ArticleGigaScience2019
Nanopore sequencing of long ribosomal DNA amplicons enables portable and simple biodiversity assessments with high phylogenetic resolution across broad taxonomic scale.
Article in GigaScience, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 88 papers.
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Who cites it
88 citing papers in PubMed.
- Species- and strain-level assessment usingGut microbesTrial
- A multiplex assay to detect mosquito species, bloodmeal host source and Plasmodium in malaria vectors using Nanopore amplicon sequencing.Medical and veterinary entomology · 2026Article
- Multi-Locus Nuclear Marker Assessment of Genetic Diversity in Swiss Orthoptera Unveils Conservation Status Limitations.Molecular ecology · 2026Article
- A Field-Deployable eDNA Metabarcoding Workflow Including De Novo Reference Assembly for Characterising Understudied Biodiversity Hotspots.Molecular ecology resources · 2026Article
- Using miniaturized laboratory equipment and DNA barcoding to improve conservation genetics training and identify illegally traded species.Conservation biology : the journal of the Society for Conservation Biology · 2026Article
- A streamlined, nanopore-compatible 5PSeq protocol for rapid phenotypic antimicrobial sensitivity testing.Cell reports methods · 2026Article
- High-throughput detection of microeukaryotic parasites in insects using Nanopore sequencing.Microbial genomics · 2026Article
- Predicting epistasis across proteins by structural logic.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Reported circulation of Zika and re-circulation of Chikungunya in Dengue-endemic Dhaka, Bangladesh in 2024.PloS one · 2026Article
- Impact of agro-industrial by-products on nutritional value and microbiota composition of black soldier fly larvae.Frontiers in microbiology · 2026Article
- Unlocking natural history collections to improve eDNA reference databases and biodiversity monitoring.Bioscience · 2025Article
- Going Mobile: Using Portable Genomic Technologies for PCR-Free In Situ Species Identification and Real-Time Molecular Systematics.Ecology and evolution · 2025Article
- Perfoliate Pondweed Meadows in Northern Coastal Areas-Reservoirs of Diverse Bacteria With Pathogenic Traits and Complex Carbon Metabolism.Environmental microbiology reports · 2025Article
- Decoding the Peruvian Amazon with in situ DNA barcoding of vertebrate and plant taxa.Scientific data · 2025Article
- Synthesis of large single-transcript pathways from oligonucleotide pools: Design of STARBURST, an autobioluminescent reporter.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Fast-tracking bespoke DNA reference database generation from museum collections for biomonitoring and conservation.Molecular ecology resources · 2025Article
- Development of a semicomprehensive detection method for paramyxoviruses and its validation using Indonesian bats.Scientific reports · 2025Article
- The Impact of Viral Concentration Method on Quantification and Long Amplicon Nanopore Sequencing of SARS-CoV-2 and Noroviruses in Wastewater.Microorganisms · 2025Article
- Article
- A new species ofIMA fungus · 2025Article
28 more citing papers are in PubMed but not listed here.
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Authors and funding
11 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundIn light of the current biodiversity crisis, DNA barcoding is developing into an essential tool to quantify state shifts in global ecosystems. Current barcoding protocols often rely on short amplicon sequences, which yield accurate identification of biological entities in a community but provide limited phylogenetic resolution across broad taxonomic scales. However, the phylogenetic structure of communities is an essential component of biodiversity. Consequently, a barcoding approach is required that unites robust taxonomic assignment power and high phylogenetic utility. A possible solution is offered by sequencing long ribosomal DNA (rDNA) amplicons on the MinION platform (Oxford Nanopore Technologies).
findingsUsing a dataset of various animal and plant species, with a focus on arthropods, we assemble a pipeline for long rDNA barcode analysis and introduce a new software (MiniBar) to demultiplex dual indexed Nanopore reads. We find excellent phylogenetic and taxonomic resolution offered by long rDNA sequences across broad taxonomic scales. We highlight the simplicity of our approach by field barcoding with a miniaturized, mobile laboratory in a remote rainforest. We also test the utility of long rDNA amplicons for analysis of community diversity through metabarcoding and find that they recover highly skewed diversity estimates.
conclusionsSequencing dual indexed, long rDNA amplicons on the MinION platform is a straightforward, cost-effective, portable, and universal approach for eukaryote DNA barcoding. Although bulk community analyses using long-amplicon approaches may introduce biases, the long rDNA amplicons approach signifies a powerful tool for enabling the accurate recovery of taxonomic and phylogenetic diversity across biological communities.
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