Novel Variants of Citrus Viroid-III in Fars Province

Document Type : Research Paper



Citrus viroid-III (CVd-III) has narrow host range and induces specific symptoms on Etrog citron consist of petiole wrinkle and browning plus leaf twist, leaf droop and bent leaf induced by point necroses of the mid vein. Citrus Viroid-III causes significant reduction of the trunk cross section in Valencia scion and trifoliate rootstock, and the canopy volume of infected trees. In this study a number of citrus trees with or without symptoms were sampled and subjected to RNA extraction followed by RT-PCR, cloning and sequencing of PCR products. Molecular properties (nucleotide composition, primary and secondary structures, molecular weights, phylogenetic relationships and percent nucleotide similarity) of viroid variants were compared. Three novel variants of CVd-III (1, 2 and 3) from Fars were selected and used for comparison with a number of other CVd-III sequences from GenBank. CVd-III-2 had 99 % sequence homology to CVd-III-3 but these two variants had only 93% homology with CVd-III-1. It was shown that on the basis of homology, CVd-III isolates from Fars province clustered in different groups.


Citrus viroids, CVd-III , Phylogeny

Alavi M, Hashemi Sohi H, Ahoomanesh A, Rahimian H (2005). Molecular analysis and identification of Citrus exocortis viroid isolates in Mazandaran province. MSc. Thesis, College of Agriculture, Esfahan University. 86 P.
Alavi SM, Ahoonmanesh A, Rahimian H (2006). Nucleotide sequence of Hop stunt viroid cDNA from Cachexia-infected citrus plants in Mazandaran province. Iranian Journal of Plant Pathology 43: 49-64.
Bernad L, Duran-Vila N (2006). A novel RT-PCR approach for detection and characterization of citrus viroids. Molecular and Cellular Probes 20: 105–113.
Diener TO (1972). Viroids and Viroid Diseases. John-Wiley and Sons. 252 P.
Elleuch A, Khouaja FD, Hamdi I, Bsais N, Perreault JP, Marrakchi M, Fakhfakh H (2006). Sequence analysis of three citrus viroids infecting a single Tunisian citrus tree (Citrus, reticulata, Clementine). Genetics and Molecular Biology 29: 705-10.
Gora-Sochacka A (2004). Viroids: Unusual small pathogenic RNAs. Acta Biochimia Polonica 51: 587-607.
Holmes DS, Quigley M (1981). A rapid boiling method for the preparation of bacterial plasmids. Analytical Biochemistry 114: 193-197.
Owens RA, Yang G, Gundersen-Rindal D, Hammond RW, Candresse T, Bar-Joseph M (2000). Both point mutation and RNA recombination contribute to the sequence diversity of citrus viroid III. Virus Genes 20: 243-251.
Roistacher CN, Bash JA, Semancik JS (1993). Distinct disease symptoms in Poncirus trifoliata induced by three citrus viroids from three specific groups. In: 12th Conf. IOCV., IOCV, Riverside, p. 173-179.
Saitou N, Nei M (1987). The neighbor-joining method: a new method for reconstructing phylogenetic trees. Molecular Biology and Evolution 4: 406–425.
Serra P, Gago S, Duran-Vila N (2008). A single nucleotide change in Hop stunt viroid modulates citrus cachexia symptoms. Virus Research 138: 130–134.
Tabler M, Tsagris M (2004). Viroids: Petite RNA pathogens with distinguished talents. Trends in Plant Science 9: 339-348.
Yang X, Hadidi A, Garnsey SM (1992). Enzymatic cDNA amplification of citrus exocortis and cachexia viroids from infected citrus hosts. Phytopathology 82: 279-285.