title: Targeted Capture of Complete Coding Regions across Divergent Species.
abstract: 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.
authors.affiliation: Department of Ecology and Evolutionary Biology, University of Toronto, Ontario, Canada.
authors.forename: Ryan K
authors.initials: RK
authors.lastname: Schott
authors.affiliation: Department of Cell and Systems Biology, University of Toronto, Ontario, Canada.
authors.forename: Bhawandeep
authors.initials: B
authors.lastname: Panesar
authors.affiliation: Department of Biology, University of Texas at Arlington, Arlington, TX.
authors.forename: Daren C
authors.initials: DC
authors.lastname: Card
authors.affiliation: Department of Cell and Systems Biology, University of Toronto, Ontario, Canada.
authors.forename: Matthew
authors.initials: M
authors.lastname: Preston
authors.affiliation: Department of Biology, University of Texas at Arlington, Arlington, TX.
authors.forename: Todd A
authors.initials: TA
authors.lastname: Castoe
authors.affiliation: Department of Ecology and Evolutionary Biology, University of Toronto, Ontario, Canada.|Department of Cell and Systems Biology, University of Toronto, Ontario, Canada.|Centre for the Analysis of Genomes and Function, University of Toronto, Canada.
authors.forename: Belinda S W
authors.initials: BS
authors.lastname: Chang
mesh_terms: D000465:Algorithms; D000818:Animals; D001717:Birds / Q000235:genetics; D019143:Evolution, Molecular; D016366:Open Reading Frames; D012104:Reptiles / Q000235:genetics; D016415:Sequence Alignment / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*
keywords: comparative studies of protein-coding genes; cross-species sequence capture; hybrid enrichment of complete coding sequences