UCE raw data: Bet_UCE_108_Glenosema_sp_1
Sheared samples were dried down to 13 L and used as input for library preparation using the Kapa Hyper Prep Kit (Kapa Biosystems, Wilmington, MA). A-tailing, end-repair and ligation reactions were performed at a quarter volume relative to the standard protocol to reduce cost, while library amplification was performed at full volume. Custom, dual-indexing adapter-primers were used to allow for in silico de-multiplexing of each sample (Glenn et al., 2016). Following stub ligation and PCR, adapter-dimers were removed by performing a 0.8-1.0 bead cleaning using an AMPure substitute (Rohland and Reich, 2012). Samples were pooled at equimolar concentrations in groups of 810 libraries for enrichment, with 500 ng of DNA input at each enrichment reaction. UCE enrichment was performed using a custom probe library developed targeting 2590 loci (Hymenoptera v2 by Branstetter et al., 2017b). Enrichment protocols followed the standard MYBaits kit procedure (Blumenstiel et al., 2010), except using a 0.2 concentration for probes and 0.7 l of 500 M custom blocking oligos designed against our custom sequence tags. Incubation of 24 hours at 65C was followed by a series of cleanups with Streptavidin beads (Thermo Fisher Scientific Inc., Waltham, MA) and a final PCR step using Kapa reagents. Post-enrichment DNA concentration was measured using either quantitative PCR (Kapa qPCR reagents; ViiA7 instrument, Thermo Fisher Scientific Inc.) or standard Qubit essays, and pools of bethylid samples were combined at equimolar ratios with pools from other samples for a total of 100120 samples per sequencing run. Final pools were size-selected to a range of 250600 bp using a Blue Pippin size selection instrument (Sage Science, Beverly, MA).