Genomic SNP Dataset and Functional Analysis Results for Prosopis cineraria (Ghaf) from the UAE

This dataset contains genome-wide SNP genotype data and downstream functional analysis results for 204 individuals of Prosopis cineraria (Ghaf tree), the national tree of the United Arab Emirates. The dataset was generated as part of a population genomics study to assess genetic diversity, population structure, and adaptive variation across natural Ghaf populations. Genotyping was performed using DNBSEQ technology, and SNPs were called using the GATK HaplotypeCaller pipeline. After quality filtering, a total of 432,753 high-quality bi-allelic SNPs were retained. A linkage disequilibrium (LD)-pruned subset of 57,183 SNPs is also provided and was used in PCA and structure analyses. In addition to raw genotype data, the dataset includes: Sample metadata (sample ID, geographic location, admixture percentages) A list of genes with high population differentiation (top FST) Results of Gene Ontology (GO) enrichment analysis Results of KEGG pathway enrichment analysis These resources provide a foundation for conservation genomics and functional population analysis of Ghaf across arid ecosystems. This dataset supports the population genomics analysis described in the preprint:Gkanogiannis, A., et al. (2025). Uncovering the Genetic Blueprint of the UAE’s National Tree: Genomic Evidence to Guide Prosopis cineraria (L.) Druce Conservation. bioRxiv. https://doi.org/10.1101/2025.07.15.663052 All files are provided in open formats (VCF, CSV, TSV) and released under a CC-BY-4.0 license.本数据集包含阿联酋国树银叶金合欢（Prosopis cineraria，俗称Ghaf树）共204个个体的全基因组单核苷酸多态性（SNP, Single Nucleotide Polymorphism）基因型数据及下游功能分析结果。该数据集作为一项群体基因组学研究的一部分生成，用于评估天然Ghaf种群的遗传多样性、群体结构及适应性变异。 基因分型采用DNBSEQ技术完成，单核苷酸多态性（SNP）的调用使用GATK HaplotypeCaller流程。经过质量过滤后，共保留432,753个高质量双等位基因单核苷酸多态性（SNP）。同时还提供了经连锁不平衡（LD, Linkage Disequilibrium）修剪的57,183个单核苷酸多态性（SNP）子集，该子集被用于主成分分析（PCA, Principal Component Analysis）及群体结构分析。 除原始基因型数据外，本数据集还包含： 1. 样本元数据（样本ID、地理位置、血统比例） 2. 高群体分化（Top FST）基因列表 3. 基因本体（GO, Gene Ontology）富集分析结果 4. 京都基因与基因组百科全书（KEGG, Kyoto Encyclopedia of Genes and Genomes）通路富集分析结果 上述资源为干旱生态系统中Ghaf树的保护基因组学及功能群体分析提供了坚实基础。 本数据集支持预印本中所述的群体基因组学分析：Gkanogiannis, A. 等(2025). 揭示阿联酋国树的遗传蓝图：指导银叶金合欢（Prosopis cineraria (L.) Druce）保护的基因组证据. bioRxiv. https://doi.org/10.1101/2025.07.15.663052 所有文件均采用开放格式（VCF、CSV、TSV）存储，并以CC-BY-4.0协议发布。