Location: Crop Improvement and Protection ResearchTitle: PAMDB, A Multilocus Sequence Typing & Analysis Database and Website for Plant-Associated Microbes Author
Submitted to: Journal of Phytopathology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 12/2/2009
Publication Date: 3/1/2010
Citation: Almeida, N., Yan, S., Cai, R., Morris, C.E., Schaad, N.W., Schuenzel, E., Lacy, G.H., Sun, X., Jones, J.B., Castillo, J.A., Bull, C.T., Leman, S., Gutman, D.S., Setubal, J.C., Vinatzer, B.A. PAMDB, 2010. A Multilocus Sequence Typing & Analysis Database and Website for Plant-Associated Microbes. Phytopathology. 100:208-215. Interpretive Summary: In understanding of bacterial pathogen diversity and rapid identification of pathogens are important to prevent the spread of new and emerging diseases. These usually require comparison of the novel pathogens to formerly characterized pathogens. The cost and government regulations prevent scientists from maintaining large collections of plant pathogens for comparison purposes. DNA sequencing and web databases hold promise to increase the study of plant associated bacteria because data generated in one laboratory can be compared to data generated in another. This manuscript reports on the generation and evaluation of a database with web interface specifically designed for plant-associated and plant-pathogenic bacteria. The database, called PAMDB (Plant Associated Microbes Database) is comprised of the DNA sequences for several genes that are useful in identifying plant associated bacteria and studying diversity among bacteria. This database is usable by scientists world-wide and will become more valuable as scientists can add their novel results. The database should allow for more rapid identification of plant pathogens and reduce duplication in research efforts since data can be shared.
Technical Abstract: 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. PAMDB (Plant Associated Microbes Database) is comprised, so far, of data from multilocus sequence typing and analysis (MLST/MLSA) studies of Axonopodis avenae, 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 species 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.