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

Autor: Trevor Hawkins, Iain Anderson, Eugene Selkov, William S. Feil, Helene Feil, Athanasios Lykidis, Ross Overbeek, Robert Edwards, Axel Bernal, Stephanie Stilwagen, Gary Reznik, Natalia Ivanova, Paul Predki, Niels Larsen, Mark D'Souza, Theresa L. Walunas, Vinayak Kapatral, Alexander H. Purcell, Tamara Los, Robert Haselkorn, Nikos C. Kyrpides, Anamitra Bhattacharyya
Rok vydání: 2002
Předmět:
Zdroj: Genome Research. 12:1556-1563
ISSN: 1549-5469
1088-9051
DOI: 10.1101/gr.370702
Popis: Xylella fastidiosa is a Gram-negative bacterium belonging to the gamma subgroup of the proteobacteria (Wells et al. 1987). This microorganism is an important plant pathogen causing many economically important crop diseases, such as Pierce's disease (PD) of grapevine and citrus variegated chlorosis in citrus (Moller et al. 1974; Purcell 1997). Almond leaf scorch was first described in 1974 (Moller et al. 1974), and electron microscope studies indicated the presence in almond of the same bacterium previously associated with PD of grapevines (Mircetich et al. 1976). Cross-inoculation studies showed that PD and the almond leaf scorch strains were pathogenic to both almond and grape (Davis and Thompson 1980). Oleander leaf scorch was first noticed in 1994 in southern California. The glassy-winged sharpshooter, Homalodisca coagulata, was found to be the vector for this bacterium. It is possible that several other varieties of sharpshooters can transmit X. fastidiosa between oleander plants (Purcell et al. 1999). The oleander leaf scorch strain could not be reisolated from grapevine in a greenhouse after inoculation using needle puncture (Purcell et al. 1999). This result provides evidence for host specificity among strains of X. fastidiosa. Previous studies classified X. fastidiosa as a single species, but differentiated members of the species, depending on such criteria as host specificity and pathogenicity (Hendson et al. 2001 and references therein). We define each strain of X. fastidiosa to be a pathovar for a specific plant, as suggested previously (Hendson et al. 2001). We will therefore refer throughout to the citrus, almond, and oleander strains as Xf pv citrus (XFA), Xf pv almond (XFX), and Xf pv oleander (XFY). The complete genome sequence of the X. fastidiosa 9a5c strain (XFA), which causes citrus variegated chlorosis , was recently published (Simpson et al. 2000). In this study, we report the gapped-genome sequences of Xf pv almond (Dixon strain) (XFX) and Xf pv oleander (Ann-1 strain) (XFY) and compare them to the complete genomic sequence of XFA. Here we present highlights of the first functional reconstruction of a phytopathogenic microbe based on the three sequenced genomes. This approach has led us to the identification of a putative drug target in the aerobic respiratory chain of this organism, as well as to a prediction of the specific growth requirements of this bacterium, which were used to develop a defined medium for optimal growth. Furthermore, based on a global alignment of the proteomes for these genomes, we identified a region in XFA that is absent in the other two genomes that potentially encodes host-specific functions. Comparisons of curated pathways and their components present in the complete XFA genome relative to the gapped XFY and XFX genomes allows the prediction of functions potentially missed during gapped-genome sequencing. Such an approach provides an added level of quality control to the analysis of sequenced genomes.
Databáze: OpenAIRE
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