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A Sanger/pyrosequencing hybrid approach for the generation of high-quality draft assemblies of marine microbial genomes

  1. Susanne M. D. Goldberg * , † , ‡ ,
  2. Justin Johnson * , † , ‡ ,
  3. Dana Busam *,
  4. Tamara Feldblyum § ,
  5. Steve Ferriera *,
  6. Robert Friedman *,
  7. Aaron Halpern *,
  8. Hoda Khouri § ,
  9. Saul A. Kravitz *,
  10. Federico M. Lauro ,
  11. Kelvin Li *,
  12. Yu-Hui Rogers *,
  13. Robert Strausberg *,
  14. Granger Sutton *,
  15. Luke Tallon § ,
  16. Torsten Thomas ‖ ,
  17. Eli Venter *,
  18. Marvin Frazier *, and
  19. J. Craig Venter * , ‡
  1. *J. Craig Venter Institute, 9704 Medical Center Drive, Rockville, MD 20850;
  2. §Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850;
  3. Scripps Institution of Oceanography, University of California at San Diego, La Jolla, CA 92093-0202; and
  4. ‖School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney UNSW 2052, Australia

  1. Contributed by J. Craig Venter, June 8, 2006

  2. ↵ †S.M.D.G. and J.J. contributed equally to this work.

Abstract

Since its introduction a decade ago, whole-genome shotgun sequencing (WGS) has been the main approach for producing cost-effective and high-quality genome sequence data. Until now, the Sanger sequencing technology that has served as a platform for WGS has not been truly challenged by emerging technologies. The recent introduction of the pyrosequencing-based 454 sequencing platform (454 Life Sciences, Branford, CT) offers a very promising sequencing technology alternative for incorporation in WGS. In this study, we evaluated the utility and cost-effectiveness of a hybrid sequencing approach using 3730xl Sanger data and 454 data to generate higher-quality lower-cost assemblies of microbial genomes compared to current Sanger sequencing strategies alone.

Footnotes

  • ‡To whom correspondence may be addressed. E-mail: sgoldberg{at}venterinstitute.org, jjohnson{at}venterinstitute.org, or jcventer{at}venterinstitute.org

  • Author contributions: R.F., Y.-H.R., and M.F. designed research; S.M.D.G., J.J., and D.B. performed research; S.F., A.H., S.A.K., F.M.L., K.L., G.S., T.T., and E.V. contributed new reagents/analytic tools; S.M.D.G., J.J., D.B., T.F., A.H., H.K., K.L., Y.-H.R., G.S., L.T., E.V., M.F., and J.C.V. analyzed data; and S.M.D.G., J.J., R.F., Y.-H.R., R.S., M.F., and J.C.V. wrote the paper.

  • Conflict of interest statement: No conflicts declared.

  • ↵**Although we labeled these as 5.3× coverage, there may have been more if slight contamination of the sample skewed our initial estimates of the genome size. This coverage estimate is for the main organism only; no contaminant is included.

  • Freely available online through the PNAS open access option.

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