ArticleScientific reports2017
High-throughput sequencing of multiple amplicons for barcoding and integrative taxonomy.
Article in Scientific reports, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 42 papers.
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Who cites it
42 citing papers in PubMed.
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- Physicochemical convergence in antibody CDR3-VH repertoires recognizing phosphorothioate-modified oligonucleotides backbone.Frontiers in immunology · 2026Article
- Unexpected microbial rhodopsin dynamics in sync with phytoplankton blooms.Nature communications · 2025Article
- Large-Scale Integrative Taxonomy of the Smallest Insects Reveals Astonishing Temperate Diversity (Hymenoptera: Chalcidoidea: Mymaridae).Molecular ecology · 2025Article
- The CODEX Approach: High-Throughput Sequencing of the Cox-1 Barcode Fragment in Neogastropods (Mollusca, Gastropoda).Molecular ecology resources · 2025Article
- Environmental factors and host sex influence the skin microbiota structure of Hong Kong newt (Paramesotriton hongkongensis) in a coldspot of chytridiomycosis in subtropical East Asia.Integrative zoology · 2025Article
- Scalable genotyping of microbial colonies.Microbial genomics · 2025Article
- DNA barcoding, integrative taxonomy, citizen science, and Bush Blitz surveys combine to reveal 34 new species ofZooKeys · 2025Article
- Barcode 100K Specimens: In a Single Nanopore Run.Molecular ecology resources · 2025Article
- Longitudinal survey of total airborne bacterial and archaeal concentrations and bacterial diversity in enriched colony housing and aviaries for laying hens.Poultry science · 2024Article
- Cost-efficient PCR based DNA barcoding of marine invertebrate specimens with NovaSeq amplicon sequencing.Molecular biology reports · 2024Article
- Capillary-Electrophoresis-Based Species Barcoding of Big Cats: CR-mtDNA-Length Polymorphism.Life (Basel, Switzerland) · 2024Article
- Deep Mutational Scanning of an Oxygen-Independent Fluorescent Protein CreiLOV for Comprehensive Profiling of Mutational and Epistatic Effects.ACS synthetic biology · 2023Article
- Highly-multiplexed and efficient long-amplicon PacBio and Nanopore sequencing of hundreds of full mitochondrial genomes.BMC genomics · 2023Article
- The impact of nucleosome structure on CRISPR/Cas9 fidelity.Nucleic acids research · 2023Article
- Sex-determining region complements traditionally used in phylogenetic studies nuclear and chloroplast sequences in investigation ofFrontiers in plant science · 2023Article
- Development and Complex Application of Methods for the Identification of Mutations in thePlants (Basel, Switzerland) · 2022Article
- Article
- Concurrent molecular characterization of sand flies and Leishmania parasites by amplicon-based next-generation sequencing.Parasites & vectors · 2022Article
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Until now, the potential of NGS for the construction of barcode libraries or integrative taxonomy has been seldom realised. Here, we amplified (two-step PCR) and simultaneously sequenced (MiSeq) multiple markers from hundreds of fig wasp specimens. We also developed a workflow for quality control of the data. Illumina and Sanger sequences accumulated in the past years were compared. Interestingly, primers and PCR conditions used for the Sanger approach did not require optimisation to construct the MiSeq library. After quality controls, 87% of the species (76% of the specimens) had a valid MiSeq sequence for each marker. Importantly, major clusters did not always correspond to the targeted loci. Nine specimens exhibited two divergent sequences (up to 10%). In 95% of the species, MiSeq and Sanger sequences obtained from the same sampling were similar. For the remaining 5%, species were paraphyletic or the sequences clustered into divergent groups on the Sanger + MiSeq trees (>7%). These problematic cases may represent coding NUMTS or heteroplasms. Our results illustrate that Illumina approaches are not artefact-free and confirm that Sanger databases can contain non-target genes. This highlights the importance of quality controls, working with taxonomists and using multiple markers for DNA-taxonomy or species diversity assessment.
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