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Applications of Oxford Nanopore Sequencing in Schizosaccharomyces pombe

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Yeast Protocols

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2196))

Abstract

Recent years have seen great progresses in third-generation sequencing. New commercial platforms from Oxford Nanopore Technologies (ONT) can generate ultra-long reads from single-molecule nucleic acid fragments of kilobases up to megabases, exceeding the limitation of short reads and dependency on template amplification suffered by the previous generation of sequencing technologies. Moreover, it can detect epigenetic modifications directly, as well as providing all-around field usage, being pocket-sized and low cost. It has already been applied to yeast research in many aspects, such as complete de novo genome assemblies, the phylogeny of large-brewing yeasts, gene isoform identification, and base modification detection. These applications have delivered novel insights into yeast genomic and transcriptomic analysis.

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References

  1. Sanger F, Nicklen S, Coulson AR (1977) DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci U S A 74:5463–5467

    Article  CAS  Google Scholar 

  2. Hyman ED (1988) A new method of sequencing DNA. Anal Biochem 174:423–436

    Article  CAS  Google Scholar 

  3. Mardis ER (2008) Next-generation DNA sequencing methods. Annu Rev Genomics Hum Genet 9:387–402

    Article  CAS  Google Scholar 

  4. Turcatti G, Romieu A, Fedurco M, Tairi AP (2008) A new class of cleavable fluorescent nucleotides: synthesis and optimization as reversible terminators for DNA sequencing by synthesis. Nucleic Acids Res 36:e25–e25

    Article  CAS  Google Scholar 

  5. Jain M, Koren S, Miga KH, Quick J, Rand AC, Sasani TA, Tyson JR, Beggs AD, Dilthey AT, Fiddes IT et al (2018) Nanopore sequencing and assembly of a human genome with ultra-long reads. Nat Biotechnol 36:338–345

    Article  CAS  Google Scholar 

  6. Wang Y, Yang Q, Wang Z (2014) The evolution of nanopore sequencing. Front Genet 5:449

    PubMed  Google Scholar 

  7. van Dijk EL, Jaszczyszyn Y, Naquin D, Thermes C (2018) The third revolution in sequencing technology. Trends Genet 34:666–681

    Article  CAS  Google Scholar 

  8. Marx V (2015) Nanopores: a sequencer in your backpack. Nat Methods 12:1015–1018

    Article  CAS  Google Scholar 

  9. Simpson JT, Workman RE, Zuzarte PC, David M, Dursi LJ, Timp W (2017) Detecting DNA cytosine methylation using nanopore sequencing. Nat Methods 14:407–410

    Article  CAS  Google Scholar 

  10. Rand AC, Jain M, Eizenga JM, Musselman-Brown A, Olsen HE, Akeson M, Paten B (2017) Mapping DNA methylation with high-throughput nanopore sequencing. Nat Methods 14:411–413

    Article  CAS  Google Scholar 

  11. Garalde DR, Snell EA, Jachimowicz D, Sipos B, Lloyd JH, Bruce M, Pantic N, Admassu T, James P, Warland A et al (2018) Highly parallel direct RNA sequencing on an array of nanopores. Nat Methods 15:201–206

    Article  CAS  Google Scholar 

  12. Salazar AN, Gorter de Vries AR, van den Broek M, Wijsman M, de la Torre Cortes P, Brickwedde A, Brouwers N, Daran JG, Abeel T (2017) Nanopore sequencing enables near-complete de novo assembly of Saccharomyces cerevisiae reference strain CEN.PK113-7D. FEMS Yeast Res 17:fox074

    Article  CAS  Google Scholar 

  13. Istace B, Friedrich A, d'Agata L, Faye S, Payen E, Beluche O, Caradec C, Davidas S, Cruaud C, Liti G et al (2017) de novo assembly and population genomic survey of natural yeast isolates with the Oxford Nanopore MinION sequencer. Gigascience 6:1–13

    Article  CAS  Google Scholar 

  14. Fournier T, Gounot JS, Freel K, Cruaud C, Lemainque A, Aury JM, Wincker P, Schacherer J, Friedrich A (2017) High-quality de novo genome assembly of the Dekkera bruxellensis yeast using Nanopore MinION sequencing. G3 (Bethesda) 7:3243–3250

    Article  CAS  Google Scholar 

  15. Salazar AN, Gorter de Vries AR, van den Broek M, Brouwers N, de la Torre Cortès P, Kuijpers NGA, Daran J-MG, and Abeel T (2019). Nanopore sequencing and comparative genome analysis confirm lager-brewing yeasts originated from a single hybridization. bioRxiv

    Google Scholar 

  16. Lanfear R, Schalamun M, Kainer D, Wang W, Schwessinger B (2019) MinIONQC: fast and simple quality control for MinION sequencing data. Bioinformatics 35:523–525

    Article  CAS  Google Scholar 

  17. Koren S, Walenz BP, Berlin K, Miller JR, Bergman NH, Phillippy AM (2017) Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation. Genome Res 27:722–736

    Article  CAS  Google Scholar 

  18. Antipov D, Korobeynikov A, McLean JS, Pevzner PA (2016) hybridSPAdes: an algorithm for hybrid assembly of short and long reads. Bioinformatics 32:1009–1015

    Article  CAS  Google Scholar 

  19. Kurtz S, Phillippy A, Delcher AL, Smoot M, Shumway M, Antonescu C, Salzberg SL (2004) MUMmer3 versatile and open software for comparing large genomes. Genome Biol 5:R12

    Article  Google Scholar 

  20. Gurevich A, Saveliev V, Vyahhi N, Tesler G (2013) QUAST: quality assessment tool for genome assemblies. Bioinformatics 29:1072–1075

    Article  CAS  Google Scholar 

  21. Li H (2018) Minimap2 pairwise alignment for nucleotide sequences. Bioinformatics 34(18):3094–3100

    Google Scholar 

  22. Sedlazeck FJ, Rescheneder P, Smolka M, Fang H, Nattestad M, von Haeseler A, Schatz MC (2018) Accurate detection of complex structural variations using single-molecule sequencing. Nat Methods 15:461–468

    Google Scholar 

  23. Gong L, Wong CH, Cheng WC, Tjong H, Menghi F, Ngan CY, Liu ET, Wei CL (2018) Picky comprehensively detects high-resolution structural variants in nanopore long reads. Nat Methods 15:455–460

    Google Scholar 

  24. Byrne A, Beaudin AE, Olsen HE, Jain M, Cole C, Palmer T, DuBois RM, Forsberg EC, Akeson M, Vollmers C (2017) Nanopore long-read RNAseq reveals widespread transcriptional variation among the surface receptors of individual B cells. Nat Commun 8:16027

    Google Scholar 

  25. Depledge DP, Srinivas KP, Sadaoka T, Bready D, Mori Y, Placantonakis DG, Mohr I, Wilson AC (2019) Direct RNA sequencing on nanopore arrays redefines the transcriptional complexity of a viral pathogen. Nat Commun 10:754

    Google Scholar 

  26. Workman RE, Tang A, Tang PS, Jain M, Tyson JR, Zuzarte PC, Gilpatrick T, Razaghi R, Quick J, Sadowski N, et al. (2018). Nanopore native RNA sequencing of a human poly(A) transcriptome. bioRxiv

    Google Scholar 

  27. Liu H, Begik O, Lucas MC, Ramirez JM, Mason CE, Wiener D, Schwartz S, Mattick JS, Smith MA, Novoa EM (2019) Accurate detection of m(6)A RNA modifications in native RNA sequences. Nat Commun 10:4079

    Google Scholar 

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Acknowledgments

This work is supported by funding from the Hundred-Talent Program of the Chinese Academy of Sciences (Y9CAS61107), the Strategic Priority Research Program of the Chinese Academy of Sciences (XDA16010603), the National Natural Science Foundation of China (31970597), the National Key Research and Development Program of China (2019YFA0802202), and K.C. Wong Education Foundation (GJTD-2019-08). We thank Liuming Wang and Zihao Wang for their discussion and assistance in figure generation.

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Correspondence to Jie Ren .

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He, M., Chi, X., Ren, J. (2021). Applications of Oxford Nanopore Sequencing in Schizosaccharomyces pombe. In: Xiao, W. (eds) Yeast Protocols. Methods in Molecular Biology, vol 2196. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-0868-5_9

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  • DOI: https://doi.org/10.1007/978-1-0716-0868-5_9

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-0867-8

  • Online ISBN: 978-1-0716-0868-5

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