A universal microarray detection method for identification of multiple phytophthora spp. using padlock probes

Phytopathology

Volumn 102, Issue 6, 2012, Pages 635-645

  Sikora, Katarzyna ^a   Verstappen, Els ^b   Mendes, Odette ^b   Schoen, Cor ^c   Ristaino, Jean ^a   Bonants, Peter ^b  

^a FOREST RESEARCH INSTITUTE   (Poland)

^b WAGENINGEN UNIVERSITY   (Netherlands)

^c NORTH CAROLINA STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

PRIMER DNA; RIBOSOMAL SPACER DNA;

ANIMAL; ARTICLE; CLASSIFICATION; COLORIMETRY; DNA MICROARRAY; EQUIPMENT; GENETICS; ISOLATION AND PURIFICATION; METHODOLOGY; MOLECULAR DIAGNOSIS; MULTIPLEX POLYMERASE CHAIN REACTION; OLIGONUCLEOTIDE PROBE; PARASITOLOGY; PHYTOPHTHORA; PLANT; PLANT DISEASE; REPRODUCIBILITY; SENSITIVITY AND SPECIFICITY;

ANIMALS; COLORIMETRY; DNA PRIMERS; DNA, RIBOSOMAL SPACER; MOLECULAR DIAGNOSTIC TECHNIQUES; MULTIPLEX POLYMERASE CHAIN REACTION; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; OLIGONUCLEOTIDE PROBES; PHYTOPHTHORA; PLANT DISEASES; PLANTS; REPRODUCIBILITY OF RESULTS; SENSITIVITY AND SPECIFICITY;

PHYTOPHTHORA;

EID: 84861496179     PISSN: 0031949X     EISSN: None     Source Type: Journal    
DOI: 10.1094/PHYTO-11-11-0309     Document Type: Article

References (44)

1. Anderson, N. M., Szemes, M., O'Brien, P. A., de Weerdt, M., Schoen, C. D., Boender, P. J., and Bonants, P. J. M. 2006. Use of hybridization melting kinetics for detecting Phytophthora species using three dimensional microarrays. Mycol. Res. 110:664-671.
2. Bala, K., Robideau, G. P., Lévesque, C. A., de Cock, A. W. A. M., Abad, Z. G., Lodhi, A. M., Shahzad, S., Ghaffar, A., and Coffey, M. D. 2010. Phytopythium Abad, de Cock, Bala, Robideau & Levesque, gen. nov. and Phytopythium sindhum Lodhi, Shahzad & Levesque, sp. nov. Persoonia 24:136-137.
3. Bilodeau, G. J., Lévesque, C. A., de Cock, A. W. A. M., Duchaine , C., Brière, S. Uribe, P., Martin, F. N., and Hamelin, R. C. 2007. Molecular detection of Phytophthora ramorum by real-time polymerase chain reaction using TaqMan, SYBR Green, and molecular beacons. Phytopathology 97:632-642. (Pubitemid 46652631)
4. Blair, J. E., Coffey, M. D., Park, S.-Y., Geiser, D. M., and Kang, S. 2008. A multi-locus phylogeny for Phytophthora utilizing markers derived from complete genome sequences. Fungal Genet. Biol. 45:266-277. (Pubitemid 351192342)
5. Bonants, P. J. M., Hagenaar-de Weerdt, M., van Gent-Pelzer, M., Lacourt, I., Cooke, D. E., and Duncan, J. M. 1997. Detection and identification of Phytophthora fragariae Hickman by the polymerase chain reaction. Eur. J. Plant Pathol. 103:345-355. (Pubitemid 27253433)
6. Bonants, P. J. M., van Gent-Pelzer, M. P. E., Hooftman, R., Cooke, D. E. L., Guy, D. C., and Duncan, J. M. 2004. A combination of baiting and different PCR formats, including measurement of real time quantitative fluorescence, for the detection of Phytophthora fragariae in strawberry plants. Eur. J. Plant Pathol. 110:689-702. (Pubitemid 39252075)
7. Brasier, C. M., Cooke, D. E. L., and Duncan, J. M. 1999. Origin of a new Phytophthora pathogen through interspecific hybridization. Proc. Natl. Acad. Sci. USA 96:5878-83. (Pubitemid 29234712)
8. Cooke, D. E. L., Drenth, A., Duncan, J. M., Wagels, G., and Brasier, C. M. 2000. A molecular phylogeny of Phytophthora and related oomycetes. Fungal Genet. Biol. 30:17-32. (Pubitemid 30666584)
9. Cooke, D. E. L., Schena, L., and Cacciola, S. O. 2007. Tools to detect, identify and monitor Phytophthora species in natural ecosystems. J. Plant Pathol. 89:13-28. (Pubitemid 46625664)
10. de Bary, H. A. 1876. Researches into the nature of the potato fungus Phytophthora infestans. J. Bot. 14:105-126.
11. Duncan, J. M. 1980. A technique for detecting red stele (Phytophthora fragariae) infection of strawberry stocks before planting. Plant Dis. 64:1023-1025.
12. Erwin, D. C., and Ribeiro, O. K. 1996. Phytophthora Diseases Worldwide. American Phytopathological Society Press, St. Paul, MN.
13. Gallegly, M. E., Hong, C., Richardson, P., and Kong, P. 2010. Phytophthora pini Leonian, a valid and distinct species. (Abstr.) Phytopathology 100:S207.
14. Gunderson, J. H., Elwood, H., Ingold, H., Kindle, A., and Sogin, M. L. 1987. Phylogenetic relationships between chlororphytes, chrysophytes, and oomycetes. Proc. Natl. Acad. Sci. USA 84:5823-5827.
15. 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. (Pubitemid 44211987)
16. Hayden, K., Rizzo, D., Tse, J., and Garbelotto, M. 2004. Detection and Quantitation of Phytophthora ramorum from California forests using realtime polymerase chain reaction assay. Phytopathology 94:1075-1083. (Pubitemid 39290280)
17. Hughes, K. J. D., Tomlinson, J. A., Griffin, R. L., Boonham, N., Inman, A. J., and Lane, C. R. 2006. Development of a one-step real-time polymerase chain reaction assay for diagnosis of Phytophthora ramorum. Phytopathology 96:975-981. (Pubitemid 44300199)
18. Ippolito A., Schena L., and Nigro F. 2002. Detection of Phytophthora nicotianae and P. citrophthora in citrus roots and soils by nested PCR. Eur. J. Plant Pathol. 108:855-868. (Pubitemid 36035333)
19. Jung, T., and Burgess, T. I. 2009. Re-evaluation of Phytophthora citricola isolates from multiple woody hosts in Europe and North America reveals a new species, Phytophthora plurivora sp. nov. Persoonia 22:95-110.
20. Kong, P., Hong, C. X., Tooley, P. W., Ivors, K., Garbelotto, M., and Richardson, P. A. 2004. Rapid identification of Phytophthora ramorum using PCR-SSCP analysis of ribosomal DNA ITS-1. Lett. Appl. Microbiol. 38:433-439. (Pubitemid 38534811)
21. Kox, L., Heurneman, I., van den Vossenberg, B., van den Beld, I., Bonants, P., and de Gruyter, H. 2007. Diagnostic values and utility of immunological, morphological and molecular methods for in planta detection of Phytophthora ramorum. Phytopathology 97:1119-1129. (Pubitemid 47441526)
22. Kroon, L. P. N. M. 2010. The genus Phytophthora; phylogeny, speciation and host specificity. Ph.D. thesis, Wageningen University.
23. 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. (Pubitemid 38829187)
24. Lievens, B., and Thomma, B. P. H. 2005. Recent developments in pathogen detection arrays: Implications for fungal plant pathogens and use in practice. Phytopathology 95:1374-1380. (Pubitemid 41692643)
25. Liew, E. C. Y., MacLean, D. J., and Irwin, J. A. G. 1998. Specific PCR based detection of Phytophthora medicaginis using the intergenic spacer region of the ribosomal DNA. Mycol. Res.102:73-80. (Pubitemid 28159071)
26. 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. H. 2009. Evaluation of molecular markers for Phytophthora ramorum detection and identification: Testing for specificity using a standardized library of isolates. Phytopathology 99:290-403.
27. Martin, F. N., and Tooley, P. W. 2003. Phylogenetic relationships among Phytophthora species inferred from sequence analysis of the mitochondrially encoded cytochrome oxidase I and II genes. Mycologia 95:269-284. (Pubitemid 36557826)
28. Ristaino, J. B., Madritch, M., Trout, C. L., and Parra, G. 1998. PCR amplification of ribosomal DNA for species identification in the plant pathogen genus Phytophthora. Appl. Environ. Microbiol. 68:948-954. (Pubitemid 28108469)
29. Robideau, G. P., de Cock, A. W. A. M., Coffey, M. D., Voglmayr, H., Bonants, P. J. M., Verstappen, E. C. P., Ristaino, J. B. Hu, J., Chitty, D., Rintoul, T. L., Brouwer, H., Désaulniers, N., Eggertson, Q. A., Bala, K., Zhang, Y., Sarhan, E., Gachon, C. M. M., and Lévesque, C. A. 2011. DNA barcoding of oomycetes with cytochrome c oxidase subunit I (COI) and internal transcribed spacer (ITS). Mol. Ecol. Res. Mol. Ecol. Res. 11:1002-1011.
30. Schena, L., Duncan, J. M., and Cooke, D. E. L. 2008. Development and application of a PCR-based 'molecular tool box' for the identification of Phytophthora species damaging forests and natural ecosystems. Plant Pathol. 57:64-75.
31. 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. (Pubitemid 44337796)
32. Stamps, D. J., Newhook, F. J., Waterhouse, G. M., and Hall, G. S. 1990. Revised tabular key to the species of Phytophthora de Bary. CAB Int. Mycol. Inst. Mycol. Pap. No. 162. Commonwealth Mycological Institute, Kew, Surrey, England.
33. Stenberg, J., Nilsson, M., and Landegren, U. 2005. ProbeMaker: An extensible framework for design of sets of oligonucleotide probes. BMC Bioinf. 6:229.
34. Szemes, M., Bonants, P., de Weerdt, M., Banner, J., Landegren, U., and Schoen, C. 2005. Diagnostic application of padlock probes-multiplex detection of plant pathogens using universal microarray. Nucleic Acids Res. 33:1-13. (Pubitemid 41511298)
35. Tooley, P. W., Bunyard, B. A., Carras, M. M., and Hatziloukas, E. 1997. Development of PCR primers from Internal Transcribed Spacer region 2 for detection of Phytophthora species infecting potatoes. Appl. Environ. Microbiol. 63:1467-1475. (Pubitemid 27174856)
36. 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.
37. Trout, C. L, Ristaino, J. B., Madritch, M., and Wangsomboondee, T. 1997. Rapid Detection of Phytophthora infestans in late blight infected tissue of potato and tomato using PCR. Plant Dis. 81:1042-1048.
38. van Doorn, R., Slawiak, M., Szemes, M., Dullemans, A. M., Bonants, P., Kowalchuk, G. A., and Schoen, C. D. 2009. Robust detection and identification of multiple oomycetes and fungi in environmental samples by using novel cleavable padlock probe-based ligation detection assay. Appl. Environ. Microbiol. 75:4185-4193.
39. van Doorn, R., Szemes, M., Bonants, P., Sallas, J., Ortenberg, E., and Schoen, C. D. 2007. Quantitative multiplex detection of plant pathogens using a novel ligation probe-based system coupled with universal, ultrahigh- throughput real-time PCR on OpenArrays. BMC Genomics 8:276.
40. Waterhouse, G. M. 1963. Key to the species of Phytophthora de Bary. Mycol. Pap. 92. Commonwealth Mycological Institute, Kew, Surrey, England.
41. Waterhouse, G. M. Newhook, F. J., and Stamps, D. J. 1983. Present criteria for classification of Phytophthora. Pages 139-147 in: Phytophthora: Its Biology, Taxonomy, Ecology, and Pathology. D. C. Erwin, S. Bartnicki-Garcia, and P. H. Tsao, eds. American Phytopathological Society Press, St. Paul, MN.
42. White, T. J., Bruns, T., Lee, S., and Taylor, J. 1990. Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. Pages 315-322 in: PCR Protocols. A Guide to Methods and Applications. M. A. Innis, D. H. Gelfand, J. J. Sninsky, and T. J. White, eds. Academic Press, Inc., San Diego, CA.
43. 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. (Pubitemid 34475881)
44. Zang, N., McCarthy, M. L., and Smart, C. D. 2008. A macroarray system for the detection of fungal and oomycete pathogens of solanaceous crops. Plant Dis. 92:953-960. (Pubitemid 351954919)