Ultraconserved element target capture of Gonocerus insidiator
Genomic DNA was extracted using a Qiagen DNeasy Blood and Tissue kit (see Forthman et al., 2019) or 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. Target enrichment was done with a hybridization mixture of 1/2 volume of baits for samples derived from fresh material and 1/4 volume of baits for samples derived from pinned material. We followed Forthman et al.'s (2022) enrichment protocol. Bait-target hybrids were bound to Dynabeads M-280 Streptavidin beads, washed 60C, and resuspended in 30 uL IDTE. 2.5 uL each of 5 uM iTru P5/P7 primers (Glenn et al., 2019) for the post-capture PCR amplification mix. 14-18 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.