Data from: 3RAD-guided SNP discovery for species identification and conservation of the medicinal southern African tree genus <em>Greyia</em> Hook. &amp; Harv.

Accurate species identification is vital for conserving and managing plants that provide important ecosystem services and have ethnobotanical value. The Greyia tree genus (G. sutherlandii, G. radlkoferi and G. flanaganii) is endemic to southern Africa and certain genotypes have medicinal value as a treatment for skin hyper-pigmentation. However, species identification presents unique difficulties due to overlapping phenotypes and the limitations of standard DNA barcoding. To address this, a robust molecular assay was developed through a two-phase approach. First, de novo SNP discovery using 3RAD identified genome-wide SNPs (n= 47,726) from two to three plants per species-specific geographic location, namely G. radlkoferi in the northern Limpopo province, G. sutherlandii in the eastern KwaZulu-Natal province, and G. flanaganii in the south-eastern Eastern Cape province of South Africa. PCA analysis and co-ancestry matrices revealed three distinct genetic clusters, supporting division of the Greyia genus into the three species. A subset of 200 SNPs that reciprocated the three clusters was extracted to make the final selection of a 23-SNP panel, which included five SNPs from barcoding genes (ITS, trnL-F, matK). Second, the 23-SNP panel was converted to allele-specific fluorescent PCR (SNP TypeTM) assays for genotyping on the BioMark™ HD system. The 23-SNP TypeTM assay panel was first validated by showing that it could differentiate the three Greyia species using gDNA from two trees of each species used for the 3RAD libraries.  Subsequently, it was applied to 73 Greyia trees from natural populations sampled over a 1000 km transect from the Eastern Cape to the Limpopo province.  Genetic clustering analyses (PCA, UPGMA, and ADMIXTURE) assigned all trees to one of three genetic groups that matched the expected biogeographical distribution of each species. Finally, in a case study, the 23-SNP TypeTM assay identified 33 Greyia trees of unknown provenance and medicinal potency from production orchards.  This study offers an efficient molecular tool for species identification, guiding conservation strategies and supporting the sustainable management of Greyia populations. # Data from: 3RAD-guided SNP discovery for species identification and conservation of the medicinal southern African tree genus *Greyia* Hook. & Harv. Dataset DOI: [10.5061/dryad.1ns1rn97b](doi.org) ## Description of the data and file structure This repository contains two files: (i) Bioinformatic pipeline for processing the 3RADseq dataset and species-diagnostic SNP selection (`Greyia-3RAD-Project-Bioinformatics-Pipeline.html`), and (ii) SNP genotype data generated with the Biomark HD platform for SNP characterisation and valuation (`GREYIA-FULL-DATA_GDA_10122025SM.csv`). Headers of `GREYIA-FULL-DATA_GDA_10122025SM.csv`file: * TreeID: Identification number of trees * Provenance: Tree growing in the wild or cultivated * Genetic Species ID: Species identity determined using SNP genotype profiles * Greyia_3RAD_D1_16417.28_A1: Nuclear SNP locus allele 1 * Greyia_3RAD_D1_16417.28_A2: Nuclear SNP locus allele 2 * Greyia_3RAD_D1_17901.48_A1: Nuclear SNP locus allele 1 * Greyia_3RAD_D1_17901.48_A2: Nuclear SNP locus allele 2 * Greyia_3RAD_D1_20015.167_A1: Nuclear SNP locus allele 1 * Greyia_3RAD_D1_20015.167_A2: Nuclear SNP locus allele 2 * Greyia_3RAD_D1_16438.7_A1: Nuclear SNP locus allele 1 * Greyia_3RAD_D1_16438.7_A2: Nuclear SNP locus allele 2 * Greyia_3RAD_D1_18402.102_A1: Nuclear SNP locus allele 1 * Greyia_3RAD_D1_18402.102_A2: Nuclear SNP locus allele 2 * Greyia_3RAD_D1_20179.46_A1: Nuclear SNP locus allele 1 * Greyia_3RAD_D1_20179.46_A2: Nuclear SNP locus allele 2 * Greyia_3RAD_D1_16444.229_A1: Nuclear SNP locus allele 1 * Greyia_3RAD_D1_16444.229_A2: Nuclear SNP locus allele 2 * Greyia_3RAD_D1_19009.73_A1: Nuclear SNP locus allele 1 * Greyia_3RAD_D1_19009.73_A2: Nuclear SNP locus allele 2 * Greyia_BarSNP_its2_01_A1: Nuclear ITS2 DNA barcoding SNP locus allele 1 * Greyia_BarSNP_its2_01_A2: Nuclear ITS2 DNA barcoding SNP locus allele 2 * Greyia_3RAD_D1_16938.173_A1: Nuclear SNP locus allele 1 * Greyia_3RAD_D1_16938.173_A2: Nuclear SNP locus allele 2 * Greyia_3RAD_D1_19082.71_A1: Nuclear SNP locus allele 1 * Greyia_3RAD_D1_19082.71_A2: Nuclear SNP locus allele 2 * Greyia_BarSNP_its2_02_A1: Nuclear ITS2 DNA barcoding SNP locus allele 1 * Greyia_BarSNP_its2_02_A2: Nuclear ITS2 DNA barcoding SNP locus allele 2 * Greyia_3RAD_D1_16946.51_A1: Nuclear SNP locus allele 1 * Greyia_3RAD_D1_16946.51_A2: Nuclear SNP locus allele 2 * Greyia_3RAD_D1_19227.91_A1: Nuclear SNP locus allele 1 * Greyia_3RAD_D1_19227.91_A2: Nuclear SNP locus allele 2 * Greyia_BarSNP_its2_03_A1: Nuclear ITS2 DNA barcoding SNP locus allele 1 * Greyia_BarSNP_its2_03_A2: Nuclear ITS2 DNA barcoding SNP locus allele 2 * Greyia_3RAD_D1_17188.43_A1: Nuclear SNP locus allele 1 * Greyia_3RAD_D1_17188.43_A2: Nuclear SNP locus allele 2 * Greyia_3RAD_D1_19287.52_A1: Nuclear SNP locus allele 1 * Greyia_3RAD_D1_19287.52_A2: Nuclear SNP locus allele 2 * Greyia_BarSNP_matK_01_A1: Plastidial matK DNA barcoding SNP locus allele 1 * Greyia_BarSNP_matK_01_A2: Plastidial matK DNA barcoding SNP locus allele 2 * Greyia_3RAD_D1_17357.154_A1: Nuclear SNP locus allele 1 * Greyia_3RAD_D1_17357.154_A2: Nuclear SNP locus allele 2 * Greyia_3RAD_D1_19922.176_A1: Nuclear SNP locus allele 1 * Greyia_3RAD_D1_19922.176_A2: Nuclear SNP locus allele 2 * Greyia_BarSNP_trnLH_01_A1: Plastidial trnLH DNA barcoding SNP locus allele 1 * Greyia_BarSNP_trnLH_01_A2: Plastidial trnLH DNA barcoding SNP locus allele 2 * Greyia_3RAD_D1_17371.56_A1: Nuclear SNP locus allele 1 * Greyia_3RAD_D1_17371.56_A2: Nuclear SNP locus allele 2 * Greyia_3RAD_D1_19983.195_A1: Nuclear SNP locus allele 1 * Greyia_3RAD_D1_19983.195_A2: Nuclear SNP locus allele 2