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Xylella fastidiosa comparative genomics
Genome Biology volume 3, Article number: reports0064 (2002)
Comparison of the genome sequences of Xylella fastidiosa strains reveals new drug targets
Significance and context
The Gram-negative plant pathogenic bacterium Xylella fastidiosa is responsible for economically important diseases in grapevine and citrus. These include, for instance, citrus variegated chlorosis, which affects all commercial sweet orange varieties. Symptoms include variegations on older leaves with chlorotic zones and brownish lesions with gum-like material. Affected fruit has no commercial value. In grapevines, X. fastidiosa may cause the so-called Pierce disease. X. fastidiosa is transmitted by sharpshooter leafhopper, and treatment of the disease is currently based mainly on the use of insecticides and the removal of infected shoots. X. fastidiosa also causes leaf scorch on oleander and almond. Bhattacharyya et al. compared the draft genome sequences of the X. fastidiosa strain XFY (X. fastidiosa pv. oleander) and XFX (X. fastidiosa pv. almond) with the previously published genome sequence of XFA (X. fastidiosa pv. citrus).
The genome sequences contained 2,731,748 (XFA), 2,625,581 (XFY) and 2,434,849 (XFX) base-pairs (bp). The G+C content was about equal for the three genomes at 52%. The genomes contain 2,985 (XFA), 2,870 (XFY) and 2,681 (XFX) open reading frames (ORFs), 58%, 62% and 62% of which were assigned functions. The XFY and XFX genomes contain a plasmid, of 30,270 and 51,158 bp, respectively, with a slightly lower G+C content of about 49%. The XFY plasmid carries genes encoding a type IV secretion system, a putative transcription regulator and a nickase. Pathway analysis revealed that the genomes contain 958 (XFA), 965 (XFY) and 938 (XFX) pathways. Compared to the genome of XFA, some functions were missing in the other two genomes. These include functions involving ribosomal SSU (1 missing in XFY, 10 missing in XFX), ribosomal LSU (4 missing in XFY, 17 missing in XFX), and aminoacyl-tRNA (1 missing in XFY, 2 missing in XFX). In addition, it was suggested that all X. fastidiosa strains possess a simple aerobic respiratory complex, enabling aerobic respiration only under high oxygen concentrations. No indications of the presence of a cytochrome c oxidase or other type of quinol oxidase as terminal oxidases were noticed. Thus, because cytochrome o (bo) ubiquinone is the only terminal oxidase present in these bacteria, it would be a suitable candidate drug target. Functional reconstruction using data revealed by the genome sequence, enabled growth media to be developed on which X. fastidiosa strains were more easily cultivated.
Bhattacharyya et al. compared the genome sequences of three plant pathogenic X. fastidiosa strains and performed a functional reconstruction to deduce new growth medium compositions that may facilitate the cultivation of those bacteria. New functions were revealed that might be involved in host-range determination and in plant pathogenicity. Extensive mutant screening, and phenotypic and biochemical analyses will be required to pinpoint pivotal functions for survival of X. fastidiosa strains in soil and infection of agronomically important crops. This may uncover bacterium-specific drug targets that can be used to protect crops against these severe plant pathogens.
Bhattacharyya A, Stilwagen S, Reznik G, Feil H, Feil WS, Anderson I, Bernal A, D'Souza M, Ivanova N, Kapatral V, et al: Draft sequencing and comparative genomics of Xylella fastidiosa strains reveal novel biological insights. Genome Res. 2002, 12: 1556-1563.
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Cite this article
D'Haeze, W. Xylella fastidiosa comparative genomics . Genome Biol 3, reports0064 (2002). https://doi.org/10.1186/gb-2002-3-12-reports0064
- Sweet Orange
- Terminal Oxidase
- Publish Genome Sequence
- Functional Reconstruction