title: UCE target enrichment of Allorhogas_sp_CNIN3390: whole organism
design: Genomic DNA was extracted using the Spin Column Genomic DNA Minipreps Kit (Bio Basic). Digestion of protein components was carried out overnight in 300 L of digestion solution and 20 L of proteinase K, and the supernatant was subsequently processed following the manufacturers protocol. All DNA extractions were quantified using a Qubit 2.0 (Life Technologies) and for each sample up to 50 ng of extracted DNA was fragmented to a mean fragment size of 400-600 bp using either a BioRuptor Pico sonication device or a Qsonica Q800R sonicator. Libraries were generated using Kapa Hyper Prep kits (Kapa Biosystems Inc., Wilmington, MA) and custom, TruSeq-style dual-indexing barcodes. For enrichment, we pooled libraries at equimolar concentrations and used the two Mybaits RNA bait libraries developed for Hymenoptera and synthesized by Arbor Biosciences (formerly MYcroarray, Ann Arbor, MI) following the standard enrichment protocol for UCEs (available from ultraconserved.org). The final enriched library pool quality was verified using an Agilent TapeSation 2200 (Agilent Tech). A first enriched pool was sent for sequencing to the University of Utah Genomics Core Facility on an Illumina HiSeq 2500 instrument (PE125, v4 chemistry), and a second to the Georgia Genomics Facility, University of Georgia, Athens, USA, on an Illumina NextSeq v2 300 cycle kit. Sequenced libraries produced 125 and 150 nucleotide paired-end reads respectively.