ArticleScientific reports2017
Field-based species identification of closely-related plants using real-time nanopore sequencing.
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 37 papers.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
37 citing papers in PubMed.
- Fragmentation of Long Reads Enables Reliable Mitogenome Assembly From Whole-Genome Amplification Data With Pervasive Palindromic Reads.Molecular ecology resources · 2026Article
- Heat but Not Cold Tolerance Is Phylogenetically Constrained in Greenlandic Terrestrial Arthropods Under Future Global Warming.Global change biology · 2026Article
- Phylogenetic clustering of microbial communities as a biomarker for chemical pollution.FEMS microbiology ecology · 2025Article
- Application and Prospects of Long-Read Sequencers for Preimplantation Genetic Testing for Structural Rearrangements.Methods in molecular biology (Clifton, N.J.) · 2025Review
- Nanopore sequencing in veterinary medicine: from concepts to clinical applications.Frontiers in cellular and infection microbiology · 2025Review
- Custom barcoded primers for influenza A nanopore sequencing: enhanced performance with reduced preparation time.Frontiers in cellular and infection microbiology · 2025Article
- Rapid on-site universal vertebrate species identification via multi-barcode nanopore sequencing.PloS one · 2025Article
- A new species ofIMA fungus · 2025Article
- The Applications of Nanopore Sequencing Technology in Animal and Human Virus Research.Viruses · 2024Review
- Identification of non-model mammal species using the MinION DNA sequencer from Oxford Nanopore.PeerJ · 2024Article
- Article
- Field-based detection of bacteria using nanopore sequencing: Method evaluation for biothreat detection in complex samples.PloS one · 2023Article
- Supporting in situ conservation of the genetic diversity of crop wild relatives using genomic technologies.Molecular ecology · 2022Review
- NanoRTax, a real-time pipeline for taxonomic and diversity analysis of nanopore 16S rRNA amplicon sequencing data.Computational and structural biotechnology journal · 2022Article
- Envisaging an Effective Global Long-Term Agrobiodiversity Conservation System That Promotes and Facilitates Use.Plants (Basel, Switzerland) · 2021Review
- Diversity Indices of Plant Communities and Their Rhizosphere Microbiomes: An Attempt to Find the Connection.Microorganisms · 2021Article
- Article
- Long-Reads-Based Metagenomics in Clinical Diagnosis With a Special Focus on Fungal Infections.Frontiers in microbiology · 2021Review
- A framework for in situ molecular characterization of coral holobionts using nanopore sequencing.Scientific reports · 2020Article
- Mitochondrial Genome ofPlants (Basel, Switzerland) · 2020Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Advances in DNA sequencing and informatics have revolutionised biology over the past four decades, but technological limitations have left many applications unexplored. Recently, portable, real-time, nanopore sequencing (RTnS) has become available. This offers opportunities to rapidly collect and analyse genomic data anywhere. However, generation of datasets from large, complex genomes has been constrained to laboratories. The portability and long DNA sequences of RTnS offer great potential for field-based species identification, but the feasibility and accuracy of these technologies for this purpose have not been assessed. Here, we show that a field-based RTnS analysis of closely-related plant species (Arabidopsis spp.) has many advantages over laboratory-based high-throughput sequencing (HTS) methods for species level identification and phylogenomics. Samples were collected and sequenced in a single day by RTnS using a portable, "al fresco" laboratory. Our analyses demonstrate that correctly identifying unknown reads from matches to a reference database with RTnS reads enables rapid and confident species identification. Individually annotated RTnS reads can be used to infer the evolutionary relationships of A. thaliana. Furthermore, hybrid genome assembly with RTnS and HTS reads substantially improved upon a genome assembled from HTS reads alone. Field-based RTnS makes real-time, rapid specimen identification and genome wide analyses possible.
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Registered trials
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.