ArticleGenome biology and evolution2011
Targeted amplicon sequencing (TAS): a scalable next-gen approach to multilocus, multitaxa phylogenetics.
Article in Genome biology and evolution, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 81 papers.
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Who cites it
81 citing papers in PubMed.
- High polymorphism detected by massively parallel sequencing of autosomal STRs using old blood samples from a Chinese Han population.Scientific reports · 2019Trial
- Significant differences in fecal microbiota are associated with various stages of glucose tolerance in African American male veterans.Translational research : the journal of laboratory and clinical medicine · 2015Trial
- scASprofiler: profiling single-cell RNA splicing with a deep convolutional generative network.Briefings in bioinformatics · 2026Article
- Review
- The evolution of diagnostic microbiology: integrating culture-based methods and genomic advances.PeerJ · 2026Review
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- MKDESIGNER and TASEQ: a set of tools for plant genotyping by targeted amplicon sequencing.BMC bioinformatics · 2025Article
- Foxa deficiency restricts hepatitis B virus biosynthesis through epigenic silencing.Journal of virology · 2024Article
- Multi-omics analyses reveal aberrant differentiation trajectory with WNT1 loss-of-function in type XV osteogenesis imperfecta.Journal of bone and mineral research : the official journal of the American Society for Bone and Mineral Research · 2024Article
- Ten-eleven translocation (Tet) methylcytosine dioxygenase-dependent viral DNA demethylation mediatesJournal of virology · 2024Article
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- Deep Sequencing of Porcine Reproductive and Respiratory Syndrome Virus ORF7: A Promising Tool for Diagnostics and Epidemiologic Surveillance.Animals : an open access journal from MDPI · 2023Article
- Carryover Contamination-Controlled Amplicon Sequencing Workflow for Accurate Qualitative and Quantitative Detection of Pathogens: a Case Study on SARS-CoV-2.Microbiology spectrum · 2023Article
- Clinical features and molecular characterization of Chinese patients with FKBP10 variants.Molecular genetics & genomic medicine · 2023Article
- Article
- Design and implementation of multiplexed amplicon sequencing panels to serve genomic epidemiology of infectious disease: A malaria case study.Molecular ecology resources · 2022Article
- The Effect of Necrotic Enteritis Challenge on Production Performance, Cecal Microbiome, and Cecal Tonsil Transcriptome in Broilers.Pathogens (Basel, Switzerland) · 2022Article
- Comparative Analysis of Metagenomics and Metataxonomics for the Characterization of Vermicompost Microbiomes.Frontiers in microbiology · 2022Article
- Phenotypic Spectrum and Molecular Basis in a Chinese Cohort of Osteogenesis Imperfecta With Mutations in Type I Collagen.Frontiers in genetics · 2022Article
- Enumeration of citrus endophytic bacterial communities based on illumine metagenomics technique.PloS one · 2022Article
21 more citing papers are in PubMed but not listed here.
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Authors and funding
9 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Next-gen sequencing technologies have revolutionized data collection in genetic studies and advanced genome biology to novel frontiers. However, to date, next-gen technologies have been used principally for whole genome sequencing and transcriptome sequencing. Yet many questions in population genetics and systematics rely on sequencing specific genes of known function or diversity levels. Here, we describe a targeted amplicon sequencing (TAS) approach capitalizing on next-gen capacity to sequence large numbers of targeted gene regions from a large number of samples. Our TAS approach is easily scalable, simple in execution, neither time-nor labor-intensive, relatively inexpensive, and can be applied to a broad diversity of organisms and/or genes. Our TAS approach includes a bioinformatic application, BarcodeCrucher, to take raw next-gen sequence reads and perform quality control checks and convert the data into FASTA format organized by gene and sample, ready for phylogenetic analyses. We demonstrate our approach by sequencing targeted genes of known phylogenetic utility to estimate a phylogeny for the Pancrustacea. We generated data from 44 taxa using 68 different 10-bp multiplexing identifiers. The overall quality of data produced was robust and was informative for phylogeny estimation. The potential for this method to produce copious amounts of data from a single 454 plate (e.g., 325 taxa for 24 loci) significantly reduces sequencing expenses incurred from traditional Sanger sequencing. We further discuss the advantages and disadvantages of this method, while offering suggestions to enhance the approach.
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