Data from: An evaluation of transcriptome-based exon capture for frog phylogenomics across multiple scales of divergence (Class: Amphibia, Order: Anura)

Custom sequence capture experiments are becoming an efficient approach for
gathering large sets of orthologous markers in nonmodel organisms.
Transcriptome-based exon capture utilizes transcript sequences to design
capture probes, typically using a reference genome to identify intron–exon
boundaries to exclude shorter exons (<200 bp). Here, we test
directly using transcript sequences for probe design, which are often
composed of multiple exons of varying lengths. Using 1260 orthologous
transcripts, we conducted sequence captures across multiple phylogenetic
scales for frogs, including outgroups ~100 Myr divergent from the ingroup.
We recovered a large phylogenomic data set consisting of sequence
alignments for 1047 of the 1260 transcriptome-based loci (~561 000 bp) and
a large quantity of highly variable regions flanking the exons in
transcripts (~70 000 bp), the latter improving substantially by only
including ingroup species (~797 000 bp). We recovered both shorter
(<100 bp) and longer exons (>200 bp), with no major
reduction in coverage towards the ends of exons. We observed significant
differences in the performance of blocking oligos for target enrichment
and nontarget depletion during captures, and differences in PCR
duplication rates resulting from the number of individuals pooled for
capture reactions. We explicitly tested the effects of phylogenetic
distance on capture sensitivity, specificity, and missing data, and
provide a baseline estimate of expectations for these metrics based on a
priori knowledge of nuclear pairwise differences among samples. We provide
recommendations for transcriptome-based exon capture design based on our
results, cost estimates and offer multiple pipelines for data assembly and
analysis.