ArticleApplications in plant sciences2021
Lineage-specific vs. universal: A comparison of the Compositae1061 and Angiosperms353 enrichment panels in the sunflower family.
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 21 papers.
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21 citing papers in PubMed.
- Tracing Species Boundaries Through Genomic Baits: Diagnostic SNP Panels for Genotyping Orchid Pollinaria.Evolutionary applications · 2026Article
- Enrichment Probe Sets Combining Universal and Lineage-Specific Targets Help Resolve Recalcitrant Lineages.Molecular ecology resources · 2026Article
- Nuclear phylogenomic analysis of Allium (Amaryllidaceae) species from Kazakhstan reveals incomplete lineage sorting and gene flow.BMC plant biology · 2026Article
- Evolutionary history of Australian samphires (Salicornieae, Amaranthaceae).Annals of botany · 2026Article
- Unravelling phylogenetic relationships of the tribe Cereeae using target enrichment sequencing.Annals of botany · 2023Article
- Chloroplast Genomes and Phylogenetic Analysis of ThreeInternational journal of molecular sciences · 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
- Increased resolution in the face of conflict: phylogenomics of the Neotropical bellflowers (Campanulaceae: Lobelioideae), a rapid plant radiation.Annals of botany · 2022Article
- 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
- New Insights Into the Relationships Within Subtribe Scorzonerinae (Cichorieae, Asteraceae) Using Hybrid Capture Phylogenomics (Hyb-Seq).Frontiers in plant science · 2022Article
- Exploring Angiosperms353: Developing and applying a universal toolkit for flowering plant phylogenomics.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
- How to Tackle Phylogenetic Discordance in Recent and Rapidly Radiating Groups? Developing a Workflow UsingFrontiers in plant science · 2021Article
- Phylogeny ofPeerJ · 2021Article
- A target enrichment probe set for resolving phylogenetic relationships in the coffee family, Rubiaceae.Applications in plant sciencesArticle
- Compositae-ParaLoss-1272: A complementary sunflower-specific probe set reduces paralogs in phylogenomic analyses of complex systems.Applications in plant sciencesArticle
- Target capture and genome skimming for plant diversity studies.Applications in plant sciencesArticle
- Astragalean819: An Astragalean clade-specific bait set to resolve phylogenetic relationships inApplications in plant sciencesArticle
- A roadmap of phylogenomic methods for studying polyploid plant genera.Applications in plant sciencesArticle
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10 authors.
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No grant is acknowledged in the PubMed record.
Abstract
premisePhylogenetic studies in the Compositae are challenging due to the sheer size of the family and the challenges they pose for molecular tools, ranging from the genomic impact of polyploid events to their very conserved plastid genomes. The search for better molecular tools for phylogenetic studies led to the development of the family-specific Compositae1061 probe set, as well as the universal Angiosperms353 probe set designed for all flowering plants. In this study, we evaluate the extent to which data generated using the family-specific kit and those obtained with the universal kit can be merged for downstream analyses.
methodsWe used comparative methods to verify the presence of shared loci between probe sets. Using two sets of eight samples sequenced with Compositae1061 and Angiosperms353, we ran phylogenetic analyses with and without loci flagged as paralogs, a gene tree discordance analysis, and a complementary phylogenetic analysis mixing samples from both sample sets.
resultsOur results show that the Compositae1061 kit provides an average of 721 loci, with 9-46% of them presenting paralogs, while the Angiosperms353 set yields an average of 287 loci, which are less affected by paralogy. Analyses mixing samples from both sets showed that the presence of 30 shared loci in the probe sets allows the combination of data generated in different ways. DISCUSSION: Combining data generated using different probe sets opens up the possibility of collaborative efforts and shared data within the synantherological community.
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