Evaluation of target regions
If exons are on average small, many probes may span exon boundaries within ORFs and may be inefficient for subsequent target enrichment with genomic DNA. We examined this issue using the Venustaconcha ellipsiformis genome (Renaut et al., 2018), the only genome for Unionidae available at the time. We generated error-free reads for our target regions (ORFs and UCEs) with ART (ART_Illumina) v. 2.5.8 (Huang et al., 2012). Each read had a length of 100 nt and reads were tilled to cover each base at 4×, resulting in a total of 84,848 reads. These reads were mapped to the Venustaconcha genome with Stampy v. 1.0.32 (Lunter & Goodson, 2011) and mapping statistics were examined with SAMTools v.1.10 (H. Li et al., 2009). Subsequently, we produced a .bed file with functions of BEDTools v. 2.29 (Quinlan & Hall, 2010), and we used IGV v.2.6.3 (Robinson et al., 2011) to visualize hits for a subset of ORFs and UCEs.