First Characterization of Apple scar skin viroid from Apple and pear cultivars in Iran and determination of genetic diversity

پژوهش های حفاظت گیاهان ایران

Article 2, Volume 28, Issue 3 - Serial Number 25, September 2014, Pages 277-284   

Document Type: Research Article

DOI: 10.22067/jpp.v28i3.43538

Authors

A. Yazarlou^{* 1}; B. Jafarpour; M. Koohi Habibi; S. Tarighi¹; J. W. Randles²

¹Ferdowsi University of Mashhad

²University of Adelaide

Abstract

Apple scar skin viroid (ASSVd) is one of the most destructive viroid diseases in pome fruits orchards which can cause significant economic losses. Symptoms of this viroid including scaring, distortion and dappling were seen in some apple orchards in east-northern of Iran. Sampling was carried out from apple and pear orchards. The RNA was extracted by Silica capture method from leaves. ASSVd was detected by RT-PCR. The purified PCR products were cloned into pGEM®-T Easy Vector and recombinant plasmids were sequenced and sequencing analysis was done. We reported 12 new variants of ASSVd from apple and pear hosts with variable length between 329 to 334 nucleotides. Phylogenetic analysis by the neighbour joining method showed that the Iranian isolates were distinct from other isolates of ASSVd. Mutation sites were indicated along the secondary structure of ASSVd molecule. This study provides the first report of detection and molecular characterization of ASSVd in apple and pear in Iran.

Keywords

ASSVd; Secondary structure; Cloning; Phylogenetic analysis

References

1- Behl M.K., Khurana S.M.P., and Parakh D.B. 1998. Bumpy fruit and other viroid and viroid-like diseases of apple in HP, India. Acta Horticulturae, 472:627-629.

2- Campbell A.I., and Sparks T.R. 1976. Experiments with dapple apple virus. Acta Hort, 67:261-264.

3- Chen W., Yang X.C., Tien P. 1987. Pear rusty skin a viroid disease. In: 7th International Congress of Virology, Edmonton, Canada. pp 300.

4- Daros J.A., Elena S., and Flores R. 2006. Viroids: an Ariadne’s thread into the RNA labyrinth. EMBO Rep, 7:593-598.

5- Desvignes J.C., Grasseau N., Boye R., and Cornaggia D. 1999. Biological Properties of Apple Scar Skin Viroid: Isolates, Host Range, Different Sensitivity of Apple Cultivars, Elimination, and Natural Transmission. Plant Disease, 83:768-772.

6- Di Serio F., Malfitano M., Alioto D., Rogozzino A., and Flores R. 2002. Apple dimple fruit viroid: sequence variability and its specific detection by multiplex fluorescent RT-PCR in the presence of apple scar skin viroid. Plant Pathology, 84:27-34.

7- Flores R., Randles J.W., Bar-Joseph M., and Diener T.O. 2000. Subviral agent: Viroids. In: Virus taxonomy 7th report of the international committee on Taxonomy of viruses. pp 1009-1024.

8- Foissac X., Svanella-Dumas L., Gentit P., Dulucq M.J., Marais A., and Candresse T. 2005. Polyvalent degenerate oligonucleotides reverse transcription-polymerase chain reaction: A polyvalent detection and characterization tool for tichoviruses, capilloviruses, and foveaviruses. Phytopathology, 95:617-625.

9- Hadidi A., Hansen A.J., Parish C.L., and Yang X. 1991. Scar skin and dapple apple viroids are seed-borne and persistent in infected apple trees. Research in Virology, 142:289-296.

10- Hadidi A., Huang C., Hammond R.W., and Hashimoto J. 1990. Homology of the agent associated with dapple apple disease to apple scar skin viroid and molecular detection of these viroids. Phytopathology, 80:263-268.

11- Hall T.A. 1999. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acid Symp Ser, 41:95–98.

12- Hashimoto J., and Koganezawa H. 1987. Nucleotide sequence and secondary structure of apple scar skin viroid. Nucleic Acids Research, 15:7045-7052.

13- Keese P., and Symons R.A. 1985. Domains in viroids: Evidence of intermolecular rearrangement and their contribution to viroid evolution. Proceedings of the National Academy of Sciences, 82:4582-4586.

14- Koganezawa H., Yang X., Zhu S.F., Hashimoto J., and Hadidi A. 2003. Apple scar skin viroid in apple. In: Hadidi A., Flores R., Randles J.W., and Semancik J.S. (eds.) Viroids. CSIRO Publishing, Australia. pp 137-141.

15- Koganezawa H. 1986. Further evidence for viroid etiology of apple scar skin and dapple diseases. Acta Hortic, 193:29-33.

16- Kumar S., Dudley J., Nei M., and Tamura K. 2008. MEGA: a biologistcentric software for evolutionary analysis of DNA and protein sequences. Briefings Bioinformatics, 9:299–306.

17- Kyriakopoulou P.E., Giunchedi L., and Hadidi A. 2001. Peach latent mosaic and pome fruit viroids in naturally infected cultivated pear Pyrus communis and wild pear P. amygdaliformis: implications on possible origin of these viroids in the Mediterranean region. Plant Pathology, 83:51-62.

18- Larkin M.A., Blackshields G., Brown N.P., Chenna R., McGettigan P.A., McWilliam H., Valentin F., Wallace I.M., Wilm A., Lopez R., Thompson J.D., Gibson T.J., and Higgins D.G. 2007. Clustal W and Clustal X version 2.0. Bioinformatics, 23:2947–2948. Ohtsuka Y. 1938. On Manshu-sabika-byo of apple, graft transmission and symptom variation in cultivars. Journal of the Japanese Society for Horticultural, 9:282-286.

19- Puchta H., Luckinger R., Yang X., Hadidi A., and Sänger H.L. 1990. Nucleotide sequence and secondary structure of apple scar skin viroid (ASSVd) from China. Plant Molecular Biology, 14:1065-1067.

20- Sano T., Candresse T., Hammond R.W., Diener T.O., and Owens R.A. 1992. Identification of multiple structural domains regulating viroid pathogenicity. Proc Natl Acad Sci, 89:10104–10108.

21- Walia Y., Kumar Y., Tanuja R., Bhardwaj P., Ram R., Thakur P.D., Sharma U., Hallan V., and Zaidi A.A. 2009. Molecular characterization and variability analysis of Apple scar skin viroid in India. Gen Plant Pathology, 75:307–311.

22- Welsh M.F., and Keene F.W.L. 1961. Diseases of apple in British Columbia that are caused by viruses or have characteristics of virus diseases. Can Plant Dis Surv, 41:123-147.

23- Yang X., Hadidi A., and Hammond R.W. 1992. Nucleotide sequence of apple scar skin viroid reverse transcribed in host extracts and amplified by the polymerase chain reaction. Acta Hort, 309:305-309.

24- Zhu S.F., Hadidi A., Hammond R.W., Yang X., Hansen A.J. 1995. Nucleotide sequence and secondary structure of pome fruit viroids from dapple apple diseased apples, pear rusty skin diseased pears and apple scar skin symptomless pears. Acta Horticulturae, 386:554-559.

25- Zucker M., and Stiegler P. 1981. Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information. Nucleic Acids Research, 9:133-148.