ردیابی و شناسایی مولکولی جدایه‌های ویروئید کوتولگی رازک آلوده کننده درختان مو در برخی از مناطق ایران

نوع مقاله : مقاله پژوهشی

نویسندگان

1 دانش‌آموخته کارشناسی ارشد بیماری‌شناسی گیاهی، دانشکده کشاورزی، دانشگاه شهید باهنر کرمان، کرمان، ایران.

2 استاد، گروه بیماری‌شناسی گیاهی، دانشکده کشاورزی، دانشگاه شهید باهنر کرمان، کرمان، ایران

3 دانش‌آموخته دکتری بیماری‌شناسی ‌گیاهی، دانشکده کشاورزی، دانشگاه‌ شهید‌ باهنر کرمان، کرمان، ایران.

4 استاد، گروه بیماری‌شناسی گیاهی، دانشکده کشاورزی، دانشگاه شهید باهنر کرمان، کرمان، ایران.

5 دانشیار، گروه بیماری‌شناسی گیاهی، دانشکده کشاورزی، دانشگاه شهید باهنر کرمان، کرمان، ایران.

چکیده

هدف: ویروئید کوتولگی رازک، (Hop stunt viroid, HSVd) گسترده‌ترین دامنه میزبانی را در بین ویروئیدها دارا می‌باشد و از مناطق مختلف دنیا گزارش شده‌است. هدف از این تحقیق، ردیابی، شناسایی و تعیین جایگاه تاکسونومیکی جدایه‌های ویروئید کوتولگی رازک در تاکستان‌های استان کرمان و برخی نقاط دیگر کشور می‌باشد.
مواد و روش‌ها: در طی تابستان سال‌های 1397 تا 1399، در مجموع 74 نمونه‌ی برگی از درختان انگور استان کرمان و دو استان آذربایجان‌شرقی (تبریز) و فارس (بیضا) جمع‌آوری شد و آلودگی نمونه‌ها به HSVd توسط آزمون RT-PCR مورد بررسی قرار گرفت. توالی ژنوم کامل هفت جدایه HSVd حاصل تعیین ترادف گردید و با توالی‌های موجود در بانک ژن مقایسه شدند. جهت بررسی روابط فیلوژنتیکی ترادف‌های بدست آمده با سایر ترادف‌های این ویروئید، از نرم افزار (version 7)MEGA  و روش neighbor-joining استفاده شد. همچنین میزان همولوژی جدایه‌ها نیز توسط نرم افزار SDT v1.2  بررسی شد. جهت تعیین دامنه میزبانی و بررسی علائم از هشت گونه و رقم گیاهی استفاده گردید.
نتایج: مطابق با گزارش‌های پیشین توالی‌های HSVd به پنج گروه فیلوژنتیکی Citrus، Hop، Plum، Plum-Hop/cit3 و Plum-Citrus تقسیم‌بندی شدند. نتایج این تحقیق نشان داد اندازه ژنوم جدایه‌های تعیین توالی شده از درختان انگور متغیر (بین 297 تا 300 نوکلئوتید) و با یکدیگر، 7/98 - 3/93 درصد تشابه داشتند. براین اساس، هفت جدایه گزارش شده در این بررسی همراه با چند جدایه گزارش شده دیگر از درختان انگور از ایران و نیز کشور آلمان در گروه اصلی Hop واقع گردیدند. سه جدایه حاصل از درختان انگور باغات استان کرمان به همراه چهار جدایه گزارش شده از این درختان، از کشور آلمان و ایران، یک زیر گروه در گروه رازک تشکیل دادند. همچنین چهار جدایه ایرانی شناسایی شده از درختان پسته در استان کرمان با تعدادی جدایه گزارش شده از درختان پسته کشور تونس (با منشاء ایرانی) نیز در گروه رازک قرار گرفتند.
نتیجه‌گیری: از آنجائی که آلودگی درختان انگور در ایران نسبت به HSVd قبل از آلودگی درختان پسته گزارش گردیده، بنابراین احتمالاً آلودگی گیاهان پسته به HSVd در ایران به‌واسطه‌ی آلودگی متقاطع و انتقال آلودگی از درختان انگور به درختان پسته رخ داده است. براین اساس با توجه به نتایج حاصل از مطالعات ملکولی و شواهد موجود، درختان انگور می‌توانند به عنوان مبداء آلودگی درختان پسته در ایران باشند.

کلیدواژه‌ها

عنوان مقاله [English]

Molecular detection and identification of Hop stunt viroid isolates infecting grapevines in some regions of Iran

نویسندگان [English]

  • Sahar Barani 1
  • Hossein Massumi 2
  • Mohammad Maddahian 3
  • Jahangir Heydarnejad 4
  • Akbar Hosseinipour 5
1 MSc Student, Department of Plant Pathology, College of Agriculture, Shahid Bahonar University of Kerman, Kerman, Iran.
2 Professor, Department of Plant Pathology, College of Agriculture, Shahid Bahonar University of Kerman, Kerman, Iran
3 Ph.D. Student, Department of Plant Pathology, College of Agriculture, Shahid Bahonar University of Kerman, Kerman, Iran.
4 Professor, Department of Plant Pathology, College of Agriculture, Shahid Bahonar University of Kerman, Kerman, Iran.
5 Associate professor, Department of Plant Pathology, College of Agriculture, Shahid Bahonar University of Kerman, Kerman, Iran.
چکیده [English]

Objective
The Hop stunt viroid has the widest host range among viroids and is prevalent worldwide. This research aims to detect and characterize HSVd variants in the vineyards of Kerman province and some other parts of Iran and analyze the variants' phylogenetic status.
Materials and methods
Seventy-four leaf samples were collected from grapevines in Kerman, East Azerbaijan (Tabriz), and Fars (Beyza) provinces during the summers of 2018–2020. The samples were processed and subjected to RT-PCR to detect HSVd using specific primers. Then, complete genomes of seven HSVd variants were sequenced and blasted into GenBank. In the MEGA 7.0 program, the neighbor-joining statistical method was used to construct a phylogenetic tree to consider relationships between the detected HSVd variants and those obtainable in GenBank. Furthermore, the homology of the grapevine-related variants was analyzed by SDT v1.2 software. Finally, eight plant species and varieties were experimentally inoculated by two HSVd variants to study symptom expression and determine host range.
Results
Throughout the world, HSVd variants have been grouped into five phylogenetic groups: Citrus, Hop, Plum, Plum-Hop/cit3, and Plum-Citrus. Accordingly, the identified seven HSVd variants in this study and several previously reported variants from grapevines in Iran and Germany were classified under the main group, Hop. The HSVd variants from grapevine had genome lengths ranging from 297 to 300 nucleotides, with 93.3–98.7% nucleotide sequence similarity. Three of the seven HSVd isolates identified in Kerman province vineyards and four isolates previously reported from grapevines in Iran and Germany formed a subgroup within the Hop cluster. In addition, the Hop group included four Iranian pistachio HSVd isolates from the Kerman province and some Tunisian pistachios HSVd isolates with Iranian provenance.
Conclusions
Given that HSVd infection of grapevines has been documented in Iran before pistachio infection, pistachios were most likely infected via HSVd inocula transferred from affected grapevines. Therefore, based on molecular studies and available evidence, grapevines can be assumed to be the source of infection for pistachio trees.

کلیدواژه‌ها [English]

  • Hop stunt viroid
  • Grapevine
  • Phylogeny

مراجع

Al Rwahnih M, Rowhani A, Westrick N, et al. (2018) Discovery of viruses and virus-like pathogens in pistachio using high-throughput sequencing. Plant Dis 102, 1419-1425.
Amari K, Canizares MC, Myrta A, et al. (2001) Tracking Hop stunt viroid (HSVd) infection in apricot trees during a whole year by non-isotopic tissue printing hybridization. Acta Hortic 550, 315-320.
Amiri-Mazhar M, Bagherian SAA, Izadpanah K (2014a) Variants of Hop stunt viroid associated with mulberry vein clearing in Iran. J Phytopathol 162, 269-271.
Amiri-Mazhar M, Bagherian SAA, Salahi-Ardakani AA, Izadpanah K (2014b) Nucleotide sequence and structural features of Hop stunt viroid and Citrus bent leaf viroid variants from blighted citrus plants in kohgiluyeh-boyerahmad province of Iran. J Agr Sci Tech 16, 657-665.
Astruc N, Marcos JF, Macquaire G, et al. (1996) Studies on the diagnosis of Hop stunt viroid in fruit trees: identification of new hosts and application of a nucleic acid extraction procedure based on non-organic solvants. Eur J Plant Pathol 102, 837-846.
Bani‐Hashemian SN, Bani‐Hashemian SM, Ashkan SM (2016) Determination of the dominant variants of Hop stunt viroid in two different cachexia isolates from north and south of Iran. J Agr Sci Tech 18, 1431-1440.
Di Serio F, Li SF, Pallas V, et al. (2017) Viroid Taxonomy. In: Viroids and Satellites. Hadidi A, Flores R, Randles JW, Palukaitis P (Eds.), Elsevier AP pp 135-146.
Diener TO (1971) Potato spindle tuber “virus”: IV. A replicating, low molecular weight RNA. Virology 45, 411-428
Diener TO (1987) Potato spindle tuber. In: The Viroids. Diener TO (Eds.), Plenum Press, New York, NY pp. 221-233.
Eastwell KC, Nelson ME (2007) Occurrence of viroids in commercial hop (Humulus lupulus L.) production areas of Washington State. Plant Health Prog 8(1), 1.
Ebrahimi-Moghadam L, Bani-Hashemian SM, Elahi-Nia SA, Bani-Hashemian SN (2014) Identification of citrus viroids in commercial citrus varieties by molecular techniques J Plant Protect 28, 250-253.
Elbeaino T, Abou Kubaa R, Choueiri E, et al. (2012a) Occurrence of Hop stunt viroid in Mulberry (Morus alba) in Lebanon and Italy. J Phytopathol 160, 48-51.
Elbeaino T, Abou Kubaa R, Ismaeil E, et al. (2012b) Viruses and Hop stunt viroid of fig trees in Syria. J Plant Pathol 94, 687-691.
Elbeaino T, Choueiri E, Digiaro M (2013) First report of hop stunt viroid in Lebanese fig trees. J Plant Pathol 95, 218.
Elleuch A, Hamdi I, Ellouze O, H et al. (2013) Pistachio (Pistacia vera L.) Is a new natural host of Hop stunt viroid. Virus Genes 47, 330-337.
Flores R, Durnan-Vila N, Pallas V, Semancik JS (1985) Detection of viroid and viroid-like RNAs from grapevine. J Gen Virol 66, 2095-2102.
Flores R, Hernández C, Alba AEMD, et al. F (2005) Viroids and viroid-host interactions. Annu. Rev Phytopathol 43, 117-139.
Flores R, Randles JW, Bar-Joseph M, Diener TO (1998) A proposed scheme for viroid classification and nomenclature. Arch Virol 143, 623-629.
Gambino G, Navarro B, Torchetti EM, et al. (2014) Survey on viroids infecting grapevine in Italy: identification and characterization of Australian grapevine viroid and Grapevine yellow speckle viroid 2. Eur J Plant Pathol 140, 199-205.
Gora-Sochacka A, Kierzek A, Candresse T, Zagorski W (1997) The genetic stability of Potato spindle tuber viroid (PSTVd) molecular variants. RNA 3(1), 68-74.
Guo L, Liu S, Wu Z, et al. (2008) Hop stunt viroid (HSVd) newly reported from hop in Xinjiang, China. Plant Pathol 57, 764.
Gursoz S, Gokoglu S, Ak BN (2010) Determination of mineral nutrition contents of grape and pistachio cultivars grown as inter planted orchard. Options Méditerr 94, 25-30.
Hadidi A, Candresse T (2003) Polymerase Chain Reaction. In: Viroids. Hadidi A, Flores R, Randles JW, Semanick JS (Eds). CSIRO Publishing. Collingwood, Australia. pp.115-122.
Hadidi A, Vidalakis G, Sano T (2017) Economic Significance of Fruit Tree and Grapevine. In: Viroids and Satellites. Hadidi A, Flores R, Randles JW, Palukaitis P (Eds). AP is an imprint of Elsevier pp. 15-25.
Hajizadeh M, Navarro B, Bashir NS, et al. (2012) Development and validation of a multiplex RT-PCR method for the simultaneous detection of five grapevine viroids. J Virol. Methods 179, 62-69.
Hajizadeh M, Torchetti EM, Sokhandan-Bashir N, et al. (2015) Grapevine viroids and Grapevine fanleaf virus in north-west of Iran. J Plant Pathol 97, 363-369.
Hassen IF, Kummert J, Marbot S, et al. (2004) First report of pear blister canker viroid, peach latent mosaic viroid, and hop stunt viroid infecting fruit trees in Tunisia. Plant Dis 88, 1164.
Hataya T, Tsushima T, Sano T (2017) Hop Stunt Viroid. In: Viroids and Satellites. Hadidi A, Flores R, Randles JW, Palukaitis P (Eds). AP is an imprint of Elsevier pp. 199-209.
Hurtt SS, Podleckis EV, Howell WE (1996) Integrated molecular and biological assays for rapid detection of Apple scar skin viroid in pear. Plant Dis 80, 458-462.
Jahanshahi Z, Izadpanah K, Afsharifar AR, Behjatnia SAA (2015) New hosts and comparison of biological and molecular characteristics of fig, mulberry, and citrus isolates of Hop Stunt Viroid in Iran. Iran J Virol 9, 22-30.
Kaponi M, Luigi M, Kyriakopoulou PE (2012) Mixed infections of pome and stone fruit viroids in cultivated and wild trees in Greece. New Dis Rep 26, 8.
Kawaguchi-Ito Y, Li SF, Tagawa M, et al. (2009). Cultivated grapevines represent a symptomless reservoir for the transmission of Hop stunt viroid to hop crops: 15 years of evolutionary analysis. PLoS One 4(12), e8386.
Keese P, Symons RH (1985) Domains in viroids: evidence of intermolecular RNA rearrangements and their contribution to viroid evolution. Proc Natl Acad Sci USA 82, 4582-4586.
Kofalvi SA, Marcos JF, Canizares M.C, et al. (1997) Hop stunt viroid (HSVd) sequence variants from Prunus species: evidence for recombination between HSVd isolates. J Gen Virol 78, 3177-3186.
Koltunow AM, Rezaian MA (1989) A scheme for viroid classification. Intervirology 30, 194-204.
Kumar S, Stecher G, Tamura K (2016) MEGA7: Molecular evolutionary genetics analysis version 7.0 for bigger datasets. Molecular Biol Evol 33, 1870-1874.
Lemmetty A, Werkman AW, Soukainen M (2011) First report of hop stunt viroid in greenhouse cucumber in Finland. Plant Dis 95, 615.
Luigi M, Manglli A, Tomassoli L, Faggioli F (2013) First report of hop stunt viroid in Hibiscus rosa-sinensis in Italy. New Dis Rep 27, 14.
Maddahian M, Massumi H, Heydarnejad J, et al. (2019) Biological and molecular characterization of hop stunt viroid variants from pistachio trees in Iran. J Phytopathol 167, 163-173.
Martelli GP (2014) Directory of virus and virus-like diseases of the grapevine and their agents. J Plant Pathol 96, 1-136.
Matousek J, Orctova L, Patzak J, et al. (2003) Molecular sampling of Hop stunt viroid (HSVd) from grapevines in hop production areas in the Czech Republic and hop protection. Plant Soil Envir 49, 168-175.
Matsushita Y, Usugi T, Tsuda S (2009) Host range and properties of Tomato chlorotic dwarf viroid. Eur J Plant Pathol 124, 349-352.
Moradi R, Koolivand D, Gandomani OE, Hajizadeh M (2018) Identification of some important viroids in vineyards from Zanjan. Proc. 23th Iran Plant Protection Cong, Gorgan, Iran pp. 625.
Muhire BM, Varsani A, Martin DP (2014) SDT: A virus classification tool based on pairwise sequence alignment and identity calculation. PLoS ONE 9, 1-8.
Ohno T, Takamatsu N, Meshi T, Okada Y (1983) Hop stunt viroid: Molecular cloning and nucleotide sequence of the complete cDNA copy. Nucleic Acids Res 11, 6185-6187.
Ohshima K, Sako T, Uyeda I, Shikata E (1988) Comparative studies on host range and the infectivity of hop stunt viroid-cucumber isolate (cucumber pale fruit viroid) native RNA and its cDNA. Arch Phytopathol Plant Pro 24, 475-484.
Owens RA, Flores R, Di Serio F, et al. (2012) Viroids. In: Virus Taxonomy -Ninth Report on the International Committee on Taxonomy of Viruses. King AMQ, Adams MJ, Carstens EB, Lefkowitz EJ (Eds). AP is an imprint of Elsevier pp. 1221-1234.
Owens RA, Hammond RW (2009) Viroid pathogenicity: one process, many faces. Viruses 1, 298-316.
Polivka H, Staub U, Gross HJ (1996) Variation of viroid profiles in individual grapevine plants: novel Grapevine yellow speckle viroid 1 mutants show alterations in hairpin I. J Gen Virol 77, 155-161.
Radisek S, Majer A, Jakse A, et al. (2012) First report of hop stunt viroid infecting hop in Slovenia. Plant Dis 96, 592.
Reanwarakorn K, Semancik JS (1999) Correlation of Hop stunt viroid variants to cachexia and xyloporosis diseases of citrus. Phytopathol 897, 568-574.
Rezaian MA, Koltunow AM, Krake LR (1988) Isolation of three viroids and a circular RNA from grapevines. J Gen Virol 69, 413-422.
Roistacher CN (1996) Indexing for viruses in citrus. Pages 301-319 in: Plant virus disease control. A Hadidi A, Khetarpal RK, Koganezawa H (Eds). APS Press: St Paul MN pp. 301-319.
Salami S, Moradi R, Hajizadeh M, Koolivand D (2022) Detection and phylogenetic analysis of four important viroids from vineyards in Zanjan province. J Appl Res Plant Prot 10(4): 71-80.
Sano T (2003) Hop stunt viroid. In: Viroids. Hadidi A, Flores R, Randles JW, Semancik JS (Eds). CSIRO Publishing, Collingwood, Australia pp. 207-212.
Sano T, Candresse T, Hammond RW, et al. (1992) Identification of multiple structural domains regulating viroid pathogenicity. Proc Nat Acad Sci USA 89, 10104-10108.
Sano T, Hataya T, Shikata E (1988) Complete nucleotide sequence of a viroid isolated from Etrog citron, a new member of hop stunt viroid group. Nucleic Acids Res 16, 347.
Sano T, Hataya T, Terai Y, Shikata E (1989) Hop stunt viroid strains from dapple fruit disease of plum and peach in Japan. J Gen Virol 70, 1311-1319.
Sano T, Mimura R, Ohshima K (2001) Phylogenetic Analysis of Hop and Grapevine Isolates of Hop stunt viroid supports a Grapevine Origin for Hop Stunt Disease. Virus Genes 22, 53-59.
Sano T, Oshima K, Hataya T, et al. (1985) A viroid-like RNA isolated from grapevine has high sequence homology with hop stunt viroid. J Gen Virol 66, 333-338.
Sano T, Ohshima K, Hataya T, et al (1986) A viroid resembling Hop stunt viroid in grapevines from Europe, the United States and Japan. J Gen Virol 67, 1673-1678.
Sano T, Uyeda I, Shikata E, et al. (1984) Nucleotide sequence of cucumber pale fruit viroid: homology to hop stunt viroid. Nucleic Acids Res 12, 3427-3434.
Sasaki M, Shikata E (1977) On some properties of hop stunt disease agent, a viroid. Proc Japan Acad 53B, 109112.
Semancik JS, Roistacher CN, Rivera-Bustamante R, Duran-Vila N (1988) Citrus cachexia viroid, a new viroid of citrus: relationship to viroids of the exocortis disease complex. J Gen Virol 69, 3059-3068.
Serra P, Gago S, Duran-Vila N (2008) A single nucleotide change in Hop stunt viroid modulates citrus cacheixa symptoms. Virus Res 138, 130-134.
Sharifi M, Massumi H, Heydarnejad J, et al. (2008) Analysis of biological and molecular variability of Watermelon mosaic virus isolates from Iran. Virus Genes 37, 304-313.
Shikata E (1990) New viroids from Japan. Semin Virol 1, 107-115.
Singh RP, Ready KFM (2003) Biological indexing. In: Viroids. Hadidi A, Flores R, Randles JW, Semancik JS (Eds) CSIRO Publishing, Collingwood, Australia. pp 89-94.
Singh R, Ready KFM, Hadidi A (2003) Viroids in North America and global distribution of viroid diseases. In: Viroids. Hadidi A, Flores R, Randles JW, Semancik JS (Eds). CSIRO Publishing, Collingwood, Australia pp. 255-264.
Staub U, Polivka H, Herrmann JV, Gross HJ (1995) Transmission of grapevine viroids is not likely to occur mechanically by regular pruning. Vitis 34, 119-123.
Taylor RH, Woodham RC (1972) Grapevine yellow speckle a newly recognized graft-transmissible disease of Vitis. Aust J Agric Res 23, 447-452.
Van Dorst HJM, Peters D (1974) Some biological observations on pale fruit, a viroid-incited disease of cucumber. Neth J Plant Pathol 80, 85-96.
Walia Y, Dhir S, Ram R, et al. (2014) Identification of the herbaceous host range of Apple scar skin viroid and analysis of its progeny variants. Plant Pathol 63, 684-690.
Wassenegger M, Spieker RL, Thalmeir S, et al. (1996) A single nucleotide substitution converts potato spindle tuber viroid (PSTVd) from a noninfectious to an infectious RNA for Nicotiana tabacum. Virology 226(2), 191-197.
Yakoubi S, Elleuch A, Besaies N, et al. (2007) First report of hop stunt viroid and citrus exocortis viroid on fig with symptoms of fig mosaic disease. J Phytopathol 155, 125-128.
Zaki-aghl M, Izadpanah K (2004) Identification and Transmission of Grapevine Yellow Speckle Disease in Iran. Proc. 16th Iran Plant Protection Cong, Tabriz, Iran pp. 359.
Zaki-aghl M, Izadpanah K (2006) Sequencing and genome analysis of Iranian isolate of grapevine yellow speckle viroid 1. Proc. 17th Iran. Plant Protection. Cong., Karaj, Iran, pp. 358.
Zaki-aghl M, Izadpanah K (2010) Identification and partial molecular characterization of grapevine viroids in Fars Province. Iran. J Plant Pathol 46(3), 249-262.
Zhang BL, Liu GY, Liu CQ, et al. (2009) Characterization of Hop stunt viroid (HSVd) isolates from jujube trees (Ziziphus jujuba). Eur J Plant Pathol 125, 665-669.
Zhang YP, Uyemoto JK, Kirkpatrick BC (1998) A small-scale procedure for extracting nucleic acids from woody plants infected with various phytopathogens for PCR assay. J Virol Methods 71, 45-50.
Zhang Z, Shuishui-Qi S, Tang N, et al. (2014) Discovery of replicating circular RNAs by RNA-seq and computational algorithms. PLoS Pathog 10, e1004553.
Zhang Z, Zhou Y, Guo R, et al. (2012) Molecular characterization of Chinese hop stunt viroid isolates reveals a new phylogenetic group and possible cross transmission between grapevine and stone fruits. Eur J Plant Pathol 134, 217-225.
Zhou Y, Guo R, Cheng Z, et al. (2006) First report of hop stunt viroid from Prunus persica with dapple fruit symptoms in China. Plant Pathol 55, 564.
Zuker M (2003) Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res 31, 3406-3415.
مجله بیوتکنولوژی کشاورزی
دوره 14، شماره 3
مهر 1401
صفحه 127-150

فایل ها

هم رسانی

ارجاع به این مقاله

آمار