Cornales (10 families; 42 genera; ~605 species) is an order of flowering plants with an extensive history of inconsistent taxonomic treatments. Due to these inconsistencies, the late Dr. Richard H. Eyde (1988) described the group as a "dustbin", the collection area for a plethora of different reassignments from authors with differing opinions. Despite these inconsistencies, a few morphological characters were used to unite Cornalean lineages including relatively inconspicuous flowers with inferior ovaries that develop into a drupe (Edye, 1988). With the emergence of DNA sequencing, molecular phylogenetic studies have drastically improved understanding of

Targeted enrichment methods allow for the extraction of hundreds of low-copy loci, which is useful for phylogenomic inference under the multispecies coalescent model (Lemmon et al., 2012;Heyduk et al., 2016). However, the bait sets required for target enrichment can be costly to produce and require genomic resources including reference genomes or transcriptome sequences (Hale et al., 2020). Universal bait sets, such as Angiosperms353 (Johnson et al., 2019), can ameliorate these challenges by enabling the generation of target gene sequences across a broad phylogenetic scale. Although this is an attractive option for some phylogenetic investigations, a "one-size-fits-all" approach may not be sufficient for disentangling phylogenetic relationships at lower taxonomic levels in many groups. Rapid species radiations, low sequence divergence, and gene and genome duplications (all rampant within the angiosperm clade) are likely to reduce the efficacy of using a universal bait set for species-level phylogeny reconstruction. Rather, it is likely that lineage-specific bait sets will be necessary to obtain sufficient variation to address questions at lower phylogenetic scales.In this study, we address this issue by generating a single-copy gene bait set for the hyperdiverse Orchidaceae, the second-largest

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.

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