title: UCE target enrichment of Ectatomma_lugens_ECTA15_TTGGTGAG+GCCAATAC () [Raw reads]
design: DNA was extracted destructively or non-destructively from adult workers using a DNeasy Blood and Tissue Kit (Qiagen, Valencia, CA, USA). We quantified DNA for each sample using a Qubit fluorometer (High sensitivity kit, Life Technologies, Inc.) and sheared 5.7 271 ng (x = 47 ng) of DNA to a target size of approximately 600 bp by sonication (Qsonica). The sheared DNA was used as input for a modified genomic DNA library preparation protocol (Kapa Hyper Prep Library Kit, Kapa Biosystems) that incorporated with-bead cleanup steps (Fisher et al., 2011) and a generic SPRI substitute (Roland and Reich, 2012), speedbeads hereafter, as described by (Faircloth et al., 2015). We used TruSeq-style dual indexing adapters during adapter ligation (Glenn et al., 2019), and PCR-amplified 50% of the resulting library volume. After rehydrating and purifying reactions, we combined groups of ten libraries at equimolar ratios into enrichment pools having final concentrations of 153178 ng/L. We enriched each pool using a set of 9,898 custom-designed probes (MYcroarray, Inc., now Arbor Biosciences) targeting 2,524 UCE loci specific for ants (Branstetter et al., 2017; hym-v2-ant-specific). We followed library enrichment procedures for the MYcroarray MYBaits kit (Blumenstiel et al., 2010), except we used a 0.1X concentration of the standard MYBaits concentration and added 0.7 L of 500 M custom blocking oligos designed against our custom sequence tags. We ran the hybridization reaction for 24 h at 65 C, subsequently bound all pools to streptavidin beads (MyOne C1; Life Technologies), and washed bound libraries according to a standard target enrichment protocol (Faircloth et al., 2012). We used the with-bead approach for PCR recovery of enriched libraries as described in Faircloth et al. (2012). We combined 15 L of streptavidin bead-bound, enriched library with 25 L HiFi Ready Mix (Kapa Biosystems), 5 L of Illumina TruSeq primer mix (2.5 M each), and 5 L of ddH2O. We purified resulting reactions using 1.0X speedbeads, and we rehydrated the enriched pools in 22 L EB. We quantified 2 L of each enriched pool using a Qubit fluorometer (broad range kit). Enriched DNA samples were sequenced on four Illumina HiSeq 2500 lanes (2x125bp v4 chemistry) at the High Throughput Genomics Lab at the University of Utah. All of the UCE laboratory work was conducted at the University of Utah.