با همکاری انجمن‏‌ بیماری شناسی گیاهی ایران

نوع مقاله : بیماری‌شناسی گیاهی

نویسندگان

1 دانشجوی کارشناسی ارشد بیماری شناسی گیاهی، دانشگاه کردستان

2 استادیار گروه گیاهپزشکی، دانشگاه کردستان

چکیده

پروتئین پوششی نقش‌های متعددی را در مراحل سیکل آلودگی به عهده دارد و گزینه مناسبی برای مطالعات تبارزایی و تنوع ژنتیکی به حساب می‌آید. به منظور بررسی آنالیز تبارزایی، تنوع ژنتیکی و فشار انتخاب بر ژن پروتئین پوششی جدایه‌های ویروس موزاییک زرد کدو (ZYMV)، هفت جدایه B10، B21، B22، H7، W5، Z3 و Z14 از غرب کشور و از میزبان‌های متفاوت تعیین توالی و با 65 جدایه قابل دسترس در پایگاه داده‌های نوکلئوتیدی مورد مقایسه قرار گرفتند. درخت تبارزایی جدایه‌های این ویروس بر اساس 432 نوکلئوتید از ژن پروتئین پوششی در نرم‌افزار MEGA6 ترسیم و برآوردهای تنوع ژنتیکی و فشار انتخاب وارد بر پروتئین پوششی با نرم‌افزار DnaSP انجام شد. در آنالیز تبارزایی، جدایه‌ها در سه گروه مجزا تفکیک شدند که جدایه‌های B10، B21، B22، H7 و Z3 در گروه جدایه‌های ایرانی و اروپایی و دو جدایه Z14 و W5 در گروهی مجزا همراه با جدایه‌های شرقی قرار گرفتند. تنوع ژنتیکی (π) بر اساس قسمتی از ژن پروتئین پوششی(CP) نشان داد که جدایه‌های شرق نسبت به جدایه‌های ایران، اروپا و آمریکا بیشترین تنوع (π=0.104) را دارند. همچنین، این قسمت از ژنCP در جدایه‌های آمریکا از کمترین تنوع (π=0.0211) برخوردار بود. کمتر از یک شدن نسبت جانشینی مترادف (dS)به غیر مترادف (dN) بیانگر نقش مؤثر انتخاب منفی در تکامل این ژن بوده است. بررسی نوترکیبی با نرم‌افزار version 4.63 RDP4 حاکی از عدم نوترکیبی در این بخش از ژنوم بود و به نظر می‌رسد که تغییرات آن در اثر جهش حاصل شده باشد.

کلیدواژه‌ها

موضوعات

عنوان مقاله [English]

Genetic diversity of Zucchini yellow mosaic virus isolates based on the partial coat protein gene

نویسندگان [English]

  • H. R. MAGHAMNIA 1
  • M. HAJIZADEH 2
  • A. AZIZI 2

چکیده [English]

Coat protein in plant viruses plays multiple roles in all infection cycle steps and commonly used in phylogenetic studies. To order phylogenetic analysis, genetic diversity and selection forces on partial coat protein of Zucchini yellow mosaic virus isolates, seven isolates B10, B21, B22, H7, W5, Z3 and Z14 from west of Iran were sequenced of several hosts and compared to 64 isolates retrieved from the GenBank. Phylogenetic tree were constructed based on 432 nucleotides of CP gene in MEGA6 software and estimation of genetic diversity and selection forces were performed in DnaSP version 5.10.05. In phylogenetic analysis, isolates B10, B21, B22, H7, Z3 were placed into European and Iranian group whereas, W5 and Z14 were placed in distinct group with east isolates. The largest nucleotide diversity (π=0.104) was obtained for the east isolates were in compared to Iranian, European and American isolates whereas, lowest diversity (π=0.0211) were found for the American isolates. Negative selection forces in CP gene history were deduced by ratio of non-synonymous nucleotide diversity to synonymous nucleotide diversity (dN/dS) was less than one. No recombination events were detected in this part of ZYMV-CP isolates and seems that genetic diversity in this part of genome resulted from nucleotide mutations

کلیدواژه‌ها [English]

  • Negative selection
  • phylogeny
  • Recombination
  • ZYMV
AL-ANI, R. A., M. A. ADHAB, A. A. ALI and S. N. DIWAN, 2011. Zucchini yellow mosaic virus: Characterization and management in Iraq, International Journal of Current Research, 11: 220-224.
AZARFAR, A., K. IZADPANAH, A. AFSHARIFAR and M. MASSUMI, 2012. Purification and the complete genome sequence of Zucchini yellow mosaic virus-Fars isolate, Iranian Journal of Plant Pathology, 48: 403-409. (in Persian with English summary).
BANANEJ, K., T. KESHAVARZ, A. VAHDAT, G. HOSSEINI SALEKDEH and M. GLASA, 2008. Biological and molecular variability of Zucchini yellow mosaic virus in Iran, Journal of Phytopathology, 156: 654-659.
BIEBRICHER, C. and M. EIGEN, 2006. What is a quasispecies? In Quasispecies: Concept and Implications for Virology, 1-31 pp.
COUTTS, B. A., M. A. KEHOE, C. G. WEBSTER, S. J. WYLIE and R. A. C. JONES, 2011. Zucchini yellow mosaic virus: biological properties, detection procedures and comparison of coat protein gene sequences, Archives of Virology, 156: 2119-2131.
DESBIEZ, C., C. WIPF-SCHEIBEL, F. GRANIER, C. ROBAGLIA, T. DELAUNAY and H. LECOQ, 1996. Biological and molecular variability of Zucchini yellow mosaic virus in the island of Martinique, Plant Disease, 80: 203–207.
DESBIEZ, C., C. WIPF-SCHEIBEL and H. LECOQ, 2002. Biological and serological variability evolution and molecular epidemiology of Zucchini yellow mosaic virus (ZYMV, Potyvirus) with special reference to Caribbean islands, Virus Research, 85: 5-16.
FOISSAC, X., L. SAVALLE-DUMAS, P. GENTIT, M. J. DULUCQ and T. CANDRESSE, 2000. Polyvalent detection of fruit tree Tricho, Chapillo and Faveaviruses by nested RT-PCR using degenerated and inosine containing primers (PDO RT-PCR), Acta Horticulture, 357: 52-59.
GHORBANI, S. 1988. Isolation of Zucchini yellow mosaic virus in the Tehran Province, Iranian Journal of Plant Pathology, 24: 13-15. (In Farsi With English Summary).
GLASA, M. and S. PITTNEROVÁ, 2006. Complete genome sequence of a Slovak isolate of Zucchini yellow mosaic virus (ZYMV) provides further evidence of a close molecular relationship among central European ZYMV isolates, Journal of Phytopathology, 154: 436-440.
GLASA, M., J. SVOBODA and S. NOVÁKOVÁ, 2007. Analysis of the molecular and biological variability of Zucchini yellow mosaic virus isolates from Slovakia and Czech Republic, Virus Genes, 35: 415-421.
HASIÓW-JAROSZEWSKA, B., N. RYMELSKA, N. BORODYNKO and H. POSPIESZNY, 2013. Biological and molecular characterization of the polish Zucchini yellow mosaic virus isolates, Acta Scientiarum Polonorum, Hortorum Cultus, 12: 75-85.
HALL, T. A. 1999. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT, Nucleic Acids Symposium Series, 41: 95-98.
KWON, S. W., M. S. KIM, H. S. CHOI and K. H. KIM, 2005. Biological characteristics and nucleotide sequences of three Korean isolates of Zucchini yellow mosaic virus, Journal of General Plant Pathology, 71: 80-85.
LECOQ, H., C. WIPF-SCHEIBEL, C. CHANDEYSSON, A. LE VAN, F. FABRE and C. DESBIEZ, 2009. Molecular epidemiology of Zucchini yellow mosaic virus in France: an historical overview, Virus Research, 141: 190-200.
LIBRADO, P. and J. ROZAS, 2009. DnaSP v5: a software for comprehensive analysis of DNA polymorphism data, Bioinformatics, 25: 1451-1452.
LIN, S. S., R. F. HOU and S. D. YEH, 2001. Complete genome sequence and genetic organization of a Taiwan isolate of Zucchini yellow mosaic virus, Botanical Bulletin of Academia Sinica, 42: 243-250.
LISA, V., G. BOCCARDO, G. D’AGOSTINO, G. DELLAVALLE and M. D’AQUILIO, 1981. Characterization of a potyvirus that causes zucchini yellow mosaic virus, Phytopathology, 71: 667-672.
MARTIN, D. P., B. MURRELL, M. GOLDEN, A. KHOOSAL and B. MUHIRE, 2015. RDP4: Detection and analysis of recombination patterns in virus genomes, Virus Evolution, 1 (1), vev003, doi: 10.1093/ve/vev003.
MASSUMI, H., M. SHAABANIAN, J. HEYDARNEJAD, A. H. HOSSEINI POUR and H. RAHIMIAN, 2011. Host range and phylogenetic analysis of Iranian isolates of Zucchini yellow mosaic virus, Journal of Plant Pathology, 93: 187-193.
MIRHOSSEINI, H., H. RAHIMIAN, V. BABAEIZAD and S. NORI, 2014. Phylogenetic analysis of Cylindrical Inclusion gene in Zucchini yellow mosaic virus isolated from Mazandaran Province. First National Congress on Biology and Natural Sciences in Iran, Tehran.
MOHAMMADI, K. 2015. Detection of some cucurbit infecting viruses in Kurdistan province by RT-PCR method. M.SC Thesis, University of Kurdistan, p. 112. (In Persian with English summary).
MUHIRE, B. M., A. VARSANI, D. P. MARTIN, 2014. SDT: A Virus Classification Tool Based on Pair wise Sequence Alignment and Identity Calculation, PLOS one, 9: e108277.
NOVÁKOVÁ, S., J. SVOBODA and M. GLASA, 2014. Analysis of the complete sequences of two biologically distinct Zucchini yellow mosaic virus isolates further evidences the involvement of a single amino acid in the virus pathogenicity, Acta Virologica, 58: 364-367.
ROOSSINCK, M. J. 1997. Mechanisms of plant virus evolution, Annual Review of Phytopathology, 35:191–209
SAFAEIZADEH, M. 2008. Comparative biological and molecular variability of Zucchini yellow mosaic virus in Iran, Asian Journal Plant Pathology, 2: 30-39.
SHAABANIAN, M., H. MASSUMI, A. HOSSEINI POUR, J. HEYDARNEJAD and N. PORAMINI, 2005. Detection and distribution of Zucchini yellow mosaic virus based on Immunocapture RT-PCR in some parts of Iran, The Fourth National Biotechnology Conference Islamic Republic of Iran, Kerman. P. 2098.
SHIMOMOTO, Y. and S. TAKEUCHI, 2006. Simultaneous detection of three Potyvirus species from Cucurbitaceae crops by multiplex RT-PCR, Japanese Journal of Phytopathology. 72: 146-149.
SIMMONS, H. E., E. C. HOLMES and A. G. STEPHENSON, 2008. Rapid evolutionary dynamics of zucchini yellow mosaic virus, Journal of General Virology, 89: 1081-1085.
SOKHANDAN-BASHIR, N. and U. MELCHER, 2012. Population genetic analysis of grapevine fan leaf virus, Archives of virology, 157: 1919-1929.
TAMURA, K., G. STECHER, D. PETERSON, A. FILIPSKI, and S. KUMAR, 2013. MEGA6: Molecular Evolutionary Genetics Analysis version 6.0, Molecular Biology and Evolution, 30: 2725–2729.
TOBIAS, I., B. SZABO, K. SALANKI, L. SARI, H. KUHLMANN, L. PALKOVICS and M. PITRAT, 2008. Seedborne transmission of Zucchini yellow mosaic virus and Cucumber mosaic virus in Styrian Hulless group of Cucurbita pepo. In: Proceedings of the IXth EUCARPIA meeting on genetics and breeding of Cucurbitaceae. INRA, Avignon (France), May 21-24th, p. 189-197.
ZHAO, M. F., J. CHEN, H. Y. ZHENG, M. J. ADAMS and J. P. CHEN, 2003. Molecular analysis of Zucchini yellow mosaic virus isolates from Hangzhou, China, Journal of Phytopathology, 151: 307-311.