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Complete Genome Sequence of Citrus Huanglongbing Bacterium, ‘Candidatus Liberibacter asiaticus’ Obtained Through Metagenomics

August 2009 , Volume 22 , Number  8
Pages  1,011 - 1,020

Yongping Duan,1 Lijuan Zhou,2 David G. Hall,1 Wenbin Li,3 Harshavardhan Doddapaneni,4 Hong Lin,4 Li Liu,5 Cheryl M. Vahling,1 Dean W. Gabriel,2 Kelly P. Williams,6 Allan Dickerman,6 Yijun Sun,5 and Tim Gottwald1

1USDA-ARS-USHRL, Fort Pierce, FL 34945, U.S.A.; 2Dept. of Plant Pathology, University of Florida, Gainesville, FL 32653, U.S.A.; 3USDA-APHIS-PPQ-CPHST, Beltsville, MD 20705, U.S.A.; 4USDA-ARS, Parlier, CA 93648, U.S.A.; 5ICBR, University of Florida, Gainesville, FL, U.S.A.; 6Virginia Bioinformatics Institute Virginia Tech, Blacksburg, VA 24061, U.S.A.

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Accepted 15 April 2009.

Citrus huanglongbing is the most destructive disease of citrus worldwide. It is spread by citrus psyllids and is associated with a low-titer, phloem-limited infection by any of three uncultured species of α-Proteobacteria, ‘Candidatus Liberibacter asiaticus’, ‘Ca. L. americanus’, and ‘Ca. L. africanus’. A complete circular ‘Ca. L. asiaticus’ genome has been obtained by metagenomics, using the DNA extracted from a single ‘Ca. L. asiaticus’--infected psyllid. The 1.23-Mb genome has an average 36.5% GC content. Annotation revealed a high percentage of genes involved in both cell motility (4.5%) and active transport in general (8.0%), which may contribute to its virulence. ‘Ca. L. asiaticus’ appears to have a limited ability for aerobic respiration and is likely auxotrophic for at least five amino acids. Consistent with its intracellular nature, ‘Ca. L. asiaticus’ lacks type III and type IV secretion systems as well as typical free-living or plant-colonizing extracellular degradative enzymes. ‘Ca. L. asiaticus’ appears to have all type I secretion system genes needed for both multidrug efflux and toxin effector secretion. Multi-protein phylogenetic analysis confirmed ‘Ca. L. asiaticus’ as an early-branching and highly divergent member of the family Rhizobiaceae. This is the first genome sequence of an uncultured α-proteobacteria that is both an intracellular plant pathogen and insect symbiont.

The American Phytopathological Society, 2009