1887

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Volume 72, Issue 7

Identification of potyviruses using the polymerase chain reaction with degenerate primers Free

Abstract

Local areas of conserved amino acid sequence in the replicase and coat proteins of potyviruses were used to select nucleotide sequences for use in the construction of sets of degenerate oligonucleotide primers for amplification of DNA fragments on potyvirus-specific templates in a combined assay of reverse transcription and the polymerase chain reaction (RT-PCR). Sequences selected for the construction of degenerate primers included the coat protein gene sequence of tulip breaking virus from lily, which is reported in this paper. It is shown that the degenerate primers support potyvirus-specific amplification, but do not support amplification on carlavirus and potexvirus templates. A panel consisting of definite and prospective members of the potyvirus group occurring in bulbous crops was subjected to the degenerate primer RT-PCR assay; amplified fragments were used in cross-hybridization experiments and restriction fragment length polymorphism analysis to detect relationships among these potyviruses. A partially characterized virus isolated from was positively identified as a potyvirus by specific amplification and subsequent sequence analysis of an amplified DNA fragment.

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© Journal of General Virology 1991
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1991-07-01
2024-04-20
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References

  1. Allen T. C. 1972; Lily symptomless virus. CMI/AAB Descriptions of Plant Viruses no 96:
     [Google Scholar]
  2. Allison R. F., Sorenson J. C., Kelly M. E., Armstrong F. B., Dougherty W. G. 1985; Sequence determination of the capsid protein gene and flanking regions of tobacco etch virus: evidence for synthesis and processing of a polyprotein in potyvirus gene expression. Proceedings of the National Academy of Sciences, U.S.A 82:3969–3972
     [Google Scholar]
  3. Allison R., Johnston R. E., Dougherty W. G. 1986; The nucleotide sequence of the coding region of tobacco etch virus genomic RNA: evidence for the synthesis of a single protein. >Virology 154:9–20
     [Google Scholar]
  4. Asjies C. J., de Vos N. P., van Slogteren D. H. M. 1973; Brown ring formation and streak mottle, two distinct syndromes in lilies associated with complex infections of lily symptomless virus and tulip breaking virus. Netherlands Journal of Plant Pathology 79:23–35
     [Google Scholar]
  5. Balasingam G., Ellison N., Milne K. S., Forster R. L. S. 1988; Sensitive and specific detection of two filamentous viruses from nerines using cloned cDNA probes. Acta horticulturae 234:267–274
     [Google Scholar]
  6. Barnett O. W. 1986; Application of new test procedures to surveys: merging the new with the old. In Developments in Applied Biology vol 1 pp 247–267 Edited by Jones R. A. C., Torrance L. Wellesboume: Association of Applied Biologists;
     [Google Scholar]
  7. Bos L. 1970; Bean yellow mosaic virus. CMI/AAB Descriptions of Plant Viruses no 40
     [Google Scholar]
  8. Brunt A. A. 1977; Some hosts and properties of narcissus latent virus, a carlavirus commonly infecting narcissus and bulbous iris. Annals of Applied Biology 87:355–364
     [Google Scholar]
  9. Brunt A. A. 1986; Iris mild mosaic virus. CMI/AAB Descriptions of Plant Viruses no 324
     [Google Scholar]
  10. Brunt A. A., Derks A. F. L. M., Barnett O. W. 1988; Iris severe mosaic virus. CMI/AAB Descriptions of Plant Viruses no 338
     [Google Scholar]
  11. Carrington J. C., Dougherty W. G. 1987; Processing of the tobacco etch virus 49K protease requires autoproteolysis. Virology 160:355–362
     [Google Scholar]
  12. Chang C. A., Hiebert E., Purcifull D. E. 1988; Analysis of in vitro translation of bean yellow mosaic virus RNA: inhibition of proteolytic processing by antiserum to the 49K nuclear inclusion proteins. Journal of General Virology 69:1117–1122
     [Google Scholar]
  13. Derks A. F. L. M., Vink-van den Abeele J. L. 1980; Hyacinth mosaic virus: symptoms in hyacinths, serological detection, and relationships with other potyviruses. Acta horticulturae 109:495–502
     [Google Scholar]
  14. Derks A. F. L. M., Vink-van den Abeele J. L., van Schadewijk A. R. 1982; Purification of tulip breaking virus and production of antisera for use in ELISA. Netherlands Journal of Plant Pathology 88:87–98
     [Google Scholar]
  15. Devereux J., Haeberli P., Smithies O. 1984; A comprehensive set of sequence analysis programs for the VAX. Nucleic Acids Research 12:387–395
     [Google Scholar]
  16. Domier L. L., Franklin K. M., Shahabuddin M., Hellmann G. M., Overmeyer J. H., Hiremath S., Slaw M. F. E., Lomonossoff G. P., Shaw J. G., Rhoads R. E. 1986; The nucleotide sequence of tobacco vein mottling virus RNA. Nucleic Acids Research 14:5417–5430
     [Google Scholar]
  17. Dougherty W. G., Allison R. F., Parks T. D., Johnston R. E., Feild M. J., Armstrong F. B. 1985; Nucleotide sequence of the 3′ terminus of pepper mottle virus genomic RNA: evidence for an alternative mode of potyvirus capsid protein gene organization. Virology 146:282–291
     [Google Scholar]
  18. Dougherty W. G., Carrington J. C., Cary S. M., Parks T. D. 1988; Biochemical and mutational analysis of a plant virus polyprotein cleavage site. EMBO Journal 7:1281–1287
     [Google Scholar]
  19. Eggenberger A. L., Stark D. M., Beachy R. N. 1989; The nucleotide sequence and expression of a soybean mosaic virus coat protein-coding region and its expression in Escherichia coli, Agrobacterium tumefaciens and tobacco callus. Journal of General Virology 70:1853–1860
     [Google Scholar]
  20. Feinberg A. P., Vogelstein B. 1983; A technique for radiolabeling DNA restriction fragments to high specific activity. Analytical Biochemistry 132:6–13
     [Google Scholar]
  21. Gough K. H., Azad A. A., Hanna P. J., Shukla D. D. 1987; Nucleotide sequence of the capsid and nucler inclusion protein genes from the Johnson grass strain of sugarcane mosaic virus RNA. Journal of General Virology 68:297–304
     [Google Scholar]
  22. Gubler U., Hoffman B. J. 1983; A simple and very efficient method for generating cDNA libraries. Gene 25:263–269
     [Google Scholar]
  23. Hammond J., Hammond R. W. 1989; Molecular cloning, sequencing and expression in Escherichia coli of the bean yellow mosaic virus coat protein gene. Journal of General Virology 70:1961–1974
     [Google Scholar]
  24. Hari V. 1979; >The RNA of tobacco etch virus contains poly(A). Virology 92:568–571
     [Google Scholar]
  25. Hari V. 1981; The RNA of tobacco etch virus: further characterization and detection of protein linked to RNA. Virology 112:391–399
     [Google Scholar]
  26. Hellmann G. M., Shaw J. G., Rhoads R. E. 1988; In vitro analysis of tobacco vein mottling virus NIa cistron: evidence for a virus-encoded protease. Virology 163:554–562
     [Google Scholar]
  27. Hollings M., Brunt A. A. 1981; Potyvirus group. CMI/AAB Descriptions of Plant Viruses no 245
     [Google Scholar]
  28. Hsu H. T., Franssen J. M., van der Hulst C. T. C., Derks A. F. L. M., Lawson R. H. 1988; Factors affecting selection of epitope specificity of monoclonal antibodies to tulip breaking virus. Phytopathology 78:1337–1340
     [Google Scholar]
  29. Jordan R. 1989; Mapping of potyvirus-specific and group-common antigenic determinants with monoclonal antibodies by Western-blot analysis and coat protein amino acid sequence comparisons. Phytopathology 79:1157
     [Google Scholar]
  30. Kamer G., Argos P. 1984; Primary structural comparison of RNA-dependent polymerases from plant, animal and bacterial viruses. Nucleic Acids Research 12:7269–7282
     [Google Scholar]
  31. Keohavong P., Thilly W. G. 1989; Fidelity of DNA polymerases in DNA amplification. Proceedings of the National Academy of Sciences, U.S.A 86:9253–257
     [Google Scholar]
  32. Kieny M. P., Lathe R., Lecocq J. R. 1983; New versatile cloning and sequencing vectors based on bacteriophage Ml3. Gene 25:263–269
     [Google Scholar]
  33. Knoth K., Roberds S., Poteet C., Tamkun M. 1988; Highly degenerate, inosine-containing primers specifically amplify rare cDNA using the polymerase chain reaction. Nucleic Acids Research 16:10932
     [Google Scholar]
  34. Koenig R., Lesemann D. E. 1974; A potyvirus from Gloriosa rothschildiana. Phytopathologische Zeitschrift 80:136–142
     [Google Scholar]
  35. Maat D. Z., Huttinga H., Hakkaart F. A. 1978; Nerine latent virus: some properties and serological detectability in Nerine bowdenii. Netherlands Journal of Plant Pathology 84:47–59
     [Google Scholar]
  36. Mack D. H., Sninsky J. J. 1988; A sensitive method for the identification of uncharacterized viruses related to known virus groups: hepadnavirus model system. Proceedings of the National Academy of Sciences, U.S.A 85:6977–6981
     [Google Scholar]
  37. Maiss E., Timpe U., Brisske A., Jelkmann W., Casper R., Himmler G., Mattanovich D., Katinger H. W. D. 1989; The complete nucleotide sequence of plum pox virus RNA. Journal of General Virology 70:513–524
     [Google Scholar]
  38. Memelink J., van der Vlugt C. I. M., Linthorst H. J. M., Derks A. F. L. M., Asjes C. J., Bol J. F. 1990; Homologies between the genomes of a carlavirus (lily symptomless virus) and a potexvirus (lily virus X) from lily plants. Journal of General Virology 71:917–924
     [Google Scholar]
  39. Moghal S. M., Francki R. I. B. 1976; Towards a system for the identification and classification of potyviruses. I. Serology and amino acid composition of six distinct viruses. Virology 73:350–362
     [Google Scholar]
  40. Moghal S. M., Francki R. I. B. 1981; Towards a system for the identification and classification of potyviruses II. Virus particle length, symptomatology and cytopathology of six distinct viruses. Virology 112:210–216
     [Google Scholar]
  41. Ravelonandro M., Varveri C., Delbos R., Dunez J. 1988; Nucleotide sequence of the capsid protein gene of plum pox potyvirus. Journal of General Virology 69:1509–1516
     [Google Scholar]
  42. Robaglia C., Durand-Tardif M., Tronchet M., Boudazin G., Astier-Manifacier S., CasseDelbart F. 1989; Nucleotide sequence of potato virus Y (N strain) genomic RNA. Journal of General Virology 70:935–947
     [Google Scholar]
  43. Rybicki E. P., Hughes F. L. 1990; Detection and typing of maize streak virus and other distantly related geminiviruses of grasses by polymerase chain reaction amplification of a conserved viral sequence. Journal of General Virology 71:2519–2526
     [Google Scholar]
  44. Sambrook J., Fritsch E. F., Maniatis T. 1989; Molecular Cloning: A Laboratory Manual. New York: Cold Spring Harbor Laboratory;
     [Google Scholar]
  45. Sanger F., Nicklen S., Coulson A. R. 1977; DNA sequencing with chain-terminating inhibitors. Proceedings of the National Academy of Sciences, U.S.A 74:5463–5467
     [Google Scholar]
  46. Shahabuddin M., Shaw J. G., Rhoads R. E. 1988; Mapping of the tobacco vein mottling virus VPg cistron. Virology 163:635–637
     [Google Scholar]
  47. Shukla D. D. 1986; Coat protein of potyviruses. 2. Amino acid sequence of the coat protein of potato virus Y. Virology 152:118–125
     [Google Scholar]
  48. Allen T. C. 1972; Lily symptomless virus. CMI/AAB Descriptions of Plant Viruses no. 96
     [Google Scholar]
  49. Shukla D. D., Ward C. W. 1988; Amino acid sequence homology of coat proteins as a basis for identification and classification of the potyvirus group. Journal of General Virology 69:2703–2710
     [Google Scholar]
  50. Shukla D. D., Ward C. W. 1989; Structure of potyvirus coat proteins and its application in the taxonomy of the potyvirus group. Advances in Virus Research 36:273–314
     [Google Scholar]
  51. Tautz D., Renz M. 1983; An optimized freeze-squeeze method for the recovery of DNA fragments from agarose gels. Analytical Biochemistry 132:14–19
     [Google Scholar]
  52. Van Koot Y., van Slogteren D. H. M., Cremer M. C., Camfferman J. 1954; Virus diseases in freesias. Netherlands Journal of Plant Pathology 60:157–192
     [Google Scholar]
  53. Zuidema D., Linthorst H. J. M., Huisman M. J., Asjes C. J., Bol J. F. 1989; Nucleotide sequence of narcissus mosaic virus RNA. Journal of General Virology 70:267–276
     [Google Scholar]
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Identification of potyviruses using the polymerase chain reaction with degenerate primers
J. Gen. Virol. 72, 1531 (1991); https://doi.org/10.1099/0022-1317-72-7-1531
/content/journal/jgv/10.1099/0022-1317-72-7-1531
/content/journal/jgv/10.1099/0022-1317-72-7-1531
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