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PAMDB, A Multilocus Sequence Typing and Analysis Database and Website for Plant-Associated Microbes

March 2010 , Volume 100 , Number  3
Pages  208 - 215

Nalvo F. Almeida, Shuangchun Yan, Rongman Cai, Christopher R. Clarke, Cindy E. Morris, Norman W. Schaad, Erin L. Schuenzel, George H. Lacy, Xiaoan Sun, Jeffrey B. Jones, Jose A. Castillo, Carolee T. Bull, Scotland Leman, David S. Guttman, JoÃo C. Setubal, and Boris A. Vinatzer

First, second, third, fourth, eighth, and sixteenth authors: Department of Plant Pathology, Physiology, and Weed Science, Virginia Tech, Blacksburg 24061; first and fifteenth authors: Virginia Bioinformatics Institute, Virginia Tech; first author: Department of Computing and Statistics, Federal University of Mato Grosso do Sul, Brazil; fifth author: Unité de Pathologie Végétale UR407, INRA, F-84140 Montfavet, France; sixth and seventh authors: United States Department of Agriculture–Agricultural Research Service (USDA-ARS), Foreign Disease-Weed Science Research, Ft. Detrick, MD 21702-5023; ninth author: Department of Agriculture and Consumer Services, Division of Plant Industry, Gainesville, FL 32608; tenth author: University of Florida, Plant Pathology Department, P.O. Box 110680, Gainesville 32611; eleventh author: PROINPA Foundation, P.O. Box 4285, Cochabamba, Bolivia; twelfth author: USDA-ARS, Salinas, CA 93905; thirteenth author: Department of Statistics, Virginia Tech; fourteenth author: Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Ontario, M5S3B2 Canada; and fifteenth author: Department of Computer Science, Virginia Tech., Blacksburg 24061.

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Accepted for publication 3 November 2009.

Although there are adequate DNA sequence differences among plant-associated and plant-pathogenic bacteria to facilitate molecular approaches for their identification, identification at a taxonomic level that is predictive of their phenotype is a challenge. The problem is the absence of a taxonomy that describes genetic variation at a biologically relevant resolution and of a database containing reference strains for comparison. Moreover, molecular evolution, population genetics, ecology, and epidemiology of many plant-pathogenic and plant-associated bacteria are still poorly understood. To address these challenges, a database with web interface was specifically designed for plant-associated and plant-pathogenic microorganisms. The Plant-Associated Microbes Database (PAMDB) comprises, thus far, data from multilocus sequence typing and analysis (MLST/MLSA) studies of Acidovorax citrulli, Pseudomonas syringae, Ralstonia solanacearum, and Xanthomonas spp. Using data deposited in PAMDB, a robust phylogeny of Xanthomonas axonopodis and related bacteria has been inferred, and the diversity existing in the Xanthomonas genus and in described Xanthomonas spp. has been compared with the diversity in P. syringae and R. solanacearum. Moreover, we show how PAMDB makes it easy to distinguish between different pathogens that cause almost identical diseases. The scalable design of PAMDB will make it easy to add more plant pathogens in the future.

Additional keywords:bacterial plant pathogens, plant disease diagnostics.

© 2010 The American Phytopathological Society