تعیین مشخصات مولکولی و تبارزایی ویروئید لکه زردی-1 مو (Grapevine yellow speckle viroid-1) از تاکستان¬های شمال¬غرب کشور

نوع مقاله : مقاله پژوهشی

نویسندگان

1 استادیار گروه گیاهپزشکی، دانشکده کشاورزی، دانشگاه کردستان

2 دانشیار گروه گیاهپزشکی، دانشکده کشاورزی، دانشگاه تبریز

چکیده

به­منظور تعیین مشخصات مولکولی و بررسی ساختارهای ثانویه ویروئید لکه زردی- 1 مو، 137 نمونه از تاکستان­های استان­های اردبیل، آذربایجان­­­ شرقی و آذربایجان­ غربی جمع­آوری گردید. اسید نوکلئیک کل از بافت برگ نمونه­ها استخراج و پس از ساخت دی­ان­ای مکمل با استفاده از آغازگر شش­نوکلئوتیدی تصادفی، طول کامل این ویروئید با روش پی­سی­آر و با استفاده از آغازگرهای اختصاصی ویروئید لکه زردی -1 مو،  تکثیر شد. محصول پی­سی­آر پس از همسانه­سازی در حامل pGEMT-easy، تعیین­توالی گردید. نتایج نشان داد که واریانت­های شناسایی­شده در این تحقیق، دارای 367 یا 368 نوکلئوتید هستند و در مجموع هفت واریانت جدید از این ویروئید تشخیص داده شد. درخت تبارزایی نشان داد که واریانت 6 مشابه اعضای تیپ یک این ویروئید و شش واریانت بعدی در کنار تعدادی جدایه و واریانت دیگر تشکیل یک تیپ جداگانه (به­نام پیشنهادی تیپ 4) را می­دهند. در ساختار ثانویه واریانت­های به­دست­آمده در این تحقیق، بیشترین تفاوت در منطقه متغیر و قسمت انتهایی چپ قرار داشت. ویروئید لکه زردی-1 مو برای اولین بار از استان­های آذربایجان­شرقی و اردبیل گزارش می­شود.

کلیدواژه‌ها


عنوان مقاله [English]

Identification, Molecular and Phylogenetic Analyses of Grapevine yellow speckle viroid-1 from the Northwest Region of Iran

نویسندگان [English]

  • Mohammad Hajizadeh 1
  • Nemat Sokhandan Bashir 2
1 Assistant Professor, Dept of Plant Protection, Faculty of Agriculture, University of Kurdistan, Sanandaj, Iran
2 Associate Professor, Dept of Plant Protection, Faculty of Agriculture, University of Tabriz, Tabriz, Iran
چکیده [English]

Totally, 137 grapevines samples were collected from vineyards in East and West Azerbaijan and Ardabil provinces of Iran and tested for molecular characterization and study on the secondary structure of Grapevine yellow speckle viroid-1 (GYSVd-1). Total nucleic acid was extracted from leaves and first-strand cDNA synthesized using random hexamer primer. PCR fragments corresponding to full length GYSVd-1 were amplified by the use of specific primers and cloned in pGEM-T-easy for sequencing. Results showed that the Iranian isolates were 367-368 nt in length, and accordingly seven new GYSVd-1 variants were identified. Phylogenetic analysis revealed that variant 6 was identical to the type 1 of GYSVd-1, whereas the other six variants together with some other isolates and variants of GYSVd-1 formed a distinct clad, which named as GYSVd-1 type 4. These variants were most different from other isolates in variable and left terminal domains of their secondary structure. This is the first report of grapevine infection with GYSVd-1 from Ardabil and East Azarbaijan provinces.

کلیدواژه‌ها [English]

  • Grapevine
  • RT-PCR
  • Secondary structure
  • Variant
زکی عقل م و ایزدپناه ک، 1389. شناسایی و تعیین برخی مشخصات مولکولی ویروئیدهای مو در استان فارس. بیماریهای گیاهی، جلد چهل و ششم، شماره 3، صفحه­های 249 تا 262.
 
Flores R, Hernández C, Martínez de Alba AE, Daros JA and Di Serio F, 2005. Viroids and viroid–host interactions. Annual Review of Phytopathology 43: 117–139.
Foissac X, Savalle-Dumas L, Gentit P, Dulucq MJ and Candresse T, 2000. Polyvalent detection of fruit tree Tricho, Capillo and Foveaviruses by nested RT-PCR using degenerated and inosine containing primers (PDO RT-PCR). Acta Horticulture 357: 52–59.
Gazel M and Onelge N, 2003. First report of grapevine viroids in the East Mediterranean region of Turkey. Plant Pathology, New Disease Report 52: 405.
Hadidi A, Flores R, Randles JW and Semanick JS, 2003. Viroids. CSIRO Publishing, Collingwood, Australia.
Hajizadeh M, Navarro B, Bashir NS and Di Serio F, 2010. Multiple viroid infections in Iranian grapevines. Journal of Plant Pathology 92(S 4): 107-122.
Hajizadeh M, Navarro B, Bashir NS, Torchetti EM and Di Serio F, 2012a. Development and validation of a multiplex RT-PCR method for the simultaneous detection of five grapevine viroids. Journal of Virological Methods 179(1): 62-69.
Hajizadeh M, Navarro B, Bashir NS and Di Serio F, 2012b. Grapevine yellow speckle-1 Type 4: A new proposed type of grapevine yellow speckle-1. Pp. 108-109. Proceeding of the 17th Meeting of ICVG. California, Davis, USA.
 Jiang D, Peng S, Wu Z, Cheng Z and Li S, 2009. Genetic diversity and phylogenetic analysis of Australian Grapevine viroid (AGVd) isolated from different grapevines in China. Virus Genes 38: 178-183.
King AMQ, Lefkowitz E, Adams MJ and Carstens EB, 2012. Virus Taxonomy: Ninth report of the international committee on taxonomy of viruses. Elsevier, USA.
Koltunow MA and Rezaian MA, 1988. Grapevine yellow speckle viroid: structural features of a new viroid group. Nucleic Acids Research 16: 849-864.
Little A and Rezaian MA, 2003. Grapevine viroids. Pp. 195-206 In: Hadidi A, Flores R, Randles JW and Semancik JS (eds.), Viroids. CSIRO Publishing, Collingwood, Australia.
Minafra A, Martelli GP and Savino V, 1990. Viroids of grapevine in Italy. Vitis 29: 173-182.
Polivka H, Staub U and Gross HJ, 1996. Variation of viroid profiles in individual grapevine plants: Novel grapevine yellow speckle viroid-1 mutants show alterations of hairpin I. Journal of General Virology 77: 155–161.
Rigden JE and Rezaian MA, 1992. In vitro synthesis of an infectious viroid: Analysis of infectivity of monomeric linear CEV. Virology 186: 201-206.
Sano T, Kobayashi T, Ishiguro A and Motomura Y, 2000. Two types of Grapevine yellow speckle viroid-1 isolated from commercial grapevine had the nucleotide sequence of yellow speckle symptom-inducing type. Journal of General Plant Pathology 66: 68-70.
Semancik JS, 2003. Pathogenesis. Pp. 61-66 In: Hadidi A, Flores R, Randles JW and Semancik JS (eds.), Viroids. CSIRO Publishing, Collingwood, Australia.
Shikata E, Sano T and Uyeda I, 1984. An infectious low molecular weight RNA was detected in grapevines by molecular hybridization with hop stunt viroid cDNA. Proceeding of the Japan Academy, Series B 60: 202.
Sokhandan NB, Gillings MR and Bowyer JW, 1997. Polymerase chain reaction detection and assessment of genetic variation in New South Wales isolates of Passionfruit woodiness potyvirus. Australasian Plant Pathology 26: 155-164.
Stellmach G and Goheen AC, 1988. Other virus and virus-like diseases. Pp 53-54 In: Pearson RC and Goheen AC, (eds.) Compendium of Grape Diseases. American Phytopathological Society Press, St Paul, Minnesota.
Szychowski JA, Credi R, Reanwarakorn K and Semancik JS, 1998. Population diversity in Grapevine yellow speckle viroid-1 and the relationship to disease expression. Virology 248: 432-444.
Szychowski JA, McKenry MV, Walker MA, Wolpert JA, Credi R and Semancik JS, 1995. The vein-banding disease syndrome: A synergistic reaction between grapevine viroids and fanleaf virus. Vitis 34: 229–232.
Tajima F and Nei M, 1984. Estimation of evolutionary distance between nucleotide sequences. Molecular Biology and Evolution 1: 269-285.
Tamura K, Peterson D, Peterson N, Glen Stecher, Nei M and Kumar S, 2011. MEGA5: Molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Molecular Biology and Evolution. 28: 2731- 2739.
Taylor RH and Woodham RC, 1972. Grapevine yellow speckle-a newly recognized graft-transmissible disease of vitis. Australian Journal of Agriculture Research 23: 447–452.
Vuittenz A, 1970. Fanleaf of grapevine. Pp. 217-228 In: Frazier NW (ed.). Virus Disease of Small Fruits and Grapevine. University of California, Berkeley.
Wan Chow Wah YF and Symons RH, 1997. A high sensitivity RT-PCR assay for the diagnosis of grapevine viroids in field and tissue culture samples. Journal of Virological Methods 63: 57-69.
Ward LI, Bumip GM, Liefting LW, Harper SJ and Clover RG, 2011. First report of Grapevine yellow speckle viroid 1 and Hop stunt viroid in grapevine (Vitis vinifera) in New Zealand. Plant Disease
95(5): 617.
Wassenegger M, Spieker RL, Thalmeir S, Gast FU, Riedel L and Sanger HL, 1996. A single nucleotide substitution converts Potato spindle tuber viroid (PSTVd) from a noninfectious to an infectious RNA for Nicotiana tabacum. Virology 226: 191-197.
Wolpert JA, Szychowski JA and Semancik JS, 1995. Effect of viroids on growth, yield, and maturity indices of cabernet sauvignon grapevines. American Journal of Enology and Viticulture 47(1): 21-24.
Zaki-Aghl M and Izadpanah K, 2009. Identification and partial characterization of grapevine viroids in Southern Iran. Pp. 354-355. Proceeding of the 16th Meeting of ICVG, Dijon, France.
Zuker M. 1989. On finding all suboptimal foldings of an RNA molecule. Science 244: 48-52