ArticleApplications in plant sciences2021
The best of both worlds: Combining lineage-specific and universal bait sets in target-enrichment hybridization reactions.
Article in Applications in plant sciences, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed, 38 citations in OpenAlex.
- Unravelling Complex Hybrid and Polyploid Evolutionary Relationships Using Phylogenetic Placement of Homologous Gene Copies from Target Enrichment Data.Systematic biology · 2026Article
- Mitoplastomic discordance in Brassicaceae phylogenomics confirms the complex evolutionary history of the family.Annals of botany · 2026Article
- Phasing Hyb-Seq loci from two combined bait sets to investigate phylogenetic patterns of hybridization within Boechera s.s. (Brassicaceae).Annals of botany · 2026Article
- Urticaceae542 as a novel probe set combining universal and lineage-specific loci for phylogenomics of Urticaceae.Scientific reports · 2025Article
- Toward a phylogenomic classification of magnoliids.American journal of botany · 2025Article
- Complementing model species with model clades.The Plant cell · 2024Review
- The evolution of the hypotetraploidFrontiers in plant science · 2023Article
- A target Capture Probe Set Useful for Deep- and Shallow-Level Phylogenetic Studies in Cactaceae.Genes · 2022Article
- A New Approach Using Targeted Sequence Capture for Phylogenomic Studies across Cactaceae.Genes · 2022Article
- A Comprehensive Phylogenomic Platform for Exploring the Angiosperm Tree of Life.Systematic biology · 2022Article
- Phylogenomic assessment prompts recognition of the Serianthes clade and confirms the monophyly ofPhytoKeys · 2022Article
- The best of both worlds: Combining lineage-specific and universal bait sets in target-enrichment hybridization reactions.Applications in plant sciences · 2021Article
- Relative performance of customized and universal probe sets in target enrichment: A case study in subtribe Malinae.Applications in plant sciences · 2021Article
- Lineage-specific vs. universal: A comparison of the Compositae1061 and Angiosperms353 enrichment panels in the sunflower family.Applications in plant sciences · 2021Article
- Exploring Angiosperms353: Developing and applying a universal toolkit for flowering plant phylogenomics.Applications in plant sciences · 2021Article
- Target capture and genome skimming for plant diversity studies.Applications in plant sciencesArticle
- HybSuite: An integrated pipeline for hybrid capture phylogenomics from reads to trees.Applications in plant sciencesArticle
- A target enrichment probe set for resolving phylogenetic relationships in the coffee family, Rubiaceae.Applications in plant sciencesArticle
- Truly the best of both worlds: Merging lineage-specific and universal probe kits to maximize phylogenomic inference.Applications in plant sciencesArticle
- A roadmap of phylogenomic methods for studying polyploid plant genera.Applications in plant sciencesArticle
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Authors and funding
18 authors at 11 institutions in 6 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
premiseResearchers 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
resultsUsing 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%).
conclusionsHigh 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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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.