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.2004年至2014年间，研究人员从全球16个不同国家、跨越多种气候带与海拔梯度采集了实夜蛾亚科蛾类（Heliothine moths）样本，相关采样信息详见附表S1与附表S2，其中多数采样点的背景信息已在Behere等人（2007）与Tay等人（2013）的研究中发表。样本采集方式包括：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，或是在生物测定后采集幼虫；样本保存方式为置于体积分数>95%的乙醇或RNAlater中，或在DNA提取前保存于-20℃环境。使用DNeasy血液与组织试剂盒（Qiagen公司）从样本中提取基因组DNA，随后采用Qubit 2.0荧光定量仪对DNA进行定量分析。基因组分型测序（Genotyping-by-Sequencing, GBS）文库构建与测序工作由美国纽约州康奈尔大学基因组多样性研究中心完成。样本相关信息与测序产出数据详见补充材料（附表S1）。简要而言，取50 ng基因组DNA使用PstI限制性内切酶进行酶切，随后按照Elshire等人（2011）的方法构建文库，并利用Illumina Hiseq测序平台完成测序。每一批测序板均设置阴性对照。使用Stacks v.1.30软件（Catchen等人，2013b）对原始数据进行质量评估与处理：首先通过process_radtags工具对样本进行多重索引拆分、将测序读段修剪至90 bp并评估读段质量，随后将处理后的读段输入至denovo_map模块，采用默认参数运行该模块；之后运行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倍的基因座；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。