Rapid and affordable size-selected PacBio single-molecule real-time sequencing template library construction using the bead-beating DNA extraction method
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Keywords
bead-beating, library preparation, PacBio, SMRT sequencing
Abstract
This study demonstrated that bead-beating method facilitates a simple and rapid protocol for genomic DNA isolation for Pacific BioSciences (PacBio) sequencing with library construction of sufficient length. The protocol may also be beneficial for inactivating pathogens by simultaneous and instant DNA fragmentation, with no special equipment required to obtain large DNA fragments. This protocol was comparable in terms of quality to the standard protocol suggested by PacBioand represents an alternative, rapid shortcut for performing accurate PacBio sequencing.
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References
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2. Goodwin S, McPherson JD, McCombie WR (2016) Coming of age: ten years of next-generation sequencing technologies. Nat Rev Genet 17: 333-351.
3. Reich D, Green RE, Kircher M, Krause J, Patterson N, et al. (2010) Genetic history of an archaic hominin group from Denisova Cave in Siberia. Nature 468: 1053-1060.
4. Green RE, Krause J, Briggs AW, Maricic T, Stenzel U, et al. (2010) A draft sequence of the Neandertal genome. Science 328: 710-722.
5. Rhoads A, Au KF (2015) PacBio sequencing and its applications. Genomics Proteomics Bioinformatics 13: 278-289.
6. Chin CS, Alexander DH, Marks P, Klammer AA, Drake J, et al. (2013) Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data. Nat Methods 10: 563-569.
7. Akiba M, Sekizuka T, Yamashita A, Kuroda M, Fujii Y, et al. (2016) Distribution and relationships of antimicrobial resistance determinants among extended-spectrum-cephalosporin-resistant or carbapenem-resistant Escherichia coli isolates from rivers and sewage treatment plants in India. Antimicrob Agents Chemother 60: 2972-2980.
8. Mayjonade B, Gouzy J, Donnadieu C, Pouilly N, Marande W, et al. (2016) Extraction of high-molecular-weight genomic DNA for long-read sequencing of single molecules. Biotechniques 61: 203-205.
9. McDonnell G, Russell AD (1999) Antiseptics and disinfectants: activity, action, and resistance. Clin Microbiol Rev 12: 147-179.
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Published
Sep 13, 2017
Article Details
How to Cite
1.
Kato K, Hashino M, Ito T, Matsui M, Suzuki S, Kai K, Kitazume M, Sekizuka T, Kuroda M. Rapid and affordable size-selected PacBio single-molecule real-time sequencing template library construction using the bead-beating DNA extraction method. J Biol Methods [Internet]. 2017 Sep. 13 [cited 2024 Apr. 25];4(3):e79. Available from: https://jbmethods.org/index.php/jbm/article/view/169
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