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Bacterial Genome Sequencing

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Molecular Epidemiology of Microorganisms

Part of the book series: Methods in Molecular Biology™ ((MIMB,volume 551))

Abstract

For over 30 yr, the Sanger method has been the standard for DNA sequencing. Instruments have been developed and improved over time to increase throughput, but they always relied on the same technology. Today, we are facing a revolution in DNA sequencing with many drastically different platforms that have become or will soon become available on the market. We review a number of sequencing technologies and provide examples of applications. We also discuss the impact genomics and new DNA sequencing approaches have had on various fields of biological research.

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References

  1. Fleischmann, R. D., Adams, M. D., White, O., Clayton, R. A., Kirkness, E. F., Kerlavage, A. R., et al (1995). Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science 269, 496–512.

    Article  PubMed  CAS  Google Scholar 

  2. Fonstein, M., and Haselkorn, R. (1995). Physical mapping of bacterial genomes. J. Bacteriol. 177, 3361–3369.

    PubMed  CAS  Google Scholar 

  3. Frangeul, L., Nelson, K. E., Buchrieser, C., Danchin, A., Glaser, P., and Kunst, F. (1999). Cloning and assembly strategies in microbial genome projects. Microbiology 145, 2625–2634.

    PubMed  CAS  Google Scholar 

  4. Delcher, A. L., Bratke, K. A., Powers, E. C., and Salzberg, S. L. (2007). Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics 23, 673–679.

    Article  PubMed  CAS  Google Scholar 

  5. Besemer, J., and Borodovsky, M. (2005). GeneMark: Web software for gene finding in prokaryotes, eukaryotes and viruses. Nucleic Acids Res. 33, 451–454.

    Article  Google Scholar 

  6. Altschul, S. F., Madden, T. L., Schaffer, A. A., Zhang, J., Zhang, Z., Miller, W., et al (1997). Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25, 3389–3402.

    Article  PubMed  CAS  Google Scholar 

  7. Riley, M. (1993). Functions of the gene products of Escherichia coli. Microbiol. Rev. 57, 862–952.

    PubMed  CAS  Google Scholar 

  8. Ashburner, M., Ball, C. A., Blake, J. A., Botstein, D., Butler, H., Cherry, J. M., et al (2000). Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat. Genet. 25, 25–29.

    CAS  Google Scholar 

  9. Bateman, A., Birney, E., Durbin, R., Eddy, S. R., Howe, K. L., and Sonnhammer, E. L. (2000). The Pfam protein families database. Nucleic Acids Res. 28, 263–266.

    Article  PubMed  CAS  Google Scholar 

  10. Haft, D. H., Selengut, J. D., and White, O. (2003). The TIGRFAMs database of protein families. Nucleic Acids Res. 31, 371–373.

    Article  PubMed  CAS  Google Scholar 

  11. Venter, J. C., Remington, K., Heidelberg, J. F., Halpern, A. L., Rusch, D., Eisen, J. A., et al (2004). Environmental genome shotgun sequencing of the Sargasso Sea. Science 304, 66–74.

    Article  PubMed  CAS  Google Scholar 

  12. Daniel, R. (2005). The metagenomics of soil. Nat. Rev. Microbiol. 3, 470–478.

    Article  PubMed  CAS  Google Scholar 

  13. Turnbaugh, P. J., Ley, R. E., Hamady, M., Fraser-Liggett, C. M., Knight, R., and Gordon, J. I. (2007). The human microbiome project. Nature 449, 804–810.

    Article  PubMed  CAS  Google Scholar 

  14. Fox, J. A., McMillan, S., and Ouellette, B. F. (2007). Conducting research on the web: 2007 update for the bioinformatics links directory. Nucleic Acids Res. 35, 3–5.

    Article  Google Scholar 

  15. Sanger, F., and Coulson, A. R. (1975). A rapid method for determining sequences in DNA by primed synthesis with DNA polymerase. J. Mol. Biol. 94, 441–448.

    Article  PubMed  CAS  Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

  17. Margulies, M., Egholm, M., Altman, W. E., Attiya, S., Bader, J. S., Bemben, L. A., et al (2005). Genome sequencing in microfabricated high-density picolitre reactors. Nature 437, 376–380.

    PubMed  CAS  Google Scholar 

  18. Ronaghi, M., Uhlen, M., and Nyren, P. (1998). A sequencing method based on real-time pyrophosphate. Science 281, 363–365.

    Article  PubMed  CAS  Google Scholar 

  19. Kartalov, E. P., and Quake, S. R. (2004). Microfluidic device reads up to four consecutive base pairs in DNA sequencing-by-synthesis. Nucleic Acids Res. 32, 2873–2879.

    Article  PubMed  CAS  Google Scholar 

  20. Goldberg, S. M., Johnson, J., Busam, D., Feldblyum, T., Ferriera, S., Friedman, R., et al (2006). A Sanger/pyrosequencing hybrid approach for the generation of high-quality draft assemblies of marine microbial genomes. Proc. Natl. Acad. Sci. U S A 103, 11240–11245.

    Article  PubMed  CAS  Google Scholar 

  21. McCutcheon, J. P., and Moran, N. A. (2007). Parallel genomic evolution and metabolic interdependence in an ancient symbiosis. Proc. Natl. Acad. Sci. U S A 104, 19392–19397.

    Article  PubMed  CAS  Google Scholar 

  22. Bennett, S. T., Barnes, C., Cox, A., Davies, L., and Brown, C. (2005). Toward the 1,000 dollars human genome. Pharmacogenomics 6, 373–382.

    Article  PubMed  CAS  Google Scholar 

  23. Levene, M. J., Korlach, J., Turner, S. W., Foquet, M., Craighead, H. G., and Webb, W. W. (2003). Zero-mode waveguides for single-molecule analysis at high concentrations. Science 299, 682–686.

    Article  PubMed  CAS  Google Scholar 

  24. Korlach, J., Marks, P. J., Cicero, R. L., Gray, J. J., Murphy, D. L., Roitman, D. B., et al (2008). Selective aluminum passivation for targeted immobilization of single DNA polymerase molecules in zero-mode waveguide nanostructures. Proc. Natl. Acad. Sci. U S A 105, 1176–1181.

    Article  PubMed  CAS  Google Scholar 

  25. Korbel, J. O., Urban, A. E., Affourtit, J. P., Godwin, B., Grubert, F., Simons, J. F., et al (2007). Paired-end mapping reveals extensive structural variation in the human genome. Science 318, 420–426.

    Article  PubMed  CAS  Google Scholar 

  26. Emrich, S. J., Barbazuk, W. B., Li, L., and Schnable, P. S. (2007). Gene discovery and annotation using LCM-454 transcriptome sequencing. Genome Res. 17, 69–73.

    Article  PubMed  CAS  Google Scholar 

  27. Torres, T. T., Metta, M., Ottenwalder, B., and Schlotterer, C. (2008). Gene expression profiling by massively parallel sequencing. Genome Res. 18, 172–177.

    Article  PubMed  CAS  Google Scholar 

  28. Hafner, M., Landgraf, P., Ludwig, J., Rice, A., Ojo, T., Lin, C., et al (2008). Identification of microRNAs and other small regulatory RNAs using cDNA library sequencing. Methods 44, 3–12.

    Article  PubMed  CAS  Google Scholar 

  29. Mardis, E. R. (2007). ChIP-seq: welcome to the new frontier. Nat. Methods 4, 613–614.

    Article  PubMed  CAS  Google Scholar 

  30. Cokus, S. J., Feng, S., Zhang, X., Chen, Z., Merriman, B., Haudenschild, C. D., et al (2008). Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning. Nature 452, 215–219.

    Article  PubMed  CAS  Google Scholar 

  31. Schones, D. E., Cui, K., Cuddapah, S., Roh, T. Y., Barski, A., Wang, Z., et al (2008). Dynamic regulation of nucleosome positioning in the human genome. Cell 132, 887–898.

    Article  PubMed  CAS  Google Scholar 

  32. Pop, M., and Salzberg, S. L. (2008). Bioinformatics challenges of new sequencing technology. Trends Genet. 24, 142–149.

    Article  PubMed  CAS  Google Scholar 

  33. Fraser-Liggett, C. M. (2005). Insights on biology and evolution from microbial genome sequencing. Genome Res. 15, 1603–1610.

    Article  PubMed  CAS  Google Scholar 

  34. Grifantini, R., Bartolini, E., Muzzi, A., Draghi, M., Frigimelica, E., Berger, J., et al (2002). Previously unrecognized vaccine candidates against group B meningococcus identified by DNA microarrays. Nat. Biotechnol. 20, 914–921.

    Article  PubMed  CAS  Google Scholar 

  35. Pieper, R., Gatlin-Bunai, C. L., Mongodin, E. F., Parmar, P. P., Huang, S. T., Clark, D. J., et al (2006). Comparative proteomic analysis of Staphylococcus aureus strains with differences in resistance to the cell wall-targeting antibiotic vancomycin. Proteomics 6, 4246–4258.

    Article  PubMed  CAS  Google Scholar 

  36. Oldiges, M., Lutz, S., Pflug, S., Schroer, K., Stein, N., and Wiendahl, C. (2007). Metabolomics: current state and evolving methodologies and tools. Appl. Microbiol. Biotechnol. 76, 495–511.

    Article  PubMed  CAS  Google Scholar 

  37. Collura, V., and Boissy, G. (2007). From protein-protein complexes to interactomics. Subcell. Biochem. 43, 135–183.

    Article  PubMed  Google Scholar 

  38. Kitano, H. (2002). Systems biology: a brief overview. Science 295, 1662–1664.

    Article  PubMed  CAS  Google Scholar 

  39. Lartigue, C., Glass, J. I., Alperovich, N., Pieper, R., Parmar, P. P., Hutchison, C. A., 3rd, et al (2007). Genome transplantation in bacteria: changing one species to another. Science 317, 632–638.

    Article  PubMed  CAS  Google Scholar 

  40. Gibson, D. G., Benders, G. A., Andrews-Pfannkoch, C., Denisova, E. A., Baden-Tillson, H., Zaveri, J., et al (2008). Complete chemical synthesis, assembly, and cloning of a Mycoplasma genitalium genome. Science 319, 1215–1220.

    Article  PubMed  CAS  Google Scholar 

  41. Grabowski, M., Joachimiak, A., Otwinowski, Z., and Minor, W. (2007). Structural genomics: keeping up with expanding knowledge of the protein universe. Curr. Opin. Struct. Biol. 17, 347–353.

    Article  PubMed  CAS  Google Scholar 

  42. Rappuoli, R., and Covacci, A. (2003). Reverse vaccinology and genomics. Science 302, 602.

    Article  PubMed  CAS  Google Scholar 

  43. Tettelin, H., Saunders, N. J., Heidelberg, J., Jeffries, A. C., Nelson, K. E., Eisen, J. A., et al (2000). Complete genome sequence of Neisseria meningitidis serogroup B strain MC58. Science 287, 1809–1815.

    Article  PubMed  CAS  Google Scholar 

  44. Pizza, M., Scarlato, V., Masignani, V., Giuliani, M. M., Aricò, B., Comanducci, M., et al (2000). Identification of vaccine candidates against serogroup B meningococcus by whole-genome sequencing. Science 287, 1816–1820.

    Article  PubMed  CAS  Google Scholar 

  45. Telford, J. L., Margarit, I., Maione, D., Masignani, V., Tettelin, H., Bensi, G.et al, (2004). Vaccines against pathogenic streptococci, in Genomics, Proteomics and Vaccines (Grandi, G. , ed.)., Wiley, London, pp. 205–222.

    Google Scholar 

  46. Goldschneider, I., Gotschlich, E. C., and Artenstein, M. S. (1969). Human immunity to the meningococcus. I. The role of humoral antibodies. J. Exp. Med. 129, 1307–1326.

    CAS  Google Scholar 

  47. Giuliani, M. M., Adu-Bobie, J., Comanducci, M., Aricò, B., Savino, S., Santini, L., et al (2006). A universal vaccine for serogroup B meningococcus. Proc. Natl. Acad. Sci. U S A 103, 10834–10839.

    Article  PubMed  CAS  Google Scholar 

  48. Tettelin, H., Masignani, V., Cieslewicz, M. J., Donati, C., Medini, D., Ward, N. L., et al (2005). Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: implications for the microbial “pan-genome.” Proc. Natl. Acad. Sci. U S A 102, 13950–13955.

    Article  CAS  Google Scholar 

  49. Medini, D., Donati, C., Tettelin, H., Masignani, V., and Rappuoli, R. (2005). The microbial pan-genome. Curr. Opin. Genet. Dev. 15, 589–594.

    Article  PubMed  CAS  Google Scholar 

  50. Maione, D., Margarit, I., Rinaudo, C. D., Masignani, V., Mora, M., Scarselli, M., et al (2005). Identification of a universal Group B streptococcus vaccine by multiple genome screen. Science 309, 148–150.

    Article  PubMed  CAS  Google Scholar 

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© 2009 Humana Press, a part of Springer Science+Business Media, LLC

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Tettelin, H., Feldblyum, T. (2009). Bacterial Genome Sequencing. In: Caugant, D. (eds) Molecular Epidemiology of Microorganisms. Methods in Molecular Biology™, vol 551. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-60327-999-4_18

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  • DOI: https://doi.org/10.1007/978-1-60327-999-4_18

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  • Publisher Name: Humana Press, Totowa, NJ

  • Print ISBN: 978-1-60327-998-7

  • Online ISBN: 978-1-60327-999-4

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