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.