Miniprimer PCR assay targeting multiple genes: A new rapid and reliable tool for genotyping Pantoea stewartii subsp. stewartii

Letters in Applied Microbiology

Volumn 50, Issue 2, 2010, Pages 216-222

  Xu, R ^a   Chen, Q ^a,b   Robleh Djama, Z ^a   Tambong, J T ^a  

^a AGRICULTURE AND AGRI FOOD CANADA   (Canada)

^b SICHUAN AGRICULTURAL UNIVERSITY   (China)

Author keywords

Bacteria; Fingerprinting; Maize; Miniprimer; Stewart's wilt of corn; Titanium Taq

Indexed keywords

BACTERIA; BACTERIOLOGY; DNA; GENE ENCODING; TITANIUM;

AMPLICONS; BACTERIAL SPECIES; BACTERIAL WILT; BANDING PATTERNS; CLAVIBACTER; DNA FRAGMENT; DNA POLYMERASE; ENCODING GENES; ERWINIA; FINGERPRINTING; GENOTYPING; MULTIPLE GENES; OPTIMAL REACTION CONDITION; PANTOEA; PCR ASSAY; PSEUDOMONAS SPP; RACEMASE; SECRETION SYSTEMS; ZEAXANTHIN;

CLONING;

ASPARAGINE; BACTERIAL DNA; BACTERIAL PROTEIN; DNA FRAGMENT; GLUCOSIDE; GLUTAMIC ACID; NUCLEOTIDE; PSAU PROTEIN; RACEMASE; TAQ POLYMERASE; UNCLASSIFIED DRUG; ZEAXANTHIN;

BACTERIUM; BIOASSAY; CLONE; DNA FINGERPRINTING; GENOTYPE; MAIZE; POLYMERASE CHAIN REACTION; PROTEIN;

AMPLICON; ARTICLE; BACTERIAL STRAIN; CONTROLLED STUDY; ERWINIA; GENE SEQUENCE; GENE TARGETING; GENOTYPE; MAIZE; MOLECULAR CLONING; NONHUMAN; NUCLEOTIDE SEQUENCE; OPERON; PANTOEA; PANTOEA STEWARTII; POLYMERASE CHAIN REACTION; PSEUDOMONAS; REPRODUCIBILITY; SEQUENCE HOMOLOGY; TYPE III SECRETION SYSTEM;

BACTERIA (MICROORGANISMS); CLAVIBACTER MICHIGANENSIS; ERWINIA; PANTOEA STEWARTII; PANTOEA STEWARTII SUBSP. STEWARTII; PECTOBACTERIUM; PSEUDOMONAS; ZEA MAYS;

EID: 74049157403     PISSN: 02668254     EISSN: 1472765X     Source Type: Journal    
DOI: 10.1111/j.1472-765X.2009.02780.x     Document Type: Article

References (23)

1. Blakemore, E.J.A., Law, J.R. Reeves, J.C. (1999) PCR identification of Erwinia stewartii and its comparison with two other methods. Seed Sci Technol 27, 385 396.
2. Bulat, S.A. Mironenko, N.V. (1990) Species identity of the phytopathogenic fungi Pyrenophora teres Dreschler and P. graminea Ito & Kuribayashi. Mikol Fitopatol 24, 435 441 (In Russian).
3. Bulat, S.A. Mironenko, N.V. (1996) Identification of fungi and analysis of their genetic diversity by polymerase chain reaction (PCR) with gene specific and nonspecific primers. Russ J Genet 32, 143 159.
4. Bulat, S.A., Lubeck, M., Alekhina, I.A., Jensen, D.F., Knudsen, I.M. Lubeck, P.S. (2000) Identification of a universally primed-PCR-derived sequence-characterized amplified region marker for an antagonistic strain of Clonostachys rosea and development of a strain-specific PCR detection assay. Appl Environ Microbiol 66, 4758 4763.
5. Bulat, S.A., Lubeck, M., Mironenko, N., Jensen, D.F. Lubeck, P.S. (1998) UP-PCR analysis and ITS1 ribotyping of strains of Trichoderma and Gliocladium. Mycol Res 102, 933 943.
6. Cocconcelli, P.S., Porro, D., Galandini, S. Senini, L. (1995) Development of RAPD protocol for typing of strains of lactic acid bacteria and enterococci. Lett Appl Microbiol 21, 376 379.
7. Coplin, D.L., Majerczak, D.R., Zhang, Y., Kim, W.-S., Jock, S. Geider, K. (2002) Identification of Pantoea stewartii subsp. stewartii by PCR and strain differentiation by PFGE. Plant Dis 86, 304 311.
8. Danovaro, R., Luna, G.M., Dell'anno, A. Pietrangeli, B. (2006) Comparison of two fingerprinting techniques, terminal restriction fragment length polymorphism and automated ribosomal intergenic spacer analysis, for determination of bacterial diversity in aquatic environments. Appl Environ Microbiol 72, 5982 5989.
9. Isenbarger, T.A., Finney, M., Rios-Velazquez, C., Handelsman, J. Ruvkun, G. (2008) Miniprimer PCR, a new lens for viewing the microbial world. Appl Environ Microbiol 74, 840 849.
10. Jensen, A.B., Thomsen, L. Eilenberg, J. (2001) Intraspecific variation and host specificity of Entomophthora muscae sensu stricto isolates revealed by random amplified polymorphic DNA, universal primed PCR, PCR-restriction fragment length polymorphism, and conidial morphology. J Invertebrate Pathol 78, 251 259.
11. Jiang, S.C., Matte, M., Matte, G., Huq, A. Colwell, R.R. (2000) Genetic diversity of clinical and environmental isolates of Vibrio cholerae determined by amplified fragment length polymorphism fingerprinting. Appl Environ Microbiol 66, 148 153.
12. Lane, D.J. (1991) 16S/23S rRNA sequencing. In Nucleic Acid Techniques in Bacterial Systematics ed. Stackebrandt, E. Goodfellow, M. pp. 115 148. New York : John Wiley & Sons, Inc.
13. Milling, A., Smalla, K., Xaver, M.F., Schloter, M. Munch, J.C. (2004) Effects of transgenic potatoes with an altered starch composition on the diversity of soil and rhizosphere bacteria and fungi. Plant Soil 266, 23 39.
14. Nielsen, O. Lübeck, P.S. (2002) Characterisation of symbionts of entomopathogenic nematodes by universally primed-PCR (UP-PCR) and UP-PCR product cross-hybridisation. FEMS Microbiol Lett 215, 63 68.
15. Ruiz, P., Izquierdo, P.M., Sesena, S. Palop, M.L. (2008) Intraspecific genetic diversity of lactic acid bacteria from malolactic fermentation of Cencibel wines as derived from combined analysis of RAPD-PCR and PFGE patterns. Food Microbiol 25, 942 948.
16. Tambong, J.T., de Cock, A.W., Tinker, N.A. Levesque, C.A. (2006) Oligonucleotide array for identification and detection of Pythium species. Appl Environ Microbiol 72, 2691 2706.
17. Tambong, J.T., Mwange, K.N., Bergeron, M., Ding, T., Mandy, F., Reid, L.M. 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.
18. Waleron, M., Waleron, K., Podhajska, A.J. Lojkowska, E. (2002) Genotyping of bacteria belonging to the former Erwinia genus by PCR-RFLP analysis of a recA gene fragment. Microbiology 148, 583 595.
19. Wang, Y., Prosen, D.E., Mei, L., Sullivan, J.C., Finney, M. Vander Horn, P.B. (2004) A novel strategy to engineer DNA polymerases for enhanced processivity and improved performance in vitro. Nucleic Acids Res 32, 1197 1207.
20. Williams, J.G.K., Kubelik, A.R., Livak, K.J., Rafalski, J.A. Tingey, S.V. (1990) DNA polymorphisms amplified by arbitrary primers are useful as genetic markers. Nucleic Acids Res 18, 6531 6535.
21. Wilson, W.J., Wiedmann, M., Dillard, H.R. Batt, C.A. (1994) Identification of Erwinia stewartii by a ligase chain reaction assay. Appl Environ Microbiol 60, 278 284.
22. Zapparoli, G., Reguant, C., Bordons, A., Torriani, S. Dellaglio, F. (2000) Genomic DNA fingerprinting of Oenococcus oeni strains by pulsed-field gel electrophoresis and randomly amplified polymorphic DNA-PCR. Curr Microbiol 40, 351 355.
23. Zhang, Z., Schwartz, S., Wagner, L. Miller, W. (2000) A greedy algorithm for aligning DNA sequences. J Comput Biol 7, 203 214.