Abstract
Differentiation and classification of phytoplasmas have been primarily based on the highly conserved 16S rRNA gene. RFLP analysis of 16S rRNA gene sequences has identified 31 16S rRNA (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 (rp) genes, 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 resolves 16Sr subgroups within a given 16Sr group, but also provides finer differentiation of closely related phytoplasma strains. Many individual 16Sr subgroups can be further differentiated into two or more distinct rp subgroups.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Similar content being viewed by others
References
Zhao Y et al (2010) Recent advances in 16S rRNA gene-based phytoplasma differentiation, classification and taxonomy. In: Weintraub PG, Jones P (eds) Phytoplasmas: genomes, plant hosts and vectors. CAB International, Wallingford, pp 64–92
Lee I-M et al (2011) ‘Candidatus Phytoplasma costaricanum’ a new phytoplasma associated with a newly emerging disease in soybean in Costa Rica. Int J Syst Evol Microbiol. doi:10.1099/ijs.0.029041-0
Lee I-M, Zhao Y, Davis RE (2010) Prospects of multiple gene-based systems for differentiation and classification of phytoplasmas. In: Weintraub PG, Jones P (eds) Phytoplasmas: genomes, plant hosts and vectors. CAB International, Wallingford, pp 51–63
Lee I-M et al (1998) Revised classification scheme of phytoplasmas based on RFLP analyses of 16S rRNA and ribosomal protein gene sequences. Int J Syst Bacteriol 48:1153–1169
Lee I-M et al (2004) ‘Candidatus Phytoplasma asteris’, a novel phytoplasma taxon associated with aster yellows and related diseases. Int J Syst Evol Microbiol 54:1037–1048
Lee I-M et al (2004) Classification of phytoplasma strains in the elm yellows group (16SrV) and proposition of ‘Candidatus Phytoplasma ulmi’ for the phytoplasma associated with elm yellows. Int J Syst Evol Microbiol 54:337–347
Martini M et al (2002) Genetic variability among flavescence dorée phytoplasmas from different origins in Italy and France. Mol Cell Probes 16:197–208
Martini M et al (2007) Ribosomal protein gene-based phylogeny for finer differentiation and classification of phytoplasmas. Int J Syst Evol Microbiol 57:2037–2051
Lim P-O, Sears BB (1992) Evolutionary relationships of a plant-pathogenic mycoplasmalike organism and Acholeplasma laidlawii deduced from two ribosomal protein gene sequences. J Bacteriol 174:2606–2611
Lee I-M et al (2003) Ecological implications from a molecular analysis of phytoplasmas involved in an aster yellows epidemic in various crops in Texas. Phytopathology 93:1368–1377
Martini M (2004) Ribosomal protein gene-based phylogeny: a basis for phytoplasma classification. PhD dissertation, University of Udine, Udine, Italy, p 106
Martini M et al (2008) Molecular differentiation of ‘Candidatus Phytoplasma mali’ and its spreading in Friuli Venezia Giulia region (north-east Italy). Acta Hortic 781:395–402
Gundersen DE et al (1996) Genomic diversity and differentiation among phytoplasma strains in 16S rRNA group I (aster yellows and related phytoplasmas) and III (X-disease and related phytoplasmas). Int J Syst Bacteriol 46:64–75
Griffiths HM et al (1999) The phytoplasma associated with ash yellows and lilac witches’-broom: ‘Candidatus Phytoplasma fraxini’. Int J Syst Bacteriol 49:1605–1614
Durante G et al (2008) Bois noir in Lombardy (northern Italy): identification of molecular markers for diagnosis and characterization of 16SrXII-A phytoplasmas. Proceedings of the: 4th National Workshop on Phytoplasma Diseases. Rome, Italy 28–30 May 2008, p 300–303
Streten C, Gibb KS (2005) Genetic variation in Candidatus Phytoplasma australiense. Plant Pathol 54:8–14
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2013 Springer Science+Business Media, LLC
About this protocol
Cite this protocol
Martini, M., Lee, IM. (2013). PCR and RFLP Analyses Based on the Ribosomal Protein Operon. In: Dickinson, M., Hodgetts, J. (eds) Phytoplasma. Methods in Molecular Biology, vol 938. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-62703-089-2_15
Download citation
DOI: https://doi.org/10.1007/978-1-62703-089-2_15
Published:
Publisher Name: Humana Press, Totowa, NJ
Print ISBN: 978-1-62703-088-5
Online ISBN: 978-1-62703-089-2
eBook Packages: Springer Protocols