Abstract
Salmonella enterica serovars often have a broad host range, and some cause both gastrointestinal and systemic disease. But the serovars Paratyphi A and Typhi are restricted to humans and cause only systemic disease. It has been estimated that Typhi arose in the last few thousand years. The sequence and microarray analysis of the Paratyphi A genome indicates that it is similar to the Typhi genome but suggests that it has a more recent evolutionary origin. Both genomes have independently accumulated many pseudogenes among their ∼4,400 protein coding sequences: 173 in Paratyphi A and ∼210 in Typhi. The recent convergence of these two similar genomes on a similar phenotype is subtly reflected in their genotypes: only 30 genes are degraded in both serovars. Nevertheless, these 30 genes include three known to be important in gastroenteritis, which does not occur in these serovars, and four for Salmonella-translocated effectors, which are normally secreted into host cells to subvert host functions. Loss of function also occurs by mutation in different genes in the same pathway (e.g., in chemotaxis and in the production of fimbriae).
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Acknowledgements
We thank K.M. Wylie for coordinating the fosmid production and sequencing, J. Reen and C. Choy for assistance with microarrays, M. Gibson for assistance with the circular genome and F. Long for assistance with the website. This work was supported by grants from the US National Institute of Allergy and Infectious Diseases to R.W. and M. McClelland and by the generosity of S. Kimmel.
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Supplementary information
Supplementary Figure 1
Genome annotation: Salmonella enterica serovar Paratyphi A ATCC9150. (PDF 352 kb)
Supplementary Fig. 2
Detection of phage SPA-3 DNA in supernatants of SPA liquid cultures after Mitomycin C treatment. (PDF 89 kb)
Supplementary Table 1
Genome annotation: Salmonella enterica serovar Paratyphi A ATCC9150. (XLS 7125 kb)
Supplementary Table 2
Comparison of gene content among twelve Paratyphi A strains. (PDF 6 kb)
Supplementary Table 3
Pseudogenes in Paratyphi A. (XLS 55 kb)
Supplementary Table 4
Putative orthologs of genes in Paratyphi A that are predicted to be pseudogenes in Typhi, Shigella flexneri, or Yersinia pestis. (XLS 354 kb)
Supplementary Table 5
New predicted pseudogenes in Typhi. (PDF 7 kb)
Supplementary Note
Further examples of potential functional consequences of pseudogenes. (PDF 17 kb)
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McClelland, M., Sanderson, K., Clifton, S. et al. Comparison of genome degradation in Paratyphi A and Typhi, human-restricted serovars of Salmonella enterica that cause typhoid. Nat Genet 36, 1268–1274 (2004). https://doi.org/10.1038/ng1470
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DOI: https://doi.org/10.1038/ng1470
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