RAD-Seq of Sclerocactus in Colorado, Utah, and New Mexico: Sclerocactus glaucus, S. dawsonii, S. parviflorus, S. brevispinus, and S. wetlandicus
DNA samples and library preparation were processed according to a modified double digest RADseq (ddRAD) protocol (Parchman et al., 2012; Tripp et al., 2017) using EcoR1 and Mse1 enzymes (New England Biolabs, Ipswich, MA). Illumina adapters and barcodes (Tripp et al., 2017) were ligated to opposing ends of the fragments through a single ligation step followed by two separate PCR enrichments which were combined. The fragments were quality filtered and size selected using BluePippin (Sage Science, Beverly, MA) at the University of Oregon Genomics and Cell Characterization Core Facility (GC3F; Eugene, OR). Fragments between 200-400 bp were chosen for library construction and sequenced using a HiSeq 4000 or a NovaSeq 6000 (Illumina, San Diego, CA) by GC3F. The resulting sequence data were cleaned and trimmed of single end adapters using TRIMMOMATIC v 0.39 (Bolger et al., 2014), and then demultiplexed using FASTQ-MULTX (Aronesty, 2013).