ReviewFrontiers in genetics2019
A Guide to Carrying Out a Phylogenomic Target Sequence Capture Project.
Review in Frontiers in genetics, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 54 papers.
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Who cites it
54 citing papers in PubMed.
- Simultaneous Inference of Flora-Wide Nuclear and Plastid Phylogenies Using Angiosperms353 Sequence Capture Data.Molecular ecology resources · 2026Article
- A global phylogenetic framework for Diospyros L. (Ebenaceae, Ericales): enhanced taxon and sample coverage through NGS, Sanger sequencing and herbariomics.Annals of botany · 2026Article
- 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
- Target Capture Sequencing Provides Insights Into Hybridogenetic Water Frogs.Ecology and evolution · 2026Article
- Five Hidden Species in a Widespread European Vertebrate: Disentangling the Alpine Newt Cryptic Species Complex Through Genomic Phylogeography.Molecular ecology · 2026Article
- The frequency and importance of polyploidy in tropical rainforest tree radiations.The New phytologist · 2026Article
- Resolving relationships in the radiation of Australia's largest pea clade (Fabaceae tribe Mirbelieae) with target-capture sequencing.Annals of botany · 2025Article
- NewtCap: An Efficient Target Capture Approach to Boost Genomic Studies in Salamandridae (True Salamanders and Newts).Ecology and evolution · 2025Article
- OLTA: Optimizing bait seLection for TArgeted sequencing.Bioinformatics (Oxford, England) · 2025Article
- VenomCap: An exon-capture probe set for the targeted sequencing of snake venom genes.Molecular ecology resources · 2024Article
- Phylogenomic analysis reveals five independently evolved African forage grass clades in the genus Urochloa.Annals of botany · 2024Article
- Hybrid-Capture Target Enrichment in Human Pathogens: Identification, Evolution, Biosurveillance, and Genomic Epidemiology.Pathogens (Basel, Switzerland) · 2024Review
- The effect of missing data on evolutionary analysis of sequence capture bycatch, with application to an agricultural pest.Molecular genetics and genomics : MGG · 2024Article
- History and prospects of flax genetic markers.Frontiers in plant science · 2024Review
- Target enrichment sequencing coupled with GWAS identifiesFrontiers in plant science · 2024Article
- Resolving the phylogeny of Thladiantha (Cucurbitaceae) with three different target capture pipelines.BMC ecology and evolution · 2023Article
- Assessment and validation of enrichment and target capture approaches to improveJournal of clinical microbiology · 2023Article
- Next-generation fungal identification using target enrichment and Nanopore sequencing.BMC genomics · 2023Article
- Identifying Climatic Drivers of Hybridization with a New Ancestral Niche Reconstruction Method.Systematic biology · 2023Article
Corrections and comments
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Authors and funding
11 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
High-throughput DNA sequencing techniques enable time- and cost-effective sequencing of large portions of the genome. Instead of sequencing and annotating whole genomes, many phylogenetic studies focus sequencing effort on large sets of pre-selected loci, which further reduces costs and bioinformatic challenges while increasing coverage. One common approach that enriches loci before sequencing is often referred to as target sequence capture. This technique has been shown to be applicable to phylogenetic studies of greatly varying evolutionary depth. Moreover, it has proven to produce powerful, large multi-locus DNA sequence datasets suitable for phylogenetic analyses. However, target capture requires careful considerations, which may greatly affect the success of experiments. Here we provide a simple flowchart for designing phylogenomic target capture experiments. We discuss necessary decisions from the identification of target loci to the final bioinformatic processing of sequence data. We outline challenges and solutions related to the taxonomic scope, sample quality, and available genomic resources of target capture projects. We hope this review will serve as a useful roadmap for designing and carrying out successful phylogenetic target capture studies.
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