Dataset: NCBI accession numbers and related metadata for an SRA archive of the Pacific oyster, Magallana gigas

Sampling was conducted at several locations: South Korea, Japan, USA, European coastlines, Argentina, and Chile.

At each site, we collected approximately 20 individuals at least 1 meter apart from natural and artificial substrata outside of obvious aquacultural infrastructure to target naturally-settled spat. The two exceptions were in Chile, which were a mix of aquacultural (n=17) and feral (n=3) samples collected from the same estuary (Estero Tongoy), and New Zealand, where oysters were naturally settled within aquaculture farms. Shells were pulled by hand off of hard substrata. Whole or mantle tissue was preserved in 95% ethanol and shipped to Charleston, South Carolina (USA) for DNA extraction using Macherey-Nagel Nucleospin Tissue kits, using the manufacturer's instructions.

To generate libraries for RADseq (restriction-site associated DNA sequencing), we digested gDNA with two restriction enzymes, EcoRI and MseI, and ligated adaptors containing unique 8 to 10 bp barcodes to the digested DNA of each individual. The products were then PCR amplified in two independent reactions with standard Illumina primers. All amplicons were pooled and shipped to the University of Texas Genomic Sequencing and Analysis Facility or the Tufts University Core Facility, which used Pippin Prep® to isolate the 300 – 450 bp fraction. This fraction was then single-read sequenced (100 or 150 basepairs) with Illumina Novaseq, HiSeq 2500 and/or HiSeq 4000 machines. We used custom scripts to demultiplex into sample-specific FASTQ-formatted files.