Molecular cloning, secondary structure, and phylogeny of three pospiviroids from ornamental plants

Canadian Journal of Plant Pathology

Volumn 27, Issue 4, 2005, Pages 592-602

  Nie, Xianzhou ^a   Singh, Rudra P ^a   Bostan, Hidayet ^b  

^a FREDERICTON RESEARCH AND DEVELOPMENT CENTRE   (Canada)

^b ATATÜRK UNIVERSITY   (Turkey)

Author keywords

CEVd; Chrysanthemum stunt viroid; Citrus exocortis viroid; CSVd; Iresine viroid; IrVd; Molecular cloning; Ornamental plants; Phylogeny; Pospiviroids; Secondary structure

Indexed keywords

CHRYSANTHEMUM; CHRYSANTHEMUM STUNT VIROID; CITRUS; CITRUS EXOCORTIS VIROID; IMPATIENS; IRESINE VIROID 1; POSPIVIROID; POSPIVIROIDAE; VERBENA; VERBENACEAE; VINCA; VINCA MAJOR; VIROIDS;

EID: 33645383068     PISSN: 07060661     EISSN: 17152992     Source Type: Journal    
DOI: 10.1080/07060660509507260     Document Type: Article

References (40)

1. Bostan, H., Nie, X., and Singh, R. P., 2004. An RT-PCR primer pair for the detection of Pospiviroid and its application in surveying ornamental plants for viroids. J. Virol. Methods, 116:189–193.
2. Elena, S. F., Dopazo, J., de la Peña, M., Flores, R., Diener, T. O., and Moya, A., 2001. Phylogenetic analysis of viroid and viroid-like satellite RNAs from plants:a reassessment. J. Mol. Evol., 53:155–159.
3. Elliott, D. R., Alexander, B. J. R., Smales, T. E., Tang, Z., and Clover, G. R. G., 2001. First report of Potato spindle tuber viroid in tomato in New Zealand. Plant Dis., 85:1027
4. European and Mediterranean Plant Protection Organization. 2004. Occurrence of Potato Spindle Tuber Pospiviroid (PSTVd) in tomato plants in Germany, Paris:EPPO Reporting Service. No. 01, 2004/2006
5. Fadda, Z., Daros, J. A., Flores, R., and Duran-Vila, N., 2003. Identification in eggplant of a variant of citrus exocortis viroid (CEVd) with a 96 nucleotide duplication in the right terminal region of the rod-like secondary structure. Virus Res., 97:145–149.
6. Felsenstein, J., 1993. “ PHYLIP (Phylogeny inference package) [computer program]. Version 3.5c ”. In Department of Genetics, University of Washington Seattle, Wash
7. Flores, R., Delgado, S., Gas, M. E., Carbonell, A., Molina, D., Gago, S., and De la Peña, M., 2004. Viroids:the minimal non-coding RNAs with autonomous replication. FEBS Lett., 567:42–48.
8. Góra-Sochacka, A., 2004. Viroids:unusual small pathogenic RNAs. Acta Biochim. Pol, 51:587–607.
9. Gozmanova, M., Denti, M. A., Minkov, I. N., Tsagris, M., and Tabler, M., 2003. Characterization of the RNA motif responsible for the specific interaction of potato spindle tuber viroid RNA (PSTVd) and the tomato protein Virp1. Nucleic Acids Res., 31:5534–5543.
10. Hammond, R., Smith, D. R., and Diener, T. O., 1989. Nucleotide sequence and proposed secondary structure of Columnea latent viroid:a natural mosaic of viroid sequences. Nucleic Acids Res., 17:10 083–10 094.
11. Ito, T., Ieki, H., Ozaki, K., Iwanami, T., Nakahara, K., Hataya, T., Ito, T., Isaka, M., and Kano, T., 2002. Multiple citrus viroids in citrus from Japan and their ability to produce exocortis-like symptoms in citron. Phytopathology, 92:542–547.
12. Mackie, A. E., McKirdy, S. J., Rodoni, B., and Kumar, S., 2002. Potato spindle tuber viroid eradicated in Western Australia. Australas. Plant Pathol., 31:311–312.
13. Matoušek, J., Orctov'a, L., Steger, G., Škopek, J., Moors, M., Dědič, P., and Riesner, D., 2004. Analysis of thermal stress-mediated PSTVd variation and biolistic inoculation of progeny of viroids “thermomutants” to tomato and Brassica species. Virology, 323:9–23.
14. Mumford, R. A., Jarvis, B., and Skelton, A., 2003. The first report of Potato spindle tuber viroid (PSTVd) in commercial tomatoes in the UK. The British Society for Plant Pathology., New Dis. Rep. [serial online], 8 (August 2003–January 2004)http://www.bspp.org.uk/ndr/jan2004/2003-68.asp
15. National Center for Biotechnology Information. 2005. NCBI BLAST, Rockville Pike, Bethesda, Md:National Center for Biotechnology Information. [online]. [updated 28 August 2005].http://www.ncbi.nlm.nih.gov/blast
16. Nie, X., and Singh, R. P., 2001. Differential accumulation of Potato virus A and expression of pathogenesis-related genes in resistant potato cv. Shepody upon graft inoculation. Phytopathology, 91:197–203.
17. Pelchat, M., Rocheleau, L., Perreault, J., and Perreault, J. P., 2003. SubViral RNA:a database of the smallest known auto-replicable RNA species. Nucleic Acids Res., 31:444–445.
18. Singh, R. P., 1973. Experimental host range of the potato spindle tuber “virus. Am. Potato J., 50:111–123.
19. Singh, R. P., 1983. Viroids and their potential danger to potatoes in hot climates. Can. Plant Dis. Surv., 63:13–18.
20. Singh, R. P., 1989. “ Plant viroids:a biochemical novelty ”. In Plant viruses. Vol. I. Structure and replication, Edited by:Manahar, C. L., 260–288. Boca Raton, Fla:CRC Press.
21. Singh, R. P., and Clark, M. C., 1971. Infectious low-molecular weight ribonucleic acid from tomato. Biochem. Biophys. Res. Commun., 44:1077–1083.
22. Singh, R. P., Finnie, R. F., and Bagnall, R. H., 1971. Losses due to the potato spindle tuber virus. Am. Potato J., 48:262–267.
23. Singh, R. P., Boucher, A., and Singh, A., 1991. High incidence of transmission and occurrence of a viroid in commercial seeds of Coleus in Canada. Plant Dis., 75:184–187.
24. Singh, R. P., Lakshman, D. K., Boucher, A., and Tavantzis, S. M., 1992. A viroid from Nematanthus wettsteinii plants closely related to Columnea latent viroid. J. Gen. Virol., 73:2769–2774.
25. Singh, R. P., Nie, X., and Singh, M., 1999. Tomato chlorotic dwarf viroid:an evolutionary link in the origin of pospiviroids. J. Gen. Virol, 80:2823–2828.
26. Singh, R. P., Ready, K. F. M., and Nie, X., 2003. “ Viroids of solonaceous species ”. In Viroids, Edited by:Hadidi, A., Flores, R., Randles, J. W., and Semancik, J. S., 125–133. Collingwood, Victoria, B.C.:Commonwealth Scientific and Industrial Research Organization (CSIRO) Publishing.
27. Slack, S. A., and Singh, R. P., 1998. “ Control of viruses affecting potatoes through seed potato certification programs ”. In Plant virus disease control, Edited by:Hadidi, A., Khetarpal, R. K., and Koganezawa, H., 249–260. St. Paul, Minn:American Phytopathological Society Press.
28. Spieker, R. L., 1996a. The molecular structure of Iresine viroid, a new viroid species from Iresine herbstii (“beefsteak plant”). J. Gen. Virol., 77:2631–2635.
29. Spieker, R. L., 1996b. A viroid from Brunfelsia undulata closely related to the Columnea latent viroid. Arch. Virol, 141:1823–1832.
30. Stasys, R. A., Dry, I. B., and Rezaian, M. A., 1995. The termini of a new citrus viroid contain duplications of the central conserved regions from two viroid groups. FEBS Lett., 358:182–184.
31. Steger, G., and Riesner, D., 2003. “ Molecular characteristics ”. In Viroids, Edited by:Hadidi, A., Flores, R., Randles, J. W., and Semancik, J. S., 15–29. Collingwood, Victoria, B.C.:Commonwealth Scientific and Industrial Research Organization (CSIRO) Publishing.
32. Szychowski, J. A., Vidalakis, G., and Semancik, J. S., 2005. Host-directed processing of Citrus exocortis viroid. J. Gen. Virol., 86:473–477.
33. Tabler, M., and Tsagris, M., 2004. Viroids:petite RNA pathogens with distinguished talents. Trends Plant Sci., 9:339–348.
34. Thompson, J. D., Higgins, D. G., and Gibson, T. J., 1994. CLUSTAL W:improving the sensitivity of progressive multiple sequence alignment through sequence weighting, positions-specific gap penalties and weight matrix choice. Nucleic Acids Res., 22:4673–4680.
35. Verhoeven, J. T. J., Arts, M. S. J., Owens, R. A., and Roenhorst, J. W., 1998. Natural infection of petunia by chrysanthemum stunt viroid. Eur. J. Plant Pathol., 104:383–386.
36. Verhoeven, J. T. J., Jansen, C. C. C., Willemen, T. M., Kox, L. F. F., Owens, R. A., and Roenhorst, J. W., 2004. Natural infections of tomato by Citrus exocortis viroid, Columnea latent viroid, Potato spindle tuber viroid and Tomato chlorotic dwarf viroid. Eur. J. Plant Pathol., 110:823–831.
37. Verni`re, C., Perrier, X., Dubois, C., Dubois, A., Botella, L., Chabrier, C., Bové, J. M., and Duran Vila, N., 2004. Citrus viroids:symptom expression and effect on vegetative growth and yield of clementine trees grafted on trifoliate orange. Plant Dis, 88:1189–1197.
38. Werkman, A. W., Verhoeven, J. T. J., Jansen, C. C. C., and Roenhorst, J. W., Identification of viroids occurring in potato and tomato, and possible consequences for future testing. The 12th European Association for Potato Research (EAPR) Virology Section Meeting. June13–192004, Rennes, France. Abstract No. 40. pp. 63Rennes, France:Institut national de la recherche agronomique. [online]. Compiled by Dani`le Giblot-Ducray. [accessed November 2005]http://www.rennes.inra.fr/eapr2004/abstracts.htm
39. Zuker, M., 2003. Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res., 31:3406–3415.
40. Zuker, M., and Stiegler, P., 1981. Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information. Nucleic Acids Res., 9:133–148.