Ultraconserved element (UCE) probe set design: Base genome and initial design parameters critical for optimization

Grey T. Gustafson, Alana Alexander, John S. Sproul, James M. Pflug, David R. Maddison, Andrew E.Z. Short

Research output: Contribution to journalArticlepeer-review

15 Scopus citations


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.

Original languageEnglish (US)
Pages (from-to)6933-6948
Number of pages16
JournalEcology and Evolution
Issue number12
StatePublished - Jun 2019
Externally publishedYes


  • bait design
  • genomics
  • phylogenetics
  • phylogenomics
  • probe design
  • ultraconserved elements

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Ecology
  • Nature and Landscape Conservation


Dive into the research topics of 'Ultraconserved element (UCE) probe set design: Base genome and initial design parameters critical for optimization'. Together they form a unique fingerprint.

Cite this