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Genomic 'valleys of death'

This month's Genome Watch considers the features of the latest streptococcal genomes in light of a common problem — cloning bias.

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Figure 1: Clone coverage in Shewanella spp.


  1. 1

    Sorek, R. et al. Genome-wide experimental determination of barriers to horizontal gene transfer. Science 318, 1449–1452 (2007).

    CAS  Article  Google Scholar 

  2. 2

    Xu, P. et al. Genome of the opportunistic pathogen Streptococcus sanguinis. J. Bacteriol. 189, 3166–3175 (2007).

    CAS  Article  Google Scholar 

  3. 3

    Conner, C. P., Heithoff, D. M., Julio, S. M., Sinsheimer, R. L. & Mahan, M. J. Differential patterns of acquired virulence genes distinguish Salmonella strains. Proc. Natl Acad. Sci. USA 95, 4641–4645 (1998).

    CAS  Article  Google Scholar 

  4. 4

    Vickerman, M. M., Iobst, S., Jesionowski, A. M. & Gill, S. R. Genome-wide transcriptional changes in Streptococcus gordonii in response to competence signaling peptide. J. Bacteriol. 189, 7799–7807 (2007).

    CAS  Article  Google Scholar 

  5. 5

    Avery, O. T., MacLeod, C. M. & McCarty, M. Studies on the chemical nature of the substance inducing transformation of pneumococcal types. Inductions of transformation by a desoxyribonucleic acid fraction isolated from pneumococcus type III. J. Exp. Med. 79, 137–158 (1944).

    CAS  Article  Google Scholar 

  6. 6

    Hoskins, J. et al. Genome of the bacterium Streptococcus pneumoniae strain R6. J. Bacteriol. 183, 5709–5717 (2001).

    CAS  Article  Google Scholar 

  7. 7

    Lanie, J. A. et al. Genome sequence of Avery's virulent serotype 2 strain D39 of Streptococcus pneumoniae and comparison with that of unencapsulated laboratory strain R6. J. Bacteriol. 189, 38–51 (2007).

    CAS  Article  Google Scholar 

  8. 8

    Rutherford, K. et al. Artemis: sequence visualization and annotation. Bioinformatics 16, 944–945 (2000).

    CAS  Article  Google Scholar 

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Entrez Genome Project

Escherichia coli

S. gordonii strain substr. CH1 Challis

S. pneumoniae strain D39

S. sanguinis strain SK36

Salmonella enterica serovar Typhimurium


454 Life Sciences


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Bentley, S. Genomic 'valleys of death'. Nat Rev Microbiol 6, 260–261 (2008).

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