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

  • Keith R. Mitchelson
  • Salvatore Moricca
Part of the Integrated Management of Plant Pests and Diseases book series (IMPD, volume 3)


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.


Amplify Fragment Length Polymorphism Ribosomal Gene Massively Parallel Signature Sequencing Nucleic Acid Research Strand Displacement Amplification 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.


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  1. 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.PubMedGoogle Scholar
  2. 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.CrossRefGoogle Scholar
  3. 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
  4. 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
  5. 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.PubMedCrossRefGoogle Scholar
  6. Beadle, J., Wright, M., McNeely, L. & Bennett, J. W. (2003). Electrophoretic karyotype analysis in fungi. Advanced Applied Microbiology, 53, 243-270.CrossRefGoogle Scholar
  7. 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.PubMedCrossRefGoogle Scholar
  8. Bensch, S., & Akesson, M. (2005). Ten years of AFLP in ecology and evolution: why so few animals? Molecular Ecology, 14, 2899-2914.PubMedCrossRefGoogle Scholar
  9. 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.PubMedGoogle Scholar
  10. 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
  11. 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.CrossRefGoogle Scholar
  12. 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.CrossRefGoogle Scholar
  13. 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.PubMedCrossRefGoogle Scholar
  14. 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.PubMedGoogle Scholar
  15. 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.PubMedCrossRefGoogle Scholar
  16. Carroll G. (1995). Forest endophytes: pattern and process. Canadian Journal of Botany, 73 (Suppl. 1), 1316-1324.CrossRefGoogle Scholar
  17. 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.PubMedCrossRefGoogle Scholar
  18. 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.CrossRefGoogle Scholar
  19. 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.CrossRefGoogle Scholar
  20. Chen, T. (2006). DNA microarrays - an armory for combating infectious diseases in the new century. Current Drug Targets - Infectious Disorders, 6, 263-279.CrossRefGoogle Scholar
  21. 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.PubMedCrossRefGoogle Scholar
  22. 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.PubMedCrossRefGoogle Scholar
  23. 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.PubMedCrossRefGoogle Scholar
  24. 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.CrossRefGoogle Scholar
  25. 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.CrossRefGoogle Scholar
  26. 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.CrossRefGoogle Scholar
  27. Edwards, S., O’Callaghan, J., & Dobson, A. D. W. (2002). PCR-based detection and quantification of mycotoxigenic fungi. Mycological Research, 106, 1005-1025.CrossRefGoogle Scholar
  28. 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.PubMedCrossRefGoogle Scholar
  29. 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.PubMedCrossRefGoogle Scholar
  30. 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.PubMedCrossRefGoogle Scholar
  31. 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.PubMedCrossRefGoogle Scholar
  32. 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.PubMedCrossRefGoogle Scholar
  33. 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.PubMedCrossRefGoogle Scholar
  34. 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.CrossRefGoogle Scholar
  35. 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
  36. 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.CrossRefGoogle Scholar
  37. 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
  38. 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.CrossRefGoogle Scholar
  39. 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.PubMedCrossRefGoogle Scholar
  40. 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.PubMedCrossRefGoogle Scholar
  41. 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
  42. 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.CrossRefGoogle Scholar
  43. 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.PubMedCrossRefGoogle Scholar
  44. 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.CrossRefGoogle Scholar
  45. 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.CrossRefGoogle Scholar
  46. 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.PubMedCrossRefGoogle Scholar
  47. 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.PubMedCrossRefGoogle Scholar
  48. 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.PubMedCrossRefGoogle Scholar
  49. 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.PubMedCrossRefGoogle Scholar
  50. 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.PubMedCrossRefGoogle Scholar
  51. 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.PubMedCrossRefGoogle Scholar
  52. 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.PubMedCrossRefGoogle Scholar
  53. 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.CrossRefGoogle Scholar
  54. 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.CrossRefGoogle Scholar
  55. 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.PubMedCrossRefGoogle Scholar
  56. 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.PubMedCrossRefGoogle Scholar
  57. 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.PubMedCrossRefGoogle Scholar
  58. 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.CrossRefGoogle Scholar
  59. 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.PubMedCrossRefGoogle Scholar
  60. Käller, M., Lundeberg, J., & Ahmadian, A. (2007). Arrayed identification of DNA signatures. Expert Review of Molecular Diagnostics, 7, 65-76.PubMedCrossRefGoogle Scholar
  61. 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.PubMedCrossRefGoogle Scholar
  62. 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.CrossRefGoogle Scholar
  63. 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.PubMedCrossRefGoogle Scholar
  64. 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.PubMedGoogle Scholar
  65. 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.CrossRefGoogle Scholar
  66. 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.PubMedCrossRefGoogle Scholar
  67. 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
  68. 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
  69. 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.PubMedCrossRefGoogle Scholar
  70. 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.PubMedCrossRefGoogle Scholar
  71. Lasker, B. A. (2006). Nucleotide sequence-based analysis for determining the molecular epidemiology of Penicillium marneffei. Journal of Clinical Microbiology, 44, 3145-3153.PubMedCrossRefGoogle Scholar
  72. Lay, M. J., & Wittwer, C.T. (1997). Real-time fluorescence genotyping of factor V Leiden during rapid-cycle PCR. Clinical Chemistry, 43, 2262-2267.PubMedGoogle Scholar
  73. 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
  74. 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.PubMedCrossRefGoogle Scholar
  75. 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.CrossRefGoogle Scholar
  76. 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.PubMedCrossRefGoogle Scholar
  77. 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.PubMedCrossRefGoogle Scholar
  78. Lephart, P. R. & Magee, P. T. (2006). Effect of the major repeat sequence on mitotic recombination in Candida albicans. Genetics, 174, 1737-1744.PubMedCrossRefGoogle Scholar
  79. 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.PubMedCrossRefGoogle Scholar
  80. 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.PubMedCrossRefGoogle Scholar
  81. 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.PubMedCrossRefGoogle Scholar
  82. 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.PubMedCrossRefGoogle Scholar
  83. Liu, C. N., Toriello, N. M., & Mathies, R. A. (2006). Multichannel PCR-CE microdevice for genetic analysis. Analytical Chemistry, 78, 5474-5479.PubMedCrossRefGoogle Scholar
  84. 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.CrossRefGoogle Scholar
  85. 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.CrossRefGoogle Scholar
  86. 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.PubMedCrossRefGoogle Scholar
  87. 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.PubMedGoogle Scholar
  88. 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.PubMedCrossRefGoogle Scholar
  89. 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.PubMedCrossRefGoogle Scholar
  90. 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.PubMedGoogle Scholar
  91. 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
  92. 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.PubMedCrossRefGoogle Scholar
  93. 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.PubMedCrossRefGoogle Scholar
  94. McCartney, H. A., Foster, S. J., Fraaije, B. A., & Ward, E. (2003). Molecular diagnostics for fungal plant pathogens. Pest Management Science, 59, 129-142.PubMedCrossRefGoogle Scholar
  95. 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.PubMedGoogle Scholar
  96. 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.PubMedCrossRefGoogle Scholar
  97. 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.CrossRefGoogle Scholar
  98. 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.PubMedGoogle Scholar
  99. 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.PubMedCrossRefGoogle Scholar
  100. Mitchelson, K. R. (2003). The use of capillary electrophoresis for DNA polymorphism analysis. Molecular Biotechnology, 24, 41-68.PubMedCrossRefGoogle Scholar
  101. 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.PubMedCrossRefGoogle Scholar
  102. 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.CrossRefGoogle Scholar
  103. 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.PubMedCrossRefGoogle Scholar
  104. 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
  105. 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.CrossRefGoogle Scholar
  106. 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
  107. 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.CrossRefGoogle Scholar
  108. 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.CrossRefGoogle Scholar
  109. 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.PubMedGoogle Scholar
  110. Mumford, R. A., Walsh, K., & Boonham, N. (2000). A comparison of molecular methods for the routine detection of viroids. EPPO Bulletin, 30, 431-435.CrossRefGoogle Scholar
  111. 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.PubMedCrossRefGoogle Scholar
  112. 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.CrossRefGoogle Scholar
  113. 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.PubMedCrossRefGoogle Scholar
  114. 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.PubMedCrossRefGoogle Scholar
  115. 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.PubMedCrossRefGoogle Scholar
  116. 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.PubMedGoogle Scholar
  117. Parro, V., Moreno-Paz, M., & Gonzalez-Toril, E. (2007). Analysis of environmental transcriptomes by DNA microarrays. Environmental Microbiology, 9, 453-464.Google Scholar
  118. 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.PubMedCrossRefGoogle Scholar
  119. 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.CrossRefGoogle Scholar
  120. 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.CrossRefGoogle Scholar
  121. 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.PubMedCrossRefGoogle Scholar
  122. 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.PubMedCrossRefGoogle Scholar
  123. 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.PubMedCrossRefGoogle Scholar
  124. 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.PubMedGoogle Scholar
  125. 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.PubMedCrossRefGoogle Scholar
  126. 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.PubMedCrossRefGoogle Scholar
  127. 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.PubMedCrossRefGoogle Scholar
  128. 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.PubMedGoogle Scholar
  129. Remington, K. A., Heidelberg, K., & Venter, J. C. (2005). Taking metagenomic studies in context. Trends in Microbiology, 13, 404.PubMedCrossRefGoogle Scholar
  130. 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.CrossRefGoogle Scholar
  131. 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.PubMedCrossRefGoogle Scholar
  132. 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.PubMedCrossRefGoogle Scholar
  133. 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.CrossRefGoogle Scholar
  134. 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.PubMedCrossRefGoogle Scholar
  135. 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.Google Scholar
  136. 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.PubMedCrossRefGoogle Scholar
  137. Shendure, J., Mitra, R. D., Varma, C., & Church, G. M. (2004). Advanced sequencing technologies: methods and goals. Nature Reviews Genetics, 5, 335-344.PubMedCrossRefGoogle Scholar
  138. 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.PubMedCrossRefGoogle Scholar
  139. 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.PubMedCrossRefGoogle Scholar
  140. Soll, D. R. (2000). The ins and outs of DNA fingerprinting the infectious fungi. Clinical Microbiology Review, 13, 332-370.CrossRefGoogle Scholar
  141. 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.CrossRefGoogle Scholar
  142. 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.PubMedCrossRefGoogle Scholar
  143. Syvänen, A.C. (2005). Toward genome-wide SNP genotyping. Nature Genetics, 37 (Suppl.), S5-10.PubMedCrossRefGoogle Scholar
  144. 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.PubMedCrossRefGoogle Scholar
  145. 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.PubMedCrossRefGoogle Scholar
  146. 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.CrossRefGoogle Scholar
  147. Tyagi, S., & Kramer, F. R. (1996). Molecular beacons: probes that fluoresce upon hybridization. Nature Biotechnology, 14, 303-308.PubMedCrossRefGoogle Scholar
  148. 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.PubMedCrossRefGoogle Scholar
  149. 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
  150. 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.PubMedCrossRefGoogle Scholar
  151. 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.CrossRefGoogle Scholar
  152. 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.CrossRefGoogle Scholar
  153. 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.PubMedCrossRefGoogle Scholar
  154. Venter, J. C., Smith, H. O., & Hood, L. (1996). A new strategy for genome sequencing. Nature, 381, 364-366.PubMedCrossRefGoogle Scholar
  155. 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.PubMedCrossRefGoogle Scholar
  156. 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
  157. 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
  158. 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.PubMedCrossRefGoogle Scholar
  159. 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
  160. 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.CrossRefGoogle Scholar
  161. 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.PubMedGoogle Scholar
  162. 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
  163. 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.PubMedCrossRefGoogle Scholar
  164. 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.PubMedCrossRefGoogle Scholar
  165. 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.PubMedCrossRefGoogle Scholar
  166. 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.PubMedCrossRefGoogle Scholar
  167. 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
  168. 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.CrossRefGoogle Scholar
  169. 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.CrossRefGoogle Scholar
  170. 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
  171. 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.PubMedCrossRefGoogle Scholar
  172. 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.CrossRefGoogle Scholar
  173. 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.CrossRefGoogle Scholar
  174. 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.PubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media B.V. 2008

Authors and Affiliations

  • Keith R. Mitchelson
    • 1
    • 2
  • Salvatore Moricca
    • 3
  1. 1.National Engineering Research Centre for Beijing Biochip TechnologyChina
  2. 2.The Medical Systems Biology Research Center Tsinghua University School of MedicineChina
  3. 3.Dipartimento di Biotecnologie agrarie Sezione di Patologia vegetaleUniversità di FirenzeItaly

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