Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
Comparative Study
. 2002 Oct;12(10):1556-63.
doi: 10.1101/gr.370702.

Draft sequencing and comparative genomics of Xylella fastidiosa strains reveal novel biological insights

Anamitra Bhattacharyya  1 , Stephanie Stilwagen, Gary Reznik, Helene Feil, William S Feil, Iain Anderson, Axel Bernal, Mark D'Souza, Natalia Ivanova, Vinayak Kapatral, Niels Larsen, Tamara Los, Athanasios Lykidis, Eugene Selkov Jr, Theresa L Walunas, Alexander Purcell, Rob A Edwards, Trevor Hawkins, Robert Haselkorn, Ross Overbeek, Nikos C Kyrpides, Paul F Predki
Affiliations
Comparative Study

Draft sequencing and comparative genomics of Xylella fastidiosa strains reveal novel biological insights

Anamitra Bhattacharyya et al. Genome Res. 2002 Oct.

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 for Xylella.

PubMed Disclaimer

Figures

Figure 1
Figure 1
Comparative disposition of functional roles in cellular subsystems in Xf genomes. The number of functional roles present in the each of the described subsystems was plotted for each of the Xylella genomes.
Figure 2
Figure 2
Graphical alignment of Xylella fastidiosa (Xf) proteomes using GenomeWalk. A unique 65-kb phage insertion region (red rectangle, brown shading) in the Xf citrus strain (XFA) is absent in the Xf almond (XFX) and oleander (XFY) strains (arrow).
Figure 3
Figure 3
Graphical visualization of the functional reconstruction of Xylella fastidiosa aerobic and anaerobic respiration. (A) Diagrammatic representation of aerobic respiration. Three-dimensional boxes show the presence of functional components and filled arrows indicate electron flow. (B) Detailed spatial disposition of membrane components of aerobic respiratory chain. The absence of cytochrome c oxidase is designated by the cross and arrow. (C) Overview of the anaerobic respiratory chain. Reconstructions show proton translocation and oxidative phosphorylation.
Figure 3
Figure 3
Graphical visualization of the functional reconstruction of Xylella fastidiosa aerobic and anaerobic respiration. (A) Diagrammatic representation of aerobic respiration. Three-dimensional boxes show the presence of functional components and filled arrows indicate electron flow. (B) Detailed spatial disposition of membrane components of aerobic respiratory chain. The absence of cytochrome c oxidase is designated by the cross and arrow. (C) Overview of the anaerobic respiratory chain. Reconstructions show proton translocation and oxidative phosphorylation.
Figure 3
Figure 3
Graphical visualization of the functional reconstruction of Xylella fastidiosa aerobic and anaerobic respiration. (A) Diagrammatic representation of aerobic respiration. Three-dimensional boxes show the presence of functional components and filled arrows indicate electron flow. (B) Detailed spatial disposition of membrane components of aerobic respiratory chain. The absence of cytochrome c oxidase is designated by the cross and arrow. (C) Overview of the anaerobic respiratory chain. Reconstructions show proton translocation and oxidative phosphorylation.
See this image and copyright information in PMC

References

    1. Bhattacharyya A, Stilwagen S, Ivanova N, D'Souza M, Bernal A, Lykidis A, Kapatral V, Anderson I, Larsen N, Los T, et al. Proc. Natl. Acad. Sci. 2002. in press. - PMC - PubMed
    1. Davis MJ, Thompson SV. Etiological role of a xylem-limited bacterium causing Pierce's disease in almond leaf scorch. Phytopathology. 1980;70:472–475.
    1. Davis MJ, Purcell AH, Thompson SV. Pierce's disease of grapevines: Isolation of the causal bacterium. Science. 1978;199:75–77. - PubMed
    1. Davis MJ, Whitcomb RF, Gillespie AG., Jr . Fastidious bacteria of plant vascular tissue and invertebrates (including so called rickettsia-like bacteria) In: Starr MP, Stolp H, Truper HG, Balows A, Schlegel HG, editors. The prokaryotes: A handbook on habits, isolation, and identification of bacteria. Heidelberg: Springer-Verlag; 1981a. pp. 2172–2188.
    1. Davis MJ, French WJ, Schaad NW. Axenic culture of the bacteria associated with phony disease of peach and plum leaf scald. Curr Microbiol. 1981b;6:309–314.

Publication types

MeSH terms

Associated data

LinkOut - more resources