Dataset: RADseq SNP genotypes of Perkinsus marinus and Crassostrea virginica from the Gulf of Mexico and eastern Atlantic shorelines collected from 2011-2019

For each oyster sampled, animals were cleaned, measured and shucked to expose soft tissues. Gill and mantle were extracted from each oyster and preserved in 95% ethanol for genetic analysis. DNA was extracted using a QIAGEN QIAamp DNA Mini Kit. Genomic DNA concentration was measured with a Nanodrop spectrophotometer to ensure the concentration was ≥100 ng μL⁻¹. All positive samples in microcentrifuge tubes were randomly mixed before transport in case there was an error in future sequencing steps that could cause a loss in representation of an entire population. Once the microcentrifuge tubes containing the extracted DNA were thoroughly mixed, 20 μL of each of the 64 samples were used in subsequent library construction. The DNA of each individual oyster was digested separately with 2 restriction enzymes, EcoRI and MseI. The digested DNA fragments were then ligated to Illumina adaptors at the MseI end and with Illumina adaptors coupled with an 8–10 bp unique barcode to the EcoRI end to allow identification of the individual in silico. The restriction-ligation products were then PCR-amplified in 2 separate reactions using standard Illumina primers. The final PCR products were pooled and shipped for sequencing.

Fifty-nine P. marinus-positive samples were sequenced in 2020 at the Tufts University Genomic Services (200–400 bp fraction; single-end sequencing on an Illumina HiSeq 2500 using SE125), 42 samples were sequenced in 2022 at the University of Texas Genomic Sequencing and Analysis Facility (300–450 bp fraction; single-end sequencing on an Illumina NovaSeq SP using SR100) and 37 of each of those samples were sequenced in both runs.

Organism identifiers (Life Science Identifier (LSID)):
Crassostrea virginica (urn:lsid:marinespecies.org:taxname:140657)
Perkinsus marinus  (urn:lsid:marinespecies.org:taxname:562957)