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Population structure of Drosophila suzukii and signals of multiple invasions in the continental United States

Citation

Chiu, Joanna (2021), Population structure of Drosophila suzukii and signals of multiple invasions in the continental United States, Dryad, Dataset, https://doi.org/10.25338/B89P86

Abstract

Drosophila suzukii, or spotted-wing drosophila, is now an established pest in many parts of the world, causing significant damage to numerous fruit crop industries. Native to East Asia, D. suzukii infestations started in the United States a decade ago, occupying a wide range of climates. To better understand invasion ecology of this pest, knowledge of past migration events, population structure, and genetic diversity is needed. In this study, we sequenced whole genomes of 237 individual flies collected across the continental U.S., as well as several representative sites in Europe, Brazil, and Asia, to identify hundreds of thousands of genetic markers for analysis. We analyzed these markers to detect population structure, to reconstruct migration events, and to estimate genetic diversity and differentiation within and among the continents. We observed strong population structure between West and East Coast populations in the U.S., but no evidence of any population structure North to South, suggesting there is no broad-scale adaptations occurring in response to the large differences in regional weather conditions. We also found evidence that repeated migration events from Asia into North America have provided increased levels of genetic diversity, which does not appear to be the case for Brazil or Europe. This large genomic dataset will spur future research into the genomic adaptations underlying D. suzukii pest activity and development of novel control methods for this agricultural pest.

Methods

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.

Funding

U.S. Department of Agriculture, Award: USDA SCRI 2015-51181-24252

U.S. Department of Agriculture, Award: USDA SCRI 2020-67013-30976