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Oral Bacterial Genome Sequencing Using the High-Throughput Roche Genome Sequencer FLX System

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Oral Biology

Part of the book series: Methods in Molecular Biology ((MIMB,volume 666))

Abstract

For over 30 years, the chain termination method of DNA sequencing (commonly known as Sanger sequencing) has been the mainstay of any DNA sequencing project. In the past, whole-genome sequencing employing exclusively Sanger chemistry has been a labor-intensive and costly exercise and an option unfeasible for the average research group. However, within the last 4 years, the introduction of three high-throughput sequencing technologies (454, SOLiD, and Illumina) has revolutionized genomics by facilitating unprecedented levels (up to gigabasepairs) of reliable DNA sequence output in a relatively short time frame and at a much lower cost per sequenced basepair. Here, we provide laboratory and bioinformatic protocols that will allow the average research group to undertake high-throughput sequencing of oral bacterial genomes using the Roche Genome Sequencer FLX System which employs 454 pyrosequencing technology.

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Acknowledgments

This research was supported by grants from the Otago Medical Research Foundation, the New Zealand Lottery Grants Board (Lottery Health), and the New Zealand Dental Association Research Foundation. N.C.K.H. wishes to acknowledge the dedication and perseverance of Nurul Haji-Ishak and Andrew Wong (University of Otago Division of Health Sciences Summer Students) during the annotation and partial gap closure phases of the oral Streptococcus genome sequencing projects.

Author information

Authors and Affiliations

  1. Faculty of Dentistry, Sir John Walsh Research Institute, University of Otago, Dunedin, New Zealand

    Nicholas C.K. Heng

  2. Department of Anatomy and Structural Biology, Otago High-Throughput DNA Sequencing Facility, University of Otago, Dunedin, New Zealand

    Jo-Ann L. Stanton

Authors
  1. Nicholas C.K. Heng
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  2. Jo-Ann L. Stanton
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Editor information

Editors and Affiliations

  1. Faculty of Dentistry, Department of Oral Sciences, University of Otago, Great King Street 310, Dunedin, 9016, New Zealand

    Gregory J. Seymour

  2. Faculty of Dentistry, Department of Oral Sciences, University of Otago, Great King Street 310, Dunedin, 9016, New Zealand

    Mary P. Cullinan

  3. Faculty of Dentistry, Sir John Walsh Research Institute, University of Otago, Great King Street 310, Dunedin, 9016, New Zealand

    Nicholas C.K. Heng

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© 2010 Springer Science+Business Media, LLC

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Heng, N.C., Stanton, JA.L. (2010). Oral Bacterial Genome Sequencing Using the High-Throughput Roche Genome Sequencer FLX System. In: Seymour, G., Cullinan, M., Heng, N. (eds) Oral Biology. Methods in Molecular Biology, vol 666. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-60761-820-1_14

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  • DOI: https://doi.org/10.1007/978-1-60761-820-1_14

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  • Publisher Name: Humana Press, Totowa, NJ

  • Print ISBN: 978-1-60761-819-5

  • Online ISBN: 978-1-60761-820-1

  • eBook Packages: Springer Protocols

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