Dryad.