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Title: PCR and RFLP analyses based on the ribosomal protein operon

item MARTINI, MARTA - University Of Udine
item Lee, Ing Ming

Submitted to: Book Chapter
Publication Type: Book / Chapter
Publication Acceptance Date: 8/11/2011
Publication Date: 9/21/2012
Citation: Martini, M., Lee, I. 2012. PCR and RFLP analyses based on the ribosomal protein operon. In: Dickinson, M., Hodgetts, J., editors. Springer Protocols: Methods in Molecular Biology. New York, NY: Humana Press. p. 173-188.

Interpretive Summary:

Technical Abstract: Differentiation and classification of phytoplasmas have been primarily based on the highly conserved 16Sr RNA gene. RFLP analysis of 16Sr RNA gene sequences has identified 31 16Sr RNA (16Sr) groups and more than 100 16Sr subgroups. Classification of phytoplasma strains can however, become more refined and specific if moderately conserved genes, such as the ribosomal protein gene (rp), are used as genetic markers. The use of additional genetic markers enhances the resolving power of phytoplasma classification. This chapter describes the methodology of detection, differentiation and classification of phytoplasma strains based on rp gene sequences. RFLP analysis of amplicons obtained by group- or subgroup- specific rp gene-based primers is used for finer differentiation of phytoplasma strains within a given group or subgroup. The rp-gene based classification not only readily resolved 16Sr subgroups within a given 16Sr group, but also provided finer differentiation of closely related phytoplasma strains. Many individual 16Sr subgroups can be further differentiated into two or more distinct rp subgroups.