We received either flash-frozen or ethanol-preserved samples of Drosophila suzukii for genomic analysis. Japanese samples were a lab strain from the Kyoto Japanese Stock Center; Hawaiian samples were wild-caught in 2009 and kept as a lab colony until DNA extraction in 2017; all other samples were field-collected. Ethanol-preserved samples were re-hydrated in 100uL water prior to DNA extraction. Flies were individually disrupted using a 3mm diameter steel bead in a TissueLyser (Qiagen, Germantown, MD) for 30 seconds at 30Hz in 100uL of 2mg/mL Proteinase K in PK buffer (MagMAX™, Thermofisher Scientific, Pleasanton, CA) before being spun down in a centrifuge for 1 minute at 10,000rpm and incubated for 2 hours at 56°C. 100uL of MagMAX DNA lysis buffer was added to each sample, followed by a 10 minute incubation, before proceeding to DNA purification using a BioSprint DNA Blood Kit on a BioSprint 96 Workstation (Qiagen), using protocol “BS96 DNA Tissue” as per manufacturer’s instructions. Illumina sequencing libraries were prepared using either the Kappa HyperPlus Kit (Roche, South San Francisco, CA) (lanes 2-4) or Qiaseq FX DNA Library Kit (Qiagen) (lanes 5-8) using 50 ng of input DNA. We followed the manufacturer’s instructions for both library preparation kits with few exceptions. With the Kappa HyperPlus Kit, we fragmented DNA at 30°C for 20 minutes and increased adapter incubation time to 1 hour. We also added a 0.6X and 0.7X size selection with AmPure XP beads (Beckman Coulter Life Sciences, Indianapolis, IN) following 5 cycles of PCR amplification with an Eppendorf Master Cycler Pro (ThermoFisher Scientific). With the Qiagen FX kit, we fragmented DNA at 30°C for 15 minutes, and amplified with 7 cycles of PCR. In both cases, DNA library concentration and fragment size were quantified on a Qubit (ThermoFisher Scientific) and a Bioanalyzer High-Sensitivity DNA chip (Agilent, Santa Clara, CA). Paired-end 150 base-pair sequencing was performed by Novogene, Inc. (Sacramento, CA) on the Illumina HiSeq 4000 platform.