title: Ultraconserved element target capture of  Latimbus concolor
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).