Streptococcus mutans strain UA159 Genome Sequencing


Streptococcus mutans strain UA159 Genome Sequencing Progress

We have produced and have sequenced both ends of the pUC sub-clones from shotgun libraries from genomic DNA isolated from Streptococcus mutans serotype C, strain UA159 (ATCC700610) obtained from Page Caufield at University Alabama Birmingham. This NIH funded project is a joint collaboration between our Genome Center at the University of Oklahoma in Norman, OK and Dr. Joe Ferretti's laboratory at in the Department of Microbiology and Immunology at the University of Oklahoma Health Sciences Center in Oklahoma City, OK.
  • Our strategy was to sequence approximately 12,000 individual, shotgun-based, double stranded templates generated from a randomly sheared library of the Streptococcus mutans genome, with both the universal forward and reverse pUC sequencing primers. When this shotgun phase was completed we moved to a directed custom synthetic primer-based approach for closure and quality improvement to complete the sequence of the genome to a high level of accuracy.
  • All of our data in contigs greater that 1kb is publically available in accord with the Bermuda Agreement on this web site.
  • As of 10-29-98 we switched to Phred980904.a and Phrap980831 and also increased our database assembly stringency from the default values of PHRAP's min_match and min_score by doubling them to produce high stringency assembled data that is more accurate.
  • As of 04-12-01 the Streptococcus mutans strain UA159 Genome shotgun and closure phase have been completed and the genomic sequence has been assembled into one, circular contig.

  • View the latest high stringency Streptococcus mutans Statistics

  • Search the Streptococcus mutans Genome sequence data


    Obtaining the sequence data via ftp

    All of our shotgun sequence data is available via ftp (see below) but at the present time, the various contigs are in "random" order and do not correspond to any specific relationship one to another. Please be aware that the order and contig number will change with each new release of data.

    Caution: the data has been neither proof read nor edited and thus should be considered preliminary raw sequence data. Also, because the sequence assembly program, Phrap, has the tendency to include inaccurate sequence reads on the ends of contigs, be cautious when using sequences within 1-200 bases of the ends of individual contigs. Please take this into account when using this data

  • Obtaining the Streptococcus mutans Sequencing Data via ftp

  • If instead, you would rather ftp this file directly, you can ftp to ftp.genome.ou.edu (logon as anonymous with password your e-mail address). Read the 00readme file in the ftp directory to determine which files you are interested in.

    Clone Availability

  • The Streptococcus mutans strain being sequenced can be obtained from the ATCC as ATCC700610.
  • At the present time, none of the shotgun clones are available, but we anticipate at some point to generate a set of ordered sub-clones that will be made available throught the ATCC.

    Literature Reference Describing Strain being sequenced

  • Murchison HH et al. Transformation of Streptococcus mutans with chromosomal and shuttle plasmid (pYA629) DNAs. Infect. Immun. 54: 273-282, 1986
  • Wexler DL et al. Characteristics and cariogenicity of a fructanase-defective Streptococcus mutants strain. Infect. Immun. 60: 3673-3681, 1992.
  • Tao L et al. Transformation efficiency of EMS-induced mutants of Streptococcus mutans of altered cell shape. J. Dent. Res. 72: 1032-1039, 1993
  • Quivey RG Jr et al. Acid adaptation in Streptococcus mutans UA159 alleviates sensitization to environmental stress due to RecA deficiency. FEMS Microbiol. Lett. 126: 257-261, 1995
  • Burne RA et al. Cariogenicity of Streptococcus mutans strains with defects in fructan metabolism assessed in a program-fed specific-pathogen-free rat model. J. Dent. Res. 75: 1572-1577, 1996

    Acknowledgment

    Should you find this data useful and wish to reference it, please acknowledge the Streptococcal mutans Genome Sequencing Project funded by USPHS/NIH grant from the Dental Institute and B. A. Roe, R. Y. Tian, H. G. Jia, Y. D. Qian, S. P. Lin, S. Li, S. Kenton, H. Lai, J. D. White, R. E. McLaughlin, M. McShan, D. Ajdic and J. Ferretti.

    If possible, please send us both the literature citation once published, and a copy of the manuscript.

    Thanks, Bruce Roe, RunYing Tian, HongGui Jia, YuDong Qian, Shaoping Lin, Suling Li, Steve Kenton, HongShing Lai, Jim D. White, Bob McLaughlin, Mike McShan, Dragana Ajdic and Joseph Ferretti.
    The University of Oklahoma, Department of Chemistry and Biochemistry, Norman, Oklahoma 73019 and The University of Oklahoma Health Sciences Center, Department of Microbiology and Immunology, Oklahoma City, Oklahoma 73190

    Joe Ferretti, Joseph-Ferretti@uokhsc.edu

    Bob McLaughlin, bob-mclaughlin@ouhsc.edu
    Dragana Ajdic, dragana-ajdic@ouhsc.edu
    Mike McShan, wmcshan@REX.RE.uokhsc.edu
    Bruce Roe, broe@ou.edu

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    Bruce Roe, broe@ou.edu