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DNA Fingerprinting Methods for Microbial Pathogens: Application to Diagnostics, Taxonomy and Plant Disease Management

  • Chapter
Integrated Management of Diseases Caused by Fungi, Phytoplasma and Bacteria

Part of the book series: Integrated Management of Plant Pests and Diseases ((IMPD,volume 3))

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Abstract

Advanced molecular genetic techniques enhance our capabilities to identify and characterize microbial pathogens, resulting in accurate testing for pathogen identification, sub-species-level DNA fingerprinting, pathogen-load testing and disease spread monitoring. These applications are instrumental to the study of plant disease epidemiology, so that adequate control measures can be accordingly implemented. In this chapter, a survey of the most popular DNA profiling techniques is presented together with some of the newer and most discriminating molecular methods. Combinations of different analytical techniques are also proposed as a useful approach for low throughput bioassays. Advantages and disadvantages of each single test are taken into account and key issues (sampling, validation, large-scale testing, etc.), encountered in the practical application of these assays, are discussed. An outline of emerging high-throughput molecular technologies expected to improve diagnostic approaches and aid disease management is also provided.

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References

  • Abd-Elsalam, K. A., Guo, J. R., Schneider, F., Asran-Amal, A. M. & Verreet, J. A. (2004). Comparative assessment of genotyping methods for study genetic diversity of Fusarium oxysporum isolates. Polish Journal of Microbiology, 53, 167-174.

    PubMed  Google Scholar 

  • Abulencia, C. B., Wyborski, D. L., Garcia, J. A., Podar, M., Chen, W., Chang, S. H., et al. (2006). Environmental whole-genome amplification to access microbial populations in contaminated sediments. Applied Environmental Microbiology, 72, 3291-3301.

    Article  CAS  Google Scholar 

  • Alemeida, A. M., Matsumoto, M. T., Baeza, L. C., de Olivera e Silva, R. B., Kleiner, A. A., Melhem-Mde, S., & Mendes-Giannini, M. J. (2007). Molecular typing and antifungal susceptibility of clinical sequential isolates of Cryptococcus neoformans from Sao Paulo State, Brazil. FEMS Yeast Research, 7, 152-164.

    Google Scholar 

  • Azumi, M., & Goto-Yamamoto, N. (2001). AFLP analysis of type strains and laboratory and industrial strains of Saccharomyces sensu stricto and its application to phenetic clustering. Yeast, 18, 1145-1154.

    Google Scholar 

  • Bäumler, S., Sierotzki, H., Gisi, U., Mohler, V., Felsenstein, F. G. & Schwartz, G. (2003). Evaluation of Erysiphe graminis f sp triticifield isolates for resistance to strobilurin fungicides with different SNP detection systems. Pest Management Science, 59, 310-314.

    Article  PubMed  CAS  Google Scholar 

  • Beadle, J., Wright, M., McNeely, L. & Bennett, J. W. (2003). Electrophoretic karyotype analysis in fungi. Advanced Applied Microbiology, 53, 243-270.

    Article  CAS  Google Scholar 

  • Ben-Ari, G., Zenvirth, D., Sherman, A., Simchen, G., Lavi, U. & Hillel, J. (2005). Application of SNPs for assessing biodiversity and phylogeny among yeast strains. Heredity, 95, 493-501.

    Article  PubMed  CAS  Google Scholar 

  • Bensch, S., & Akesson, M. (2005). Ten years of AFLP in ecology and evolution: why so few animals? Molecular Ecology, 14, 2899-2914.

    Article  PubMed  CAS  Google Scholar 

  • Bohaychuk, V. M., Gensler, G. E., McFall, M. E., King, R. K., & Renter, D. G. (2007). A real-time PCR assay for the detection of Salmonella in a wide variety of food and food-animal matricest. Journal of Food Protection, 70, 1080-1087.

    PubMed  CAS  Google Scholar 

  • Böhm, J., Hahn, A., Schubert, R., Bahnweg, G., Adler, N., Nechwatal, J., Oehlmann, R. & Oβwald, W. (1999). Real-time quantitative PCR: DNA determination in isolated spores of the mycorrhizal fungus Glomus mosseae and monitoring of Phytophthora infestans and Phytophthora citricola in their respective host plants. Journal of Phytopathology, 147, 409-416.

    Google Scholar 

  • Boonham, N., Walsh, K., Mumford, R. A. & Barker, I. (2000). Use of multiplex real-time PCR (TaqMan) for the detection of potato viruses. EPPO Bulletin, 30, 427-430.

    Article  Google Scholar 

  • Bourassa, M., Bernier, L., & Hamelin, R. C. (2005). Direct genotyping of the poplar leaf rust fungus, Melampsora medusae f. sp. deltoidae, using codominant PCR-SSCP markers. Forest Pathology, 35, 245-261.

    Article  Google Scholar 

  • Brenner, S., Johnston, M., Bridgham, J., Golda, G., Lloyd, D. H., Johnson, D., et al. (2000). Gene expression analysis by massively parallel signature sequencing (MPSS) on microbead arrays. Nature Biotechnology, 18, 630-634.

    Article  PubMed  CAS  Google Scholar 

  • Cadez, N., Raspor, P., de Cock, A.W., Boekhout, T. & Smith, M.T. (2002). Molecular identification and genetic diversity within species of the genera Hanseniaspora and Kloeckera. FEMS Yeast Research, 1, 279-289.

    PubMed  CAS  Google Scholar 

  • Canales, R .D., Luo, Y., Willey, J. C., Austermiller, B., Barbacioru, C .C., Boysen, C., et al. (2006). Evaluation of DNA microarray results with quantitative gene expression platforms. Nature Biotechnology, 24, 1115-1122.

    Article  PubMed  CAS  Google Scholar 

  • Carroll G. (1995). Forest endophytes: pattern and process. Canadian Journal of Botany, 73 (Suppl. 1), 1316-1324.

    Article  Google Scholar 

  • Castrillo, L. A., Thomsen, L., Juneja, P., & Hajek, A. E. (2007). Detection and quantification of Entomophaga maimaiga resting spores in forest soil using real-time PCR. Mycological Research, 111, 324-331.

    Article  PubMed  CAS  Google Scholar 

  • Chang, P. L., Hsieh, W. S., Chiang, C. L., Tuohy, M. J., Hall, G. S., Procop, G. W., et al. (2007). The hsp65 gene patterns of less common Mycobacterium and Nocardia spp. by polymerase chain reaction-restriction fragment length polymorphism analysis with capillary electrophoresis. Diagnostic Microbiology & Infectious Disease, 58, 315-323.

    Article  CAS  Google Scholar 

  • Chen, Q. H., Wag, Y. C., Li, A. N., Zhang, Z. G., & Zheng, X. B. (2007). Molecular mapping of two cultivar-specific avirulence genes in the rice blast fungus Magnaporthe grisea. Molecular Genetics & Genomics, 277, 139-148.

    Article  CAS  Google Scholar 

  • Chen, T. (2006). DNA microarrays - an armory for combating infectious diseases in the new century. Current Drug Targets - Infectious Disorders, 6, 263-279.

    Article  CAS  Google Scholar 

  • Cocolin, L., Urso, R., Rantsiou, K., Cantoni, C. & Comi, G. (2006). Dynamics and characterization of yeasts during natural fermentation of Italian sausages. FEMS Yeast Research, 6, 692-701.

    Article  PubMed  CAS  Google Scholar 

  • Consolandi, C., Severgnini, M., Fronsini, A., Caramenti, G., De Fazio, M., Ferrara, F., et al. (2006). Polymerase chain reaction of 2-kb cyanobacterial gene and human anti-alpha1-chymotrypsin gene from genomic DNA on the In-Check single-use microfabricated silicon chip. Analytical Biochemistry, 353, 191-197.

    Article  PubMed  CAS  Google Scholar 

  • Coton, M., Laplace, J. M., Auffray, Y. & Coton, E. (2006). Polyphasic study of Zymomonas mobilis strains revealing the existence of a novel subspecies Z. mobilis subsp. francensis subsp. nov., isolated from French cider. International Journal of Systematic and Evolutionary Microbiology, 56, 121-125.

    Article  PubMed  CAS  Google Scholar 

  • De Souza, F. A., Kowalchuk, G. A., Leeflang, P., Van Veen, J. A. & Smit, E. (2004). PCR-denaturing gradient gel electrophoresis profiling of inter- and intraspecies 18S rRNA gene sequence heterogeneity is an accurate and sensitive method to assess species diversity of arbuscular mycorrhizal fungi of the genus Gigaspora. Applied Environmental Microbiology, 70, 1413-1424.

    Article  CAS  Google Scholar 

  • Di Maria, S., Basso, A. L., Santoro, E., Grazia, L. & Coppola, R. (2002). Monitoring of Staphylococcus xylosus DSM 20266 added as starter during fermentation and ripening of soppressata molisana, a typical Italian sausage. Journal of Applied Microbiology, 92, 158-164.

    Article  Google Scholar 

  • Doddapaneni, H., & Yadav, J. S. (2005). Microarray-based global differential expression profiling of P450 monooxygenases and regulatory proteins for signal transduction pathways in the white rot fungus Phanerochaete chrysosporium. Molecular Genetics & Genomics, 274, 454-466.

    Article  CAS  Google Scholar 

  • Edwards, S., O’Callaghan, J., & Dobson, A. D. W. (2002). PCR-based detection and quantification of mycotoxigenic fungi. Mycological Research, 106, 1005-1025.

    Article  CAS  Google Scholar 

  • Emrich, C. A., Tian, H., Medintz, I. L., & Mathies, R. A. (2002). Microfabricated 384-lane capillary array electrophoresis bioanalyser for ultra high-throughput genetic analysis. Analytical Chemistry, 74, 5076-5083.

    Article  PubMed  CAS  Google Scholar 

  • Feau, N., Weiland, J. E., Stanosz, G. R. & Bernier, L. (2005). Specific and sensitive PCR-based detection of Septoria musiva, S. populicola and S. populi, the causes of leaf spot and stem canker on poplars. Mycological Research, 109, 1015-1028.

    Article  PubMed  CAS  Google Scholar 

  • Fischer, A., Lenhard, A., Tronecker, H., Lorat, Y., Kraenzle, M., Sorgenfrei, O., et al. (2007). iGentifier: indexing and large-scale profiling of unknown transcriptomes. Nucleic Acids Research, 35, 4640-4648.

    Article  PubMed  CAS  Google Scholar 

  • Forche, A., Magee, P. T., Magee, B. B. & May, G. (2004). Genome-wide single-nucleotide polymorphism map for Candida albicans. Eukaryotic Cell, 3, 705-714.

    Article  PubMed  CAS  Google Scholar 

  • Forche, A., May, G., & Magee, P. T. (2005). Demonstration of loss of heterozygosity by single-nucleotide polymorphism microarray analysis and alterations in strain morphology in Candida albicans strains during infection. Eukaryotic Cell, 4, 156-165.

    Article  PubMed  CAS  Google Scholar 

  • Foulet, F., Nicolas, N., Eloy, O., Botterel, F., Gantier, J. C., Costa, J. M. & Bretagne, S. (2005). Microsatellite marker analysis as a typing system for Candida glabrata. Journal of Clinical Microbiology, 43, 4574-4579.

    Article  PubMed  CAS  Google Scholar 

  • Fouqué, B., Brachet, A. G., Gétin, S., Pégon, P., Obeïd, P., Delapierre, G., & Chatelain, F. (2007). Improvement of yeast biochip sensitivity using multilayer inorganic sol-gel substrates. Biosensensors and Bioelectronics, 22, 2151-2157.

    Article  CAS  Google Scholar 

  • Fraaije, B. A., Lovell, D. J., & Baldwin, S. (2002). Septoria epidemics on wheat: Combined use of visual assessment and PCR-based diagnostics to identify mechanisms of disease escape. Plant Protection Science, 38, 421-424.

    Google Scholar 

  • Fraaije, B. A., Lovell, D., Coelho, J. M., Baldwin, S., & Hollomon, D. W. (2001). PCR-based assays to assess wheat varietal resistance to blotch (Septoria triticiand Stagonospora nodorum) and rust (Puccinia striiformis and Puccinia recondita) diseases. European Journal of Plant Pathology, 107, 905-917.

    Article  CAS  Google Scholar 

  • Gang, D. R., & Weber, D.J. (1995). Preparation of genomic DNA for RAPD analysis from thick-walled dormant teliospores of Tilletia species. Biotechniques 19:92, 94, 96-97.

    Google Scholar 

  • Gao, H., Yang, Z. K., Gentry, T. J., Wu, L., Schadt, C. W. & Zhou, J. (2006). Microarray-based analysis of microbial community RNAs by whole-community RNA amplification. Applied Environmental Microbiology, 73, 563-571.

    Article  CAS  Google Scholar 

  • Ge, B., Larkin, C., Ahn, S., Jolley, M., Nasir, M., Meng, J., & Hall, R. H. (2002). Identification of Escherichia coli O157:H7 and other enterohemorrhagic serotypes by EHEC- hlyA targeting, strand displacement amplification, and fluorescence polarization. Molecular and Cellular Probes, 16, 85-92.

    Article  PubMed  CAS  Google Scholar 

  • Gelfi, C., Righetti, P. G., Travi, M., & Fattore, S. (1997). Temperature-programmed capillary electrophoresis for the analysis of high-melting point mutants in thalassemias. Electrophoresis, 18, 724-731.

    Article  PubMed  CAS  Google Scholar 

  • Gil-Lamaignere, C., Roilides, E., Hacker, J., & Müller, F. M. (2003). Molecular typing for fungi - a critical review of the possibilities and limitations of currently and future methods. Clinical Microbiology and Infection, 9, 172-185.

    Google Scholar 

  • Gilles, T., Evans, N., Fitt, B. D. L., & Jeger, M. J. (2000). Epidemiology in relation to forecasting light leaf spot (Pyrenopeziza brassicae) severity on winter oilseed rape (Brassica napus) in the UK. European Journal of Plant Pathology, 106, 593-605.

    Article  Google Scholar 

  • Godoy, P., Cano, J., Gené, J., Guarro, J., Höfling-Lima, A. L. & Lopes Colombo, A. (2004). Genotyping of 44 isolates of Fusarium solani, the main agent of fungal keratitis in Brazil. Journal of Clinical Microbiology, 42, 4494-4497.

    Article  PubMed  CAS  Google Scholar 

  • Goldberg, S. M., Johnson, J., Busam, D., Feldblyum, T., Ferriera, S., Friedman, R., et al. (2006). A Sanger/pyrosequencing hybrid approach for the generation of high-quality draft assemblies of marine microbial genomes. Proceedings of the National Academy of Science, USA, 103, 11240-11245.

    Article  CAS  Google Scholar 

  • Gómez-Alpizar, L., Carbone, I., & Ristaino, J. B. (2007). An Andean origin of Phytophthora infestans inferred from mitochondrial and nuclear gene genealogies. Proceedings of the National Academy of Science, USA, 104, 3306-3311.

    Article  CAS  Google Scholar 

  • González-Techera, A., Jubany, S., Carrau, F. M. & Gaggero, C. (2001). Differentiation of industrial wine yeast strains using microsatellite markers. Letters in Applied Microbiology, 33, 71-75.

    Article  PubMed  Google Scholar 

  • Grimmer, M. K., Trybush, S., Hanley, S., Francis, S. A., Karp, A. & Asher, M. J. (2007). An anchored linkage map for sugar beet based on AFLP, SNP and RAPD markers and QTL mapping of a new source of resistance to Beet necrotic yellow vein virus. Theoretical and Applied Genetics, 114, 1151-1160.

    Article  PubMed  CAS  Google Scholar 

  • Guo, J. R., Schneider, F., Abd-Elsalam, K. A., & Verreet, J. A. (2005). Rapid and efficient extraction of genomic DNA from different phytopathogenic fungi using DNAzol reagent. Biotechnology Letters, 27, 3-6.

    Article  PubMed  CAS  Google Scholar 

  • Hatsch, D., Phalip, V., & Jeltsch, J. M. (2004). Use of genes encoding cellobiohydrolase-C and topoisomerase II as targets for phylogenetic analysis and identification of Fusarium. Research in Microbiology, 155, 290-296.

    Article  PubMed  CAS  Google Scholar 

  • Healy, M., Reece, K., Walton, D., Huong, J., Shah, K. & Kontoyiannis, D. P. (2004). Identification to the species level and differentiation between strains of Aspergillus clinical isolates by automated repetitive-sequence-based PCR. Journal of Clinical Microbiology, 42, 4016-4024.

    Article  PubMed  CAS  Google Scholar 

  • Huang, A., Li, J. W., Shen, Z. Q., Wang, X. W. & Jin, M. (2006). High-throughput identification of clinical pathogenic fungi by hybridization to an oligonucleotide microarray. Journal of Clinical Microbiology, 44, 3299-3305.

    Article  PubMed  CAS  Google Scholar 

  • Huang, C. W., Cheng, Y. S., Rouvier, R., Yang, K. T., Wu, C. P. & Huang, M. C. (2007). AFLP fingerprinting for paternity testing in ducks. British Poultry Science, 48, 323-330.

    Article  PubMed  CAS  Google Scholar 

  • Huhtamellas, S., Leinonen, M., Nieminen, T., Fahnert, B., Myllykoski, L., Breitenstein, A. & Neubauer, P. (2007). RNA-based sandwich hybridisation method for detection of lactic acid bacteria in brewery samples. Journal of Microbiological Methods, 68, 543-553.

    Article  CAS  Google Scholar 

  • Hutchison, C. A., Smith, H. O., Pfannkoch, C. & Venter, J. C. (2005). Cell-free cloning using π29 DNA polymerase. Proceedings of the National Academy of Science,USA, 102, 17332-17336.

    Article  CAS  Google Scholar 

  • Irie, T., Matsumura, H., Terauchi, R. & Saitoh, H. (2003). Serial Analysis of Gene Expression (SAGE) of Magnaporthe grisea: genes involved in appressorium formation. Molecular Genetics and Genomics, 270, 181-189.

    Article  PubMed  CAS  Google Scholar 

  • Jespersen, L., Van der Kühle, A., & Petersen, K. M. (2000). Phenotypic and genetic diversity of Saccharomycescontaminants isolated from lager breweries and their phylogenetic relationship with brewing yeasts. International Journal of Food Microbiology, 60, 43-53.

    Article  PubMed  CAS  Google Scholar 

  • Johannesson, H., Kasuga, T., Schaller, R. A., Good, B., Gardner, M. J., Townsend, J. P., et al. (2006). Phase-specific gene expression underlying morphological adaptations of the dimorphic human pathogenic fungus, Coccidioides posadasii. Fungal Genetics and Biology, 43, 545-559.

    Article  PubMed  CAS  Google Scholar 

  • Jones, T., Federspiel, N. A., Chibana, H., Dungan, J., Kalman, S., Magee, B. B., et al. (2004). The diploid genome sequence of Candida albicans. Proceedings of the National Academy of Science, USA, 101, 7329-7334.

    Article  CAS  Google Scholar 

  • Jurado, M., Vázquez, C., Marín, S., Sanchis, V., Teresa González-Jaén, M. (2006). PCR-based strategy to detect contamination with mycotoxigenic Fusarium species in maize. Systematic and Applied Microbiology, 29, 681-689.

    Article  PubMed  CAS  Google Scholar 

  • Käller, M., Lundeberg, J., & Ahmadian, A. (2007). Arrayed identification of DNA signatures. Expert Review of Molecular Diagnostics, 7, 65-76.

    Article  PubMed  Google Scholar 

  • Kartalov, E. P., & Quake, S. R. (2004). Microfluidic device reads up to four consecutive base pairs in DNA sequencing-by-synthesis. Nucleic Acids Research, 32, 2873-2879.

    Article  PubMed  CAS  Google Scholar 

  • Kasuga, T., & Mitchelson, K. R. (2000). Intersterility group differentiation in Heterobasidion annosum using ribosomal IGS1 region polymorphism. European Journal of Forest Pathology, 30, 329-344.

    Article  Google Scholar 

  • Kasuga, T., Townsend, J. P., Tian, C., Gilbert, L. B., Mannhaupt, G., Taylor, J. W. & Glass, N. L. (2005). Long-oligomer microarray profiling in Neurospora crassa reveals the transcriptional program underlying biochemical and physiological events of conidial germination. Nucleic Acids Research, 33, 6469-6485.

    Article  PubMed  CAS  Google Scholar 

  • Kema, G. H., Goodwin, S. B., Hamza, S., Verstappen, E. C., Cavaletto, J. R., Van der Lee, T. A., et al. (2002). A combined amplified fragment length polymorphism and randomly amplified polymorphism DNA genetic kinkage map of Mycosphaerella graminicola, the septoria tritici leaf blotch pathogen of wheat. Genetics, 161, 1497-1505.

    PubMed  CAS  Google Scholar 

  • Keon, J., Antoniw, J., Carzaniga, R., Deller, S., Ward, J. L., Baker, J. M., et al. (2007). Transcriptional adaptation of Mycosphaerella graminicola to programmed cell death (PCD) of its susceptible wheat host. Molecular Plant Microbe Interaction, 20, 178-193.

    Article  CAS  Google Scholar 

  • Kim, N. S., Park, N. I., Kim, S. H., Kim, S. T., Han, S. S. & Kang, K. Y. (2000). Isolation of TC/AG repeat microsatellite sequences for fingerprinting rice blast fungus and their possible horizontal transfer to plant species. Molecules and Cells, 10, 127-134.

    Article  PubMed  CAS  Google Scholar 

  • Krause, L., Diaz, N. N., Bartels, D., Edwards, R. A., Pühler, A., Rohwer, F., et al. (2006). Finding novel genes in bacterial communities isolated from the environment. Bioinformatics, 22, e281-e289.

    Google Scholar 

  • Kuimelis, R. G., Livak, K. J., Mullah, B., & Andrus, A. (1997). Structural analogues of TaqMan probes for real-time quantitative PCR. Nucleic Acids Symposium Series, 37, 255-256.

    Google Scholar 

  • Langrell, S. R. (2005). Development of a nested PCR detection procedure for Nectria fuckeliana direct from Norway spruce bark extracts. FEMS Microbiology Letters, 242, 185-193.

    Article  PubMed  CAS  Google Scholar 

  • Larsen, L. A., Jespersgaard, C., & Andersen, P. S. (2007). Single-strand conformation polymorphism analysis using capillary array electrophoresis for large-scale mutation detection. Nature Protocols, 2, 1458-1466.

    Article  PubMed  CAS  Google Scholar 

  • Lasker, B. A. (2006). Nucleotide sequence-based analysis for determining the molecular epidemiology of Penicillium marneffei. Journal of Clinical Microbiology, 44, 3145-3153.

    Article  PubMed  CAS  Google Scholar 

  • Lay, M. J., & Wittwer, C.T. (1997). Real-time fluorescence genotyping of factor V Leiden during rapid-cycle PCR. Clinical Chemistry, 43, 2262-2267.

    PubMed  CAS  Google Scholar 

  • Lebech, A. M. (2002). Polymerase chain reaction in diagnosis of Borrelia burgdorferi infections and studies on taxonomic classification. Acta Pathologica, Microbiologica et Immunologica Scandinavica, (Suppl.), 105, 1-40.

    Google Scholar 

  • Lee, J. S., Shin, J. H., Kim, M. N., Jung, S. I., Park, K. H., Cho, D., et al. (2007). Kodamaea ohmeriisolates from patients in a university hospital: identification, antifungal susceptibility, and pulsed-field gel electrophoresis analysis. Journal of Clinical Microbiology, 45, 1005-1010.

    Article  PubMed  CAS  Google Scholar 

  • Legally, E. T., Scherer, J. R., Blazej, R. G., Toriello, N. M., Diep, B. A., Ramchandani, M., et al. (2004). Integrated portable genetic analysis microsystem for pathogen/infectious disease detection. Analytical Chemistry, 76, 3162-3170.

    Article  CAS  Google Scholar 

  • Legras, J. L., Ruh, O., Merdinoglu, D. & Karst, F. (2005). Selection of hypervariable microsatellite loci for the characterization of Saccharomyces cerevisiae strains. International Journal of Food Microbiology, 102, 73-83.

    Article  PubMed  CAS  Google Scholar 

  • Leisova, L., Minarkova, V., Kucera, L. & Ovesna, J. (2006). Quantification of Pyrenophora teres in infected barley leaves using real-time PCR. Journal of Microbiological Methods, 67, 446-455.

    Article  PubMed  CAS  Google Scholar 

  • Lephart, P. R. & Magee, P. T. (2006). Effect of the major repeat sequence on mitotic recombination in Candida albicans. Genetics, 174, 1737-1744.

    Article  PubMed  CAS  Google Scholar 

  • Leskelä, T., Tilsala-Timisjärvi, A., Kusnetsov, J., Neubauer, P. and Breitenstein, A. (2005). Sensitive genus-specific detection of Legionella by a 16S rRNA based sandwich hybridization assay. Journal of Microbiological Methods, 62, 167-179.

    Article  PubMed  CAS  Google Scholar 

  • Li, Q., Deka, C., Glassner, B. J., Arnold, K., Li-Sucholeiki, X. C., Tomita-Mitchell, A., er al. (2005). Design of an automated multicapillary instrument with fraction collection for DNA mutation discovery by constant denaturant capillary electrophoresis (CDCE). Journal of Separation Science, 28, 1375-1389.

    Article  PubMed  CAS  Google Scholar 

  • Lievens, B., Brouwer, M., Vanachter, A. C. R. C., Lévesque, C. A., Cammue, B. P. A., & Thomma, B. P. H. J. (2003) Design and development of a DNA array for rapid detection and identification of multiple tomato vascular wilt pathogens. FEMS Microbiology Letters, 223, 113-122.

    Article  PubMed  CAS  Google Scholar 

  • Lievens, B., Brouwer, M., Vanachter, A. C. R. C., Lévesque, C. A., Cammue, B. P. A. & Thomma, B. P. H. J. (2005). Quantitative assessment of phytopathogenic fungi in various substrates using a DNA macroarray. Environmental Microbiology, 7, 1698-1710.

    Article  PubMed  CAS  Google Scholar 

  • Liu, C. N., Toriello, N. M., & Mathies, R. A. (2006). Multichannel PCR-CE microdevice for genetic analysis. Analytical Chemistry, 78, 5474-5479.

    Article  PubMed  CAS  Google Scholar 

  • Liu, J., Maldonado-Mendoza, I., Lopez-Meyer, M., Cheung, F., Town, C. D. & Harrison, M. J. (2007a). Arbuscular mycorrhizal symbiosis is accompanied by local and systemic alterations in gene expression and an increase in disease resistance in the shoots. Plant Journal, 50, 529-544.

    Article  CAS  Google Scholar 

  • Liu, P., Seo, T. S., Bevor, N., Shin, K. J., Scherer, J. R. & Mathies, R.A. (2007b). Integrated portable polymerase chain reaction-capillary electrophoresis microsystem for rapid forensic short tandem repeat typing. Analytical Chemistry, 79,1881-1889.

    Article  CAS  Google Scholar 

  • Liu, Z. L., & Slininger, P. J. (2007). Universal external RNA controls for microbial gene expression analysis using microarray and qRT-PCR. Journal of Microbiological Methods, 68, 486-496.

    Article  PubMed  CAS  Google Scholar 

  • Lockhart, S. R., Pujol, C., Dodgson, A. R., & Soll, D. R. (2005). Deoxyribonucleotide acid fingerprinting methods for Candida species. Methods in Molecular Medicine, 118,15-25.

    PubMed  CAS  Google Scholar 

  • Lopandic, K., Zelger, S., Bánszky, L. K., Eliskases-Lechner, F., & Prillinger, H. (2006). Identification of yeasts associated with milk products using traditional and molecular techniques. Food Microbiology, 23, 341-350.

    Article  PubMed  CAS  Google Scholar 

  • Mabru, D., Douet, J. P., Mouton, A., Dupré, C., Richard, J. M., Médina, B., et al. (2004). PCR-RFLP using a SNP on the mitochondrial Lsu-rDNA as an easy method to differentiate Tuber melanosporum (Perigord truffle) and other truffle species in cans. International Journal of Food Microbiology, 94, 33-42.

    Article  PubMed  CAS  Google Scholar 

  • Margulies, M., Egholm, M., Altman, W., Attiya, S., Bader, J., Bemben, L., et al. (2005). Genome sequencing in microfabricated high-density picolitre reactors. Nature, 437, 376-380.

    PubMed  CAS  Google Scholar 

  • Martin, R. R., James, D., & Lévesque, C. A. (2000). Impacts of molecular diagnostic technologies on plant disease management. Annual Review of Phytopathology, 38, 207-239.

    Google Scholar 

  • Masoud, W., Cesar, L. B., Jespersen, L. & Jakobsen, M. (2004). Yeast involved in fermentation of Coffea arabica in East Africa determined by genotyping and by direct denaturating gradient gel electrophoresis. Yeast, 21,549-556.

    Article  PubMed  CAS  Google Scholar 

  • Maxwell, A., Jackson, S. L., Dell, B. & Hardy, G. E. (2005). PCR-identification of Mycosphaerella species associated with leaf diseases of Eucalyptus. Mycological Research, 109, 992-1004.

    Article  PubMed  CAS  Google Scholar 

  • McCartney, H. A., Foster, S. J., Fraaije, B. A., & Ward, E. (2003). Molecular diagnostics for fungal plant pathogens. Pest Management Science, 59, 129-142.

    Article  PubMed  CAS  Google Scholar 

  • McIlhatton, B. P., Keating, C., Curran, M. D., McMullin, M. F., Barr, J. G., Madrigal, J. A. & Middleton, D. (2002). Identification of medically important pathogenic fungi by reference strand-mediated conformational analysis (RSCA). Journal of Medical Microbiology, 51, 468-478.

    PubMed  CAS  Google Scholar 

  • Meyer, W., & Mitchell, T. G. (1995). Polymerase chain reaction fingerprinting in fungi using single primers specific to minisatellites and simple repetitive DNA sequences: strain variation in Cryptococcus neoformans. Electrophoresis, 16, 1648-1656.

    Article  PubMed  CAS  Google Scholar 

  • Michelmore, R. W., Paran, I., & Kesseli, R. V. (1991). Identification of markers linked to disease-resistance genes by bulked segregant analysis: a rapid method to detect markers in specific genomic regions by using segregating populations. Proceedings of the National Academy of Science,USA, 88, 9828-9832.

    Article  CAS  Google Scholar 

  • Milczarski, P., Banek-Tabor, A., Lebiecka, K., Stojałowski, S., Myśków, B. & Masojć, P. (2007). New genetic map of rye composed of PCR-based molecular markers and its alignment with the reference map of the DS2 × RXL10 intercross. Journal of Applied Genetics, 48, 11-24.

    PubMed  Google Scholar 

  • Minami, M., Kureha, O., Mori, M., Kamitsuji, H., Suzuki, K., & Irie, T. (2007). Long serial analysis of gene expression for transcriptome profiling during the initiation of ligninolytic enzymes production in Phanerochaete chrysosporium. Applied Microbiology and Biotechnology, 75, 609-618.

    Article  PubMed  CAS  Google Scholar 

  • Mitchelson, K. R. (2003). The use of capillary electrophoresis for DNA polymorphism analysis. Molecular Biotechnology, 24, 41-68.

    Article  PubMed  CAS  Google Scholar 

  • Mitchelson, K. R., Drenthe, J., Duong, H. and Chaparro, J.X. (1999). Direct sequencing of RAPD fragments using 3’-extended oligonucleotide primers and dye-terminator cycle-sequencing. Nucleic Acids Research, 27, e28.

    Article  PubMed  CAS  Google Scholar 

  • Mohali, S., Burgess, T. I., & Wingfield, M. J. (2005). Diversity and host association of the tropical tree endophyte Lasiodiplodia theobromae revealed using simple sequence repeat markers. Forest Pathology, 35, 385-396.

    Article  Google Scholar 

  • Moreno-Paz, M., & Parro, V. (2006). Amplification of low quantity bacterial RNA for microarray studies: time-course analysis of Leptospirillum ferrooxidans under nitrogen-fixing conditions. Environmental Microbiology, 8, 1064-1073.

    Article  PubMed  CAS  Google Scholar 

  • Morgan, M. R. A. (1995). Monitoring safety of plant foods: immunodiagnostics for mycotoxins and other bioactive compounds. In: H. J. Skerritt & R. Appels (Eds.), New Diagnostics in Crop Science. Biotechnology in Agriculture, No. 13, (pp. 215-242). Wallingford, UK: CAB International.

    Google Scholar 

  • Moricca, S., Raddi, P., Borja, I., & Vendramin, G. G. (2000). Differentiation of Seiridiumspecies associated with virulent cankers on cypress in the Mediterranean region by PCR- SSCP. Plant Pathology, 49, 774-781.

    Article  CAS  Google Scholar 

  • Moricca, S., Hantula, J., & Müller, M. M. (2004). Genomic and genetic perspectives on fungal endophytes. In: Ragazzi A., Moricca S. & Dellavalle, I. (Eds.), Endophytism in forest trees (pp. 51-71). Firenze: Accademia Italiana di Scienze Forestali.

    Google Scholar 

  • Moricca, S., Ragazzi, A., & Mitchelson, K. R. (1999). Molecular and conventional detection and identification of Cladosporium tenuissimum on two-needle pine rust aeciospores. Canadian Journal of Botany, 77, 339-347.

    Article  CAS  Google Scholar 

  • Moricca, S., Ragazzi, A., Kasuga, T. & Mitchelson, K. R. (1998). Detection of Fusarium oxysporum f.sp. vasinfectum in cotton tissue by polymerase chain reaction. Plant Pathology, 47, 486-494.

    Article  CAS  Google Scholar 

  • Müller, M. V., Germani J. C., & Van der Sand, S. T. (2005). The use of RAPD to characterize Bipolaris sorokiniana isolates. Genetics and Molecular Research, 4, 642-652.

    PubMed  Google Scholar 

  • Mumford, R. A., Walsh, K., & Boonham, N. (2000). A comparison of molecular methods for the routine detection of viroids. EPPO Bulletin, 30, 431-435.

    Article  Google Scholar 

  • Muraguchi, H., Ito, Y., Kamada, T. & Yanagi, S. O. (2003). A linkage map of the basidiomycete Coprinus cinereus based on random amplified polymorphic DNAs and restriction fragment length polymorphisms. Fungal Genetics and Biology, 40, 93-102.

    Article  PubMed  CAS  Google Scholar 

  • Noll, W. W., & Collins, M. (1987). Detection of human DNA polymorphisms with a simplified denaturing gradient gel electrophoresis technique. Proceedings of the National Academy of Science,USA, 84, 3339-3343.

    Article  CAS  Google Scholar 

  • Nunes, L. R., Costa de Oliveira, R., Leite, D. B., da Silva, V. S., dos Reis Marques, E., da Silva Ferreira, M. E., et al. (2005). Transcriptome analysis of Paracoccidioides brasiliensis cells undergoing mycelium-to-yeast transition. Eukaryotic Cell, 4, 2115-2128.

    Article  PubMed  CAS  Google Scholar 

  • O’Sullivan, D., Tosi, P., Creusot, F., Cooke, B. M., Phan, T. H., Dron, M., & Langin, T. (1998). Variation in genome organization of the plant pathogenic fungus Colletotrichum lindemuthianum. Current Genetics, 33, 291-298.

    Article  PubMed  CAS  Google Scholar 

  • Ottesen, E. A., Hong, J. W., Quake, S. R. & Ledbetter, J. R. (2006). Microfluidic digital PCR enables multigene analysis of individual environmental bacteria. Science, 314, 1464-1467.

    Article  PubMed  CAS  Google Scholar 

  • Palacios, G., Quan, P. L., Jabado, O. J., Conlan, S., Hirschberg, D. L., Liu, Y., et al. (2007). Panmicrobial oligonucleotide array for diagnosis of infectious diseases. Emerging Infectious Diseases, 13, 73-81.

    PubMed  CAS  Google Scholar 

  • Parro, V., Moreno-Paz, M., & Gonzalez-Toril, E. (2007). Analysis of environmental transcriptomes by DNA microarrays. Environmental Microbiology, 9, 453-464.

    Google Scholar 

  • Patterson, T. A., Lobenhofer, E. K., Fulmer-Smentek, S. B., Collins, P. J., Chu, T. M., Bao, W., et al. (2006). Performance comparison of one-color and two-color platforms within the MicroArray Quality Control (MAQC) project. Nature Biotechnology, 24, 1140-1150.

    Article  PubMed  CAS  Google Scholar 

  • Perrin, R. M., Fedorova, N. D., Bok, J. W., Cramer, R. A., Wortman, J. R., Kim, H. S., et al. (2007). Transcriptional regulation of chemical diversity in Aspergillus fumigatus by LaeA. PLoS Pathology, 3, e50.

    Article  CAS  Google Scholar 

  • Pinard, R., de Winter, A., Sarkis, G. J., Gerstein, M. B., Tartaro, K. R., Plant, R. N., et al. (2006). Assessment of whole genome amplification-induced bias through high-throughput, massively parallel whole genome sequencing. BMC Genomics, 23, 216.

    Article  CAS  Google Scholar 

  • Pingle, M. R., Granger, K., Feinberg, P., Shatsky, R., Sterling, B., Rundell, M., et al. (2007). Multiplexed identification of blood-borne bacterial pathogens by use of a novel 16S rRNA gene PCR-ligase detection reaction-capillary electrophoresis assay. Journal of Clinical Microbiology, 45, 1927-1935.

    Article  PubMed  CAS  Google Scholar 

  • Pisano, M. B., Fadda, M. E., Deplano, M., Corda, A., Casula, M., & Cosentino, S. (2007). Characterization of Fiore Sardo cheese manufactured with the addition of autochthonous cultures. Journal of Dairy Research, 74, 255-261.

    Article  PubMed  CAS  Google Scholar 

  • Plachý, R., Hamal, P., & Raclavský, V. (2005). McRAPD as a new approach to rapid and accurate identification of pathogenic yeasts. Journal of Microbiological Methods, 60, 107-113.

    Article  PubMed  CAS  Google Scholar 

  • Pramateftaki, P. V., Antoniou, P. P., & Typas, M. A. (2000). The complete DNA sequence of the nuclear ribosomal RNA gene complex of Verticillium dahliae: intraspecific heterogeneity within the intergenic spacer region. Fungal Genetics and Biology, 29,135-143.

    PubMed  CAS  Google Scholar 

  • Rajashekar, B., Samson, P., Johansson, T., & Tunlid, A. (2007). Evolution of nucleotide sequences and expression patterns of hydrophobin genes in the ectomycorrhizal fungus Paxillus involutus. New Phytologist, 174, 399-411.

    Article  PubMed  CAS  Google Scholar 

  • Rakeman, J. L., Bui, U., Lafe, K., Chen, Y. C., Honeycutt, R. J. & Cookson, B. T. (2005). Multilocus DNA sequence comparisons rapidly identify pathogenic molds. Journal of Clinical Microbiology, 43, 3324-3333.

    Article  PubMed  CAS  Google Scholar 

  • Reinartz, J., Bruyns, E., Lin, J. Z., Burcham, T., Brenner, S., Bowen, B., et al. (2002). Massively parallel signature sequencing (MPSS) as a tool for in-depth quantitative gene expression profiling in all organisms. Briefings in Functional Genomics and Proteomics, 1, 95-104.

    Article  PubMed  CAS  Google Scholar 

  • Rementeria, A., Vivanco, A. B., Cadaval, A., Ruesga, M. T., Brena, S., Pontón, J., Quindós, G. & Garaizar, J. (2004). Typing fungal isolates: molecular methods and computerized analysis. Methods in Molecular Biology, 268, 117-125.

    PubMed  CAS  Google Scholar 

  • Remington, K. A., Heidelberg, K., & Venter, J. C. (2005). Taking metagenomic studies in context. Trends in Microbiology, 13, 404.

    Article  PubMed  CAS  Google Scholar 

  • Robène-Soustrade, I., Laurent, P., Gagnevin, L., Jouen, E., & Pruvost, O. (2006). Specific detection of Xanthomonas axonopodis pv. dieffenbachiae in anthurium (Anthurium andreanum) tissues by nested PCR. Applied Environmental Microbiology, 72, 1072-1078.

    Article  CAS  Google Scholar 

  • Salathia, N., Lee, H. N., Sangster, T. A., Morneau, K., Landry, C. R., Schellenberg, K., et al. (2007). Indel arrays: an affordable alternative for genotyping. Plant Journal, 51, 727-737.

    Article  PubMed  CAS  Google Scholar 

  • Saracli, M. A., Yildiran, S. T., Sener, K., Gonlum, A., Doganci, L., Keller, S. M., & Wickes, B. L. (2006). Genotyping of Turkish environmental Cryptococcus neoformans var. neoformans isolates by pulsed field gel electrophoresis and mating type. Mycoses, 49, 124-129.

    Article  PubMed  CAS  Google Scholar 

  • Schaad, N. W., Berthier-Schaad, Y., Sechler, A., & Knorr, D. (1999). Detection of Clavibacter michiganensis subsp. sepedonicus in potato tubers by BIO-PCR and an automated real-time fluorescence detection system. Plant Disease, 83, 1095-1100.

    Article  CAS  Google Scholar 

  • Schaad, N. W., Frederick, R. D., Shaw, J., Schneider, W. L., Hickson, R., Petrillo, M. D., & Luster, D. G. (2003). Advances in molecular-based diagnostics in meeting crop biosecurity and phytosanitary issues. Annual Review of Phytopathology, 41, 305-324.

    Article  PubMed  CAS  Google Scholar 

  • Schaad, N. W., & Frederick, R. D. (2002). Real-time PCR and its application for rapid plant disease diagnostics. Canadian Journal of Plant Pathology, 24, 250-258.

    CAS  Google Scholar 

  • Scott, D. L., Clark, C. W., Fyffe, A. E., Walker, M. D., & Deah, K. L. (1998). The differentiation of Phytophthoraspecies that are pathogenic on potatoes by an asymmetric PCR combined with single-strand conformation polymorphism analysis. Letters in Applied Microbiology, 27, 39-44.

    Article  PubMed  CAS  Google Scholar 

  • Shendure, J., Mitra, R. D., Varma, C., & Church, G. M. (2004). Advanced sequencing technologies: methods and goals. Nature Reviews Genetics, 5, 335-344.

    Article  PubMed  CAS  Google Scholar 

  • Sipos, R., Székely, A. J., Palatinszky, M., Révész, S., Márialigeti, K., & Nikolausz, M. (2007). Effect of primer mismatch, annealing temperature and PCR cycle number on 16S rRNA gene-targetting bacterial community analysis. FEMS Microbiology Ecology, 60, 341-350.

    Article  PubMed  CAS  Google Scholar 

  • Siripong, S., Kelly, J. J., Stahl, D. A., & Rittmann, B. E. (2006). Impact of prehybridization PCR amplification on microarray detection of nitrifying bacteria in wastewater treatment plant samples. Environmental Microbiology, 8, 1564-1574.

    Article  PubMed  CAS  Google Scholar 

  • Soll, D. R. (2000). The ins and outs of DNA fingerprinting the infectious fungi. Clinical Microbiology Review, 13, 332-370.

    Article  CAS  Google Scholar 

  • Song, X., Sun, J., Støre, G., Eribe, E. R., Hansen, B. F., & Olsen, I. (2006). Genotypic relatedness of yeasts in thrush and denture stomatitis. Oral Microbiol Immunology, 21, 301-308.

    Article  CAS  Google Scholar 

  • Sotto, A., Richard, J. L., Jourdan, N., Combescure, C., Bouziges, N., & Lavigne, J. P. (2007). Miniaturized oligonucleotide arrays: a new tool for discriminating colonization from infection due to Staphylococcus aureus in diabetic foot ulcers. Diabetes Care, 30, 2051-2056.

    Article  PubMed  CAS  Google Scholar 

  • Syvänen, A.C. (2005). Toward genome-wide SNP genotyping. Nature Genetics, 37 (Suppl.), S5-10.

    Article  PubMed  CAS  Google Scholar 

  • Tabone, T., Sallman, G., Chiotis, M., Law, M., & Cotton, R. (2006). Chemical cleavage of mismatch (CCM) to locate base mismatches in heteroduplex DNA. Nature Protocols, 1,2297-2304.

    Article  PubMed  CAS  Google Scholar 

  • Thelwell, N., Millington, S., Solinas, A., Booth, J., & Brown, T. (2000). Mode of action and application of Scorpion primers to mutation detection. Nucleic Acids Research, 28, 3752-3761.

    Article  PubMed  CAS  Google Scholar 

  • Toriello, N. M., Liu, C. N. & Mathies, R. A. (2007). Multichannel reverse transcription-polymerase chain reaction microdevice for rapid gene expression and biomarker analysis. Analytical Chemistry, 78, 7997-8003.

    Article  CAS  Google Scholar 

  • Tyagi, S., & Kramer, F. R. (1996). Molecular beacons: probes that fluoresce upon hybridization. Nature Biotechnology, 14, 303-308.

    Article  PubMed  CAS  Google Scholar 

  • Valero, E., Cambon, B., Schuller, D., Casal, M., & Dequin, S. (2007). Biodiversity of Saccharomycesyeast strains from grape berries of wine-producing areas using starter commercial yeasts. FEMS Yeast Research, 7, 317-329.

    Article  PubMed  CAS  Google Scholar 

  • Van Eijk, M. J., Broekhof, J. L., Van der Poel, H. J., Hogers, R. C., Schneiders, H., Kamerbeek, J., et al. (2004). SNPWave: a flexible multiplexed SNP genotyping technology. Nucleic Acids Research, 32, E47.

    Google Scholar 

  • Van Elsas, J. D., Duarte, G.F., Keijzer-Wolters, A., & Smit, E. (2000). Analysis of the dynamics of fungal communities in soil via fungal-specific PCR of soil DNA followed by denaturing gradient gel electrophoresis. Journal of Microbiological Methods, 43, 133-151.

    Article  PubMed  Google Scholar 

  • Van Het Hoog, M., Rast, T. J., Martchenko, M., Grindle, S., Dignard, D., Hogues, H., et al. (2007). Assembly of the Candida albicans genome into sixteen supercontigs aligned on the eight chromosomes. Genome Biology, 8, R52.

    Article  CAS  Google Scholar 

  • Velasco, E., Infante, M., Durán, M., Pérez-Cabornero, L., Sanz, D. J., Esteban-Cardeñosa, E., & Miner, C. (2007). Heteroduplex analysis by capillary array electrophoresis for rapid mutation detection in large multiexon genes. Nature Protococols, 2, 237-246.

    Article  CAS  Google Scholar 

  • Venter, J. C., Remington, K., Heidelberg, J. F., Halpern, A. L., Rusch, D., Eisen, J. A., et al. (2004). Environmental genome shotgun sequencing of the Sargasso Sea. Science, 304, 66-74.

    Article  PubMed  CAS  Google Scholar 

  • Venter, J. C., Smith, H. O., & Hood, L. (1996). A new strategy for genome sequencing. Nature, 381, 364-366.

    Article  PubMed  CAS  Google Scholar 

  • Viaud, M., Brunet-Simon, A., Brygoo, Y., Pradier, J. M., & Levis, C. (2003). Cyclophilin A and calcineurin functions investigated by gene inactivation, cyclosporin A inhibition and cDNA arrays approaches in the phytopathogenic fungus Botrytis cinerea. Molecular Microbiology, 50, 1451-1465.

    Article  PubMed  CAS  Google Scholar 

  • Vos, P., Hogers, R., Bleeker, M., Reijans, M., Van der Lee, T., Hornes, M., et al. (1995). AFLP: a new technique for DNA fingerprinting. Nucleic Acids Research, 23, 4407-4414.

    Google Scholar 

  • Waalwijk, C., Van der Heide, R., de Vries, I., Van der Lee, T., Schoen, C., Costrel-de Corainville, G., Häuser-Hahn, I., et al. (2004). Quantitative detection of Fusarium species in wheat using TaqMan. European Journal of Plant Pathology, 110, 481-494.

    Google Scholar 

  • Walczak, E., Czaplińska, A., Barszczewski, W., Wilgosz, M., Wojtatowicz, M. & Robak, M. (2007). RAPD with microsatellite as a tool for differentiation of Candidagenus yeasts isolated in brewing. Food Microbiology, 24, 305-312.

    Article  PubMed  CAS  Google Scholar 

  • Ward, E., Foster, S. J., Fraaije, B. A. & McCartney, H. A. (2004). Plant pathogen diagnostics: Immunological and nucleic-acid approaches. Annals of Applied Biology, 145, 1-16.

    Google Scholar 

  • Ware, S. B., Verstappen, E. C., Breeden, J., Cavaletto, J. R., Goodwin, S. B., Waalwijk, C., Crous, P. W., & Kema, G. H. (2007). Discovery of a functional Mycosphaerella teleomorph in the presumed asexual barley pathogen Septoria passerinii. Fungal Genetics and Biology, 44, 369-397.

    Article  CAS  Google Scholar 

  • Weising, K., Atkinson, R. G., & Gardner, R. C. (1995). Genomic fingerprinting by microsatellite-primed PCR: a critical evaluation. PCR Methods and Applications, 4, 249-255.

    PubMed  CAS  Google Scholar 

  • White, T.J., Bruns, T., Lee, S., & Taylor, J. (1990) Amplification and direct sequencing of fungal ribosomal genes for phylogenetics. In: Innes M. A., Gelfand, D. H., Sininsky, J. J. & White T. J. (Eds.), PCR Protocols: A Guide to Methods and Applications (pp. 315-322). San Diego: Academic Press.

    Google Scholar 

  • Williams, J. G. K., Kubelik, A. R., Livak, K. J., Rafalski, J. A., & Tingey, S. V. (1990). DNA polymorphisms amplified by arbitary primers are useful as genetic markers. Nucleic Acids Research, 18, 6531-6535.

    Article  PubMed  CAS  Google Scholar 

  • Wise, M. G., Healy, M., Reece, K., Smith, R., Walton, D., Dutch, W., et al. (2007). Species identification and strain differentiation of clinical Candida isolates using the DiversiLab system of automated repetitive sequence-based PCR. Journal of Medical Microbiology, 56, 778-787.

    Article  PubMed  CAS  Google Scholar 

  • Wu, J. H., & Liu, W. T. (2007). Quantitative multiplexing analysis of PCR-amplified ribosomal RNA genes by hierarchical oligonucleotide primer extension reaction. Nucleic Acids Research, 35, E82.

    Article  PubMed  CAS  Google Scholar 

  • Wu, L., Liu, X., Schadt, C. W., & Zhou, J. (2006). Microarray-based analysis of subnanogram quantities of microbial community DNAs by using whole-community genome amplification. Applied and Environmental Microbiology, 72, 4931-4941.

    Article  PubMed  CAS  Google Scholar 

  • Yergeau, E., Filion, M., Vujanovic, V., & St-Arnaud, M. (2005). A PCR-denaturing gradient gel electrophoresis approach to assess Fusarium diversity in asparagus. Journal of Microbiological Methods, 60, 143-154.

    Google Scholar 

  • Yeung, S. H., Greenspoon, S. A., McGuckian, A., Crouse, C. A., Emrich, C. A., Ban, J., & Mathies, R. A. (2006a). Rapid and high-throughput forensic short tandem repeat typing using a 96-lane microfabricated capillary array electrophoresis microdevice. Journal of Forensic Science, 51, 740-747.

    Article  CAS  Google Scholar 

  • Yeung, S. W., Lee, T. M., Cai, H., & Hsing, I. M. (2006b). A DNA biochip for on-the-spot multiplexed pathogen identification. Nucleic Acids Research, 34, E118.

    Article  Google Scholar 

  • Yu, K., & Pauls, K. P. (1993). Optimization of DNA extraction PCR procedures for random amplified polymorphic DNA (RAPD) analysis in plants. In: H. G. Griffen & A. M. Griffin (Eds.), PCR Technology Current Innovations (pp. 193-200). Boca Raton, FL: CRC Press.

    Google Scholar 

  • Zhong, S., Steffenson, B. J., Martinez, J. P., & Ciuffetti, L. M. (2002). A molecular genetic map and electrophoretic karyotype of the plant pathogenic fungus Cochliobolus sativus. Molecular Plant Microbe Interactions, 15, 481-492.

    Article  PubMed  CAS  Google Scholar 

  • Zhu, L. X., Zhang, Z. W., Liang, D., Jiang, D., Wang, C., Du, N., et al. (2007a). Multiplex asymmetric PCR-based oligonucleotide microarray for detection of drug resistance genes containing single mutations in Enterobacteriaceae. Antimicrobial Agents and Chemotherapy, 51, 3707-3713.

    Article  CAS  Google Scholar 

  • Zhu, L. X., Wang, D., Zhang, G. B., Jiang, D., Zhang, Z. W., Zhang, Q., et al. (2007b). Development of a base stacking hybridization-based microarray method for rapid identification of clinical isolates. Diagnostic Microbiology and Infectious Disease, 59, 149-156.

    Article  CAS  Google Scholar 

  • Zinger, L., Gury, J., Giraud, F., Krivobok, S., Gielly, L., Taberlet, P., & Geremia, R. A. (2007). Improvements of polymerase chain reaction and capillary electrophoresis single-strand conformation polymorphism methods in microbial ecology: toward a high-throughput method for microbial diversity studies in soil. Microbial Ecology, 54, 203-216.

    Article  PubMed  CAS  Google Scholar 

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Authors and Affiliations

  1. National Engineering Research Centre for Beijing Biochip Technology, Beijing 102206, China

    Keith R. Mitchelson

  2. The Medical Systems Biology Research Center Tsinghua University School of Medicine, Beijing 100084, China

    Keith R. Mitchelson

  3. Dipartimento di Biotecnologie agrarie Sezione di Patologia vegetale, Università di Firenze, Italy

    Salvatore Moricca

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  1. Consiglio Nazionale delle Ricerche, Dipartimento Agroalimentare Istituto per la Protezione delle Piante, Via G. Amendola 122/D, 70126 Bari, Italy

    A. Ciancio

  2. Dept. Botany, University of Delhi, New Delhi-110007, India

    K.G. Mukerji

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Mitchelson, K.R., Moricca, S. (2008). DNA Fingerprinting Methods for Microbial Pathogens: Application to Diagnostics, Taxonomy and Plant Disease Management. In: Ciancio, A., Mukerji, K. (eds) Integrated Management of Diseases Caused by Fungi, Phytoplasma and Bacteria. Integrated Management of Plant Pests and Diseases, vol 3. Springer, Dordrecht. https://doi.org/10.1007/978-1-4020-8571-0_16

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