ArticleApplications in plant sciences2018
Targeting legume loci: A comparison of three methods for target enrichment bait design in Leguminosae 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 32 papers.
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32 citing papers in PubMed.
- Resolving relationships in the radiation of Australia's largest pea clade (Fabaceae tribe Mirbelieae) with target-capture sequencing.Annals of botany · 2025Article
- Building a robust backbone for Astragalus using a clade-specific target enrichment bait set.American journal of botany · 2025Article
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- Divergence and reticulation in the Mexican white oaks: ecological and phylogenomic evidence on species limits and phylogenetic networks in the Quercus laeta complex (Fagaceae).Annals of botany · 2024Article
- New insights into polyploid evolution and dynamic nature of Ludwigia section Isnardia (Onagraceae).Botanical studies · 2023Article
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- A target capture approach for phylogenomic analyses at multiple evolutionary timescales in rosewoods (Dalbergia spp.) and the legume family (Fabaceae).Molecular ecology resources · 2022Article
- A multispecies amplicon sequencing approach for genetic diversity assessments in grassland plant species.Molecular ecology resources · 2022Article
- Target capture data resolve recalcitrant relationships in the coffee family (Rubioideae, Rubiaceae).Frontiers in plant science · 2022Article
- Highly Resolved Papilionoid Legume Phylogeny Based on Plastid Phylogenomics.Frontiers in plant science · 2022Article
- The best of both worlds: Combining lineage-specific and universal bait sets in target-enrichment hybridization reactions.Applications in plant sciences · 2021Article
- New targets acquired: Improving locus recovery from the Angiosperms353 probe set.Applications in plant sciences · 2021Article
- An Overview of the Genetics and Genomics of theFrontiers in plant science · 2021Review
- Allele Sorting as a Novel Approach to Resolving the Origin of Allotetraploids Using Hyb-Seq Data: A Case Study of the Balkan Mountain EndemicFrontiers in plant science · 2021Article
- The Effects of Herbarium Specimen Characteristics on Short-Read NGS Sequencing Success in Nearly 8000 Specimens: Old, Degraded Samples Have Lower DNA Yields but Consistent Sequencing Success.Frontiers in plant science · 2021Article
- Hybrid capture of 964 nuclear genes resolves evolutionary relationships in the mimosoid legumes and reveals the polytomous origins of a large pantropical radiation.American journal of botany · 2020Article
- Enabling evolutionary studies at multiple scales in Apocynaceae through Hyb-Seq.Applications in plant sciences · 2020Article
- Reference transcriptomes and comparative analyses of six species in the threatened rosewood genus Dalbergia.Scientific reports · 2020Article
- Strategies for reducing per-sample costs in target capture sequencing for phylogenomics and population genomics in plants.Applications in plant sciences · 2020Review
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4 authors.
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Abstract
premise of the studyThe development of pipelines for locus discovery has spurred the use of target enrichment for plant phylogenomics. However, few studies have compared pipelines from locus discovery and bait design, through validation, to tree inference. We compared three methods within Leguminosae (Fabaceae) and present a workflow for future efforts.
methodsUsing 30 transcriptomes, we compared Hyb-Seq, MarkerMiner, and the Yang and Smith (Y&S) pipelines for locus discovery, validated 7501 baits targeting 507 loci across 25 genera via Illumina sequencing, and inferred gene and species trees via concatenation- and coalescent-based methods.
resultsHyb-Seq discovered loci with the longest mean length. MarkerMiner discovered the most conserved loci with the least flagged as paralogous. Y&S offered the most parsimony-informative sites and putative orthologs. Target recovery averaged 93% across taxa. We optimized our targeted locus set based on a workflow designed to minimize paralog/ortholog conflation and thus present 423 loci for legume phylogenomics.
conclusionsMethods differed across criteria important for phylogenetic marker development. We recommend Hyb-Seq as a method that may be useful for most phylogenomic projects. Our targeted locus set is a resource for future, community-driven efforts to reconstruct the legume tree of life.
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