ReviewApplications in plant sciences2020
Strategies for reducing per-sample costs in target capture sequencing for phylogenomics and population genomics in plants.
Review in Applications in plant sciences, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 49 papers.
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Who cites it
49 citing papers in PubMed, 119 citations in OpenAlex.
- Simultaneous Inference of Flora-Wide Nuclear and Plastid Phylogenies Using Angiosperms353 Sequence Capture Data.Molecular ecology resources · 2026Article
- Contrasting Dispersal Histories Shape Distinct Evolutionary Trajectories Between Malesian and PantropicalEcology and evolution · 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
- Applying Target Capture Sequencing to Unravel thePlants (Basel, Switzerland) · 2026Article
- Accelerated development of rice near-isogenic lines based on rapid generation advance (RGA) and target capture sequencing (TCS).Molecular breeding : new strategies in plant improvement · 2026Article
- Patterns of Interploidy Admixture in Polyploid Complexes: Insights From Thymus Sect. Mastichina (Lamiaceae).Molecular ecology · 2026Article
- Genetic Diversity Unveiled: Cost-Effective Methods for Grassland Species.Molecular ecology resources · 2026Article
- Low genetic differentiation among morphologically distinct Cycas species informs the delineation of conservation management units.Annals of botany · 2026Article
- UnFATE: A Comprehensive Probe Set and Bioinformatics Pipeline for Phylogeny Reconstruction and Multilocus Barcoding of Filamentous Ascomycetes (Ascomycota, Pezizomycotina).Systematic biology · 2025Article
- Population genetic structure reveals asymmetric hybridization between Pinus pumila and P. parviflora var. Pentaphylla in the Hakkoda Mountains, Northern Japan.Scientific reports · 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
- The winner takes it all: a single genotype of Kalanchoe × houghtonii is a global invader.Annals of botany · 2025Article
- Improved genomic DNA extraction from citrus species using a modified CTAB method.Molecular biology reports · 2025Article
- Reducing costs and shortening the cetyltrimethylammonium bromide (CTAB) method to improve DNA extraction efficiency from wintersweet and some other plants.Scientific reports · 2025Article
- Insect Phylogenomics: From Experiment Planning to Post-phylogenetic Analyses.Methods in molecular biology (Clifton, N.J.) · 2025Review
- Leveraging the power of long reads for targeted sequencing.Genome research · 2024Review
- Artifactual Orthologs and the Need for Diligent Data Exploration in Complex Phylogenomic Datasets: A Museomic Case Study from the Andean Flora.Systematic biology · 2024Article
- GeCKO: user-friendly workflows for genotyping complex genomes using target enrichment capture. A use case on the large tetraploid durum wheat genome.Plant methods · 2024Article
- Divergence and reticulation in the Mexican white oaks: ecological and phylogenomic evidence on species limits and phylogenetic networks in the Quercus laeta complex (Fagaceae).Annals of botany · 2024Article
Corrections and comments
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Authors and funding
5 authors at 3 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The reduced cost of high-throughput sequencing and the development of gene sets with wide phylogenetic applicability has led to the rise of sequence capture methods as a plausible platform for both phylogenomics and population genomics in plants. An important consideration in large targeted sequencing projects is the per-sample cost, which can be inflated when using off-the-shelf kits or reagents not purchased in bulk. Here, we discuss methods to reduce per-sample costs in high-throughput targeted sequencing projects. We review the minimal equipment and consumable requirements for targeted sequencing while comparing several alternatives to reduce bulk costs in DNA extraction, library preparation, target enrichment, and sequencing. We consider how each of the workflow alterations may be affected by DNA quality (e.g., fresh vs. herbarium tissue), genome size, and the phylogenetic scale of the project. We provide a cost calculator for researchers considering targeted sequencing to use when designing projects, and identify challenges for future development of low-cost sequencing in non-model plant systems.
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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.