Advertisement

Phytoplasma pp 223-232 | Cite as

Microarrays for Universal Detection and Identification of Phytoplasmas

  • Mogens NicolaisenEmail author
  • Henriette Nyskjold
  • Assunta Bertaccini
Part of the Methods in Molecular Biology book series (MIMB, volume 938)

Abstract

Detection and identification of phytoplasmas is a laborious process often involving nested PCR followed by restriction enzyme analysis and fine-resolution gel electrophoresis. To improve throughput, other methods are needed. Microarray technology offers a generic assay that can potentially detect and differentiate all types of phytoplasmas in one assay. The present protocol describes a microarray-based method for identification of phytoplasmas to 16Sr group level.

Key words

Phytoplasma Microarray DNA chip Detection Diagnosis 16S rRNA 

References

  1. 1.
    Deng S, Hiruki C (1991) Amplification of 16S rRNA genes from culturable and nonculturable mollicutes. J Microbiol Meth 14:53–61CrossRefGoogle Scholar
  2. 2.
    Smart CD et al (1996) Phytoplasma-specific PCR primers based on sequences of the 16S–23S rRNA spacer region. Appl Environ Microbiol 62:2988–2993PubMedGoogle Scholar
  3. 3.
    Gundersen DE, Lee I-M (1996) Ultrasensitive detection of phytoplasmas by nested-PCR assays using two universal primer pairs. Phytopathol Mediterr 35:144–151Google Scholar
  4. 4.
    Lee I-M et al (1998) Revised classification scheme of phytoplasmas based an RFLP analyses of 16S rRNA and ribosomal protein gene sequences. Int J Syst Bacteriol 48:1153–1169CrossRefGoogle Scholar
  5. 5.
    François C et al (2006) Towards specific diagnosis of plant-parasitic nematodes using DNA oligonucleotide microarray technology: a case study with the quarantine species Meloidogyne chitwoodi. Mol Cell Probes 20:64–69PubMedCrossRefGoogle Scholar
  6. 6.
    Nicolaisen M et al (2005) An oligonucleotide microarray for the identification and differentiation of trichothecene producing and non-producing Fusarium species occurring on cereal grain. J Microbiol Meth 62:57–69CrossRefGoogle Scholar
  7. 7.
    Lievens B et al (2006) Detecting single nucleotide polymorphisms using DNA arrays for plant pathogen diagnosis. FEMS Microbiol Lett 255:129–139PubMedCrossRefGoogle Scholar
  8. 8.
    Tambong JT et al (2006) Oligonucleotide array for identification and detection of Pythium species. Appl Environ Microbiol 72:2691–2706PubMedCrossRefGoogle Scholar
  9. 9.
    Pelludat C, Duffy B, Frey JE (2009) Design and development of a DNA microarray for rapid identification of multiple European quarantine phytopathogenic bacteria. Eur J Plant Pathol 125:413–423CrossRefGoogle Scholar
  10. 10.
    Fessehaie A, De Boer SH, Lévesque CA (2003) An oligonucleotide array for the identification and differentiation of bacteria pathogenic on potato. Phytopathology 93:262–269PubMedCrossRefGoogle Scholar
  11. 11.
    Nicolaisen M, Bertaccini A (2007) An oligonucleotide microarray-based assay for identification of phytoplasma 16S ribosomal groups. Plant Pathol 56:332–336CrossRefGoogle Scholar
  12. 12.
    Boonham N, Tomlinson J, Mumford R (2007) Microarrays for rapid identification of plant viruses. Annu Rev Phytopathol 45:307–328PubMedCrossRefGoogle Scholar
  13. 13.
    Dufva M (2005) Fabrication of high quality microarrays. Biomol Eng 22:173–184PubMedCrossRefGoogle Scholar
  14. 14.
    Zhang L, Hurek T, Reinhold-Hurek B (2005) Position of the fluorescent label is a crucial factor determining signal intensity in microarray hybridizations. Nucleic Acids Res 33:e166PubMedCrossRefGoogle Scholar
  15. 15.
    Franke-Whittle IH et al (2006) Comparison of different labeling methods for the production of labeled target DNA for microarray hybridization. J Microbiol Meth 65:117–126CrossRefGoogle Scholar
  16. 16.
    Vora GJ et al (2008) Comparison of detection and signal amplification methods for DNA microarrays. Mol Cell Probes 22:294–300PubMedCrossRefGoogle Scholar
  17. 17.
    Prince JP et al (1993) Molecular detection of diverse mycoplasmalike organisms (MLOs) associated with grapevine yellows and their classification with aster yellows, X-disease, and elm yellows MLOs. Phytopathology 83:1130–1137CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC 2013

Authors and Affiliations

  • Mogens Nicolaisen
    • 1
    Email author
  • Henriette Nyskjold
    • 1
  • Assunta Bertaccini
    • 2
  1. 1.Department of AgroecologyAarhus UniversitySlagelseDenmark
  2. 2.DiSTA, Plant PathologyAlma Mater Studiorum—University of BolognaBolognaItaly

Personalised recommendations