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

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.

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

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

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

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

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.