Abstract
DNA barcoding is an identification method based on comparison of a short DNA sequence with known sequences from a database. A DNA barcoding tool has been developed for phytoplasma identification. This phytoplasma DNA barcoding protocol based on the tuf gene has been shown to identify phytoplasmas belonging to the following groups: 16SrI, 16SrII, 16SrIII, 16SrIV, 16SrV, 16SrVI, 16SrVII, 16SrIX, 16SrX, 16SrXI, 16SrXII, 16SrXIV, 16SrXX, and 16SrXXI.
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References
Bertaccini A (2007) Phytoplasmas: diversity, taxonomy, and epidemiology. Front Biosci 12:673–689
Bertaccini A, Duduk B, Paltrinieri S et al (2014) Phytoplasmas and phytoplasma diseases: a severe threat to agriculture. Am J Plant Sci 5:1763–1788
IRPCM Phytoplasma/ Spiroplasma Working Team—Phytoplasma taxonomy group (2004) ‘Candidatus Phytoplasma’, a taxon for the wall-less, non-helical prokaryotes that colonize plant phloem and insects. Int J Syst Evol Microbiol 54:1243–1255
Contaldo N, Bertaccini A, Paltrinieri S et al (2012) Axenic culture of plant pathogenic phytoplasmas. Phytopath Mediter 51:607–617
Lee IM, Davis RE, Chen TA et al (1992) A genotype-based system for identification and classification of mycoplasma like organisms (MLOs) in the aster yellows MLO strain cluster. Phytopathology 82:977–986
Martini M, Lee I-M, Bottner KD et al (2007) Ribosomal protein gene-based phylogeny for differentiation and classification of phytoplasmas. Int J Syst Evol Microbiol 57:2037–2051
Lee I-M, Bottner-Parker KD, Zhao Y et al (2010) Phylogenetic analysis and delineation of phytoplasmas based on secY gene sequences. Int J Syst Evol Microbiol 60:2887–2897
Lee I-M, Bottner-Parker KD, Zhao Y et al (2012) Differentiation and classification of phytoplasmas in the pigeon pea witches’ broom group (16SrIX): an update based on multiple gene sequence analysis. Int J Syst Evol Microbiol 62:2279–2285
Makarova OV, Contaldo N, Paltrinieri S et al (2012) DNA barcoding for universal identification of ‘Candidatus Phytoplasmas’ using a fragment of the elongation factor Tu gene. PLoS One 7:e52092
Wei W, Davis RE, Lee I-M et al (2007) Computer-simulated RFLP analysis of 16S rRNA genes: identification of ten new phytoplasma groups. Int J Syst Evol Microbiol 57:1855–1867
Deng S, Hiruki C (1991) Amplification of 16S rRNA genes from culturable and nonculturable mollicutes. J Microbiol Meth 14:53–61
Smart CD, Schneider B, Blomquist CL et al (1996) Phytoplasma-specific PCR primers based on sequences of the 16S-23S rRNA spacer region. Appl Environ Microbiol 62:2988–2993
Gundersen DE, Lee IM, Schaff DA et al (1996) Genomic diversity and differentiation among phytoplasma strains in 16S rRNA groups I (aster yellows and related phytoplasmas) and III (X-disease and related phytoplasmas). Int J Syst Bacteriol 46:64–75
Hodgetts J, Boonham N, Mumford R et al (2008) 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 58:1826–1837
Lee I-M, Zhao Y, Bottner KD (2006) SecY gene sequence analysis for finer differentiation of diverse strains in the aster yellows phytoplasma group. Mol Cell Probes 20:87–91
Botti S, Bertaccini A (2003) Variability and functional role of chromosomal sequences in 16SrI-B subgroup phytoplasmas including aster yellows and related strains. J Appl Microbiol 94:103–110
Marcone C, Lee I-M, Davis RE et al (2000) Classification of aster yellows-group phytoplasmas based on combined analyses of rRNA and tuf gene sequences. Int J Syst Evol Microbiol 50:1703–1713
Hebert PDN, Penton EH, Burns JM et al (2004) Ten species in one: DNA barcoding reveals cryptic species in the neotropical skipper butterfly Astraptes fulgerator. Proc Natl Acad Sci U S A 101:14812–14817
Hebert PDN, Ratnasingham S, deWaard JR (2003) Barcoding animal life: cytochrome c oxidase subunit 1 divergences among closely related species. Proc R Soc Lond B (Suppl) 270:S96–S99
Bonants P, Groenewald E, Rasplus JY et al (2010) QBOL: a new EU project focusing on DNA barcoding of Quarantine organisms. EPPO Bull 40:30–33
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Contaldo, N., Paltrinieri, S., Makarova, O., Bertaccini, A., Nicolaisen, M. (2015). Q-Bank Phytoplasma: A DNA Barcoding Tool for Phytoplasma Identification. In: Lacomme, C. (eds) Plant Pathology. Methods in Molecular Biology, vol 1302. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-2620-6_10
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DOI: https://doi.org/10.1007/978-1-4939-2620-6_10
Publisher Name: Humana Press, New York, NY
Print ISBN: 978-1-4939-2619-0
Online ISBN: 978-1-4939-2620-6
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