Construction of an interactive online phytoplasma classification tool, iPhyClassifier, and its application in analysis of the peach X-disease phytoplasma group (16SrIII)

Authors: Zhao, Yan; WEI, WEI - LIAONING CHINA; Lee, Ing Ming; Shao, Jonathan; SUO, XIAOBING - HERNDON VIRGINIA; Davis, Robert

Submitted to: International Journal of Systematic and Evolutionary Microbiology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/14/2009
Publication Date: 10/1/2009
Citation: Zhao, Y., Wei, W., Lee, I., Shao, J.Y., Suo, X., Davis, R.E. 2009. Construction of an interactive online phytoplasma classification tool, iPhyClassifier, and its application in analysis of the peach X-disease phytoplasma group (16SrIII). International Journal of Systematic and Evolutionary Microbiology. 59(10):2582-2593.

Interpretive Summary: The health of numerous agriculturally and economically important vegetable, cereal, fruit, ornamental, and forest crops around the world are constantly being threatened by infection due to a large group of small bacteria called phytoplasmas. These disease-causing bacteria live inside nutrition-transporting vessels of infected plants and are spread among vulnerable plants by insects. Phytoplasma infection often results in poor growth, commodity loss, and reduced product quality. Correct identification of widely divergent phytoplasma strains is the key to accurate disease diagnosis and proactive epidemic management. Since phytoplasmas cannot be cultivated in the laboratory, DNA fingerprinting is the best way to distinguish them from one another. Conventional DNA fingerprinting involves several complicated and expensive laboratory procedures. Recently, we developed computer programs to mimic the laboratory DNA fingerprinting procedures and significantly improved the efficiency of phytoplasma identification process. In the present study, we constructed an interactive online tool named iPhyClassifier, creating a user friendly platform for real-time identification and classification of known and discovery of new phytoplasmas. Using the online tool, we discovered four distinct phytoplasma types bearing new DNA fingerprint patterns, and we updated classification of a group of phytoplasmas including those that cause diseases in various stone fruit trees (peach X-disease phytoplasma group). The online tool constructed in this study will help phytoplasma researchers, plant doctors, and quarantine personnel to identify phytoplasmas rapidly, efficiently, and accurately.

Technical Abstract: Phytoplasmas, causal agents of numerous plant diseases, are insect vector-transmitted cell wall-less bacteria descended from ancestral low G+C Gram-positive bacteria in the Bacillus-Clostridium group. Despite their monophyletic origin, widely divergent phytoplasma lineages have evolved in adaptation to specific ecological niches. Classification and taxonomic assignment of phytoplasmas have been primarily based on molecular analysis of 16S rRNA gene sequences due to inaccessibility of measurable phenotypic characters suitable for conventional microbial characterizations. In the present study, an interactive online tool, iPhyClassifier, was developed to expand the efficacy and capacity of the current 16S rRNA gene sequence-based phytoplasma classification system. iPhyClassifier performs sequence similarity analysis, simulates laboratory restriction enzyme digestions and subsequent gel electrophoresis, and generates virtual restriction fragment length polymorphism (RFLP) profiles. Based on calculated RFLP pattern similarity coefficients and overall sequence identity scores, iPhyClassifier makes instant suggestions on tentative phytoplasma 16Sr group/subgroup classification status and ‘Candidatus Phytoplasma species’ assignment. Using iPhyClassifier, we revised and updated classification of strains affiliated with the peach X-disease phytoplasma group. iPhyClassifier can be accessed at http://www.ba.ars.usda.gov/data/mppl/iPhyClassifier.html.