Draft Sequencing and Comparative Genomics of Xylella fastidiosa Strains Reveal Novel Biological Insights

  1. Anamitra Bhattacharyya1,8,
  2. Stephanie Stilwagen2,
  3. Gary Reznik1,
  4. Helene Feil3,
  5. William S. Feil4,
  6. Iain Anderson1,
  7. Axel Bernal1,
  8. Mark D'Souza1,
  9. Natalia Ivanova1,
  10. Vinayak Kapatral1,
  11. Niels Larsen1,
  12. Tamara Los1,
  13. Athanasios Lykidis1,
  14. Eugene Selkov, Jr.1,
  15. Theresa L. Walunas1,
  16. Alexander Purcell4,
  17. Rob A. Edwards5,
  18. Trevor Hawkins2,
  19. Robert Haselkorn6,
  20. Ross Overbeek1,
  21. Nikos C. Kyrpides1, and
  22. Paul F. Predki2,7
  1. 1Integrated Genomics, Inc., Chicago, Illinois 60612, USA; 2Department of Energy, Joint Genome Institute, Walnut Creek, California 94598, USA; 3Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA; 4Department of Environmental Science, Policy, and Management, University of California, Berkeley, California 94720, USA; 5Department of Microbiology, University of Tennessee, Memphis, Tennessee 38163, USA; 6Departments of Molecular Genetics & Cell Biology and Biochemistry & Molecular Biology, Chicago, Illinois 60637, USA; 7Protometrix, Inc., Guilford, Connecticut 06437, USA

Abstract

Draft sequencing is a rapid and efficient method for determining the near-complete sequence of microbial genomes. Here we report a comparative analysis of one complete and two draft genome sequences of the phytopathogenic bacterium, Xylella fastidiosa, which causes serious disease in plants, including citrus, almond, and oleander. We present highlights of an in silico analysis based on a comparison of reconstructions of core biological subsystems. Cellular pathway reconstructions have been used to identify a small number of genes, which are likely to reside within the draft genomes but are not captured in the draft assembly. These represented only a small fraction of all genes and were predominantly large and small ribosomal subunit protein components. By using this approach, some of the inherent limitations of draft sequence can be significantly reduced. Despite the incomplete nature of the draft genomes, it is possible to identify several phage-related genes, which appear to be absent from the draft genomes and not the result of insufficient sequence sampling. This region may therefore identify potential host-specific functions. Based on this first functional reconstruction of a phytopathogenic microbe, we spotlight an unusual respiration machinery as a potential target for biological control. We also predicted and developed a new defined growth medium forXylella.

[The sequence data from this study have been submitted to GenBank under accession nos. NC_002723 (X. fastidiosa Almond [Dixon]) and NC_002722 (X. fastidiosaOleander [Ann-1]).

Footnotes

  • ↵8 Corresponding author.

  • E-MAIL anamitra{at}integratedgenomics.com; FAX (312) 226-9446.

  • Article and publication are at http://www.genome.org/cgi/doi/10.1101/gr.370702.

    • Received April 19, 2002.
    • Accepted July 30, 2002.
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  1. Published in Advance September 13, 2002, doi: 10.1101/gr.370702 Genome Res. 12: 1556-1563 Cold Spring Harbor Laboratory Press

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