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.