Show simple item record

dc.contributor.authorGustafson, Grey T.
dc.contributor.authorAlexander, Alana
dc.contributor.authorSproul, John S.
dc.contributor.authorPflug, James M.
dc.contributor.authorMaddison, David R.
dc.contributor.authorShort, Andrew E.
dc.identifier.citationGustafson, GT, Alexander, A, Sproul, JS, Pflug, JM, Maddison, DR, Short, AEZ. Ultraconserved element (UCE) probe set design: Base genome and initial design parameters critical for optimization. Ecol Evol. 2019; 9: 6933– 6948.
dc.descriptionThis work is licensed under a Creative Commons Attribution 4.0 International License.en_US
dc.description.abstractTargeted 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.en_US
dc.publisherWiley Open Accessen_US
dc.rights© 2019 The Authors. Ecology and Evolution published by John Wiley & Sons Ltd.en_US
dc.subjectBait designen_US
dc.subjectProbe designen_US
dc.subjectUltraconserved elementsen_US
dc.titleUltraconserved element (UCE) probe set design: Base genome and initial design parameters critical for optimizationen_US
kusw.kuauthorGustafson, Grey T.
kusw.kuauthorAlexander, Alana
kusw.kuauthorShort, Andrew E.
kusw.kudepartmentEcology & Evolutionary Biologyen_US
kusw.kudepartmentKU Biodiversity Instituteen_US
kusw.oanotesPer Sherpa Romeo 01/07/2021:

Ecology and Evolution [Open panel below]Publication Information TitleEcology and Evolution [English] ISSNsElectronic: 2045-7758 URL Publishers Wiley Open Access [University Publisher] European Society for Evolutionary Biology (ESEB) [Associate Organisation] Society for the Study of Evolution (SSE) [Associate Organisation] DOAJ Listing Requires APCYes [Data provided by DOAJ] [Open panel below]Publisher Policy Open Access pathways permitted by this journal's policy are listed below by article version. Click on a pathway for a more detailed view.

Published Version NoneCC BYPMC Any Website, Journal Website, +3 OA PublishingThis pathway includes Open Access publishing EmbargoNo Embargo LicenceCC BY Copyright OwnerAuthors Publisher DepositPubMed Central Location Any Website Institutional Repository Named Repository (PubMed Central) Subject Repository Journal Website Conditions Hosting site must incorporate publisher-supplied amendments or retractions issued Published source must be acknowledged Must link to published article with DOI
kusw.oaversionScholarly/refereed, publisher versionen_US
kusw.oapolicyThis item meets KU Open Access policy criteria.en_US

Files in this item


This item appears in the following Collection(s)

Show simple item record

© 2019 The Authors. Ecology and Evolution published by John Wiley & Sons Ltd.
Except where otherwise noted, this item's license is described as: © 2019 The Authors. Ecology and Evolution published by John Wiley & Sons Ltd.