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Target sequence capture in orchids: Developing a kit to sequence hundreds of single‐copy loci

https://doi.org/10.1002/aps3.11416
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1002/ajb2.1047openalex-snapshot
Phylotranscriptomic analysis and genome evolution of the Cypripedioideae (Orchidaceae)
inferredcites →https://doi.org/10.1002/aps3.11337openalex-snapshot
Strategies for reducing per‐sample costs in target capture sequencing for phylogenomics and population genomics in plants
inferredcites →https://doi.org/10.1002/aps3.11416openalex-snapshot
Target sequence capture in orchids: Developing a kit to sequence hundreds of single‐copy loci
inferredcites →https://doi.org/10.1002/aps3.11420openalex-snapshot
New targets acquired: Improving locus recovery from the Angiosperms353 probe set
inferredcites →https://doi.org/10.1007/978-1-62703-646-7_10openalex-snapshot
Phylogeny-aware alignment with PRANK
inferredcites →https://doi.org/10.1007/978-3-319-31350-4_3openalex-snapshot
Targeted DNA Region Re-sequencing
inferredcites →https://doi.org/10.1007/978-3-642-37195-0_13openalex-snapshot
Assembling Genomes and Mini-metagenomes from Highly Chimeric Reads
inferredcites →https://doi.org/10.1007/s00606-008-0105-0openalex-snapshot
Phylogenetic utility of ycf1 in orchids: a plastid gene more variable than matK
inferredcites →https://doi.org/10.1007/s10592-005-9073-xopenalex-snapshot
Development and characterization of polymorphic microsatellite loci in endangered fern Adiantum reniforme var. sinense
inferredcites →https://doi.org/10.1016/j.ympev.2018.07.014openalex-snapshot
Anchored hybrid enrichment generated nuclear, plastid and mitochondrial markers resolve the Lepanthes horrida (Orchidaceae: Pleurothallidinae) species complex
inferredcites →https://doi.org/10.1016/s0022-2836(05)80360-2openalex-snapshot
Basic Local Alignment Search Tool
inferredcites →https://doi.org/10.1038/ng.3149openalex-snapshot
The genome sequence of the orchid Phalaenopsis equestris
inferredcites →https://doi.org/10.1038/nmeth.1923openalex-snapshot
Fast gapped-read alignment with Bowtie 2
inferredcites →https://doi.org/10.1073/pnas.0409137102openalex-snapshot
An algorithm for progressive multiple alignment of sequences with insertions
inferredcites →https://doi.org/10.1080/10635150701472164openalex-snapshot
Improvement of Phylogenies after Removing Divergent and Ambiguously Aligned Blocks from Protein Sequence Alignments
inferredcites →https://doi.org/10.1089/cmb.2013.0084openalex-snapshot
Assembling Single-Cell Genomes and Mini-Metagenomes From Chimeric MDA Products
inferredcites →https://doi.org/10.1093/aob/mcu253openalex-snapshot
Phylogenetic relationships in Epidendroideae (Orchidaceae), one of the great flowering plant radiations: progressive specialization and diversification
inferredcites →https://doi.org/10.1093/bioinformatics/btq033openalex-snapshot
BEDTools: a flexible suite of utilities for comparing genomic features
inferredcites →https://doi.org/10.1093/bioinformatics/btu033openalex-snapshot
RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies
inferredcites →https://doi.org/10.1093/bioinformatics/btu170openalex-snapshot
Trimmomatic: a flexible trimmer for Illumina sequence data
inferredcites →https://doi.org/10.1093/botlinnean/box083openalex-snapshot
A review of the trade in orchids and its implications for conservation
inferredcites →https://doi.org/10.1093/oso/9780198505136.001.0001openalex-snapshot
Genera Orchidacearum
inferredcites →https://doi.org/10.1093/oso/9780198507109.001.0001openalex-snapshot
Genera Orchidacearum
inferredcites →https://doi.org/10.1093/oso/9780198507123.001.0001openalex-snapshot
Genera Orchidacearum
inferredcites →https://doi.org/10.1093/oso/9780198507130.001.0001openalex-snapshot
Genera Orchidacearum
inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a026334openalex-snapshot
Selection of Conserved Blocks from Multiple Alignments for Their Use in Phylogenetic Analysis
inferredcites →https://doi.org/10.1093/sysbio/sys049openalex-snapshot
Anchored Hybrid Enrichment for Massively High-Throughput Phylogenomics
inferredcites →https://doi.org/10.1093/sysbio/syy086openalex-snapshot
A Universal Probe Set for Targeted Sequencing of 353 Nuclear Genes from Any Flowering Plant Designed Using k-Medoids Clustering
inferredcites →https://doi.org/10.1098/rspb.2015.1553openalex-snapshot
Orchid phylogenomics and multiple drivers of their extraordinary diversification
inferredcites →https://doi.org/10.1098/rspb.2017.1182openalex-snapshot
DNA metabarcoding of orchid-derived products reveals widespread illegal orchid trade
inferredcites →https://doi.org/10.1101/gr.9.9.868openalex-snapshot
CAP3: A DNA Sequence Assembly Program
inferredcites →https://doi.org/10.1111/boj.12234openalex-snapshot
An updated classification of Orchidaceae
inferredcites →https://doi.org/10.1111/j.1558-5646.1968.tb03463.xopenalex-snapshot
POLLINATION BY EUGLOSSINE BEES
inferredcites →https://doi.org/10.1111/nph.15312openalex-snapshot
Bridging the micro‐ and macroevolutionary levels in phylogenomics: Hyb‐Seq solves relationships from populations to species and above
inferredcites →https://doi.org/10.1126/science.1158395openalex-snapshot
Phylogeny-Aware Gap Placement Prevents Errors in Sequence Alignment and Evolutionary Analysis
inferredcites →https://doi.org/10.1146/annurev.es.13.110182.002105openalex-snapshot
Biology of the Orchid Bees (Euglossini)
inferredcites →https://doi.org/10.1186/s12859-018-2129-yopenalex-snapshot
ASTRAL-III: polynomial time species tree reconstruction from partially resolved gene trees
inferredcites →https://doi.org/10.1371/journal.pbio.1002379openalex-snapshot
Phylogenomics Reveals Three Sources of Adaptive Variation during a Rapid Radiation
inferredcites →https://doi.org/10.15517/lank.v13i3.14425openalex-snapshot
Generic and Subtribal relationShipS in neotropical cymbidieae (orchidaceae) baSed on matK/ycf1 plaStid data
inferredcites →https://doi.org/10.15517/rbt.v15i1.28484openalex-snapshot
Observations on Orchids and Euglossine Bees in Panama and Costa Rica
inferredcites →https://doi.org/10.21273/hortsci.39.1.202bopenalex-snapshot
Genera Orchidacearum, Volume 3, Orchidoideae (Part Two), Vanilloideae
inferredcites →https://doi.org/10.2307/1223934openalex-snapshot
An improved method of DNA isolation from plants collected in the field and conserved in saturated NaCl/CTAB solution
inferredcites →https://doi.org/10.2307/2656837openalex-snapshot
Subtribal and generic relationships of Maxillarieae (Orchidaceae) with emphasis on Stanhopeinae: combined molecular evidence
inferredcites →https://doi.org/10.2307/2656938openalex-snapshot
A phylogenetic analysis of the Orchidaceae: evidence from rbcL nucleotide sequences
inferredcites →https://doi.org/10.3389/fpls.2019.01761openalex-snapshot
Target Nuclear and Off-Target Plastid Hybrid Enrichment Data Inform a Range of Evolutionary Depths in the Orchid Genus Epidendrum
inferredcites →https://doi.org/10.3390/genes9030132openalex-snapshot
Testing for Polytomies in Phylogenetic Species Trees Using Quartet Frequencies
inferredcites →https://doi.org/10.3732/ajb.91.1.149openalex-snapshot
An expanded plastid DNA phylogeny of Orchidaceae and analysis of jackknife branch support strategy

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.5091/plecevo.114642zenodo-depositor-declared
An overview of floral and vegetative evolution in the Asian clade of Bulbophyllum (Orchidaceae)
inferred← citeshttps://doi.org/10.1002/ajb2.1695openalex-snapshot
Reconstructing Dipsacales phylogeny using Angiosperms353: issues and insights
inferred← citeshttps://doi.org/10.1002/ajb2.1703openalex-snapshot
Exploring Angiosperms353: An open, community toolkit for collaborative phylogenomic research on flowering plants
inferred← citeshttps://doi.org/10.1002/aps3.11443openalex-snapshot
Exploring Angiosperms353: Developing and applying a universal toolkit for flowering plant phylogenomics
inferred← citeshttps://doi.org/10.1002/aps3.11537openalex-snapshot
Target capture and genome skimming for plant diversity studies
inferred← citeshttps://doi.org/10.1002/aps3.11554openalex-snapshot
A target enrichment probe set for resolving phylogenetic relationships in the coffee family, Rubiaceae
inferred← citeshttps://doi.org/10.1002/aps3.11568openalex-snapshot
Compositae‐ParaLoss‐1272: A complementary sunflower‐specific probe set reduces paralogs in phylogenomic analyses of complex systems
inferred← citeshttps://doi.org/10.1002/aps3.11597openalex-snapshot
Developing Asparagaceae1726: An Asparagaceae‐specific probe set targeting 1726 loci for Hyb‐Seq and phylogenomics in the family
inferred← citeshttps://doi.org/10.1002/aps3.11615openalex-snapshot
Truly the best of both worlds: Merging lineage‐specific and universal probe kits to maximize phylogenomic inference
inferred← citeshttps://doi.org/10.1002/aps3.11624openalex-snapshot
From phylogenomics to breeding: Can universal target capture probes be used in the development of SNP markers for kinship analysis?
inferred← citeshttps://doi.org/10.1002/aps3.70019openalex-snapshot
Advancing phylogenomics in Amaranthaceae sensu stricto: Development and application of a new nuclear target enrichment bait set
inferred← citeshttps://doi.org/10.1002/aps3.70024openalex-snapshot
Astragalean819: An Astragalean clade‐specific bait set to resolve phylogenetic relationships in Astragalus
inferred← citeshttps://doi.org/10.1002/aps3.70059openalex-snapshot
HybSuite: An integrated pipeline for hybrid capture phylogenomics from reads to trees
inferred← citeshttps://doi.org/10.1002/aps3.70063openalex-snapshot
Leveraging target enrichment and genome skimming (Hyb‐Seq) of herbarium collections to unlock timber DNA barcoding
inferred← citeshttps://doi.org/10.1002/ece3.10190openalex-snapshot
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
inferred← citeshttps://doi.org/10.1002/tax.13260openalex-snapshot
Complete genus‐level phylogenomics and new subtribal classification of the pantropical plant family Annonaceae
inferred← citeshttps://doi.org/10.1007/s10592-026-01808-4openalex-snapshot
Genetic diversity and population structure of Florida’s threatened Bletia purpurea (Orchidaceae): Insights from target capture sequencing and implications for conservation
inferred← citeshttps://doi.org/10.1007/s11240-026-03417-yopenalex-snapshot
In vitro and biotechnological approaches in Dendrobium orchid breeding: a review
inferred← citeshttps://doi.org/10.1007/s12225-022-10016-5openalex-snapshot
Systematics and conservation of British and Irish orchids: a "state of the union" assessment to accompany Atlas 2020
inferred← citeshttps://doi.org/10.1007/s44281-023-00026-zopenalex-snapshot
Integrating genomic sequencing resources: an innovative perspective on recycling with universal Angiosperms353 probe sets
inferred← citeshttps://doi.org/10.1016/j.ympev.2026.108633openalex-snapshot
Nuclear phylogenomics reveals trait- and environment-associated patterns of diversification in Prunus s.l. (Rosaceae)
inferred← citeshttps://doi.org/10.1038/s41598-025-31584-zopenalex-snapshot
Urticaceae542 as a novel probe set combining universal and lineage-specific loci for phylogenomics of Urticaceae
inferred← citeshttps://doi.org/10.1093/aob/mcad153openalex-snapshot
Unravelling phylogenetic relationships of the tribe Cereeae using target enrichment sequencing
inferred← citeshttps://doi.org/10.1093/aob/mcae161openalex-snapshot
Phylogenomic analysis of target enrichment and transcriptome data uncovers rapid radiation and extensive hybridization in the slipper orchid genus Cypripedium
inferred← citeshttps://doi.org/10.1093/aob/mcae202openalex-snapshot
Orchid phylogenetics and evolution: history, current status and prospects
inferred← citeshttps://doi.org/10.1093/botlinnean/boaf047openalex-snapshot
Rediscovery and phylogenomic placement of Feliciadamia stenocarpa (Feliciadamieae: Melastomataceae): assessing gene tree discordance
inferred← citeshttps://doi.org/10.1093/gbe/evag202openalex-snapshot
Phylotranscriptomics Allows Distinguishing Major Gene Flow Events from Incomplete Lineage Sorting in Rapidly Diversifying Mimetic Orchids (Genus Ophrys )
inferred← citeshttps://doi.org/10.1093/plcell/koad260openalex-snapshot
Complementing model species with model clades
inferred← citeshttps://doi.org/10.1093/sysbio/syaf069openalex-snapshot
Nuclear Phylogenomic Insights into Relationships, Support, and Conflict Among the Early Diverging Lineages of the Megadiverse Epidendroid Orchids
inferred← citeshttps://doi.org/10.1101/2023.07.19.549085openalex-snapshot
Compositae-ParaLoss-1272: Complementary sunflower specific probe-set reduces issues with paralogs in complex systems
inferred← citeshttps://doi.org/10.1101/2023.11.16.567445openalex-snapshot
Truly the best of both worlds: merging lineage-specific and universal baiting kits to maximize phylogenomic inference
inferred← citeshttps://doi.org/10.1111/1755-0998.13986openalex-snapshot
Orchidinae‐205: A new genome‐wide custom bait set for studying the evolution, systematics, and trade of terrestrial orchids
inferred← citeshttps://doi.org/10.1111/1755-0998.70173openalex-snapshot
Enrichment Probe Sets Combining Universal and Lineage‐Specific Targets Help Resolve Recalcitrant Lineages
inferred← citeshttps://doi.org/10.1111/eva.70315openalex-snapshot
Tracing Species Boundaries Through Genomic Baits: Diagnostic SNP Panels for Genotyping Orchid Pollinaria
inferred← citeshttps://doi.org/10.1111/jipb.13415openalex-snapshot
Phylogenomics and the flowering plant tree of life
inferred← citeshttps://doi.org/10.1111/jipb.13462openalex-snapshot
Comprehensive phylogenetic analyses of Orchidaceae using nuclear genes and evolutionary insights into epiphytism
inferred← citeshttps://doi.org/10.1111/jipb.13609openalex-snapshot
Nuclear phylogenomics of angiosperms and insights into their relationships and evolution
inferred← citeshttps://doi.org/10.1111/jipb.70315openalex-snapshot
Orchid genome evolution and trait innovation
inferred← citeshttps://doi.org/10.15517/lank.v22i3.53319openalex-snapshot
new species of Andinia (Pleurothallidinae) from Peru and an updated phylogenetic analysis of the genus with emphasis on subgenus Aenigma
inferred← citeshttps://doi.org/10.3389/fevo.2022.943361openalex-snapshot
Predictors of sequence capture in a large-scale anchored phylogenomics project
inferred← citeshttps://doi.org/10.3389/fgene.2022.1085692openalex-snapshot
A nuclear target sequence capture probe set for phylogeny reconstruction of the charismatic plant family Bignoniaceae
inferred← citeshttps://doi.org/10.3389/fpls.2022.889988openalex-snapshot
A Bird’s Eye View of the Systematics of Convolvulaceae: Novel Insights From Nuclear Genomic Data
inferred← citeshttps://doi.org/10.3389/fpls.2022.910362openalex-snapshot
Orchid Phylotranscriptomics: The Prospects of Repurposing Multi-Tissue Transcriptomes for Phylogenetic Analysis and Beyond
inferred← citeshttps://doi.org/10.3389/fpls.2026.1864920openalex-snapshot
The multichromosomal structure evolution of Dendrobium mitogenomes and new insights into interrelationships of recently radiated tribes in Epidendroideae (Orchidaceae)
inferred← citeshttps://doi.org/10.3390/d17020136openalex-snapshot
Nuclear Phylogenomics of Angiosperms and Evolutionary Implications
inferred← citeshttps://doi.org/10.3390/genes13040707openalex-snapshot
A target Capture Probe Set Useful for Deep- and Shallow-Level Phylogenetic Studies in Cactaceae
inferred← citeshttps://doi.org/10.3897/ab.e98875openalex-snapshot
Molecular identification of plants: from sequence to species
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