Identifying conserved genomic elements and designing universal bait sets to enrich them

Abstract

Summary1. Targeted enrichment of conserved genomic regions is a popular method for collecting large amounts of sequence data from non-model taxa for phylogenetic, phylogeographic and population genetic studies. For example, two available bait sets each allow enrichment of thousands of orthologous loci from >20 000 species (Faircloth et al. Systematic Biology, 61, 717-726, 2012; Molecular Ecology Resources, 15, 489-501, 2015).Unfortunately, few open-source workflows are available to identify conserved genomic elements shared among divergent taxa and to design enrichment baits targeting these regions. Those that do exist require extensive bioinformatics expertise and significant amounts of time to use. These shortcomings limit the application of targeted enrichment methods to additional organismal groups. 2. Here, I describe a universal workflow for identifying conserved genomic regions in available genomic data and for designing targeted enrichment baits to collect data from these conserved regions. These methods require less expertise, less time and better use commonly available information to identify conserved loci and design baits to capture them. 3. I apply this computational approach to the understudied arthropod groups Arachnida, Coleoptera, Diptera, Hemiptera or Lepidoptera to identify thousands of conserved loci in each group and design target enrichment baits to capture these loci. I then use in silico analyses to demonstrate that targeted enrichment of the conserved loci can be used to reconstruct the accepted relationships among genome sequences from the focal arthropod orders. 4. The software workflow I created allowed me to identify thousands of conserved loci in five diverse arthropod groups and design sequence capture baits to target them. This suite of capture bait designs should enable collection of phylogenomic data from >900 000 arthropod species. Although the examples in this manuscript focus on understudied arthropod groups, the approach I describe is applicable to all organismal groups having some form of pre-existing genomic information (e.g. other invertebrates, plants, fungi and microbes). Finally, the documentation, design steps, software code and bait sets developed here are available under an open-source license for restriction-free testing, use, and additional modification by any research group.

Advancing mite phylogenomics: Designing ultraconserved elements for Acari phylogeny

“…When we compare the “ mite‐v2‐master‐probe‐list‐baits” against the “ all‐Arachnid‐baits ” (Faircloth, ), we found that 477 loci matched at a 50% identity over 50% coverage between bait sets. If we increased the metrics of similarity to 80% identity over 80% coverage, 303 duplicated loci where found.…”

On the universality of target‐enrichment baits for phylogenomic research

“…The ability of the baits to hybridize in‐solution is tested in silico by aligning them to sequenced genomes. Hereby, a minimum of 80% sequence overlap and identity is used to predict good in‐solution capture success (Branstetter, Longino, Ward, & Faircloth, ; Faircloth, ; Faircloth et al., ).…”

BaitsTools: Software for hybridization capture bait design

“…baitstools is more flexible and covers a wider variety of hybridization capture applications than existing publicly available software, such as BaitDesigner (Broad Institute ) and the phyluce ultra‐conserved element (UCE) workflow (Faircloth, ). BaitDesigner is an unpublished oligonucleotide bait design tool included within the picard package (Broad Institute ).…”

“…The phyluce UCE workflow is designed to identify and produce baits for UCE loci from aligned genomes and sequence data (Faircloth, ). Although baitstools does not identify UCEs, it can be used to design appropriate bait sequences once these loci are identified.…”