title: Ultraconserved  element target capture of Melucha quadrivittis
design: Genomic DNA was extracted using a 1)  Gentra Puregene Tissue, 2) Qiagen DNeasy Blood and Tissue kit (see Forthman  et al., 2019), or 3) Qiagen DNeasy Blood and Tissue kit coupled with Qiagen  QIAquick PCR purification kit (see Knyschov et al., 2019). Libraries were  constructed from genomic DNA following Forthman et al. (2019). Cleaned,  amplified libraries were quantified with Qubit and subsequently combined in  equimolar amounts into 1000 ng pools. A custom MYbaits kit containing a  subset of Hemiptera UCE probes designed from pentatomomorphan species  (Faircloth, 2017) was used for target enrichment. The hybridization mixture  used half volume baits (2.75 uL) with 2.75 uL molecular-grade water. For some  samples, we followed Forthman et al. (2019) enrichment protocol (TE  protocol), while others were subjected to a modified version of the protocol  (TE-touchdown protocol). For the TE protocol, a baits were hybridized with  each library pool at 65C for 1624 hours. In the TE-touchdown protocol,  baits were to hybridize with library pools at 65C for 18 hours followed by  18 hours at 62C. However, samples were prematurely removed during the  TE-touchdown protocol before hybridization was complete. At the  recommendation of Arbor Biosciences, we added an additional 2.75 uL baits to  these samples and re-ran the hybridization protocol to completion.    Bait-target hybrids were bound to Dynabeads M-280 Streptavidin beads,  washed, and resuspended in 30 uL IDTE. 2.5 uL each of 5 uM iTru P5/P7 primers  (Glenn et al., 2016) for the post-capture PCR amplification mix. 14-17 cycles  of post-capture amplification were performed, followed by cleaning. Enriched  library pools were pooled in equimolar amounts and sequenced using a single  Illumina HiSeq3000 lane (2x100 run) at the University of Florida  Interdisciplinary Center for Biotechnology Research (ICBR).