GO2TR: a gene ontology-based workflow to generate target regions for target enrichment experiments

Although new sequencing technology has enabled biologists to examine genome-wide variation in their taxa of interest, new experimental design, analysis, and cost hurdles impede many researchers from using the benefits of next-generation sequencing. Here we present a workflow to help researchers identify genomic intervals associated with a desired gene function by using gene ontology terms to filter an annotated genome. Resulting intervals comprise a target region that can then be used to design complementary sequences or baits for capturing desired targets in a target enrichment experiment. We show that target regions produced by our workflow and Ensembl Genebuild share intervals but nonetheless differ, and then demonstrate our workflow's utility for target enrichment experiments involving non-model organisms. Using available turtle genomes and bait sequences designed to capture a workflow-generated target region, in silico analysis predicts between 48 and 86 % of baits will bind to complementary sequences in genomes across the Order Testudines (turtles and tortoises). We then use these bait sequences in an actual target enrichment experiment and show that bait performance falls within the range predicted by in silico analysis. We show that by selecting a reference genome related as closely as possible to taxa of interest and focusing on important and likely conserved gene functions, users can acquire valuable genomic data from non-model organisms.