Nanopore sequencing: Review of potential applications in functional genomics

Molecular biology has been led by various measurement technologies, and increased throughput has developed omics analysis. The development of massively parallel sequencing technology has enabled access to fundamental molecular data and revealed genomic and transcriptomic signatures. Nanopore sequencers have driven such evolution to the next stage. Oxford Nanopore Technologies Inc. provides a new type of single molecule sequencer using protein nanopore that realizes direct sequencing without DNA synthesizing or amplification. This nanopore sequencer can sequence an ultra‐long read limited by the input nucleotide length, or can determine DNA/RNA modifications. Recently, many fields such as medicine, epidemiology, ecology, and education have benefited from this technology. In this review, we explain the features and functions of the nanopore sequencer, introduce various situations where it has been used as a critical technology, and expected future applications.

[1]  Heng Li,et al.  Minimap and miniasm: fast mapping and de novo assembly for noisy long sequences , 2015, Bioinform..

[2]  R. Lewis,et al.  Molecular and mechanical characterization of aciniform silk: uniformity of iterated sequence modules in a novel member of the spider silk fibroin gene family. , 2004, Molecular biology and evolution.

[3]  Adam Ameur,et al.  Single-Molecule Sequencing: Towards Clinical Applications. , 2019, Trends in biotechnology.

[4]  Winston Timp,et al.  Detecting DNA cytosine methylation using nanopore sequencing , 2017, Nature Methods.

[5]  Daniel R. Garalde,et al.  Highly parallel direct RNA sequencing on an array of nanopores , 2016, Nature Methods.

[6]  Chengxi Ye,et al.  DBG2OLC: Efficient Assembly of Large Genomes Using Long Erroneous Reads of the Third Generation Sequencing Technologies , 2014, Scientific Reports.

[7]  N. Ricker,et al.  The limitations of draft assemblies for understanding prokaryotic adaptation and evolution. , 2012, Genomics.

[8]  Peer Bork,et al.  The genome sequence of Bifidobacterium longum reflects its adaptation to the human gastrointestinal tract , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[9]  J. C. Clemens,et al.  Drosophila Dscam Is an Axon Guidance Receptor Exhibiting Extraordinary Molecular Diversity , 2000, Cell.

[10]  James B. Brown,et al.  BasecRAWller: Streaming Nanopore Basecalling Directly from Raw Signal , 2017, bioRxiv.

[11]  Douglas J. Botkin,et al.  Nanopore DNA Sequencing and Genome Assembly on the International Space Station , 2016, bioRxiv.

[12]  Heng Li,et al.  Minimap2: pairwise alignment for nucleotide sequences , 2017, Bioinform..

[13]  Joshua Quick,et al.  Rapid draft sequencing and real-time nanopore sequencing in a hospital outbreak of Salmonella , 2015, Genome Biology.

[14]  Jacob Kraemer Tebes,et al.  New Opportunities. , 2020, American journal of community psychology.

[15]  Masaru Tomita,et al.  Orb-weaving spider Araneus ventricosus genome elucidates the spidroin gene catalogue , 2019, Scientific Reports.

[16]  D. Branton,et al.  The potential and challenges of nanopore sequencing , 2008, Nature Biotechnology.

[17]  S. Howorka,et al.  Structural and mechanistic insights into the bacterial amyloid secretion channel CsgG , 2014, Nature.

[18]  James Clarke,et al.  Nanopore development at Oxford Nanopore , 2016, Nature Biotechnology.

[19]  B. Chain,et al.  The sequence of sequencers: The history of sequencing DNA , 2016, Genomics.

[20]  M. Frith,et al.  Nanopore-based single molecule sequencing of the D4Z4 array responsible for facioscapulohumeral muscular dystrophy , 2017, Scientific Reports.

[21]  Sergey I. Nikolenko,et al.  SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing , 2012, J. Comput. Biol..

[22]  Xingang Wang,et al.  RaGOO: fast and accurate reference-guided scaffolding of draft genomes , 2019, Genome Biology.

[23]  J. Sambrook,et al.  Molecular Cloning: A Laboratory Manual , 2001 .

[24]  Yutaka Suzuki,et al.  Nanopore sequencing of drug-resistance-associated genes in malaria parasites, Plasmodium falciparum , 2018, Scientific Reports.

[25]  Ryan R. Wick,et al.  Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads , 2016, bioRxiv.

[26]  Brent S. Pedersen,et al.  Nanopore sequencing and assembly of a human genome with ultra-long reads , 2017, Nature Biotechnology.

[27]  B. Cooperman,et al.  Electrophoretic Deformation of Individual Transfer RNA Molecules Reveals Their Identity. , 2016, Nano letters.

[28]  David L. Kaplan,et al.  New Opportunities for an Ancient Material , 2010, Science.

[29]  B. Tian,et al.  RNA‐Seq methods for transcriptome analysis , 2017, Wiley interdisciplinary reviews. RNA.

[30]  David N. Nicholson,et al.  The Nephila clavipes genome highlights the diversity of spider silk genes and their complex expression , 2017, Nature Genetics.

[31]  E. Mardis.  Next-generation sequencing platforms. , 2013, Annual review of analytical chemistry.

[32]  Native RNA sequencing on nanopore arrays redefines the transcriptional complexity of a viral pathogen , 2018 .

[33]  Minh Duc Cao,et al.  Chiron: translating nanopore raw signal directly into nucleotide sequence using deep learning , 2017, bioRxiv.

[34]  M. Akeson,et al.  Capture, Unfolding, and Detection of Individual tRNA Molecules Using a Nanopore Device , 2015, Front. Bioeng. Biotechnol..

[35]  Evgeny M. Zdobnov,et al.  BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs , 2015, Bioinform..

[36]  Jin-Wu Nam,et al.  The present and future of de novo whole-genome assembly , 2016, Briefings Bioinform..

[37]  T. Blackledge,et al.  Physicochemical Property Variation in Spider Silk: Ecology, Evolution, and Synthetic Production. , 2017, Annual review of entomology.

[38]  Doug Stryke,et al.  Rapid metagenomic identification of viral pathogens in clinical samples by real-time nanopore sequencing analysis , 2015, Genome Medicine.

[39]  Qing Meng,et al.  Full-Length Minor Ampullate Spidroin Gene Sequence , 2012, PloS one.

[40]  R. Vasudeva,et al.  Draft genome of a high value tropical timber tree, Teak (Tectona grandis L. f): insights into SSR diversity, phylogeny and conservation , 2018, DNA research : an international journal for rapid publication of reports on genes and genomes.

[41]  Pavel A. Pevzner,et al.  Assembly of long error-prone reads using de Bruijn graphs , 2016, Proceedings of the National Academy of Sciences.

[42]  M. Preul,et al.  MinION rapid sequencing: Review of potential applications in neurosurgery , 2018, Surgical neurology international.

[43]  E. Zaikova,et al.  Real-Time DNA Sequencing in the Antarctic Dry Valleys Using the Oxford Nanopore Sequencer. , 2017, Journal of biomolecular techniques : JBT.

[44]  David A. Matthews,et al.  Real-time, portable genome sequencing for Ebola surveillance , 2016, Nature.

[45]  Trevor Bedford,et al.  Multiplex PCR method for MinION and Illumina sequencing of Zika and other virus genomes directly from clinical samples , 2017, Nature Protocols.

[46]  Benedict Paten,et al.  Haplotype-aware genotyping from noisy long reads , 2018, bioRxiv.

[47]  Michael Liem,et al.  Rapid de novo assembly of the European eel genome from nanopore sequencing reads , 2017, Scientific Reports.

[48]  Christina A. Cuomo,et al.  Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement , 2014, PloS one.

[49]  T. Michael,et al.  Generating a high-confidence reference genome map of the Greater Duckweed by integration of cytogenomic, optical mapping, and Oxford Nanopore technologies. , 2018, The Plant journal : for cell and molecular biology.

[50]  Paolo Piazza,et al.  Comprehensive comparison of Pacific Biosciences and Oxford Nanopore Technologies and their applications to transcriptome analysis , 2017, F1000Research.

[51]  H. Bayley,et al.  Continuous base identification for single-molecule nanopore DNA sequencing. , 2009, Nature nanotechnology.

[52]  T. Imanishi,et al.  A portable system for rapid bacterial composition analysis using a nanopore-based sequencer and laptop computer , 2017, Scientific Reports.

[53]  Yutaka Suzuki,et al.  A novel diagnostic method for malaria using loop-mediated isothermal amplification (LAMP) and MinION™ nanopore sequencer , 2017, BMC Infectious Diseases.

[54]  Kresimir Krizanovic,et al.  Evaluation of tools for long read RNA-seq splice-aware alignment , 2017, bioRxiv.

[55]  G. Reifenberger,et al.  The 2016 World Health Organization Classification of Tumors of the Central Nervous System: a summary , 2016, Acta Neuropathologica.

[56]  Complete Genome Sequence of Arthrobacter sp. Strain MN05-02, a UV-Resistant Bacterium from a Manganese Deposit in the Sonoran Desert , 2019, Journal of genomics.

[57]  Tomáš Vinař,et al.  DeepNano: Deep recurrent neural networks for base calling in MinION nanopore reads , 2016, PloS one.

[58]  Francesca Giordano,et al.  Oxford Nanopore MinION Sequencing and Genome Assembly , 2016, Genom. Proteom. Bioinform..

[59]  P. Ashton,et al.  MinION nanopore sequencing identifies the position and structure of a bacterial antibiotic resistance island , 2014, Nature Biotechnology.

[60]  Lachlan James M. Coin,et al.  npInv: accurate detection and genotyping of inversions using long read sub-alignment , 2018, BMC Bioinformatics.

[61]  Julia Zeitlinger,et al.  Highly Contiguous Genome Assemblies of 15 Drosophila Species Generated Using Nanopore Sequencing , 2018, G3: Genes, Genomes, Genetics.

[62]  A. Kasarskis,et al.  A window into third-generation sequencing. , 2010, Human molecular genetics.

[63]  J. McPherson,et al.  Coming of age: ten years of next-generation sequencing technologies , 2016, Nature Reviews Genetics.

[64]  Alexander Payne,et al.  BulkVis: a graphical viewer for Oxford nanopore bulk FAST5 files , 2018, Bioinform..

[65]  Oliver G. Pybus,et al.  Mobile real-time surveillance of Zika virus in Brazil , 2016, Genome Medicine.

[66]  W. F. Thompson,et al.  Rapid isolation of high molecular weight plant DNA. , 1980, Nucleic acids research.

[67]  M. Tomita,et al.  The bagworm genome reveals a unique fibroin gene that provides high tensile strength , 2019, Communications Biology.

[68]  John R Tyson,et al.  MinION-based long-read sequencing and assembly extends the Caenorhabditis elegans reference genome , 2018, Genome research.

[69]  Kathrin Lang,et al.  Full-Length HLA Class I Genotyping with the MinION Nanopore Sequencer. , 2018, Methods in molecular biology.

[70]  D. Branton,et al.  Three decades of nanopore sequencing , 2016, Nature Biotechnology.

[71]  Nuno R. Faria,et al.  Multiplex PCR method for MinION and Illumina sequencing of Zika and other virus genomes directly from clinical samples , 2017, Nature Protocols.

[72]  Chunlei Du,et al.  Nanopore-based Fourth-generation DNA Sequencing Technology , 2015, Genom. Proteom. Bioinform..

[73]  Heng Li,et al.  Fast and accurate long-read assembly with wtdbg2 , 2019, Nature Methods.

[74]  C. Austin,et al.  Finding Nemo: hybrid assembly with Oxford Nanopore and Illumina reads greatly improves the clownfish (Amphiprion ocellaris) genome assembly , 2018, GigaScience.

[75]  Michael C. Schatz,et al.  Accurate detection of complex structural variations using single molecule sequencing , 2017, Nature Methods.

[76]  Yutaka Suzuki,et al.  NanoPipe—a web server for nanopore MinION sequencing data analysis , 2019, GigaScience.

[77]  R. Lewis,et al.  Structure of a protein superfiber: spider dragline silk. , 1990, Proceedings of the National Academy of Sciences of the United States of America.

[78]  N. Loman,et al.  A complete bacterial genome assembled de novo using only nanopore sequencing data , 2015, Nature Methods.

[79]  W. Kloosterman,et al.  From squiggle to basepair: computational approaches for improving nanopore sequencing read accuracy , 2018, Genome Biology.

[80]  Edwin Cuppen,et al.  Mapping and phasing of structural variation in patient genomes using nanopore sequencing , 2017, Nature Communications.

[81]  S. Turner,et al.  Real-Time DNA Sequencing from Single Polymerase Molecules , 2009, Science.

[82]  B. Graveley,et al.  Determining exon connectivity in complex mRNAs by nanopore sequencing , 2015, Genome Biology.

[83]  A. Estoup,et al.  The Genomic Basis of Color Pattern Polymorphism in the Harlequin Ladybird , 2018, Current Biology.

[84]  S. Koren,et al.  Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation , 2016, bioRxiv.

[85]  Ilan Shomorony,et al.  HINGE: Long-Read Assembly Achieves Optimal Repeat Resolution , 2016, bioRxiv.

[86]  M. Schatz,et al.  Phased diploid genome assembly with single-molecule real-time sequencing , 2016, Nature Methods.

[87]  Jing Li,et al.  De novo yeast genome assemblies from MinION, PacBio and MiSeq platforms , 2017, Scientific Reports.

[88]  Arwyn Edwards,et al.  Deep Sequencing: Intra-terrestrial metagenomics illustrates the potential of off-grid Nanopore DNA sequencing , 2017, bioRxiv.

[89]  Arwyn Edwards,et al.  Extreme metagenomics using nanopore DNA sequencing : a field report from Svalbard , 78 ° N , 2016 .

[90]  Sergey Koren,et al.  Aggressive assembly of pyrosequencing reads with mates , 2008, Bioinform..

[91]  Hugh E. Olsen,et al.  The Oxford Nanopore MinION: delivery of nanopore sequencing to the genomics community , 2016, Genome Biology.

[92]  Jordan M. Eizenga,et al.  Mapping DNA Methylation with High Throughput Nanopore Sequencing , 2017, Nature Methods.

[93]  Jose Espejo Valle-Inclan,et al.  Long-Read Annotation: Automated Eukaryotic Genome Annotation Based on Long-Read cDNA Sequencing1[OPEN] , 2018, Plant Physiology.

[94]  Jessica K. Polka,et al.  Non-model model organisms , 2017, BMC Biology.

[95]  Sumio Sugano,et al.  Serotyping dengue virus with isothermal amplification and a portable sequencer , 2017, Scientific Reports.

[96]  Angela N. Brooks,et al.  Nanopore native RNA sequencing of a human poly(A) transcriptome , 2018, bioRxiv.

[97]  Michael Roberts,et al.  The MaSuRCA genome assembler , 2013, Bioinform..

[98]  Yunfan Fan,et al.  Nanopore sequencing detects structural variants in cancer , 2015, bioRxiv.

[99]  Stefan Engelen,et al.  de novo assembly and population genomic survey of natural yeast isolates with the Oxford Nanopore MinION sequencer , 2016, bioRxiv.

[100]  M. Frith,et al.  Adaptive seeds tame genomic sequence comparison. , 2011, Genome research.

[101]  Niranjan Nagarajan,et al.  Fast and accurate de novo genome assembly from long uncorrected reads. , 2017, Genome research.

[102]  K. Katoh,et al.  MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability , 2013, Molecular biology and evolution.

[103]  Hugh E. Olsen,et al.  Nanopore long-read RNAseq reveals widespread transcriptional variation among the surface receptors of individual B cells , 2017, Nature Communications.