SNP data in plink bed format from GBS analysis of Helicoverpa armigera, H. zea and H. punctigera

Heliothine moths were collected between 2004 and 2014 from 16 different countries around the world across various climatic zones and altitudes (Tables S1 and S2), many of which are described in Behere et al. (2007); and Tay et al. (2013). Samples were collected as larvae from wild and crop host plants, as adult moths via light/pheromone traps, or as larvae after bioassay, and preserved in ethanol (>95%) or RNAlater, or stored at -20°C prior to DNA extraction. DNA was extracted from samples using DNeasy blood and tissue kits (Qiagen), before being quantified with a Qubit 2.0.GBS library preparation and sequencing was performed by the Genomic Diversity Facility, Cornell University, NY, USA. Information regarding the samples used and sequencing output is recorded in the supplementary material (Table S1). Briefly, 50 ng of gDNA was digested using PstI, before library construction as in Elshire et al. (2011) and sequencing using an Illumina Hiseq. A negative control was included with each plate. Raw data were assessed for quality and processed using Stacks v. 1.30 (Catchen et al. 2013b). Briefly, process_radtags was used to demultiplex samples, trim to 90 bp and assess the quality of reads before being forwarded to denovo_map, which was run using default settings. The Populations module was then run, limiting the output to loci existing in at least 5% of samples from each sampling location, with at least 5x coverage. The Populations module was used to output SNP data in Plink format.

实夜蛾亚科蛾类（Heliothine moths）于2004至2014年间，从全球16个不同国家的多样气候带与海拔区域采集获得（表S1、表S2），其中多数样本的相关信息已在Behere等（2007）及Tay等（2013）的研究中得以详述。样本采集方式涵盖：从野生及作物寄主植物上采集幼虫、通过灯光/性信息素诱捕器采集成虫，或是经生物测定后采集幼虫；采集后的样本以体积分数≥95%的乙醇或RNAlater进行保存，或在DNA提取前置于-20℃条件下储存。使用DNeasy血液与组织试剂盒（Qiagen）对样本进行DNA提取，随后采用Qubit 2.0完成定量。基因型测序（Genotyping-by-Sequencing, GBS）文库制备与测序工作由美国纽约州康奈尔大学基因组多样性中心完成。样本相关信息及测序产出数据均记录于补充材料（表S1）中。简要而言，取50 ng基因组DNA（genomic DNA, gDNA），使用PstI进行酶切，随后按照Elshire等（2011）的方法构建文库，并利用Illumina HiSeq进行测序。每个反应平板均设置阴性对照。原始数据先进行质量评估，随后使用Stacks v.1.30（Catchen等，2013b）进行处理。具体流程为：通过process_radtags工具对样本进行解多重标签、将序列修剪至90 bp并评估测序读段（reads）的质量，随后将处理后的reads输入至denovo_map模块，以默认参数运行。随后运行Populations模块，将输出限定为至少存在于每个采样地点5%的样本中、且测序覆盖度至少为5×的位点。最终通过Populations模块输出Plink格式的单核苷酸多态性（Single Nucleotide Polymorphism, SNP）数据。