Detection of Coconut cadang-cadang viroid sequences in oil and coconut palm by ribonuclease protection assay

Annals of Applied Biology

Volumn 154, Issue 1, 2009, Pages 117-125

  Vadamalai, G ^a,b   Perera, A A F L K ^c   Hanold, D ^a   Rezaian, M A ^a   Randles, J W ^a  

^a UNIVERSITY OF ADELAIDE   (Australia)

^b UNIVERSITY PUTRA MALAYSIA   (Malaysia)

^c Coconut Research Institute ^*  (Sri Lanka)

Author keywords

African oil palm; CCCVd related RNA; Cocadviroid; Coconut cadang cadang viroid; Coconut palm; Malaysia; Ribonuclease protection assay; Sri Lanka

Indexed keywords

BIOASSAY; BIOLOGICAL SURVEY; DETECTION METHOD; ENZYME ACTIVITY; MONOCOTYLEDON; PLANTATION; VIROID;

ASIA; EURASIA; MALAYSIA; PHILIPPINES; SOUTH ASIA; SOUTHEAST ASIA; SRI LANKA;

COCADVIROID; COCONUT CADANG-CADANG VIROID; COCOS NUCIFERA; ELAEIS; ELAEIS GUINEENSIS; LYCOPERSICON ESCULENTUM; POTATO SPINDLE TUBER VIROID; SOLANUM TUBEROSUM; VIROIDS;

EID: 58249109469     PISSN: 00034746     EISSN: 17447348     Source Type: Journal    
DOI: 10.1111/j.1744-7348.2008.00278.x     Document Type: Article

References (45)

1. Ahmad N., Kuramoto I.K., Baroudy B.M. (1993) A ribonuclease protection assay for the direct detection and quantitation of hepatitis C virus RNA. Clinical and Diagnostic Virology, 1, 233 244.
2. Ali A., Randles J.W. (2001) Genomic heterogeneity in Pea seed-borne mosaic virus isolates from Pakistan, the centre of diversity of the host species, Pisum sativum. Archives of Virology, 146, 1855 1870.
3. Aranda M.A., Fraile A., Garcia-Arenal F. (1993) Genetic variability and evolution of the satellite RNA of Cucumber mosaic virus during natural epidemics. Journal of Virology, 67, 5896 5901.
4. Aranda M.A., Fraile A., Garcia-Arenal F., Malpica J.M. (1995) Experimental evaluation of the ribonuclease protection assay method for the assessment of genetic heterogeneity in populations of RNA viruses. Archives of Virology, 140, 1373 1383.
5. Baumstark T., Schroeder A.R.W., Riesner D. (1997) Viroid processing: switch from cleavage to ligation is driven by a change from a tetraloop to a loop E conformation. EMBO Journal, 16, 599 610.
6. Bonfiglioli R.G., McFadden G.I., Symons R.H. (1994) In situ hybridization localizes avocado sunblotch viroid on chloroplast thylakoid membranes and coconut cadang cadang viroid in the nucleus. The Plant Journal, 6, 99 103.
7. Cabrera O., Roossinck M.J., Scholthof K.-B.G. (2000) Genetic diversity of Panicum mosaic virus satellite RNAs in St. Augustine grass. Phytopathology, 90, 977 980.
8. Coulter J.K., Rosenquist E.A. (1955) Mineral nutrition of the oil palm. A study of the chemical composition of the frond in relation to chlorosis and yield. Malayan Agricultural Journal, 38, 214 236.
9. Flores R., Daros J.A., Navarro J.A. (2003a) Replication. In Viroids, pp. 55 60. Eds A. Hadidi, R. Flores, J.W. Randles and J.S. Semancik. Collingwood, Australia : CSIRO.
10. Flores R., Randles J.W., Owens R.A. (2003b) Classification. In Viroids, pp. 71 75. Eds A. Hadidi, R. Flores, J.W. Randles and J.S. Semancik. Collingwood, Australia : CSIRO.
11. Forde S.C.M., Leyritz M.J.P. (1968) A study of confluent orange spotting of the oil palm in Nigeria. Journal of the Nigerian Institute for Oil Palm Research, 4, 371 380.
12. Gas M.E., Hernandez C., Flores R., Daros J.A. (2007) Processing of nuclear viroids in vivo: an interplay between RNA conformations. PLoS Pathology, 3, 1813 1826.
13. Gomez G., Pallas V. (2007) Mature monomeric forms of Hop stunt viroid resist RNA silencing in transgenic plants. The Plant Journal, 51, 1041 1049.
14. Hanold D., Randles J.W. (1991) Detection of coconut cadang-cadang viroid-like sequences in oil and coconut palm and other monocotyledons in the south-west Pacific. Annals of Applied Biology, 118, 139 151.
15. Hanold D., Randles J.W. (Eds 1998) Report on ACIAR-Funded Research on Viroids and Viruses of Coconut Palm and other Tropical Monocotyledons 1985-1993. ACIAR Monograph No. 45. Canberra, Australia : Australian Centre for International Agricultural Research.
16. Hanold D., Randles J.W. (2003) CCCVd-related molecules in oil palms, coconut palms and other monocotyledons outside the Philippines. In Viroids, pp. 336 344. Eds A. Hadidi, R. Flores, J.W. Randles and J.S. Semancik. Collingwood, Australia : CSIRO.
17. Haseloff J., Mohamed N.A., Symons R.H. (1982) Viroid RNAs of cadang-cadang disease of coconuts. Nature, 299, 316 321.
18. Hodgson R.A.J., Randles J.W. (1999) Detection of coconut cadang-cadang viroid-like sequences. In Current Plant Science and Biotechnology In Agriculture, Current Advances in Coconut Biotechnology, Vol. 35, pp. 227 246. Eds C. Oropeza, J.L. Verdeil, G.R. Ashburner, R. Cardena and J.M. Santamaria. London, UK : Kluwer Academic Publishers.
19. Hodgson R.A.J., Wall G.C., Randles J.W. (1998) Specific identification of coconut tinangaja viroid (CTiVd) for differential field diagnosis of viroids in coconut palm. Phytopathology, 88, 774 781.
20. Imperial J.S., Rodriguez M.J.B., Randles J.W. (1981) Variation in the viroid-like RNA associated with cadang-cadang disease: evidence for an increase in molecular weight with disease progress. Journal of General Virology, 56, 77 85.
21. Imperial J.S., Bautista R.M., Randles J.W. (1985) Transmission of the coconut cadang-cadang viroid to six species of palm by inoculation with nucleic acid extracts. Plant Pathology, 34, 391 401.
22. Kurath G., Palukaitis P. (1989a) RNA sequence heterogeneity in natural populations of three satellite RNAs of cucumber mosaic virus. Virology, 173, 231 240.
23. Kurath G., Palukaitis P. (1989b) Satellite RNAs of Cucumber mosaic virus: recombinants constructed in vitro reveal independent functional domains for chlorosis and necrosis in tomato. Molecular Plant-Microbe Interactions, 2, 91 96.
24. Lakshman D.K., Tavantzis S.M. (1992) RNA progeny of an infectious two-base deletion cDNA mutant of Potato spindle tuber viroid (PSTV) acquire two nucleotides in planta. Virology, 187, 565 572.
25. Liu Y.H., Symons R.H. (1998) Specific RNA self-cleavage in coconut cadang-cadang viroid: potential for a role in rolling circle replication. RNA, 4, 418 429.
26. Lopez-Galindez C., Lopez J.A., Melero J.A., De La Fuente L., Martinez C., Ortin J., Perucho M. (1988) Analysis of genetic variability and mapping of point mutations in influenza virus by the RNAse A mismatch cleavage method. Proceedings of the National Academy of Sciences of the United States of America, 85, 3522 3526.
27. Mohamed N.A., Haseloff J., Imperial J.S., Symons R.H. (1982) Characterization of the different electrophoretic forms of the cadang-cadang viroid. Journal of General Virology, 63, 181 188.
28. Pacumbaba E.P., Zelazny B., Orense J.C., Rillo E.P. (1994) Evidence for pollen and seed transmission of the coconut cadang-cadang viroid in Cocos nucifera. Journal of Phytopathology, 142, 37 42.
29. Palukaitis P., Roossinck M.J., Garcia-Arenal F. (1994) Applications of ribonuclease protection assay in plant virology. In Molecular Virology Techniques, Part A, pp. 237 250. Ed. K.W. Adolph. San Diego, CA, USA : Academic Press Inc.
30. Ranasinghe C.S., Wijesekara R., Wimalasekara R. (2002) Rapid decline syndrome of coconut (Cocos nucifera L.) - preliminary report of a new condition. Palms, 46, 167 171.
31. Randles J.W. (1985) Coconut cadang-cadang viroid. In Subviral Pathogens of Plants and Animals: Viroids and Prions, pp. 39 74. Eds K. Maramorosch and J.J. McKelvey Jr. Orlando, FL, USA : Academic Press Inc.
32. Randles J.W., Rodriguez M.J.B. (2003) Coconut cadang-cadang viroid. In Viroids, pp. 233 241. Eds A. Hadidi, R. Flores, J.W. Randles and J.S. Semancik. Collingwood, Australia : CSIRO.
33. Randles J.W., Boccardo G., Imperial J.S. (1980) Detection of the cadang-cadang RNA in African oil palm and buri palm. Phytopathology, 70, 185 189.
34. Randles J.W., Hanold D., Pacumbaba E.P., Rodriguez M.J.B. (1992) Cadang-cadang disease of coconut palm. In Plant Diseases of International Importance. Eds A.N. Mukhopadhyay, J. Kumar, H.S. Chaube and U.S. Singh. Englewood Cliffs, NJ, USA : Prentice Hall Inc.
35. Robertson J.S., Prendergast A.G., Sly J.M.A. (1968) Diseases and disorders of the oil palm (Elaeis guineensis) in West Africa. Journal of the Nigerian Institute for Oil Palm Research, 4, 381 409.
36. Rodriguez M.J.B. (1993) Molecular variation in coconut cadang-cadang viroid (CCCVd). PhD Thesis. The University of Adelaide, Adelaide.
37. Rodriguez M.J.B., Randles J.W. (1993) Coconut cadang-cadang viroid (CCCVd) mutants associated with severe disease vary in both the pathogenicity domain and the central conserved region. Nucleic Acids Research, 21, 2771
38. Rosenau C., Kaboord B., Qoronfleh M.W. (2002) Development of a chemiluminescence-based ribonuclease protection assay. BioTechniques, 33, 1354 1358.
39. Smilde K.W. (1962) 10th Annual Report of the West African Institute for Oil Palm Research, pp. 71 78. Benin City, Nigeria : West African Institute for Oil Palm Research.
40. Smilde K.W. (1963) 11th Annual Report of the West African Institute for Oil Palm Research, pp. 67 76. Benin City, Nigeria : West African Institute for Oil Palm Research.
41. Steger G., Riesner D. (2003) Molecular characteristics. In Viroids, pp. 15 29. Eds A. Hadidi, R. Flores, J.W. Randles and J.S. Semancik. Collingwood, Australia : CSIRO.
42. Turner P.D. (1981) Oil Palm Diseases and Disorders, pp. 280. Kuala Lumpur, Malaysia : Oxford University Press.
43. Vadamalai G. (2005) An investigation of oil palm orange spotting disorder. PhD Thesis. The University of Adelaide, Adelaide. [WWW document]. URL http://thesis.library.adelaide.edu.au/public/adt-SUA20060321.085810/index.html
44. Vadamalai G., Hanold D., Rezaian M.A., Randles J.W. (2006) Variants of the Coconut cadang-cadang viroid isolated from an African oil palm (Elaeis guineensis Jacq.) in Malaysia. Archives of Virology, 151, 1447 1456.
45. Winter E., Yamamoto F., Almoguera C., Perucho M. (1985) A method to detect and characterize point mutations in transcribed genes: amplification and overexpression of the mutant c-Ki-ras allele in human tumor cells. Proceedings of the National Academy of Sciences of the United States of America, 82, 7575 7579.