ArticleApplications in plant sciences2014
Hyb-Seq: Combining target enrichment and genome skimming for plant phylogenomics.
Article in Applications in plant sciences, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 173 papers, 1 of them a synthesis that pooled it.
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173 citing papers in PubMed, 1 synthesis or guideline pooled it, 509 citations in OpenAlex.
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- Enrichment Probe Sets Combining Universal and Lineage-Specific Targets Help Resolve Recalcitrant Lineages.Molecular ecology resources · 2026Article
- Integrative utilization of genomic resources for improved phylogenetic resolution in Sonerileae (Melastomataceae).American journal of botany · 2026Article
- Next-Generation Genotyping: Innovations Driving Plant Genomic Improvement.Life (Basel, Switzerland) · 2026Review
- Applying Target Capture Sequencing to Unravel thePlants (Basel, Switzerland) · 2026Article
- Patterns of Interploidy Admixture in Polyploid Complexes: Insights From Thymus Sect. Mastichina (Lamiaceae).Molecular ecology · 2026Article
- Phylogenomics, ecomorphological evolution, and historical biogeography in Deuterocohnia (Bromeliaceae: Pitcairnioideae).American journal of botany · 2026Article
- Molecular identification and diversity assessment of Tyrrhenian Romulea species (Iridaceae).PloS one · 2026Article
- UnFATE: A Comprehensive Probe Set and Bioinformatics Pipeline for Phylogeny Reconstruction and Multilocus Barcoding of Filamentous Ascomycetes (Ascomycota, Pezizomycotina).Systematic biology · 2025Article
- PickMe: Sample Selection for Species Tree Reconstruction using Coalescent Weighted Quartets.Systematic biology · 2025Article
- Ortho2Web: a workflow for disentangling the roles of hybridization and allopolyploidization in reticulation within Campanulaceae.BMC biology · 2025Article
- Evidence of Intraspecific Adaptive Variation in the American Pika (Ochotona princeps) on a Continental Scale Using a Target Enrichment and Mitochondrial Genome Skimming Approach.Molecular ecology · 2025Article
- Article
- Evaluating the utility of deep genome skimming for phylogenomic analyses: A case study in the species-rich genusPlant diversity · 2025Article
- Phylogenetic relationships and the identification of allopolyploidy in circumpolar Silene sect. Physolychnis.American journal of botany · 2025Article
- Extensive genome-wide phylogenetic discordance is due to incomplete lineage sorting in the rapidly radiated East Asian genus Nekemias (Vitaceae).Annals of botany · 2025Article
- Genomic DNA barcodes provide novel insights into species delimitation in the complex Camellia sect. Thea (Theaceae).BMC plant biology · 2025Article
- Specimen Identification Through Multilocus Species Tree Constructed From Single-Copy Orthologs (SCOs): A Case Study inEcology and evolution · 2025Article
- Reinstatement ofPhytoKeys · 2025Article
- Low-pass nanopore sequencing for measurement of global methylation levels in plants.BMC genomics · 2024Article
113 more citing papers are in PubMed but not listed here.
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Authors and funding
7 authors at 4 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
unlabelledPREMISE OF THE STUDY: Hyb-Seq, the combination of target enrichment and genome skimming, allows simultaneous data collection for low-copy nuclear genes and high-copy genomic targets for plant systematics and evolution studies. • METHODS AND
resultsGenome and transcriptome assemblies for milkweed (Asclepias syriaca) were used to design enrichment probes for 3385 exons from 768 genes (>1.6 Mbp) followed by Illumina sequencing of enriched libraries. Hyb-Seq of 12 individuals (10 Asclepias species and two related genera) resulted in at least partial assembly of 92.6% of exons and 99.7% of genes and an average assembly length >2 Mbp. Importantly, complete plastomes and nuclear ribosomal DNA cistrons were assembled using off-target reads. Phylogenomic analyses demonstrated signal conflict between genomes. •
conclusionsThe Hyb-Seq approach enables targeted sequencing of thousands of low-copy nuclear exons and flanking regions, as well as genome skimming of high-copy repeats and organellar genomes, to efficiently produce genome-scale data sets for phylogenomics.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.