DOI: 10.5061/dryad.v0k4h
title: Data from: Identifying conserved genomic elements and designing universal bait sets to enrich them

description: 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 &gt;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. 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. 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. 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 &gt;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.
description: Arachnida Bait Design
 and Testing FilesThe ZIP archive contains
 the files used to identify, design, and test probes targeting conserved
 loci in Arachnids. The *-design-steps.md file is a description of the
 design steps followed for the group. The "BAM" directory
 contains mappings of real/simulated reads to the base genome sequence for
 the group. The "BED" directory contains BAM files converted to
 BED, as well as intermediate BED files created during BED processing. The
 "BED" directory also contains the database of putatively
 conserved loci in the exemplar+base genome taxa, and the temporary probe
 design file. The "*-probes" directory contains the database of
 temporary probe mappings to exemplar taxa, several intermediate files, and
 the principal probe design file. The "in-silico-test" directory
 contains all data from in-silico testing of the principal probe design
 file.arachnida.zipArachnida-UCE-1.1K-v1 Bait DesignA target enrichment probe set designed from 1,120 UCE loci identified among arachnids. This is a ZIP archive of a FASTA file that is ready for submission of the probe set for synthesis.Arachnida-UCE-1.1K-v1.fasta.zipColeoptera Bait Design and Testing FilesThe ZIP archive contains the files used to identify, design, and test probes targeting conserved loci in Coleoptera. The *-design-steps.md file is a description of the design steps followed for the group. The "BAM" directory contains mappings of real/simulated reads to the base genome sequence for the group. The "BED" directory contains BAM files converted to BED, as well as intermediate BED files created during BED processing. The "BED" directory also contains the database of putatively conserved loci in the exemplar+base genome taxa, and the temporary probe design file. The "*-probes" directory contains the database of temporary probe mappings to exemplar taxa, several intermediate files, and the principal probe design file. The "in-silico-test" directory contains all data from in-silico testing of the principal probe design file.coleoptera.zipColeoptera-UCE-1.1K-v1 Bait DesignA target enrichment probe set designed from 1,172 UCE loci identified among Coleoptera. This is a ZIP archive of a FASTA file that is ready for submission of the probe set for synthesis.Coleoptera-UCE-1.1K-v1.fasta.zipDiptera Bait Design and Testing FilesThe ZIP archive contains the files used to identify, design, and test probes targeting conserved loci in Diptera. The *-design-steps.md file is a description of the design steps followed for the group. The "BAM" directory contains mappings of real/simulated reads to the base genome sequence for the group. The "BED" directory contains BAM files converted to BED, as well as intermediate BED files created during BED processing. The "BED" directory also contains the database of putatively conserved loci in the exemplar+base genome taxa, and the temporary probe design file. The "*-probes" directory contains the database of temporary probe mappings to exemplar taxa, several intermediate files, and the principal probe design file. The "in-silico-test" directory contains all data from in-silico testing of the principal probe design file.diptera.zipDiptera-UCE-2.7K-v1 Bait DesignA target enrichment probe set designed from 2,711 UCE loci identified among Diptera. This is a ZIP archive of a FASTA file that is ready for submission of the probe set for synthesis.Diptera-UCE-2.7K-v1.fasta.zipHemiptera Bait Design and Testing FilesThe ZIP archive contains the files used to identify, design, and test probes targeting conserved loci in Hemiptera. The *-design-steps.md file is a description of the design steps followed for the group. The "BAM" directory contains mappings of real/simulated reads to the base genome sequence for the group. The "BED" directory contains BAM files converted to BED, as well as intermediate BED files created during BED processing. The "BED" directory also contains the database of putatively conserved loci in the exemplar+base genome taxa, and the temporary probe design file. The "*-probes" directory contains the database of temporary probe mappings to exemplar taxa, several intermediate files, and the principal probe design file. The "in-silico-test" directory contains all data from in-silico testing of the principal probe design file.hemiptera.zipHemiptera-UCE-2.7K-v1 Bait DesignA target enrichment probe set designed from 2,731 UCE loci identified among Hemiptera. This is a ZIP archive of a FASTA file that is ready for submission of the probe set for synthesis.Hemiptera-UCE-2.7K-v1.fasta.zipLepidoptera Bait Design and Testing FilesThe ZIP archive contains the files used to identify, design, and test probes targeting conserved loci in Lepidoptera. The *-design-steps.md file is a description of the design steps followed for the group. The "BAM" directory contains mappings of real/simulated reads to the base genome sequence for the group. The "BED" directory contains BAM files converted to BED, as well as intermediate BED files created during BED processing. The "BED" directory also contains the database of putatively conserved loci in the exemplar+base genome taxa, and the temporary probe design file. The "*-probes" directory contains the database of temporary probe mappings to exemplar taxa, several intermediate files, and the principal probe design file. The "in-silico-test" directory contains all data from in-silico testing of the principal probe design file.lepidoptera.zipLepidoptera-UCE-1.3K-v1 Bait DesignA target enrichment probe set designed from 1,381 UCE loci identified among Lepidoptera. This is a ZIP archive of a FASTA file that is ready for submission of the probe set for synthesis.Lepidoptera-UCE-1.3K-v1.fasta.zip