Chapter 4 : Comparative Genomics of

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The use of comparative genomics combined with robust methods for data analysis will continue and will form the basis for the development of rational intervention strategies to reduce in the food chain. This chapter reviews the salient comparative features of the four fully sequenced genomes and reveals highlights from selected whole-genome microarray studies. The publication of the first genome paved the way for comparative genomics of this species. The relative genome diversity of bacterial species varies from clonal (genetically uniform) to genetically highly variable. The majority of genes on CJIE3 are of unknown function, although 23% share homology with ATCC 51449 genomic island (HHGI1). Recent comparative phylogenomics studies have been undertaken on increasingly large collections of strains from defined origins. The chapter discusses case studies of genomic comparisons by microarray. More recently, the authors studied over 230 strains from diverse origin and have further demonstrated the split of strains into two clades. Approximately half of the human isolates from this study are not associated with the livestock clade. DNA microarrays represent a powerful enabling technology for the whole-scale comparison of bacterial genomes. This, coupled with new methods to model DNA microarray data, is facilitating the development of robust comparative phylogenomics analyses. The next challenge for microbiologists in this postgenomic era is to correlate genome to phenome. This will provide a clear and more comprehensive understanding of the biology of .

Citation: Champion O, Al-Jaberi S, Stabler R, Wren B. 2008. Comparative Genomics of , p 63-71. In Nachamkin I, Szymanski C, Blaser M (ed), , Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555815554.ch4

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Image of Figure 1.
Figure 1.

Venn diagram of the genome content of the three sequenced human isolates (NCTC 11168, CG8486, and 81-176) (adapted from ). The gene content of 81-176 is based on the results of . These estimations exclude the capsule, LOS, and flagellin posttranslational modification loci.

Citation: Champion O, Al-Jaberi S, Stabler R, Wren B. 2008. Comparative Genomics of , p 63-71. In Nachamkin I, Szymanski C, Blaser M (ed), , Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555815554.ch4
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Image of Figure 2.
Figure 2.

Comparative phylogenomics pipeline. Graphical representation of steps involved in production of a phylogenetic tree. Genomic DNA from each member of the strain collection was hybridized to a BμGS 11168 microarray with 11168 gDNA as control. Florescent intensities were calculated by BlueFuse. GeneSpring calculated intensity ratios and removed low-quality data points. GACK was used to convert ratio data to binary present/absent data. MrBayes used the binary data to construct a putative phylogeny by means of a Bayesian algorithm. The resulting tree was statistically tested for robustness. Further strains can be fed into the pipeline, and selection may be influenced by current phylogeny prediction.

Citation: Champion O, Al-Jaberi S, Stabler R, Wren B. 2008. Comparative Genomics of , p 63-71. In Nachamkin I, Szymanski C, Blaser M (ed), , Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555815554.ch4
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Generic image for table
Table 1.

Summary of genomes sequenced to date and comparison to

Citation: Champion O, Al-Jaberi S, Stabler R, Wren B. 2008. Comparative Genomics of , p 63-71. In Nachamkin I, Szymanski C, Blaser M (ed), , Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555815554.ch4

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