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

Abstract

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.

Joining forces in Ochnaceae phylogenomics: a tale of two targeted sequencing probe kits

“…We advise that when developing future taxon or family specific probe kits, the genes targeted by the Angiosperms353 probe kit be included in the specific probe kit to improve prospects of combining lineage‐specific data sets across angiosperms. Alternatively, the Angiosperms353 probe set can be easily combined with a specific probe set at the hybridization step (Hendriks et al, 2021). Although the phylogenomic analyses based on the Angiosperms353 kit did not reveal novel relationships compared to those performed with the family‐specific kit, they still provided important insights by corroborating relationships among the rapidly diverging Ochnineae as well as the three subfamilies that have long remained intractable.…”

Global Phylogeny of the Brassicaceae Provides Important Insights into Gene Discordance

“…Wet lab methods were described in Hendriks et al (2021). Briefly, we extracted genomic DNA from 25 mg of dried leaf tissue (or less if not enough material was available; in case no leaf tissue was available from any herbarium voucher available to us, we used branches and/or flowers) using the DNeasy PowerPlant Pro Kit (Qiagen, Hilden, Germany), following the manufacturer’s protocol (but with a final elution time of 1 hr).…”

A Hybrid Capture Bait Set for Begonia

“…Better integration with other studies could be achieved through combining our bait set with the Angiosperms353 set in the hybridisation step. This approach has worked well in Brassicaceae (Hendriks et al, 2021).…”