Panel of 23S rRNA gene-based real-time PCR assays for improved universal and group-specific detection of phytoplasmas

Applied and Environmental Microbiology

Volumn 75, Issue 9, 2009, Pages 2945-2950

  Hodgetts, Jennifer ^a   Boonham, Neil ^b   Mumford, Rick ^b   Dickinson, Matthew ^a  

^a UNIVERSITY OF NOTTINGHAM   (United Kingdom)

^b CENTRAL SCIENCE LABORATORY   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

MULTIPLEX ASSAYS; NESTED PCR; PHYTOPLASMA; PHYTOPLASMAS; REAL-TIME PCR ASSAY; RRNA GENES; SPECIFIC DETECTION; SR GROUP; UNIVERSAL ASSAY;

ASSAYS;

PRIMER RNA; RNA 16S; RNA 23S; BACTERIAL DNA; BACTERIAL RNA; PRIMER DNA; RIBOSOME DNA;

BIOASSAY; DETECTION METHOD; GENE EXPRESSION; PHYTOPLASMA; POLYMERASE CHAIN REACTION; REAL TIME; RNA;

ARTICLE; BACTERIAL GENE; BACTERIAL STRAIN; BACTERIUM DETECTION; CONTROLLED STUDY; MULTIPLEX POLYMERASE CHAIN REACTION; NONHUMAN; PHYTOPLASMA; REAL TIME POLYMERASE CHAIN REACTION; RNA GENE; RNA PROBE; SENSITIVITY ANALYSIS; CLASSIFICATION; EVALUATION; GENETICS; ISOLATION AND PURIFICATION; METHODOLOGY; OLIGONUCLEOTIDE PROBE; POLYMERASE CHAIN REACTION; SENSITIVITY AND SPECIFICITY;

CANDIDATUS PHYTOPLASMA;

DNA PRIMERS; DNA, BACTERIAL; DNA, RIBOSOMAL; OLIGONUCLEOTIDE PROBES; PHYTOPLASMA; POLYMERASE CHAIN REACTION; RNA, BACTERIAL; RNA, RIBOSOMAL, 23S; SENSITIVITY AND SPECIFICITY;

EID: 65549161763     PISSN: 00992240     EISSN: 10985336     Source Type: Journal    
DOI: 10.1128/AEM.02610-08     Document Type: Article

References (22)

1. Aldaghi, M., S. Massart, S. Roussel, and M. H. Jijakli. 2007. Development of a new probe for specific and sensitive detection of «Candidatus Phyto- plasma mail» in inoculated apple trees. Ann. Appl. Biol. 151:251-258.
2. Angelini, E., G. L. Bianchi, L. Filippin, C. Morassutti, and M. Borgo. 2007. A new TaqMan method for the identification of phytoplasmas associated with grapevine yellows by real-time PCR assay. J. Microbiol. Methods 68: 613-622.
3. Baric, S., and J. Dalla-Via. 2004. A new approach to apple proliferation detection: a highly sensitive real-time PCR assay. J. Microbiol. Methods 57:135-145.
4. Christensen, N. M., M. Nicolaisen, M. Hansen, and A. Schulz. 2004. Distri- bution of phytoplasmas in infected plants as revealed by real-time PCR and bioimaging. Mol. Plant-Microbe Interact. 17:1175-1184.
5. Crosslin, J. M., G. J. Vandemark, and J. E. Munyaneza. 2006. Development of a real-time, quantitative PCR for detection of the Columbia basin potato purple top phytoplasma in plants and beet leafhoppers. Plant Dis. 90:663-667.
6. Cullen, D. W., and P. R. Hirsch. 1998. Simple and rapid method for direct extraction of microbial DNA from soil for PCR. Soil Biol. Biochem. 30:983-993.
7. Doyle, J. J., and J. L. Doyle. 1990. Isolation of plant DNA from fresh tissue. Focus 12:13-15.
8. Firrao, G., K. Gibb, and C. Streten. 2005. Short taxonomic guide to the genus «Candidatus phytoplasma.» J. Plant Pathol. 87:249-263.
9. Galetto, L., B. Bosco, and C. Marzachi. 2005. Universal and group-specific real-time PCR diagnosis of flavescence dorée (16Sr-V), bois noir (16Sr-XII) and apple proliferation (16Sr-X) phytoplasmas from field-collected plant hosts and insect vectors. Ann. Appl. Biol. 147:191-201.
10. Gundersen, D. E., and I.-M. Lee. 1996. Ultrasensitive detection of phyto- plasmas by nested-PCR assays using two universal primer pairs. Phytopathol. Mediterr. 35:144-151.
11. Harrison, N. A., M. Womack, and M. L. Carpio. 2002. Detection and char- acterization of a lethal yellowing (16SrIV) group phytoplasma in Canary Island date palms affected by lethal decline in Texas. Plant Dis. 86:676-681.
12. Hodgetts, J., T. Ball, N. Boonham, R. Mumford, and M. Dickinson. 2007. Use of terminal restriction fragment length polymorphism (TRFLP) for identification of phytoplasmas in plants. Plant Pathol. 56:357-365.
13. Hodgetts, J., N. Boonham, R. Mumford, N. Harrison, and M. Dickinson. 2008. Phytoplasma phylogenetics based on analysis of the secA and 23S rRNA gene sequences for improved resolution of the «Candidatus Phyto- plasma» species. Int. J. Syst. Evol. Microbiol. 58:1826-1837.
14. Hogenhout, S. A., K. Oshima, E.-D. Ammar, S. Kakizawa, H. N. Kingdom, and S. Namba. 2008. Phytoplasmas: bacteria that manipulate plants and insects. Mol. Plant Pathol. 9:403-423.
15. Hren, M., J. Boben, A. Rotter, P. Kralj, K. Gruden, and M. Ravnikar. 2007. Real-time PCR detection system for Flavescence dorée and Bois noir phy- toplasmas in grapevine: comparison with conventional PCR detection and application in diagnostics. Plant Pathol. 56:785-796.
16. Marzachí, C., and D. Bosco. 2005. Relative quantification of chrysanthemum yellows (16Sr I) phytoplasma in its plant and insect host using real-time polymerase chain reaction. Mol. Biotechnol. 30:117-127.
17. Smart, C. D., B. Schneider, C. L. Blomquist, L. J. Guerra, N. A. Harrison, U. Ahrens, K.-H. Lorenz, E. Seemuller, and B. Kirkpatrick. 1996. Phytoplasma- specific PCR primers based on sequence of the 16S-23S rRNA spacer region. Appl. Environ. Microbiol. 62:2988-2993.
18. Torres, E., E. Bertolini, M. Cambra, C. Montón, and M. P. Martín. 2005. Real-time PCR for simultaneous and quantitative detection of quarantine phytoplasmas from apple proliferation (16SrX) group. Mol. Cell. Probes 19:334-340.
19. Wang, K., C. Hiruki, and F. Yeh. 2003. Molecular evolution of phytoplasmas based on polymorphisms in the 16S rRNA genes and the 16/23S spacer regions. Proc. Jpn. Acad. B 79:155-162.
20. Wei, W., S. Kakizawa, S. Suzuki, H. Y. Jung, H. Nishigawa, S. Miyata, K. Oshima, M. Ugaki, T. Hibi, and S. Namba. 2004. In planta dynamic analysis of onion yellows phytoplasma using localised inoculation by insect transmis- sion. Phytopathology 94:244-250.
21. Wei, W., R. E. Davis, I.-M. Lee, and Y. Zhao. 2007. Computer-simulated RFLP analysis of 16S rRNA genes: identification of ten new phytoplasma groups. Int. J. Syst. Evol. Microbiol. 57:1855-1867.
22. Weller, S. A., J. G. Elphinstone, N. C. Smtih, N. Boonham, and D. E. Stead. 2000. Detection of Ralstonia solanacearum strains with a quantitative, mul- tiplex, real-time, fluorogenic PCR (TaqMan) assay. Appl. Environ. Micro- biol. 66:2853-2858.