ArticleApplications in plant sciences2021
Relative performance of customized and universal probe sets in target enrichment: A case study in subtribe Malinae.
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 16 papers.
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16 citing papers in PubMed.
- Enrichment Probe Sets Combining Universal and Lineage-Specific Targets Help Resolve Recalcitrant Lineages.Molecular ecology resources · 2026Article
- Wide diversity in narrow geographic space: genetic, morphological and ploidy variation in three Central EuropeanAoB PLANTS · 2026Article
- Resolving the phylogeny of Thladiantha (Cucurbitaceae) with three different target capture pipelines.BMC ecology and evolution · 2023Article
- Unravelling phylogenetic relationships of the tribe Cereeae using target enrichment sequencing.Annals of botany · 2023Article
- A target capture approach for phylogenomic analyses at multiple evolutionary timescales in rosewoods (Dalbergia spp.) and the legume family (Fabaceae).Molecular ecology resources · 2022Article
- Taxon-specific or universal? Using target capture to study the evolutionary history of rapid radiations.Molecular ecology resources · 2022Article
- A New Approach Using Targeted Sequence Capture for Phylogenomic Studies across Cactaceae.Genes · 2022Article
- The relationship between transposable elements and ecological niches in the Greater Cape Floristic Region: A study on the genusFrontiers in plant science · 2022Article
- Lineage-specific vs. universal: A comparison of the Compositae1061 and Angiosperms353 enrichment panels in the sunflower family.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
- Exploring Angiosperms353: Developing and applying a universal toolkit for flowering plant phylogenomics.Applications in plant sciences · 2021Article
- Phylogeny ofPeerJ · 2021Article
- How to Tackle Phylogenetic Discordance in Recent and Rapidly Radiating Groups? Developing a Workflow UsingFrontiers in plant science · 2021Article
- Advancing phylogenomics in Amaranthaceae sensu stricto: Development and application of a new nuclear target enrichment bait set.Applications in plant sciencesArticle
- A target enrichment probe set for resolving phylogenetic relationships in the coffee family, Rubiaceae.Applications in plant sciencesArticle
- Target capture and genome skimming for plant diversity studies.Applications in plant sciencesArticle
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8 authors.
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No grant is acknowledged in the PubMed record.
Abstract
premiseCustom probe design for target enrichment in phylogenetics is tedious and often hinders broader phylogenetic synthesis. The universal angiosperm probe set Angiosperms353 may be the solution. Here, we test the relative performance of Angiosperms353 on the Rosaceae subtribe Malinae in comparison with custom probes that we specifically designed for this clade. We then address the impact of bioinformatically altering the performance of Angiosperms353 by replacing the original probe sequences with orthologs extracted from the
methodsTo evaluate the relative performance of these probe sets, we compared the enrichment efficiency, locus recovery, alignment length, proportion of parsimony-informative sites, proportion of potential paralogs, the topology and support of the resulting species trees, and the gene tree discordance.
resultsLocus recovery was highest for our custom Malinae probe set, and replacing the original Angiosperms353 sequences with a DISCUSSION: A custom probe set benefits from data completeness and can be tailored toward the specificities of the project of choice; however, Angiosperms353 was equally as phylogenetically informative as the custom probes. We therefore recommend using both a custom probe set and Angiosperms353 to facilitate large-scale systematic studies, where financially possible.
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