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Int J Syst Evol Microbiol 59 (2009), 2582-2593; DOI  10.1099/ijs.0.010249-0
© 2009 International Union of Microbiological Societies

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

Yan Zhao, Wei Wei, Ing-Ming Lee, Jonathan Shao, Xiaobing Suo and Robert E. Davis

Molecular Plant Pathology Laboratory, USDA-Agricultural Research Service, Beltsville, MD 20705, USA

Correspondence
Yan Zhao
yan.zhao{at}ars.usda.gov

Phytoplasmas, the causal agents of numerous plant diseases, are insect-vector-transmitted, cell-wall-less bacteria descended from ancestral low-G+C-content 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 based primarily on molecular analysis of 16S rRNA gene sequences because of the inaccessibility of measurable phenotypic characters suitable for conventional microbial characterization. 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 similarity scores, iPhyClassifier makes instant suggestions on tentative phytoplasma 16Sr group/subgroup classification status and ‘Candidatus Phytoplasma’ species assignment. Using iPhyClassifier, we revised and updated the classification of strains affiliated with the peach X-disease phytoplasma group. The online tool can be accessed at http://www.ba.ars.usda.gov/data/mppl/iPhyClassifier.html.

Abbreviations: RFLP, restriction fragment length polymorphism

The GenBank/EMBL/DDBJ accession numbers for the 16S rRNA gene sequences of Montana potato purple top phytoplasma PPT-MT117-1, pecan bunch phytoplasma PB1, goldenrod yellows phytoplasma GR1 and Alaska potato purple top phytoplasma PPT-AK6 determined in this study are FJ226074, FJ376626, FJ376627 and FJ376629.

Similarity coefficients derived from analysis of virtual RFLP patterns of 16S rRNA F2nR2 sequences from phytoplasma strains in the peach X-disease group (16SrIII) are available as supplementary material with the online version of this paper.






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