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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.

Author information

Affiliations

  1. Sidney Kimmel Cancer Center, 10835 Altman Row, San Diego, California 92121, USA.

    • Michael McClelland
    •  & Steffen Porwollik
  2. Department of Biological Sciences, University of Calgary, Calgary, Alberta T2N 1N4, Canada.

    • Kenneth E Sanderson
  3. Genome Sequencing Center, Washington University School of Medicine, 4444 Forest Park Boulevard, St Louis, Missouri 63108, USA.

    • Sandra W Clifton
    • , Phil Latreille
    • , Aniko Sabo
    • , Rekha Meyer
    • , Tamberlyn Bieri
    • , Phil Ozersky
    • , Michael McLellan
    • , C Richard Harkins
    • , Chunyan Wang
    • , Christine Nguyen
    • , Amy Berghoff
    • , Glendoria Elliott
    • , Sara Kohlberg
    • , Cindy Strong
    • , Feiyu Du
    • , Jason Carter
    • , Colin Kremizki
    • , Dan Layman
    • , Shawn Leonard
    • , Hui Sun
    • , Lucinda Fulton
    • , William Nash
    • , Tracie Miner
    • , Patrick Minx
    • , Kim Delehaunty
    • , Catrina Fronick
    • , Vincent Magrini
    • , Michael Nhan
    • , Wesley Warren
    • , John Spieth
    •  & Richard K Wilson
  4. Informatics Research, Celera/Applied Biosystems, 45 W. Gude Drive, Rockville, Maryland 20850, USA.

    • Liliana Florea

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Correspondence to Michael McClelland.

Supplementary information

PDF files

  1. 1.

    Supplementary Figure 1

    Genome annotation: Salmonella enterica serovar Paratyphi A ATCC9150.

  2. 2.

    Supplementary Fig. 2

    Detection of phage SPA-3 DNA in supernatants of SPA liquid cultures after Mitomycin C treatment.

  3. 3.

    Supplementary Table 2

    Comparison of gene content among twelve Paratyphi A strains.

  4. 4.

    Supplementary Table 5

    New predicted pseudogenes in Typhi.

  5. 5.

    Supplementary Note

    Further examples of potential functional consequences of pseudogenes.

Excel files

  1. 1.

    Supplementary Table 1

    Genome annotation: Salmonella enterica serovar Paratyphi A ATCC9150.

  2. 2.

    Supplementary Table 3

    Pseudogenes in Paratyphi A.

  3. 3.

    Supplementary Table 4

    Putative orthologs of genes in Paratyphi A that are predicted to be pseudogenes in Typhi, Shigella flexneri, or Yersinia pestis.

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DOI

https://doi.org/10.1038/ng1470

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