Macroarray detection of plant RNA viruses using randomly primed and amplified complementary DNAs from infected plants

Phytopathology

Volumn 97, Issue 1, 2007, Pages 119-127

  Agindotan, Bright ^a   Perry, Keith L ^a  

^a Department of Obstetrics Gynecology   (United States)

Author keywords

Anchor primers

Indexed keywords

CUCUMBER MOSAIC VIRUS; POTATO LEAFROLL VIRUS; POTATO VIRUS Y; POTYVIRUS; RNA VIRUSES; SOLANUM TUBEROSUM;

EID: 33845789113     PISSN: 0031949X     EISSN: None     Source Type: Journal    
DOI: 10.1094/PHYTO-97-0119     Document Type: Article

References (53)

1. Abdullahi, I., Koerbler, M., Stachewicz, H., and Winter, S. 2005. The 18S rDNA sequence of Synchytrium endobioticum and its utility in microarrays for the simultaneous detection of fungal and viral pathogens of potato. Appl. Microbiol. Biotechnol. 68:368-375.
2. Altschul, S. F., Madden, T. L., Schaffer, A. A., Zhang, J. H., Zhang, Z., Miller, W., and Lipman, D. J. 1997. Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Res. 25:3389-3402.
3. Banik, M. T., and Zitter, T. A. 1990. Determination of cucumber mosaic virus titer in muskmelon by enzyme-linked immunosorbent assay and correlation with aphid transmission. Plant Dis. 74:857-859.
4. Bohlander, S. K., Espinosa, R., Lebeau, M. M., Rowley, J. D., and Diaz, M. O. 1992. A method for the rapid sequence-independent amplification of microdissected chromosomal material. Genomics 13:1322-1324.
5. Boonham, N., Walsh, K., Smith, P., Madagan, K., Graham, I., and Barker, I. 2003. Detection of potato viruses using microarray technology: Towards a generic method for plant viral disease diagnosis. J. Virol. Methods 108:181-187.
6. Bowtell, D., and Sambrook, J. 2003. DNA Microarrays: A Molecular Cloning Manual. Cold Spring Harbor Laboratory, Cold Spring Harbor, NY.
7. Bystricka, D., Lenz, O., Mraz, I., Dedic, P., and Sip, M. 2003. DNA microarray: Parallel detection of potato viruses. Acta Virol. 47:41-44.
8. Bystricka, D., Lenz, O., Mraz, I., Pilterova, L., Kmoch, S., and Sip, M. 2005. Oligonucleotide-based microarray: A new improvement in microarray detection of plant viruses. J. Virol. Methods 128:176-182.
9. Chizhikov, V., Wagner, M., Ivshina, A., Hoshino, Y., Kapikian, A. Z., and Chumakov, K. 2002. Detection and genotyping of human group A rotaviruses by oligonucleotide microarray hybridization. J. Clin. Microbiol. 40:2398-2407.
10. Choi, S. K., Choi, J. K., Park, W. M., and Ryu, K. H. 1999. RT-PCR detection and identification of three species of cucumoviruses with a genus-specific single pair of primers. J. Virol. Methods 83:67-73.
11. Chong, K. Y., Chen, C. M., and Choo, K. B. 1993. Post-hybridization recovery of membrane filter-bound DNA for enzymatic DNA amplification. Biotechniques 14:575.
12. Clark, A. J., and Perry, K. L. 2002. Transmissibility of field isolates of soybean viruses by Aphis glycines. Plant Dis. 86:1219-1222.
13. Culley, A. I., Lang, A. S., and Suttle, C. A. 2003. High diversity of unknown picorna-like viruses in the sea. Nature 424:1054-1057.
14. Deyong, Z., Willingmann, P., Heinze, C., Adam, G., Pfunder, M., Frey, B., and Frey, J. E. 2005. Differentiation of cucumber mosaic virus isolates by hybridization to oligonucleotides in a microarray format. J. Virol. Methods 123:101-108.
15. 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.
16. Fitzgibbon, J. E., and Sagripanti, J. L. 2006. Simultaneous identification of orthopoxviruses and alphaviruses by oligonucleotide macroarray with special emphasis on detection of variola and Venezuelan equine encephalitis viruses. J. Virol. Methods 131:160-167.
17. Gibbs, A., and Mackenzie, A. 1997. A primer pair for amplifying part of the genome of all potyvirids by RT-PCR. J. Virol. Methods 63:9-16.
18. Ginocchio, C. C., Zhang, F., Malhotra, A., Manji, R., Sillekens, P., Foolen, H., Overdyk, M., and Peeters, M. 2005. Development, technical performance, and clinical evaluation of a NucliSens basic kit application for detection of enterovirus RNA in cerebrospinal fluid. J. Clin. Microbiol. 43:2616-2623.
19. Harju, V. A., Skelton, A., Clover, G. R. G., Ratti, C., Boonham, N., Henry, C. M., and Mumford, R. A. 2005. The use of real-time RT-PCR (TaqMan) and post-ELISA virus release for the detection of Beet necrotic yellow vein virus types containing RNA 5 and its comparison with conventional RT-PCR. J. Virol. Methods 123:73-80.
20. Kawasaki, E., 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.
21. Klaassen, C. H. W., Prinsen, C. F. M., de Valk, H. A., Horrevorts, A. M., Jeunink, M. A. F., and Thunnissen, F. 2004. DNA microarray format for detection and subtyping of human papillomavirus. J. Clin. Microbiol. 42:2152-2160.
22. Kozal, M. J., Shah, N., Shen, N. P., Yang, R., Fucini, R., Merigan, T. C., Richman, D. D., Morris, D., Hubbell, E. R., Chee, M., and Gingeras, T. R. 1996. Extensive polymorphisms observed in HIV-1 clade B protease gene using high-density oligonucleotide arrays. Nat. Med. 2:753-759.
23. Lapa, S., Mikheev, M., Shchelkunov, S., Mikhailovich, V., Sobolev, A., Blinov, V., Babkin, I., Guskov, A., Sokunova, E., Zasedatelev, A., Sandakhchiev, L., and Mirzabekov, A. 2002. Species-level identification of orthopoxviruses with an oligonucleotide microchip. J. Clin. Microbiol. 40:753-757.
24. Lee, G. P., Min, B. E., Kim, C. S., Choi, S. H., Harn, C. H., Kim, S. U., and Ryu, K. H. 2003. Plant virus cDNA chip hybridization for detection and differentiation of four cucurbit-infecting Tobamoviruses. J. Virol. Methods 110:19.
25. Levesque, C. A., Harlton, C. E., and de Cock, A. W. A. M. 1998. Identification of some oomycetes by reverse dot blot hybridization. Phytopathology 88:213-222.
26. Li, J., Chen, S., and Evans, D. H. 2001. Typing and subtyping influenza virus using DNA microarrays and multiplex reverse transcriptase PCR. J. Clin. Microbiol. 39:696-704.
27. Lievens, B., Brouwer, M., Vanachter, A., Levesque, C. A., Cammue, B. P. A., and Thomma, B. 2003. Design and development of a DNA array for rapid detection and identification of multiple tomato vascular wilt pathogens. FEMS Microbiol. Lett. 223:113-122.
28. Lin, B. C., Vora, G. J., Thach, D., Walter, E., Metzgar, D., Tibbetts, C., and Stenger, D. A. 2004. Use of oligonucleotide microarrays for rapid detection and serotyping of acute respiratory disease-associated adenoviruses. J. Clin. Microbiol. 42:3232-3239.
29. Lunello, P., Mansilla, C., Conci, V., and Ponz, F. 2004. Ultra-sensitive detection of two garlic potyviruses using a real-time fluorescent (Taqman(R)) RT-PCR assay. J. Virol. Methods 118:15.
30. Martin, R. R., James, D., and Levesque, C. A. 2000. Impacts of molecular diagnostic technologies on plant disease management. Annu. Rev. Phytopathol. 38:207-239.
31. Ng, J., and Perry, K. L. 1999. Stability of the aphid transmission phenotype in cucumber mosaic virus. Plant Pathol. 48:388-394.
32. Olmos, A., Bertolini, E., Gil, M., and Cambra, M. 2005. Real-time assay for quantitative detection of non-persistently transmitted Plum pox virus RNA targets in single aphids. J. Virol. Methods 128:151-155.
33. Owen, J., Shintaku, M., Aeschleman, P., Tahar, S. B., and Palukaitis, P. 1990. Nucleotide sequence and evolutionary relationships of cucumber mosaic virus (CMV) strains: CMV RNA 3. J. Gen. Virol. 71:2243-2249.
34. Ratti, C., Budge, G., Ward, L., Clover, G., Rubies-Autonell, C., and Henry, C. 2004. Detection and relative quantitation of Soil-borne cereal mosaic virus (SBCMV) and Polymyxa graminis in winter wheat using real-time PCR (TaqMan). J. Virol. Methods 122:95-103.
35. Rizzo, T. M., and Palukaitis, P. 1988. Nucleotide-sequence and evolutionary relationships of cucumber mosaic virus (CMV) strains: CMV RNA 2. J. Gen. Virol. 69:1777-1787.
36. Rizzo, T. M., and Palukaitis, P. 1989. Nucleotide-sequence and evolutionary relationships of Cucumber mosaic virus (CMV) strains: CMV RNA 1. J. Gen. Virol. 70:1-11.
37. Robertson, N. L., French, R., and Gray, S. M. 1991. Use of group-specific primers and the polymerase chain-reaction for the detection and identification of luteoviruses. J. Gen. Virol. 72:1473-1477.
38. Saldarelli, P., Rowhani, A., Routh, G., Minafra, A., and Digiaro, M. 1998. Use of degenerate primers in a RT-PCR assay for the identification and analysis of some filamentous viruses, with special reference to clostero- and vitiviruses of the grapevine. Eur. J. Plant Pathol. 104:945-950.
39. Sambrook, J., Fritsch, E. F., and Maniatis, T. 1989. Molecular Cloning: A Laboratory Manual. 2nd ed. Cold Spring Harbor Laboratory, Cold Spring Harbor, NY.
40. Sanchez-Navarro, J. A., Aparicio, F., Rowhani, A., and Pallas, V. 1998. Comparative analysis of ELISA, nonradioactive molecular hybridization and PCR for the detection of Prunus necrotic ringspot virus in herbaceous and Prunus hosts. Plant Pathol. 47:780-786.
41. Sanchez-Seco, M. P., Echevarria, J. M., Hernandez, L., Estevez, D., Navarro-Mari, J. M., and Tenorio, A. 2003. Detection and identification of Toscana and other phleboviruses by RT-nested-PCR assays with degenerated primers. J. Med. Virol. 71:140-149.
42. Shih, S. R., Wang, Y. W., Chen, G. W., Chang, L. Y., Lin, T. Y., Tseng, M. C., Chiang, C., Tsao, K. C., Huang, C. G., Shio, M. R., Tai, J. H., Wang, S. H., Kuo, R. L., and Liu, W. T. 2003. Serotype-specific detection of enterovirus 71 in clinical specimens by DNA microchip array. J. Virol. Methods 111:55-60.
43. Sholberg, P., O'Gorman, D., Bedford, K., and Levesque, C. A. 2005. Development of a DNA macroarray for detection and monitoring of economically important apple diseases. Plant Dis. 89:1143-1150.
44. Singh, M., and Singh, R. P. 1996. Nucleotide sequence and genome organization of a Canadian isolate of the common strain of potato virus Y (PVYO). Can. J. Plant Pathol. 18:209-224.
45. Slack, S. A. 1993. Seed certification and seed improvement programs. Pages 61-65 in: Potato Health Management. R. C. Rowe, ed. The American Phytopathological Society, St. Paul, MN.
46. Slack, S. A., and Tufford, L. A. 1995. Meristem culture for virus elimination. Pages 117-128 in: Fundamental Methods of Plant Cell, Tissue and Organ Culture and Laboratory Operations. O. L. Gamborg and G. C. Phillips, eds. Springer-Velag, Berlin.
47. Tambong, J. T., de Cock, A., Tinker, N. A., and Levesque, C. A. 2006. Oligonucleotide array for identification and detection of Pythium species. Appl. Environ. Microbiol. 72:2691-2706.
48. Tzanetakis, I. E., Keller, K. E., and Martin, R. R. 2005. The use of reverse transcriptase for efficient first- and second-strand cDNA synthesis from single- and double-stranded RNA templates. J. Virol. Methods 124:73-77.
49. Wang, D., Coscoy, L., Zylberberg, M., Avila, P. C., Boushey, H. A., Ganem, D., and DeRisi, J. L. 2002. Microarray-based detection and genotyping of viral pathogens. Proc. Natl. Acad. Sci. USA 99:15687-15692.
50. Wang, D., Urisman, A., Liu, Y. T., Springer, M., Ksiazek, T. G., Erdman, D. D., Mardis, E. R., Hickenbotham, M., Magrini, V., Eldred, J., Latreille, J. P., Wilson, R. K., Ganem, D., and DeRisi, J. L. 2003. Viral discovery and sequence recovery using DNA microarrays. PLoS Biol. 1:257-260.
51. Waterhouse, P. M., Gildow, F. E., and Johnstone, G. R. 1988. Luteoviridae. Pages Number 399 in: CMI/AAB Descriptions of Plant Viruses. B. D. Harrison and A. F. Murant, eds. Commonwealth Agricultural Bureau/Association of Applied Biologists, Kew, U.K.
52. Webster, C. G., Wylie, S. J., and Jones, M. G. K. 2004. Diagnosis of plant viral pathogens. Curr. Sci. 86:1604-1607.
53. Wilson, W. J., Strout, C. L., DeSantis, T. Z., Stilwell, J. L., Carrano, A. V., and Andersen, G. L. 2002. Sequence-specific identification of 18 pathogenic microorganisms using microarray technology. Mol. Cell. Probes 16:119-127.