DOI: 10.5061/dryad.2f62927
title: Data from: Ultraconserved element (UCE) probe set design: base genome and initial design parameters critical for optimization

description: Targeted capture and enrichment approaches have proven effective for
 phylogenetic study. Ultraconserved elements (UCEs) in particular have
 exhibited great utility for phylogenomic analyses, with the software
 package phyluce being among the most utilized pipelines for UCE
 phylogenomics, including probe design. Despite the success of UCEs, it is
 becoming increasing apparent that diverse lineages require probe sets
 tailored to focal taxa in order to improve locus recovery. However,
 factors affecting probe design and methods for optimizing probe sets to
 focal taxa remain underexplored. Here, we use newly available beetle
 (Coleoptera) genomic resources to investigate factors affecting UCE probe
 set design using phyluce. In particular, we explore the effects of
 stringency during initial design steps, as well as base genome choice on
 resulting probe sets and locus recovery. We found that both base genome
 choice and initial bait design stringency parameters greatly alter the
 number of resultant probes included in final probe sets and strongly
 affect the number of loci detected and recovered during in silico testing
 of these probe sets. In addition, we identify attributes of base genomes
 that correlated with high performance in probe design. Ultimately, we
 provide a recommended workflow for using Phyluce to design an optimized
 UCE probe set that will work across a targeted lineage, and use our
 findings to develop a new, open‐source UCE probe set for beetles of the
 suborder Adephaga.
description: Supporting_File_1_gene_markers_for_genetic_distance_esimatesZipped file containing names and fasta file of target sequences for fifty nuclear protein-coding loci from Zhang et al. (2018); fasta files of fifty nuclear protein-coding loci extracted from study taxa’s genomic assemblies; data used for maximum likelihood analysis of extracted fifty nuclear protein-coding loci and result files; fasta files of six common phylogenetic markers used for genetic distance analysis; data used for maximum likelihood analysis of six common phylogenetic markers and result files.Supporting_File_2_PHYLUCE_probe_design_results_and_final_probe_setZipped file containing PHYLUCE probe design experiment results, including monolithic fasta files, final optimized probe design fasta files, in vitro aspects of final subset of optimized probes, and Adephaga_2.9Kv1 final probe set fasta file.Amphizoa_base_bed_filesThis contains the bed/bam alignment files using the title taxon as the base genome allowing replication of the conducted probe design experiments.Bembidion_base_bed_filesThis contains the bed/bam alignment files using the title taxon as the base genome allowing replication of the conducted probe design experiments.Chlaenius_base_bed_filesThis contains the bed/bam alignment files using the title taxon as the base genome allowing replication of the conducted probe design experiments.Lionepha_base_bed_filesThis contains the bed/bam alignment files using the title taxon as the base genome allowing replication of the conducted probe design experiments.Omoglymmius_base_bed_filesThis contains the bed/bam alignment files using the title taxon as the base genome allowing replication of the conducted probe design experiments.Pterostichus_base_bed_filesThis contains the bed/bam alignment files using the title taxon as the base genome allowing replication of the conducted probe design experiments.Trachypachus_base_bed_filesThis contains the bed/bam alignment files using the title taxon as the base genome allowing replication of the conducted probe design experiments.