Spiroplasma kunkelii Strain CR2-3x Genome Sequencing

This collaborative project between our laboratory at the University of Oklahoma, Norman Campus's Advanced Center for Genome Technology, in the Department of Chemistry and Biochemistry, which is funded in part by an US Department of Agriculture, Agricultural Research Service cooperative agreement, and Dr. Robert E. Davis at the USDA. ShaoPing Lin's group has just begun this project and the data is being released nightly as it is being collected.


Spiroplasma kunkelii Strain CR2-3x Genome Sequencing Progress

  • Strain CR2-3x was obtained from Dr. Jacque Fletcher at Oklahoma State University and the genomic DNA was isolated by Dr. Robert E. Davis at the USDA.
  • Our initial sequencing strategy is to sequence generate double-stranded DNA sequencing templates from a randomly sheared library of the genomic DNA. Colonies are being picked and the sequencing templates are being isolated using the semi-automated procedures described on our protocol page .
  • Each double-stranded sequencing template is being end sequenced using the universal forward and reverse pUC/M13 sequencing primers, and the sequencing data is being collected on the ABI 3700 automated fluorescent-based capillary sequencers.
  • Final sequence proofreading will be accomplished by direct sequencing off large insert lambda clones, PCR products from genomic templates, and primer walking-based sequencing off large (4-8Kb) plasmid sub-clones.

  • View the Latest Phrap High Stringency Spiroplasma kunkelii Statistics

  • Search the Spiroplasma kunkelii Genome sequence data


    Obtaining the sequence data via ftp

    All of our shotgun sequence data is available via ftp (see below).

    Caution: Since the data presently is being proof read, it should be considered preliminary raw sequence data. Please take this into account when using this data

    The latest sequence data is available in the 'spiro-1k.fa' file on our ftp site.

  • Obtaining the Spiroplasma kunkelii Sequencing Data via ftp

  • If instead, you would rather ftp this file directly, you can ftp to ftp.spiro.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 Spiroplasma kunkelii strain CR2-3x being sequenced, will be submitted to the ATCC and given an accession number.
  • At the present time, none of the shotgun clones are available for distribution. 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



  • Other Spiroplasma related web sites

    http://www.barc.usda.gov/psi/mppl/spiroplasma/

    http://www.oardc.ohio-state.edu/spiroplasma/genome.htm


    Acknowledgment

    Should you find this data useful and wish to reference it, please acknowledge the Spiroplasma kunkelii Genome Sequencing Project funded by US Department of Agriculture, Agricultural Research Service Project Number: 1275-22000-144-02 and B. A. Roe, S. P. Lin, H.G. Jia, H.M. Wu, D. Kupfer, and R. E. Davis.

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

    Thanks, Bruce Roe, ShaoPing Lin, HongGui Jia, HongMin Wu, Doris Kupfer and Robert Davis.
    The University of Oklahoma, Department of Chemistry and Biochemistry, Norman, Oklahoma 73019 and the US Department of Agriculture, Agricultural Research Service, Beltsville, MD.

    Bruce Roe, broe@ou.edu

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    Bruce Roe, broe@ou.edu