Multiplex real-time polymerase chain reaction (PCR) for detection of Phytophthora ramorum, the causal agent of sudden oak death

References

• Bilodeau , G. J. , Lévesque , C. A. , de Cock , A. W. A. M. , Duchaine , C. , Briere , S. , Uribe , P. , Martin , F. N. and Hamelin , R. C. 2007a . Molecular detection of Phytophthora ramorum by real-time polymerase chain reaction using TaqMan, SYBR Green, and molecular beacons . Phytopathology , 97 : 632 – 642 .
   PubMed Web of Science ®Google Scholar
• Bilodeau , G. J. , Lévesque , C. A. , de Cock , A. W. A. M. , Briére , S. C. and Hamelin , R. C. 2007b . Differentiation of European and North American genotypes of Phytophthora ramorum by real-time polymerase chain reaction primer extension . Can. J. Plant Pathol. , 29 ( 4 ) : 408 – 420 .
   Web of Science ®Google Scholar
• Böhm , J. , Hahn , A. , Schubert , R. , Bahnweg , G. , Adler , N. , Nechwatal , J. , Oehlmann , R. and Osswald , 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 . J. Phytopathol. , 147 : 409 – 416 .
   Web of Science ®Google Scholar
• Braasch , D. A. and Corey , D. R. 2001 . Locked nucleic acid (LNA): fine-tuning the recognition of DNA and RNA . Chem. Biol. , 8 : 1 – 7 .
   PubMed Web of Science ®Google Scholar
• Brasier , C. M. , Cooke , D. E. L. , Duncan , J. M. and Hansen , E. M. 2003 . Multiple new phenotypic taxa from trees and riparian ecosystems in Phytophthora gonapodyides-P. megasperma ITS Clade 6, which tend to be high-temperature tolerant and either inbreeding or sterile . Mycol. Res. , 107 : 277 – 290 .
   PubMedGoogle Scholar
• Davidson , J. M. , Werres , S. , Garbelotto , M. , Hansen , E. M. and Rizzo , D. M. 2003 . “ Sudden oak death and associated diseases caused by Phytophthora ramorum ” . In Plant Health Prog. [online]. [accessed 23 September 2008].
   Google Scholar
• de Cock , A. W. A. M. , Neuvel , A. , Bahnweg , G. , de Cock , J. C. J. M. and Prell , H. H. 1992 . A comparison of morphology, pathogenicity and restriction fragment patterns of mitochondrial-DNA among isolates of Phytophthora porri Foister . Eur. J. Plant Pathol. , 98 : 277 – 289 .
   Google Scholar
• Dick , M. W. 1989 . Phytophthora undulata comb. nov . Mycotaxon , 25 : 449 – 453 .
   Google Scholar
• Gaastra , W. 1984 . “ Enzyme-linked immuno-sorbent assay ” . In Methods in molecular biology , Edited by: Walker , J. 349 – 355 . Clifton, N.J : Humana Press . Part 2
   Google Scholar
• Hayden , K. , Ivors , K. , Wilkinson , C. and Garbelotto , M. 2006 . TaqMan chemistry for Phytophthora ramorum detection and quantification, with a comparison of diagnostic methods . Phytopathology , 96 : 846 – 854 .
   PubMed Web of Science ®Google Scholar
• Hughes , K. J. D. , Giltrap , P. M. , Barton , V. C. , Hobden , E. , Tomlinson , J. A. and Barber , P. 2006a . On-site real-time PCR detection of Phytophthora ramorum causing dieback of Parrotia persica in the UK . Plant Pathol. , 55 : 813
   Web of Science ®Google Scholar
• Hughes , K. J. D. , Tomlinson , J. A. , Griffin , R. L. , Boonham , N. , Inman , A. J. and Lane , C. R. 2006b . Development of a one-step real-time polymerase chain reaction assay for diagnosis of Phytophthora ramorum . Phytopathology , 96 : 975 – 981 .
   PubMed Web of Science ®Google Scholar
• Kroon , L. P. N. M. , Bakker , F. T. , van den Bosch , G. B. M. , Bonants , P. J. M. and Flier , W. G. 2004 . Phylogenetic analysis of Phytophthora species based on mitochondrial and nuclear DNA sequences . Fungal Genet. Biol. , 41 : 766 – 782 .
   PubMed Web of Science ®Google Scholar
• Lévesque , C. A. and de Cock , A. W. A. M. 2004 . Molecular phylogeny and taxonomy of the genus Pythium . Mycol. Res , 108 : 1363 – 1383 .
   PubMed Web of Science ®Google Scholar
• Ma , Z. and Michailides , T. J. 2007 . Approaches for eliminating PCR inhibitors and designing PCR primers for the detection of phytopathogenic fungi . Crop Prot. , 26 : 145 – 161 .
   Web of Science ®Google Scholar
• Martin , F. N. , Coffey , M. , Berger , P. , Hamelin , R. , Tooley , P. , Garbelotto , M. , Hughes , K. and Kubisiak , T. 2006 . Validation of molecular markers for Phytophthora ramorum detection and identification using a standardized library of isolates . Phytopathology , 96 : S74 [Abstr.]
   Google Scholar
• Martin , F. N. , Coffey , M. D. , Zeller , K. , Hamelin , R. C. , Tooley , P. , Garbelotto , M. , Hughes , K. J. D. , Kubisiak , T. , Bilodeau , G. J. , Levy , L. , Blomquist , C. and Berger , P. 2009 . Evaluation of molecular markers for Phytophthora ramorum detection and identification: testing for specificity using a standardized library of isolates . Phytopathology , 99 : 390 – 403 .
   PubMed Web of Science ®Google Scholar
• McPherson , B. A. , Mori , S. R. , Wood , D. L. , Storer , A. J. , Svihra , P. , Kelly , N. M. and Standiford , R. B. 2005 . Sudden oak death in California: Disease progression in oaks and tanoaks . For. Ecol. Manage. , 213 : 71 – 89 .
   Web of Science ®Google Scholar
• Möller , E. M. , Bahnweg , G. , Sandermann , H. and Geiger , H. H. 1992 . A simple and efficient protocol for isolation of high-molecular-weight DNA from filamentous fungi, fruit bodies, and infected-plant tissues . Nucleic Acids Res. , 20 : 6115 – 6116 .
   PubMed Web of Science ®Google Scholar
• Osterbauer , N. and Trippe , A. 2005 . Comparing diagnostic protocols for Phytophthora ramorum in rhododendron leaves . Plant Health Prog. , [online].[accessed 23 September 2008].
   Google Scholar
• Rioux , D. , Callan , B. and McKenney , D. 2006 . Phytophthora ramorum: causal agent of sudden oak death, ramorum blight, ramorum bleeding canker, ramorum (shoot) dieback , Ottawa, Ont : Plant Health Risk Assessment Unit, Science Division, Canadian Food Inspection Agency . PRA 00-39
   Google Scholar
• Schaad , N. W. and Frederick , R. D. 2002 . Real-time PCR and its application for rapid plant disease diagnostics . Can. J. Plant Pathol. , 24 ( 3 ) : 250 – 258 .
   Web of Science ®Google Scholar
• Schena , L. , Hughes , K. J. D. and Cooke , D. E. L. 2006 . Detection and quantification of Phytophthora ramorum, P. kernoviae, P. citricola and P. quercina in symptomatic leaves by multiplex real-time PCR . Mol. Plant Pathol. , 7 : 365 – 379 .
   PubMed Web of Science ®Google Scholar
• Tomlinson , J. A. , Boonham , N. , Hughes , K. J. D. , Griffin , R. L. and Barker , I. 2005 . On-site DNA extraction and real-time PCR for detection of Phytophthora ramorum in the field . Appl. Environ. Microbiol. , 71 : 6702 – 6710 .
   PubMed Web of Science ®Google Scholar
• Tomlinson , J. A. , Barker , I. and Boonham , N. 2007 . Faster, simpler, more-specific methods for improved molecular detection of Phytophthora ramorum in the field . Appl. Environ. Microbiol. , 73 : 4040 – 4047 .
   PubMed Web of Science ®Google Scholar
• Tooley , P. W. , Martin , F. N. , Carras , M. M. and Frederick , R. D. 2006 . Real-time fluorescent polymerase chain reaction detection of Phytophthora ramorum and Phytophthora pseudosyringae using mitochondrial gene regions . Phytopathology , 96 : 336 – 345 .
   PubMed Web of Science ®Google Scholar
• Tyler , B. M. , Tripathy , S. , Zhang , X. , Dehal , P. , Jiang , R. H. Y. , Aerts , A. , Arredondo , F. D. , Baxter , L. , Bensasson , D. , Beynon , J. L. , Chapman , J. , Damasceno , C. M. B. , Dorrance , A. E. , Dou , D. , Dickerman , A. W. , Dubchak , I. L. , Garbelotto , M. , Gijzen , M. , Gordon , S. G. , Govers , F. , Grunwald , N. J. , Huang , W. , Ivors , K. L. , Jones , R. W. , Kamoun , S. , Krampis , K. , Lamour , K. H. , Lee , M.-K. , McDonald , W. H. , Medina , M. , Meijer , H. J. G. , Nordberg , E. K. , Maclean , D. J. , Ospina-Giraldo , M. D. , Morris , P. F. , Phuntumart , V. , Putnam , N. H. , Rash , S. , Rose , J. K. C. , Sakihama , Y. , Salamov , A. A. , Savidor , A. , Scheuring , C. F. , Smith , B. M. , Sobral , B. W. S. , Terry , A. , Torto-Alalibo , T. A. , Win , J. , Xu , Z. , Zhang , H. , Grigoriev , I. V. , Rokhsar , D. S. and Boore , J. L. 2006 . Phytophthora genome sequences uncover evolutionary origins and mechanisms of pathogenesis . Science (Washington, D.C.) , 313 : 1261 – 1266 .
   PubMed Web of Science ®Google Scholar
• USDA-APHIS. 2008 . APHIS list of regulated hosts and plants associated with Phytophthora ramorum 8 [accessed 23 September 2008]
   Google Scholar
• USDA-APHIS-PPQ. 2007 . Update on PPQ diagnostics for SOD: diagnostics procedures approved by APHIS and diagnostic analyses performed by APHISPPQ for Phytophthora ramorum Revised 6 May 2007. [accessed 2 February 2009].
   Google Scholar
• Werres , S. , Marwitz , R. , Man in‘tVeld , W. A. , de Cock , A. W. A. M. , Bonants , P. J. M. , de Weerdt , M. , Themann , K. , Ilieva , E. and Baayen , R. P. 2001 . Phytophthora ramorum sp. nov., a new pathogen on Rhododendron and Viburnum . Mycol. Res. , 105 : 1155 – 1165 .
   Web of Science ®Google Scholar
• White , T. J. , Bruns , T. , Lee , S. and Taylor , J. 1990 . “ Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics ” . In PCR protocols: a guide to methods and applications , Edited by: Innis , M. A. , Gelfand , D. H. , Sninsky , J. J. and White , T. J. 315 – 322 . San Diego, Calif : Academic Press Inc .
   Google Scholar
• Winton , L. M. and Hansen , E. M. 2001 . Molecular diagnosis of Phytophthora lateralis in trees, water, and foliage baits using multiplex polymerase chain reaction . For. Pathol. , 31 : 275 – 283 .
   Web of Science ®Google Scholar