Chapter 5 : Comparative Genomics of Species Other than

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The best characterized of the campylobacters is subsp. , a common commensal of warm-blooded animals, especially birds. The availability of eight new non (NJC) genomes permits genomic comparisons between the NJC group and between the NJC genomes and the subsp. genomes. This chapter compares and contrasts the genomes of species other than subsp. . The primary phenotypic marker associated with plasmids is antibiotic resistance. Genes encoding resistance to tetracycline, kanamycin, and chloramphenicol have been identified on plasmids. plasmids fall into two basic groups: cryptic plasmids and megaplasmids. Homopolymeric G: C tracts have been identified in all of the NJC genomes. Several genes within the NJC genomes are frameshifted or have other defects and are considered putative pseudogenes. In , the conjugative F episome cointegrates into the chromosome via homologous recombination between insertion sequences (IS) elements common to both the chromosome and the F plasmid, resulting in an Hfr strain. strains that possess the Entner-Doudoroff (ED) pathway contain a phosphoglucose isomerase (PGI) distinct from those found in the other Epsilonproteobacteria. A complete oxidative tricarboxylic acid (TCA) cycle is present in subsp. , as evidenced by the presence of all three subunits of succinate dehydrogenase (encoded by ). The chapter talks about restriction/modification systems, and virulence/pathogenicity loci. Genomic data for the NJC genomes will lead to new typing methods and perhaps culture methods.

Citation: Miller W. 2008. Comparative Genomics of Species Other than , p 73-95. In Nachamkin I, Szymanski C, Blaser M (ed), , Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555815554.ch5
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Image of Figure 1.
Figure 1.

Average amino acid identities of the proteomes. Pairwise BLASTP comparisons of the proteomes were performed. For each protein from each proteome, the protein with the most significant homology from the other proteomes was identified. Significant homology was defined as >30% amino acid sequence identity with at least 75% sequence overlap. From these matches, a set of 880 core proteins, conserved across the proteomes, was identified. Values represent average amino acid identities between the core protein sets of any two given proteomes. See Table 1 , footnote , for abbreviations.

Citation: Miller W. 2008. Comparative Genomics of Species Other than , p 73-95. In Nachamkin I, Szymanski C, Blaser M (ed), , Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555815554.ch5
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Image of Figure 2.
Figure 2.

Pairwise dot plot comparisons of selected genomes. Each protein in the subsp. NCTC 11168 proteome was compared with the proteomes of RM2228 (A), subsp. 269.97 (B), and RM2100 (C) by BLASTP analysis. Each dot represents a protein with significant homology, using the parameters from Fig. 1 , to a subsp. NCTC 11168 protein. The and axis values represent gene numbers.

Citation: Miller W. 2008. Comparative Genomics of Species Other than , p 73-95. In Nachamkin I, Szymanski C, Blaser M (ed), , Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555815554.ch5
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Image of Figure 3.
Figure 3.

Phylogenetic tree depicting the similarities among HsdM polypeptides from and from selected bacterial taxa. Bootstrap values (>75%) are based on 500 replicates and are indicated as percentages. HsdM proteins are bold. Representatives of the IA (IA), IB (IB), IC (IC) and ID (ID) families are included for comparison. Type I families, identified previously (A, B, AB, C, D, and F), are shaded in gray. See Table 1 , footnote , for abbreviations.

Citation: Miller W. 2008. Comparative Genomics of Species Other than , p 73-95. In Nachamkin I, Szymanski C, Blaser M (ed), , Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555815554.ch5
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Image of Figure 4.
Figure 4.

Pairwise comparisons of the cytolethal distending toxin subunits. Pairwise comparisons of the CdtA (A; lower triangle), CdtB (B) and CdtC (A; upper triangle) subunits were performed by BLASTP. Values represent amino acid identities.

Citation: Miller W. 2008. Comparative Genomics of Species Other than , p 73-95. In Nachamkin I, Szymanski C, Blaser M (ed), , Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555815554.ch5
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Generic image for table
Table 1.

General features of the sequenced genomes

Citation: Miller W. 2008. Comparative Genomics of Species Other than , p 73-95. In Nachamkin I, Szymanski C, Blaser M (ed), , Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555815554.ch5
Generic image for table
Table 2.

Localized regions of synteny within

Citation: Miller W. 2008. Comparative Genomics of Species Other than , p 73-95. In Nachamkin I, Szymanski C, Blaser M (ed), , Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555815554.ch5

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