Target enrichment bait design
Target regions were submitted to Arbor Bioscientific for development of a custom MyBaits kit. Probes were 100 nt in length and we aimed to cover targets at 2×, resulting in a raw bait set of 40,269 probes. Probes were subsequently verified with the Venustachoncha genome and ten of our TransRate-filtered transcriptomes (i.e. those of individuals E4, E8, E32, E36, Mol1-Mol6). The procedure consisted of repeated analyses with BLAST v.2.5.0+ (Camacho et al., 2009) to examinein silico how many hits these probes would produce on each genomic and transcriptomic reference under a variety of hybridization melting temperatures. After moderate filtering the probes were synthesized on magnetic beads for subsequent target enrichment.