UCE target enrichment of Plutodes costatus FLAJ150
Genomic DNA was extracted from tissue of two to three legs using the DNeasy Blood & Tissue Kit 250 (Qiagen). DNA yield was quantified using a Qubit 4 (Life Technologies) and we used aliquots of 2 to 150 ng in a volume of 100 ul of ultrapure water as input DNA. Further, DNA was sheared with cycles of 15 seconds on and 90 seconds off in a BioRuptor Pico sonicator to reach fragments between 400-600 base pairs (bp). Genomic libraries were prepared following the protocol by Branstetter et al. (2017), using a Kapa HyperPrep kit (Roche) and dual-indexing primers iTru5 and iTru7 (Glenn et al., 2019). For library UCE enrichment we pooled 6 to10 libraries at equimolar concentrations and followed the Standard Protocol from MyBaits (version 5.02). We used the Lepidoptera bait set 1.3kv1 (Arbor Biosciences) designed by Faircloth (2017) that targets 1,381 UCE loci. The enriched libraries were sent to Admera Health (New Jersey, EEUU) and sequencing was conducted on an Illumina HiSeq 2500 instrument (2x150 rapid run; Illumina Inc. San Diego, CA).