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ARS Home » Northeast Area » Beltsville, Maryland (BARC) » Beltsville Agricultural Research Center » Molecular Plant Pathology Laboratory » Research » Publications at this Location » Publication #350954

Research Project: Genome-Based Strategies and Physiological Biomarkers for Detection and Identification of plant Pathogenic Phytoplasmas and Spiroplasmas

Location: Molecular Plant Pathology Laboratory

Title: PCR-based sequence analysis on multiple genes other than 16S rRNA gene for differentiation of phytoplasmas

item MARTINI, MARTA - University Of Urbino
item Bottner, Kristi
item LEE, ING-MING - Retired ARS Employee

Submitted to: Book Chapter
Publication Type: Book / Chapter
Publication Acceptance Date: 2/23/2018
Publication Date: 10/26/2018
Citation: Martini, M., Bottner-Parker, K.D., Lee, I. 2018. PCR-based sequence analysis on multiple genes other than 16S rRNA gene for differentiation of phytoplasmas. In: Musetti, R., Pagliari, L. Phytoplasmas: Methods and Protocols. Basel, Switzerland: Springer. 1875:97-115.

Interpretive Summary:

Technical Abstract: Differentiation and classification of phytoplasmas have been primarily based on the highly conserved 16S rRNA gene, for which “universal” primers are available. To date, 36 ribosomal (16Sr) groups and more than 150 subgroups have been delineated by RFLP analysis of 16S rRNA gene sequences. However, in recent years, the use of moderately conserved genes as additional genetic markers has enhanced the resolving power in delineating distinct phytoplasma strains among members of some 16Sr subgroups. This chapter describes the methodology of amplification, differentiation and classification of phytoplasmas based on less-conserved non-16S RNA genes, namely rp and secY. Actual and virtual RFLP analyses of amplicons obtained by semi-universal or group-specific rp and secY gene-based primers are used for finer differentiation of phytoplasma strains within a given group. The rp and secY gene-based classification not only readily resolves 16Sr subgroups within a given 16Sr group, but also provides finer differentiation of closely related phytoplasma strains within a given 16Sr subgroup.