ArticleApplications in plant sciences2021
Target sequence capture in orchids: Developing a kit to sequence hundreds of single-copy loci.
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 28 papers.
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Who cites it
28 citing papers in PubMed, 43 citations in OpenAlex.
- Phylotranscriptomics Allows Distinguishing Major Gene Flow Events from Incomplete Lineage Sorting in Rapidly Diversifying Mimetic Orchids (Genus Ophrys).Genome biology and evolution · 2026Article
- Orchid genome evolution and trait innovation.Journal of integrative plant biology · 2026Review
- 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
- The multichromosomal structure evolution ofFrontiers in plant science · 2026Article
- Urticaceae542 as a novel probe set combining universal and lineage-specific loci for phylogenomics of Urticaceae.Scientific reports · 2025Article
- Orchid phylogenetics and evolution: history, current status and prospects.Annals of botany · 2025Review
- Phylogenomic analysis of target enrichment and transcriptome data uncovers rapid radiation and extensive hybridization in the slipper orchid genus Cypripedium.Annals of botany · 2024Article
- Complementing model species with model clades.The Plant cell · 2024Review
- Unravelling phylogenetic relationships of the tribe Cereeae using target enrichment sequencing.Annals of botany · 2023Article
- Nano-Strainer: A workflow for the identification of single-copy nuclear loci for plant systematic studies, using target capture kits and Oxford Nanopore long reads.Ecology and evolution · 2023Article
- A target Capture Probe Set Useful for Deep- and Shallow-Level Phylogenetic Studies in Cactaceae.Genes · 2022Article
- A Bird's Eye View of the Systematics of Convolvulaceae: Novel Insights From Nuclear Genomic Data.Frontiers in plant science · 2022Article
- A nuclear target sequence capture probe set for phylogeny reconstruction of the charismatic plant family Bignoniaceae.Frontiers in genetics · 2022Article
- Orchid Phylotranscriptomics: The Prospects of Repurposing Multi-Tissue Transcriptomes for Phylogenetic Analysis and Beyond.Frontiers in plant science · 2022Article
- Reconstructing Dipsacales phylogeny using Angiosperms353: issues and insights.American journal of botany · 2021Article
- Target sequence capture in orchids: Developing a kit to sequence hundreds of single-copy loci.Applications in plant sciences · 2021Article
- Exploring Angiosperms353: Developing and applying a universal toolkit for flowering plant phylogenomics.Applications in plant sciences · 2021Article
- Developing Asparagaceae1726: An Asparagaceae-specific probe set targeting 1726 loci for Hyb-Seq and phylogenomics in the family.Applications in plant sciencesArticle
- A target enrichment probe set for resolving phylogenetic relationships in the coffee family, Rubiaceae.Applications in plant sciencesArticle
Corrections and comments
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Authors and funding
4 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
premiseUnderstanding relationships among orchid species and populations is of critical importance for orchid conservation. Target sequence capture has become a standard method for extracting hundreds of orthologous loci for phylogenomics. Up-front cost and time associated with design of bait sets makes this method prohibitively expensive for many researchers. Therefore, we designed a target capture kit to reliably sequence hundreds of orthologous loci across orchid lineages.
methodsWe designed an Orchidaceae target capture bait set for 963 single-copy genes identified in published orchid genome sequences. The bait set was tested on 28 orchid species, with representatives of the subfamilies Cypripedioideae, Orchidoideae, and Epidendroideae.
resultsBetween 1,518,041 and 87,946,590 paired-end 150-base reads were generated for target-enriched genomic libraries. We assembled an average of 812 genes per library for Epidendroideae species and a mean of 501 genes for species in the subfamilies Orchidoideae and Cypripedioideae. Furthermore, libraries had on average 107 of the 254 genes that are included in the Angiosperms353 bait set, allowing for direct comparison of studies using either bait set. DISCUSSION: The Orchidaceae963 kit will enable greater accessibility and utility of next-generation sequencing for orchid systematics, population genetics, and identification in the illegal orchid trade.
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