Targeted enrichment of UCEs from Scytalopus krabbei LSUMZ-74122
Using ~250 ng of DNA in 25 uL volume, we performed 1/2 reactions of end-repair, A-tailing and adapter-ligation using Kapa Biosystems Hyper Prep kits. To allow for dual indexing, we ligated universal iTru stubs (Glenn et al. 2016) and incorporated iTru dual-indexes (Glenn et al. 2016) to library fragments using 9-12 cycles of PCR. Libraries were combined in pools of 8 equimolar samples for enrichment. We performed target enrichment using the Mycroarray MYbaits kit for Tetrapods UCE 5K version 1, which targets 5,060 UCE loci. Fragments recovered were PCR-amplified and sequenced in a high output paired-end run of 150 cycles on an Illumina HiSeq 4000 System.