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Chapter 2 : Comparative Genomics of : Intrastrain Diversity and Genome Plasticity

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Abstract:

As with many other gram-positive organisms, the genome of proved difficult to sequence. The majority of insertion sequence (IS) elements have undergone insertions, deletions, and/or point mutations that result in frame shifted or otherwise nonfunctional transposase genes. A primary role for the numerous repeats might be their potential contribution to genomic rearrangements using the repeats as seeds for recombination events, as discussed in this chapter. It has been noted an intriguing functional pattern for proteins that are surface-attached by alternate means. The nonshared genes represent both single-gene insertions and deletions and also a number of nonshared regions. All regions of diversity, except only region outside of the capsular region, represented genes that were present in at least one additional strain from our collection of genetically diverse strains. The mosaic distribution supports the idea that these regions are associated with genome plasticity. The significance of the high density of repeats is that they may play a significant role in generating the genome plasticity that is observed. The vast majority of clinical and nonclinical isolates of are transformable, and the frequent exchange of genetic information through transformation could permit a high degree of genetic plasticity.

Citation: Tettelin H, Hollingshead S. 2004. Comparative Genomics of : Intrastrain Diversity and Genome Plasticity, p 15-29. In Tuomanen E, Mitchell T, Morrison D, Spratt B (ed), The Pneumococcus. ASM Press, Washington, DC. doi: 10.1128/9781555816537.ch2

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Cell Wall Proteins
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Figures

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FIGURE 1

PROmer plots showing proteome-to-proteome comparisons of various species within the lactic acid group of bacteria. Genes along the diagonal represent conserved proteins, potential orthologs, that are encoded in similar positions for the cross-genome comparison. The genes encoding these proteins are still in synteny between the two genomes under comparison. Scattered dots away from the diagonal represent the detection of potential orthologs whose position has shifted since the two genomes last shared a common ancestor. The genes encoding these scattered proteins now lack synteny. While comparisons of GAS, GBS, and maintain some synteny, most comparisons with show little synteny.

Citation: Tettelin H, Hollingshead S. 2004. Comparative Genomics of : Intrastrain Diversity and Genome Plasticity, p 15-29. In Tuomanen E, Mitchell T, Morrison D, Spratt B (ed), The Pneumococcus. ASM Press, Washington, DC. doi: 10.1128/9781555816537.ch2
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Tables

Generic image for table
TABLE 1

TGenome features of the three sequenced strains of

Citation: Tettelin H, Hollingshead S. 2004. Comparative Genomics of : Intrastrain Diversity and Genome Plasticity, p 15-29. In Tuomanen E, Mitchell T, Morrison D, Spratt B (ed), The Pneumococcus. ASM Press, Washington, DC. doi: 10.1128/9781555816537.ch2
Generic image for table
TABLE 2

Major regions of nonconserved gene order between TIGR4 and R6 identified by inspection of PROmer plots ( Fig. 1 )

Citation: Tettelin H, Hollingshead S. 2004. Comparative Genomics of : Intrastrain Diversity and Genome Plasticity, p 15-29. In Tuomanen E, Mitchell T, Morrison D, Spratt B (ed), The Pneumococcus. ASM Press, Washington, DC. doi: 10.1128/9781555816537.ch2
Generic image for table
TABLE

Regions of diversity identified in CGH of 13 strains

Citation: Tettelin H, Hollingshead S. 2004. Comparative Genomics of : Intrastrain Diversity and Genome Plasticity, p 15-29. In Tuomanen E, Mitchell T, Morrison D, Spratt B (ed), The Pneumococcus. ASM Press, Washington, DC. doi: 10.1128/9781555816537.ch2

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