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).