ArticleApplications in plant sciences2018
Comparison of taxon-specific versus general locus sets for targeted sequence capture in plant phylogenomics.
Article in Applications in plant sciences, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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23 citing papers in PubMed, 49 citations in OpenAlex.
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- Taxon-specific or universal? Using target capture to study the evolutionary history of rapid radiations.Molecular ecology resources · 2022Article
- A Comprehensive Phylogenomic Platform for Exploring the Angiosperm Tree of Life.Systematic biology · 2022Article
- A nuclear target sequence capture probe set for phylogeny reconstruction of the charismatic plant family Bignoniaceae.Frontiers in genetics · 2022Article
- Reconstructing Dipsacales phylogeny using Angiosperms353: issues and insights.American journal of botany · 2021Article
- Relative performance of customized and universal probe sets in target enrichment: A case study in subtribe Malinae.Applications in plant sciences · 2021Article
- Enabling evolutionary studies at multiple scales in Apocynaceae through Hyb-Seq.Applications in plant sciences · 2020Article
- A two-tier bioinformatic pipeline to develop probes for target capture of nuclear loci with applications in Melastomataceae.Applications in plant sciences · 2020Article
- Reconstructing the Complex Evolutionary History of the PapuasianFrontiers in plant science · 2020Article
- A customized nuclear target enrichment approach for developing a phylogenomic baseline forApplications in plant sciences · 2019Article
- Tackling Rapid Radiations With Targeted Sequencing.Frontiers in plant science · 2019Article
- Capturing variation inApplications in plant sciences · 2018Article
- Comparison of taxon-specific versus general locus sets for targeted sequence capture in plant phylogenomics.Applications in plant sciences · 2018Article
- Target capture and genome skimming for plant diversity studies.Applications in plant sciencesArticle
- Calceolariaceae809: A bait set for targeted sequencing of nuclear loci.Applications in plant sciencesArticle
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Authors and funding
3 authors at 1 institution in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
premise of the studyTargeted sequence capture can be used to efficiently gather sequence data for large numbers of loci, such as single-copy nuclear loci. Most published studies in plants have used taxon-specific locus sets developed individually for a clade using multiple genomic and transcriptomic resources. General locus sets can also be developed from loci that have been identified as single-copy and have orthologs in large clades of plants.
methodsWe identify and compare a taxon-specific locus set and three general locus sets (conserved ortholog set [COSII], shared single-copy nuclear [APVO SSC] genes, and pentatricopeptide repeat [PPR] genes) for targeted sequence capture in
resultsThe taxon-specific locus set had the most target loci. Assembly success was high for all locus sets in DISCUSSION: General locus sets can be a useful source of sequence capture targets, especially if multiple genomic resources are not available for a taxon.
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