A TaqMan real-time PCR assay targeting the cytochrome o ubiquinol oxidase subunit II gene for detection of several pathovars of Pseudomonas syringae

References

• Almeida , N.F. , Yan , S. , Lindeberg , M. , Studholme , D.J. , Schneider , D.J. , Condon , B. , Liu , H. and …Vinatzer , B.A. 2009 . A draft genome sequence of Pseudomonas syringae pv. tomato T1 reveals a type III effector repertoire significantly divergent from that of P. syringae pv. tomato DC3000 . Mol. Plant-Microbe Interact. , 22 : 52 – 62 .
   PubMed Web of Science ®Google Scholar
• Arnold , D.L. , Athey-Pollard , A. , Gibbon , M.J. , Taylor , J.D. and Vivian , A. 1996 . Specific oligonucleotide primers for the identification of Pseudomonas syringae pv. pisi yield one of two possible DNA fragments by PCR amplification: evidence for phylogenetic divergence . Physiol. Mol. Plant Pathol. , 49 : 233 – 245 .
   Google Scholar
• Bakkeren , G. , Kronstad , J.W. and Lévesque , C.A. 2000 . Comparison of AFLP fingerprints and ITS sequences as phylogenetic markers in Ustilaginomycetes . Mycologia , 92 : 510 – 521 .
   Web of Science ®Google Scholar
• Behrendt , U. , Ulrich , A. and Schumann , P. 2003 . Fluorescent pseudomonads associated with the phyllosphere of grasses; Pseudomonas trivialis sp. nov., Pseudomonas poae sp. nov. and Pseudomonas congelans sp. nov . Int. J. Syst. Evol. Microbiol. , 53 : 1461 – 1469 .
   PubMed Web of Science ®Google Scholar
• Buell , C.R. , Joardar , V. , Lindeberg , M. , Selengut , J. , Paulsen , I.T. , Gwinn , M.L. , Dodson , R.J. and …Collmer , A. 2003 . The complete genome sequence of the Arabidopsis and tomato pathogen Pseudomonas syringae pv. tomato DC3000 . Proc. Natl. Acad. Sci. USA , 100 : 10181 – 10186 .
   PubMed Web of Science ®Google Scholar
• Cherpuri , V. , Lemieux , L. , Au , D.C.T. and Gennis , R.B.B. 1990 . The sequence of the cyo operon indicates substantial structural similarities between the cytochrome o ubiquinol oxidase of Escherichia coli and the aa3-type family of cytochrome c oxidases . J. Biol. Chem. , 265 : 11185 – 11192 .
   Google Scholar
• Cho , M.S. , Jeon , Y.H. , Kang , M.J. , Ahn , H.I. , Baek , H.J. , Na , Y.W. , Choi , Y.M. , Kim , T.S. and Park , D.S. 2010 . Sensitive and specific detection of phaseolotoxigenic and nontoxigenic strains of Pseudomonas syringae pv. phaseolicola by TaqMan real-time PCR using site-specific recombinase gene sequences . Microbiol. Res. , 165 : 565 – 572 .
   Google Scholar
• Cuppels , D.A. , Louws , F.J. and Ainsworth , T. 2006 . Development and evaluation of PCR-based diagnostic assays for the bacterial speck and bacterial spot pathogens of tomato . Plant Dis. , 90 : 451 – 458 .
   Web of Science ®Google Scholar
• Cuppels , D.A. and Elmhirst , J. 1999 . Disease development and changes in the natural Pseudomonas syringae pv. tomato populations on field tomato plants . Plant Dis. , 83 : 759 – 764 .
   PubMed Web of Science ®Google Scholar
• Deng , W.L. , Preston , G. , Collmer , A. , Chang , C.J. and Huang , H.C. 1998 . Characterization of the hrpC and hrpRS operons of Pseudomonas syringae pathovars syringae, tomato, and glycinea and analysis of the ability of hrpF, hrpG, hrcC, hrpT, and hrpV mutants to elicit the hypersensitive response and disease in plants . J. Bacteriol. , 180 : 4523 – 4531 .
   Google Scholar
• Fanelli , V. , Cariddi , C. and Finetti-Sialer , M. 2007 . Selective detection of Pseudomonas syringae pv. tomato using dot-blot hybridization and real-time PCR . Plant Pathol. , 56 : 683 – 691 .
   Google Scholar
• Feil , H. , Feil , W.S. , Chain , P. , Larimer , F. , Dibartolo , G. , Copeland , A. , Lykidis , A. , Trong , S. and …Lindow , S.E. 2005 . Comparison of the complete genome sequences of Pseudomonas syringae pv. syringae B728a and pv. tomato DC3000 . Proc. Natl. Acad. Sci. USA , 102 : 11064 – 11069 .
   PubMed Web of Science ®Google Scholar
• Fessehaie , A. , De Boer , S.H. and Levesque , C.A. 2003 . An oligonucleotide array for the identification and differentiation of bacteria pathogenic on potato . Phytopathology , 93 : 262 – 269 .
   PubMed Web of Science ®Google Scholar
• Gervasi , F. and Scortichini , M. 2009 . Detection of Pseudomonas avellanae from hazelnut twigs by TaqMan real-time PCR . J. Plant Pathol. (Italy) , 91 : 561 – 566 .
   Google Scholar
• Gottsberger , R.A. 2010 . Development and evaluation of a real-time PCR assay targeting chromosomal DNA of Erwinia amylovora . Lett. Appl. Microbiol , 51 : 285 – 292 .
   Google Scholar
• Green , S. , Laue , B. , Fossdal , C.G. , A'hara , S.W. and Cottrell , J.E. 2009 . Infection of horse chestnut (Aesculus hippocastanum) by Pseudomonas syringae pv. aesculi and its detection by quantitative real-time PCR . Plant Pathol. , 58 : 731 – 744 .
   Web of Science ®Google Scholar
• Hollaway , G.J. , Bretag , T.W. and Price , T.V. 2007 . The epidemiology and management of bacterial blight (Pseudomonas syringae pv. pisi) of field pea (Pisum sativum) in Australia: a review . Aust. J. Agric. Res. , 58 : 1086 – 1099 .
   Google Scholar
• Joardar , V. , Lindeberg , M. , Jackson , R.W. , Selengut , J. , Dodson , R. , Lauren , M. , Brinkac , L.M. and …Buell , C.R. 2005 . Whole-genome sequence analysis of Pseudomonas syringae pv. phaseolicola 1448A reveals divergence among pathovars in genes involved in virulence and transposition . J. Bacteriol. , 187 : 6488 – 6498 .
   PubMed Web of Science ®Google Scholar
• Kawasaki , E.S. , Saiki , R. and Erlich , H. 1993 . Genetic analysis using polymerase chain reaction-amplified DNA and immobilized oligonucleotide probes: reverse dot-blot typing . Methods Enzymol. , 218 : 369 – 381 .
   PubMed Web of Science ®Google Scholar
• Martín-Sanz , A. , Palomo , J. , Pérez De La Vega , M. and Caminero , C. 2011 . Identification of pathovars and races of Pseudomonas syringae, the main causal agent of bacterial disease in pea in North-Central Spain, and the search for disease resistance Eur . J. Plant Pathol. , 129 : 57 – 69 .
   Google Scholar
• Mohr , T.J. , Liu , H , Yan , S. , Morris , C.E. , Castillo , J.A. , Jelenska , J. and Vinatzer , B.A. 2008 . Naturally occurring non-pathogenic isolates of the plant pathogen species Pseudomonas syringae lack a type III secretion system and effector gene orthologues . J. Bacteriol. , 190 : 2858 – 2870 .
   Google Scholar
• Mulet , M. , Lalucat , J. and Garcia-Valdes , E. 2010 . DNA sequence-based analysis of the Pseudomonas species . Environ Microbiol. , 12 : 1513 – 1530 .
   PubMed Web of Science ®Google Scholar
• Nelson , K.E. , Weinel , C. , Paulsen , I.T. , Dodson , R.J. , Hilbert , H. , Martins Dos Santos , V.A. , Fouts , D.E. and …Fraser , C.M. 2002 . Complete genome sequence and comparative analysis of the metabolically versatile Pseudomonas putida KT2440 . Environ. Microbiol. , 4 : 799 – 808 .
   PubMed Web of Science ®Google Scholar
• Palacio-Bielsa , A. , Cubero , J. , Cambra , M.A. , Collados , R. , Berruete , I.M. and Lopez , M. 2011 . Development of an efficient real-time quantitative PCR protocol for detection of Xanthosomonas arboricicola pv. pruni in Prunus species . Appl. Environ. Microbiol. , 77 : 89 – 97 .
   Google Scholar
• Palleroni , N.J. 2005 . “ Genus I. Pseudomonas Migula 1894, 237AL (Nom. cons. Opin. 5, Jud. Comm. 1952, 121) ” . In Bergey's manual of systematic bacteriology , Edited by: Garrity , G.M. , Bell , J.A. and Lilburn , T. 323 – 379 . New York : Springer Press .
   Google Scholar
• Pappu , S.S. , Roy , K.L. and Bell , J.B. 1990 . Drosophila melanogaster tRNASer suppressor genes function with strict codon specificity when introduced into Saccharomyces cerevisiae . Gene , 91 : 255 – 259 .
   Google Scholar
• Paulsen , I.T. , Press , C.M. , Ravel , J. , Kobayashi , D.Y. , Myers , G.S. , Mavrodi , D.V. , Deboy , R.T. and …Loper , J.E. 2005 . Complete genome sequence of the plant commensal Pseudomonas fluorescens Pf-5 . Nat. Biotechnol. , 23 : 873 – 878 .
   PubMed Web of Science ®Google Scholar
• Phillippy , A.M. , Ayanbule , K. , Edwards , N.J. and Salzberg , S.L. 2009 . Insignia: a DNA signature search web server for diagnostic assay development . Nucl. Acids Res. , 37 : W229 – W234 .
   Google Scholar
• Prosen , D. , Hatziloukas , E. , Schaad , N.W. and Panopoulos , N.J. 1993 . Specific detection of Pseudomonas syringae pv. phaseolicola DNA in bean seed by polymerase chain reaction-based amplification of a phaseolotoxin gene region . Phytopathology , 83 : 965 – 970 .
   Web of Science ®Google Scholar
• Psallidas , P.G. 1988 . “ Pseudomonas syringae pv. tomato (Okabe) Young ” . In European handbook of plant diseases , Edited by: Smith , I.M. , Dunez , J. and Lelliot , R.A. Oxford : Blackwell Scientific .
   Google Scholar
• Rees-George , J. , Vanneste , J.L. , Cornish , D.A. , Pushparajah , I.P.S. , Yu , J. , Templeton , M.D. and Everett , K.H. 2010 . Detection of Pseudomonas syringae pv. actinidiae using polymerase chain reaction (PCR) primers based on the 16S-23S rDNA intertranscribed spacer region and comparison with PCR primers based on other gene regions . Plant Pathol. , 59 : 453 – 464 .
   Google Scholar
• Renick , L.J. , Cogal , A.G. and Sundin , G.W. 2008 . Phenotypic and genetic analysis of epiphytic Pseudomonas syringae populations from sweet cherry in Michigan . Plant Dis. , 92 : 372 – 378 .
   Google Scholar
• Schaad , N.W. , Erthier , S.Y. , Sechler , A. and Knorr , D. 1999 . Detection of Clavibacter michiganensis subsp. sepedonicus in potato tubers by BIO-PCR and an automated real-time fluorescence detection system . Plant Dis. , 83 : 1095 – 1100 .
   PubMed Web of Science ®Google Scholar
• Scheck , H.J. and Pscheidt , J.W. 1998 . Effect of copper bactericides on copper-resistant and -sensitive strains of Pseudomonas syringae pv. syringae . Plant Dis. , 82 : 397 – 406 .
   Web of Science ®Google Scholar
• Schena , L. and Ippolito , A. 2003 . Rapid and sensitive detection of Rosellinia necatrix on roots and soils by real time Scorpion-PCR . Plant Pathol. , 85 : 15 – 25 .
   Google Scholar
• Smid , E.J. , Hausen , A.H.J. and Gorris , L.G.M. 1995 . Detection of Erwinia carotovora subsp. atroseptica and Erwinia chrysanthemi in potato tubers using polymerase chain reaction . Plant Pathol. , 44 : 1058 – 1062 .
   Web of Science ®Google Scholar
• Smitley , D.R. and Mccarter , S.M. 1982 . Spread of Pseudomonas syringae pv. tomato and role of epiphytic populations and environmental conditions in disease development . Plant Dis. , 66 : 713 – 717 .
   Google Scholar
• Sorensen , K.N. , Kim , K.H. and Takemoto , J.Y. 1998 . PCR detection of cyclic lipodepsinonapeptide-producing Pseudomonas syringae pv. syringae and similarity of strains . Appl. Environ. Microbiol. , 64 : 226 – 230 .
   PubMed Web of Science ®Google Scholar
• Stover , C.K. , Pham , X.Q. , Erwin , A.L. , Mizoguchi , S.D. , Warrener , P. , Hickey , M.J. , Brinkman , F.S. and …Olson , M.V. 2000 . Complete genome sequence of Pseudomonas aeruginosa PAO1, an opportunistic pathogen . Nature , 406 : 959 – 964 .
   PubMed Web of Science ®Google Scholar
• Tambong , J.T. , De Cock , A.W. , Tinker , N.A. and Levesque , C.A. 2006 . Oligonucleotide array for identification and detection of Pythium species . Appl. Environ. Microbiol. , 72 : 2691 – 2706 .
   PubMed Web of Science ®Google Scholar
• Tambong , J.T. , Mwange , K.N. , Bergeron , M. , Ding , T. , Mandy , F. , Reid , L.M. and Zhu , X. 2008 . Rapid detection and identification of the bacterium Pantoea stewartii in maize by TaqMan real-time PCR assay targeting the cpsD gene . J. Appl. Microbiol. , 104 : 1525 – 1537 .
   PubMed Web of Science ®Google Scholar
• Tamura , K. , Dudley , J. , Nei , M. and Kumar , S. 2007 . MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0 . Mol. Biol. Evol. , 24 : 1596 – 1599 .
   PubMed Web of Science ®Google Scholar
• Webster , D.M. , Atkin , J.D. and Cross , J.E. 1983 . Bacterial blight of snap beans and their control . Plant Dis. , 67 : 935 – 939 .
   Google Scholar
• Weller , S.A. , Elphinstone , J.G. , Smith , N.C. , Boonham , N. and Stead , D.E. 2000 . Detection of Ralstonia solanacearum strains with a quantitative, multiplex, real-time, fluorogenic PCR (TaqMan) assay . Appl. Environ. Microbiol. , 66 : 2853 – 2858 .
   PubMed Web of Science ®Google Scholar
• Yan , Y. , Yang , J. , Dou , Y. , Chen , M. , Ping , S. , Peng , J. , Lu , W... and Jin , Q. 2008 . Nitrogen fixation island and rhizosphere competence traits in the genome of root-associated Pseudomonas stutzeri A1501 . Proc. Natl. Acad. Sci. USA , 105 : 7564 – 7569 .
   PubMed Web of Science ®Google Scholar
• Zaccardelli , M. , Spasiano , A. and Merighi , M. 2005 . Identification and in planta detection of Pseudomonas syringae pv. tomato using PCR amplification of hrpZPst . Eur. J. Plant Pathol. , 111 : 85 – 90 .
   Google Scholar
• Zhao , Y. , Damicone , J.P. and Bender , C.L. 2002 . Detection, survival, and sources of inoculum for bacterial diseases of leafy crucifers in Oklahoma . Plant Dis. , 86 : 883 – 888 .
   Google Scholar