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Molecular Plant Pathology Laboratory, USDA–Agricultural Research Service, Beltsville, MD 20705, USA
Correspondence
Yan Zhao
zhaoy{at}ba.ars.usda.gov
Phytoplasmas are cell wall-less bacteria that cause numerous plant diseases. As no phytoplasma has been cultured in cell-free medium, phytoplasmas cannot be differentiated and classified by the traditional methods which are applied to culturable prokaryotes. Over the past decade, the establishment of a phytoplasma classification scheme based on 16S rRNA restriction fragment length polymorphism (RFLP) patterns has enabled the accurate and reliable identification and classification of a wide range of phytoplasmas. In the present study, we expanded this classification scheme through the use of computer-simulated RFLP analysis, achieving rapid differentiation and classification of phytoplasmas. Over 800 publicly available phytoplasma 16S rRNA gene sequences were aligned using the CLUSTAL_X program and the aligned 1.25 kb fragments were exported to pDRAW32 software for in silico restriction digestion and virtual gel plotting. Based on distinctive virtual RFLP patterns and calculated similarity coefficients, phytoplasma strains were classified into 28 groups. The results included the classification of hundreds of previously unclassified phytoplasmas and the delineation of 10 new phytoplasma groups representing three recently described and seven novel putative ‘Candidatus Phytoplasma’ taxa.
This article has been cited by other articles:
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 J. Hodgetts, N. Boonham, R. Mumford, and M. Dickinson Panel of 23S rRNA Gene-Based Real-Time PCR Assays for Improved Universal and Group-Specific Detection of Phytoplasmas Appl. Envir. Microbiol., May 1, 2009; 75(9): 2945 - 2950. [Abstract] [Full Text] [PDF]
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W. Wei, I.-M. Lee, R. E. Davis, X. Suo, and Y. Zhao Automated RFLP pattern comparison and similarity coefficient calculation for rapid delineation of new and distinct phytoplasma 16Sr subgroup lineages Int J Syst Evol Microbiol, October 1, 2008; 58(10): 2368 - 2377. [Abstract] [Full Text] [PDF]
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 W. Wei, R. E. Davis, R. Jomantiene, and Y. Zhao Ancient, recurrent phage attacks and recombination shaped dynamic sequence-variable mosaics at the root of phytoplasma genome evolution PNAS, August 19, 2008; 105(33): 11827 - 11832. [Abstract] [Full Text] [PDF]
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J. Hodgetts, N. Boonham, R. Mumford, N. Harrison, and M. Dickinson Phytoplasma phylogenetics based on analysis of secA and 23S rRNA gene sequences for improved resolution of candidate species of 'Candidatus Phytoplasma' Int J Syst Evol Microbiol, August 1, 2008; 58(8): 1826 - 1837. [Abstract] [Full Text] [PDF]
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H. Cai, W. Wei, R. E. Davis, H. Chen, and Y. Zhao Genetic diversity among phytoplasmas infecting Opuntia species: virtual RFLP analysis identifies new subgroups in the peanut witches'-broom phytoplasma group Int J Syst Evol Microbiol, June 1, 2008; 58(6): 1448 - 1457. [Abstract] [Full Text] [PDF]
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