The best of both worlds: Combining lineage‐specific and universal bait sets in target‐enrichment hybridization reactions

• Published in: Applications in plant sciences Vol. 9; no. 7
• Main Authors: Hendriks, Kasper P., Mandáková, Terezie, Hay, Nikolai M., Ly, Elfy, Hooft van Huysduynen, Alex, Tamrakar, Rubin, Thomas, Shawn K., Toro‐Núñez, Oscar, Pires, J. Chris, Nikolov, Lachezar A., Koch, Marcus A., Windham, Michael D., Lysak, Martin A., Forest, Félix, Mummenhoff, Klaus, Baker, William J., Lens, Frederic, Bailey, C. Donovan
• Format: Journal Article
• Language: English
• Published: United States John Wiley & Sons, Inc 01.07.2021; John Wiley and Sons Inc; Wiley
• Subjects: Alexander, P J; Biodiversity; Brassicaceae; combining probes; DNA probes; enrichment; Gene mapping; Genetic testing; genomics; Hybridization; Hyb‐Seq; loci; nucleic acid hybridization; Phylogenetics; phylogenomics; phylogeny; Plant sciences; population biology; Protocol Note; Protocol Notes; Source studies; target enrichment; England; United Kingdom > UK; New Mexico; United States > US; Massachusetts; Germany; enrichment; combining probes; population biology; Hyb‐Seq; target enrichment; phylogeny; Brassicaceae; phylogenomics
• ISSN: 2168-0450; 2168-0450
• DOI: 10.1002/aps3.11438

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.