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Chapter 2 : Understanding the Model and the Menace: a Postgenomic View of

Authors: Roy R. Chaudhuri1, Gavin H. Thomas2
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Affiliations: 1: Division of Immunity and Infection, IBR West, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom; 2: Department of Biology, Area 10, University of York, P.O. Box 373, York YO10 5YW, United Kingdom
Content Type: Monograph
Publication Year: 2007

Category: Genomics and Bioinformatics; Bacterial Pathogenesis

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Understanding the Model and the Menace: a Postgenomic View of , Page 1 of 2

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Abstract:

This chapter discusses the insights into pathogenicity and the wider processes of genome evolution that have resulted from the sequencing of the K-12 genome, and, more recently, those from a number of pathogenic strains, including several from the related “genus” . It also discusses the available resources for genomics and the progress that has been made in recent years toward a complete understanding of biology. Genes that are acquired by horizontal transfer subsequently undergo a process of amelioration as their base composition becomes acclimatized to the new host. Programs such as BLAST can be used to identify unexpected similarities between genes in phylogenetically distinct species, although it should be noted that BLAST results do not necessarily correspond to those from more robust phylogenetic analyses. Interestingly, strains classified as group B2 are rarely found as human commensals, and the group includes many strains with extraintestinal pathogenic (ExPEC) virulence determinants. As with enterohemorrhagic (EHEC) O157:H7, serotype 2a was an obvious target for whole-genome sequencing because of its importance as a pathogen. The processes of genome evolution are clear from the genome sequences already available.

Citation: Chaudhuri R, Thomas G. 2007. Understanding the Model and the Menace: a Postgenomic View of , p 21-48. In Pallen M, Nelson K, Preston G (ed), Bacterial Pathogenomics. ASM Press, Washington, DC. doi: 10.1128/9781555815530.ch2

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Understanding the Model and the Menace: a Postgenomic View of Escherichia coli
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Citation: Chaudhuri R, Thomas G. 2007. Understanding the Model and the Menace: a Postgenomic View of , p 21-48. In Pallen M, Nelson K, Preston G (ed), Bacterial Pathogenomics. ASM Press, Washington, DC. doi: 10.1128/9781555815530.ch2
/content/10.1128/9781555815530.ch02.ch02fig01
FIGURE 1
Phylogenetic relationships between the strains in the ECOR collection, as assessed by MLEE ( ). Data were obtained from http://foodsafe.msu.edu/whittam, and a neighbor-joining tree was generated by neighbor, part of the PHYLIP package. The tree was rooted using group B2 as an outgroup ( ).
10.1128/9781555815530/f0026-01_thmb.gif
10.1128/9781555815530/f0026-01.gif
Image of FIGURE 1
FIGURE 1

Phylogenetic relationships between the strains in the ECOR collection, as assessed by MLEE ( ). Data were obtained from http://foodsafe.msu.edu/whittam, and a neighbor-joining tree was generated by neighbor, part of the PHYLIP package. The tree was rooted using group B2 as an outgroup ( ).

Citation: Chaudhuri R, Thomas G. 2007. Understanding the Model and the Menace: a Postgenomic View of , p 21-48. In Pallen M, Nelson K, Preston G (ed), Bacterial Pathogenomics. ASM Press, Washington, DC. doi: 10.1128/9781555815530.ch2
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Tables

Understanding the Model and the Menace: a Postgenomic View of Escherichia coli
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Citation: Chaudhuri R, Thomas G. 2007. Understanding the Model and the Menace: a Postgenomic View of , p 21-48. In Pallen M, Nelson K, Preston G (ed), Bacterial Pathogenomics. ASM Press, Washington, DC. doi: 10.1128/9781555815530.ch2
/content/10.1128/9781555815530.ch02.ch02tab01
TABLE 1
genome projects completed and underway as of April 2006
Generic image for table
TABLE 1

genome projects completed and underway as of April 2006

Citation: Chaudhuri R, Thomas G. 2007. Understanding the Model and the Menace: a Postgenomic View of , p 21-48. In Pallen M, Nelson K, Preston G (ed), Bacterial Pathogenomics. ASM Press, Washington, DC. doi: 10.1128/9781555815530.ch2
/content/10.1128/9781555815530.ch02.ch02tab02
TABLE 2
Selected online resources for genomics
Generic image for table
TABLE 2

Selected online resources for genomics

Citation: Chaudhuri R, Thomas G. 2007. Understanding the Model and the Menace: a Postgenomic View of , p 21-48. In Pallen M, Nelson K, Preston G (ed), Bacterial Pathogenomics. ASM Press, Washington, DC. doi: 10.1128/9781555815530.ch2

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