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New strains of fruit and nut pathogen yield their genomes

Scientists have sequenced the genomes of two strains of Xylella fastidiosa, a plant pathogen that damages fruit and nut crops throughout the world. The bacteria cause wilt disease in a variety of plant species, including Pierce's disease in grapevines and variegated chlorosis in citrus fruits.

Xylella fastidiosa pv oleander within xylem vessel of an oleander leaf.

Xylella live in the gut of insects called sharpshooters, which feed on plants by sucking out sap. The insects transmit the bacteria directly into the plant tissue, where they clog the flow of water to leaves and destroy fruits.

In two new studies, the researchers compared the sequences of Xylella strains that attack almond and oleander plants to the completed genome of a citrus strain (finished by a team of Brazilian researchers in 2000). The scientists revealed how the pathogen may survive in hosts and identified potential new targets to stop disease.

The Department of Energy's Joint Genome Institute in Walnut Creek, California sequenced the partial genomes of the almond and oleander strains—cheaper and faster than complete genome sequencing. The institute collaborated with Integrated Genomics in Chicago, Illinois to compare the two to the completed genome of the citrus strain.

"You can get a lot of useful information despite not having 100 percent of the genome," says Alexander Purcell of the University of California, Berkeley, a member of the research team.

Xylella can breathe with or without oxygen, but both energy pathways are extremely inefficient. This may be a potential target for disease control. Someday, these pathways could be targeted with drugs that would shut down respiration and kill the bacteria.

The scientists also found genes that may help Xylella survive in specific hosts. They identified genes unique to the citrus strain that are absent in both the oleander and almond strains. These genes take up and use sugars that may improve Xylella's ability to grow in its citrus host.

Anamitra Bhattacharyya, who led the project at Integrated Genomics, says that the team expected to find more differences between the three Xylella strains than they actually did. The genomes show similarly conserved genes, providing "unique information in terms of the relatedness of the three strains," the authors write in Proceedings of the National Academy of Sciences.

Purcell, who has worked with the bacteria for over thirty years, says that he and other scientists are still trying to find out why diseases like Pierce's are rampant in certain areas of the world but not in others. Despite its prevalence in California's Napa Valley, Pierce's disease has never appeared on vines in Europe.

Xylella fastidiosa cells attached to blue-green sharpshooter's foregut (pre-cibarium) two weeks after exposure to infected plants.

Recent reports of the Xylella pathogen in Kosovo and growing concern over its emergence in Australia indicate that new tools are needed to fight the bacteria. The incessantly hungry sharpshooter, with its high feeding rate, continues to spread this devastating disease.

The team first announced the new sequences in the journal Genome Research, and then provided additional analyses of the genomes in a paper published in Proceedings of the National Academy of Sciences.

The Joint Genome Institute is now collaborating with the Brazilian Genome Consortium, the Organization for Nucleotide Sequencing and Analysis, to finish the sequences of the almond and oleander strains.

The sequences of all three Xylella strains are available at Integrated Genomics

See related GNN article
»Genome of bacteria Xylella fastidiosa, a threat to fruit and nut crops, is sequenced

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Bhattacharyya, A. et al. Whole-genome comparative analysis of three phytopathogenic Xylella fastidiosa strains. Proc Natl Acad Sci USA 99, 12403-12408 (September 17, 2002).
Bhattacharyya, A. et al. Draft sequencing and comparative genomics of Xylella fastidiosa strains reveal novel biological insights. Genome Res. Published online September 13, 2002.
Simpson, A.J.G. et al. The genome sequence of the plant pathogen Xylella fastidiosa. Nature 406, 151-159 (July 13, 2000).

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