ArticleApplications in plant sciences2021
On the potential of Angiosperms353 for population genomic studies.
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 33 papers.
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33 citing papers in PubMed.
- Simultaneous Inference of Flora-Wide Nuclear and Plastid Phylogenies Using Angiosperms353 Sequence Capture Data.Molecular ecology resources · 2026Article
- Enrichment Probe Sets Combining Universal and Lineage-Specific Targets Help Resolve Recalcitrant Lineages.Molecular ecology resources · 2026Article
- A case of budding speciation in the California Floristic Province and infraspecific divergence in Abronia villosa.American journal of botany · 2026Article
- Genomic elucidation of hybridization between Liberica and excelsa coffee and its implications for coffee crop development.Scientific reports · 2026Article
- Population genetics and phylogenomic insights into the origin of economically important black pepper (Piper nigrum).American journal of botany · 2026Article
- Patterns of Interploidy Admixture in Polyploid Complexes: Insights From Thymus Sect. Mastichina (Lamiaceae).Molecular ecology · 2026Article
- Evolutionary history of Australian samphires (Salicornieae, Amaranthaceae).Annals of botany · 2026Article
- Genomic insights into population structure and conservation of wild olive (Frontiers in plant science · 2026Article
- Urticaceae542 as a novel probe set combining universal and lineage-specific loci for phylogenomics of Urticaceae.Scientific reports · 2025Article
- Genomic data define species delimitation in Liberica coffee with implications for crop development and conservation.Nature plants · 2025Article
- Looking back to look ahead: the temporal dimension of conservation seed bank collections.The New phytologist · 2025Review
- Conservation Implications for the Iberian Narrow EndemicEcology and evolution · 2025Article
- Genome-Wide Adaptation to a Complex Environmental Gradient in a Keystone Phytoplankton Species.Molecular ecology · 2025Article
- When the sand blossoms: Phylogeny, trait evolution, and geography of speciation in Linanthus.American journal of botany · 2025Article
- Range extension and re-assessment ofBiodiversity data journal · 2025Article
- Phylogenomic study ofFrontiers in plant science · 2025Article
- The evolution of the hypotetraploidFrontiers in plant science · 2023Article
- Easy353: A Tool to Get Angiosperms353 Genes for Phylogenomic Research.Molecular biology and evolution · 2022Article
- Taxon-specific or universal? Using target capture to study the evolutionary history of rapid radiations.Molecular ecology resources · 2022Article
- Phylogenomic and comparative analyses of Coffeeae alliance (Rubiaceae): deep insights into phylogenetic relationships and plastome evolution.BMC plant biology · 2022Article
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4 authors.
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Abstract
premiseThe successful application of universal targeted sequencing markers, such as those developed for the Angiosperms353 probe set, within populations could reduce or eliminate the need for specific marker development, while retaining the benefits of full-gene sequences in population-level analyses. However, whether the Angiosperms353 markers provide sufficient variation within species to calculate demographic parameters is untested.
methodsUsing herbarium specimens from a 50-year-old floristic survey in Texas, we sequenced 95 samples from 24 species using the Angiosperms353 probe set. Our data workflow calls variants within species and prepares data for population genetic analysis using standard metrics. In our case study, gene recovery was affected by genomic library concentration only at low concentrations and displayed limited phylogenetic bias.
resultsWe identified over 1000 segregating variants with zero missing data for 92% of species and demonstrate that Angiosperms353 markers contain sufficient variation to estimate pairwise nucleotide diversity (π)-typically between 0.002 and 0.010, with most variation found in flanking non-coding regions. In a subset of variants that were filtered to reduce linkage, we uncovered high heterozygosity in many species, suggesting that denser sampling within species should permit estimation of gene flow and population dynamics. DISCUSSION: Angiosperms353 should benefit conservation genetic studies by providing universal repeatable markers, low missing data, and haplotype information, while permitting inclusion of decades-old herbarium specimens.
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