SNP datasets for the genetic analysis of European flat oyster populations

These datasets comprise SNP genotype data from European flat oyster samples (Table_Populations), provided in VCF format. They were used to characterize the genetic diversity and population structure of European flat oysters. SNP Array Dataset: A subset of 487 oysters from 20 populations was genotyped at GENTYANE using the medium-density Affymetrix Axiom SNP array (Gutierrez et al., 2017). After applying multiple filtering steps, 5,090 SNPs were retained. Merged Dataset I: Genotypes of 260 oysters from 15 populations (Alves Monteiro et al., 2024) were integrated with the SNP Array Dataset, resulting in a combined dataset of 747 samples and 2,129 SNPs. Merged Dataset II: This dataset (747 samples, 1,001 SNPs) was created by retaining only those SNPs for which the difference in heterozygosity estimates between the initial 20 populations and the additional 15 populations was not significantly different from zero. English Channel Dataset: Two Belgian populations were added to a regional subset of the previous datasets, totaling 259 oysters from 12 populations. The correspondence between individual names in the VCF files and Population IDs is provided in the metadata files Metadata_747, Metadata_487, and Metadata_259. In the VCF files, marker names (ID) follow Gutierrez et al. (2017), while chromosome identification (CHROM) and SNP positions (POS) are based on Gundappa et al. (2022). The SNP Array Dataset, Merged Dataset I, and Merged Dataset II were analyzed in Lapègue et al. (2026), while the English Channel Dataset was analyzed in Sumon et al. (2026).