Wei Wei, Robert E. Davis, Ing-Ming Lee and Yan Zhao (2007)
Computer-simulated RFLP analysis of 16S rRNA genes: identification of
ten new phytoplasma groups. Int J Syst Evol Microbiol 57, 1855-1867.
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.