Comparative genome analysis of Salmonella Enteritidis PT4 and Salmonella Gallinarum 287/91 provides insights into evolutionary and host adaptation pathways

  1. Nicholas R. Thomson1,9,
  2. Debra J. Clayton2,
  3. Daniel Windhorst3,
  4. Georgios Vernikos1,
  5. Susanne Davidson2,
  6. Carol Churcher1,
  7. Michael A. Quail1,
  8. Mark Stevens2,
  9. Michael A. Jones4,
  10. Michael Watson2,
  11. Andy Barron1,
  12. Abigail Layton2,
  13. Derek Pickard1,
  14. Robert A. Kingsley1,
  15. Alex Bignell1,
  16. Louise Clark1,
  17. Barbara Harris1,
  18. Doug Ormond1,
  19. Zahra Abdellah1,
  20. Karen Brooks1,
  21. Inna Cherevach1,
  22. Tracey Chillingworth1,
  23. John Woodward1,
  24. Halina Norberczak1,
  25. Angela Lord1,
  26. Claire Arrowsmith1,
  27. Kay Jagels1,
  28. Sharon Moule1,
  29. Karen Mungall1,
  30. Mandy Sanders1,
  31. Sally Whitehead1,
  32. Jose A. Chabalgoity5,
  33. Duncan Maskell6,
  34. Tom Humphrey7,
  35. Mark Roberts8,
  36. Paul A. Barrow4,
  37. Gordon Dougan1, and
  38. Julian Parkhill1
  1. 1 The Pathogen Sequencing Unit, The Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom;
  2. 2 Division of Microbiology, Institute for Animal Health, Compton, Berkshire RG20 7NN, United Kingdom;
  3. 3 Lohmann Animal Health GmbH & Co. KG, 27472 Cuxhaven, Germany;
  4. 4 School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington, Leicestershire LE12 5RD, United Kingdom;
  5. 5 Department of Biotechnology, School of Medicine, Universidad de la Republica, Montevideo CP 11600, Uruguay;
  6. 6 Department of Veterinary Medicine, University of Cambridge, Cambridge CB3 0ES, United Kingdom;
  7. 7 School of Clinical Veterinary Science, University of Bristol, Langford, Bristol BS40 5DU, United Kingdom;
  8. 8 Institute of Comparative Medicine, Faculty of Veterinary Medicine, University of Glasgow, Glasgow G61 1QH, United Kingdom

Abstract

We have determined the complete genome sequences of a host-promiscuous Salmonella enterica serovar Enteritidis PT4 isolate P125109 and a chicken-restricted Salmonella enterica serovar Gallinarum isolate 287/91. Genome comparisons between these and other Salmonella isolates indicate that S. Gallinarum 287/91 is a recently evolved descendent of S. Enteritidis. Significantly, the genome of S. Gallinarum has undergone extensive degradation through deletion and pseudogene formation. Comparison of the pseudogenes in S. Gallinarum with those identified previously in other host-adapted bacteria reveals the loss of many common functional traits and provides insights into possible mechanisms of host and tissue adaptation. We propose that experimental analysis in chickens and mice of S. Enteritidis–harboring mutations in functional homologs of the pseudogenes present in S. Gallinarum could provide an experimentally tractable route toward unraveling the genetic basis of host adaptation in S. enterica.

Footnotes

  • ↵9 Corresponding author.

    ↵9 E-mail nrt{at}sanger.ac.uk; fax 44-(0)-1223-494919.

  • [Supplemental material is available online at www.genome.org. The genome sequence data from this study have been submitted to EMBL under accession nos. AM933172 and AM933173.]

  • Article published online before print. Article and publication date are at http://www.genome.org/cgi/doi/10.1101/gr.077404.108.

    • Received February 12, 2008.
    • Accepted June 17, 2008.
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  1. Published in Advance June 26, 2008, doi: 10.1101/gr.077404.108 Genome Res. 18: 1624-1637 Copyright © 2008, Cold Spring Harbor Laboratory Press

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