Data from: Targeted capture of complete coding regions across divergent species

Despite continued advances in sequencing technologies, there is a need for
methods that can efficiently sequence large numbers of genes from diverse
species. One approach to accomplish this is targeted capture (hybrid
enrichment). While these methods are well established for genome
resequencing projects, cross-species capture strategies are still being
developed and generally focus on the capture of conserved regions, rather
than complete coding regions from specific genes of interest. The
resulting data is thus useful for phylogenetic studies, but the wealth of
comparative data that could be used for evolutionary and functional
studies is lost. Here we design and implement a targeted capture method
that enables recovery of complete coding regions across broad taxonomic
scales. Capture probes were designed from multiple reference species and
extensively tiled in order to facilitate cross-species capture. Using
novel bioinformatics pipelines we were able to recover nearly all of the
targeted genes with high completeness from species that were up to 200 myr
divergent. Increased probe diversity and tiling for a subset of genes had
a large positive effect on both recovery and completeness. The resulting
data produced an accurate species tree, but importantly this same data can
also be applied to studies of molecular evolution and function that will
allow researchers to ask larger questions in broader phylogenetic
contexts. Our method demonstrates the utility of cross-species approaches
for the capture of full length coding sequences, and will substantially
improve the ability for researchers to conduct large-scale comparative
studies of molecular evolution and function.