PREMISE: Researchers adopting target-enrichment approaches often struggle with the decision of whether to use universal or lineage-specific probe sets. To circumvent this quandary, we investigate the efficacy of a simultaneous enrichment by combining universal probes and lineage-specific probes in a single hybridization reaction, to benefit from the qualities of both probe sets with little added cost or effort. METHODS AND RESULTS: Using 26 Brassicaceae libraries and standard enrichment protocols, we compare results from three independent data sets. A large average fraction of reads mapping to the Angiosperms353 (24-31%) and Brassicaceae (35-59%) targets resulted in a sizable reconstruction of loci for each target set (x̄ ≥ 70%). CONCLUSIONS: High levels of enrichment and locus reconstruction for the two target sets demonstrate that the sampling of genomic regions can be easily extended through the combination of probe sets in single enrichment reactions. We hope that these findings will facilitate the production of expanded data sets that answer individual research questions and simultaneously allow wider applications by the research community as a whole.

CEITEC Masaryk University Brno CZ 625 00 Czech Republic

Centre for Organismal Studies COS Biodiversity and Plant Systematics Heidelberg University 69120 Heidelberg Germany

Departamento de Botánica Universidad de Concepción Concepción Chile

Department of Biology Botany Osnabrück University Osnabrück 49076 Germany

Department of Biology Duke University Durham North Carolina 27708 USA

Department of Biology New Mexico State University Las Cruces New Mexico 88001 USA

Department of Molecular Cell and Developmental Biology University of California Los Angeles Los Angeles California 90095 USA

Division of Biological Sciences University of Missouri Columbia Missouri 65211 USA

Institute of Biology Leiden Plant Sciences Leiden University Sylviusweg 72 2333 BE Leiden The Netherlands

Naturalis Biodiversity Center Research Group Functional Traits P O Box 9517 2300RA Leiden The Netherlands

Royal Botanic Gardens Kew Richmond Surrey TW9 3AE United Kingdom

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