Genotyping-By-Sequencing of the Therophyte Geropogon hybridus

Genotyping-By-Sequencing of the Therophyte Geropogon hybridus from island-like patches of natural vegetation in Israel, in an area with a strong north-south precipitation gradient. Sampling took place in a raster-like mosaic, along a north-south transect (in the North (N1–N4), in the Center (C1–C4), and in the South (S1–S4)), at the boundary between the Mediterranean and arid climate zone. The DNA was extracted by using the DNeasy Plant Mini Kit following the manufacturer’s instructions (Qiagen, Hilden, Germany). 200 ng of genomic DNA were digested with 1 Unit MslI (NEB) by LGC (Genomics GmBH, Berlin, Germany). Sequencing took place on a Illumina HiSeq 2000 platform in one channel of 180 pooled samples (LGC Genomics GmBH, Berlin, Germany). Raw sequence data was demultiplexed by barcodes using Illumina's CASAVA data analysis software and quality filtered using BBMerge 34.30 (LGC Genomics GmBH, Berlin, Germany). We used quality trimmed data for further calculations in Stacks 1.40 (Catchen et al. 2011; Catchen et al. 2013).

本数据集包含以色列南北降水梯度显著区域内岛屿状自然植被斑块中一年生植物（Therophyte）杂种婆罗门参（Geropogon hybridus）的基因型分型测序（Genotyping-By-Sequencing，GBS）数据。采样采用类栅格镶嵌的样方布局，沿南北样带布设，涵盖北部（N1–N4）、中部（C1–C4）与南部（S1–S4）三个区域，所有采样点位均处于地中海气候与干旱气候的交界地带。基因组DNA采用DNeasy植物微量提取试剂盒（DNeasy Plant Mini Kit），严格遵循制造商说明书进行提取（凯杰公司（Qiagen），德国希尔登）。取200纳克基因组DNA，由LGC基因学有限公司（LGC Genomics GmBH，德国柏林）使用1单位限制性内切酶MslI（NEB）完成酶切反应。测序工作在因美纳（Illumina）HiSeq 2000测序平台上开展，对180个混合样本的单个测序通道进行测序（LGC基因学有限公司，德国柏林）。原始测序数据通过条形码序列，利用因美纳CASAVA数据分析软件完成解多重处理，并使用BBMerge 34.30（LGC基因学有限公司，德国柏林）进行质量过滤。本研究使用经过质量修剪的测序数据，在Stacks 1.40软件中开展后续生物信息学分析（Catchen等，2011；Catchen等，2013）。