Iranian Journal of Plant Protection Science

Iranian Journal of Plant Protection Science

Molecular and phylogenetic characteristics of sunflower isolate of Bean ‎yellow mosaic virus ‎

Document Type : Research Paper

Authors
Mohammad Morad Moradi 1
Ahmad Hosseini 2
Samin Hosseini Farhangi 3
1 Former M.Sc. Student, Department of Plant Protection, Faculty of Agriculture, Vali-e-Asr University of ‎Rafsanjan, Rafsanjan, Iran
2 Assistant Professor, Department of Plant Protection, Faculty of Agriculture, Vali-e-Asr University of ‎Rafsanjan, Rafsanjan, Iran
3 Assistant Professor, Department of Plant Protection, Faculty of Agriculture, Vali-e-Asr University of Rafsanjan, Rafsanjan, Iran
10.22059/ijpps.2019.287135.1006901
Abstract
Bean yellow mosaic virus (BYMV) is one of the most important members of the genus Potyvirus that is distributed worldwide. In the present study, the complete genome sequence and molecular characteristics of a BYMV sunflower isolate (BYSun) from Iran has been reported. The complete nucleotide sequence of BYSun was determined using degenerate and specific primers and 5`-RACE. The viral genome comprises 9547 nucleotides, excluding a 3´-terminal poly (A) sequence. The genome of BYSun has a 206 nt 5´-non coding and a 171 nt 3´-non coding region. The RNA encodes a single polyprotein of 3056 amino acid residues and has a deduced genome organization typical for the members of the genus Potyvirus and nine cleavage sites of the polyprotein were predicted. The small overlapping ORF (PIPO) in the P3 gene was also deduced. When analyzed using the RDP4 program, at least one recombination breakpoint was identified in BYSun genome. BYSun along with 23 full-length sequences of BYMV isolates from Genbank were subjected to phylogenetic analysis that showed the highest nucleotide and amino acid sequence identitywith Australian isolate of BYMV-S isolated from Broad bean. Phylogenetic analysis of different BYMV isolates sequences revealed existence of six to eight phylogenetic groupings depending on parts of investigated genome. BYSun and BYMV-S grouped apart from other isolates and were placed within a distinct group, currently designated “S”. This is the first report of a full-length sequence of a BYMV isolate from Iran.
Keywords
Bean yellow mosaic virus
full length genome sequence
sunflower
phylogeny
  1. Adams, M.J., Antoniw, J.F. & Beaudoin, F. (2005). Overview and analysis of the polyprotein cleavage sites in the family Potyviridae. Molecular Plant Pathology, 6, 471-487.
  2. Chen, J., Chen, J. & Adams, M.J. (2001). A universal PCR primer to detect members of the Potyviridae and its use to examine the taxonomic status of several members of the family. Archives of Virology, 146, 757-766.
  3. Chang, C., Hiebert, E. & Purcifull, D. E. (1988). Purification, characterization, and immunological analysis of nuclear inclusions induced by bean yellow mosaic and clover yellow vein potyviruses. Phytopathology, 78(10), 1266-1275.
  4. Chu, P., Anderson, B., Khan, M., Shukla, D. & Higgins, T. (1999). Production of Bean yellow mosaic virus resistant subterranean clover (Trifolium subterraneum) plants by transformation with the virus coat protein gene. Annals of Applied Biology, 135, 469-480.
  5. Chung, B. Y. W., Miller, W. A., Atkins, J. F. & Firth, A. E. (2008). An overlapping essential gene in the Potyviridae. Proceedings of the National Academy of Sciences, 105, 5897-5902.
  6. Clark, M. F. & Adams, A. N. (1977). Characteristics of the microplate method of enzyme-linked immunosorbent assay for the detection of plant viruses. Journal of General Virology, 34, 475-483.
  7. Dombrovsky, A., Huet, H., Chejanovsky, N. & Raccah, B. (2005). Aphid transmission of a potyvirus depends on suitability of the helper component and the N terminus of the coat protein. Archives of Virology, 150, 287-298.
  8. Gallie, D. R. & Walbot, V. (1992). Identification of the motifs within the Tobacco mosaic virus 5′-leader responsible for enhancing translation. Nucleic Acids Research, 20, 4631-4638.
  9. Gal-On, A. (2007). Zucchini yellow mosaic virus: insect transmission and pathogenicity. Molecular Plant Pathology, 8, 139-150.
  10. Goetz, R., Huth, W., Lesemann, D.E. & Maiss, E. (2002). Molecular and serological relationships of Spartina mottle virus (SpMV) strains from Spartina spec. and from Cynodon dactylon to other members of the Potyviridae. Archives of Virology, 147, 379-391.
  11. Guyatt, K. J., Proll, D. F., Menssen, A. & Davidson, A. D. (1996). The complete nucleotide sequence of bean yellow mosaic potyvirus RNA. Archives of Virology, 141(7), 1231-1246.
  12. Ha, C., Coombs, S., Revill, P.A., Harding, R.M., Vu, M. & Dale, J. L. (2008). Design and application of two novel degenerate primer pairs for the detection and complete genomic characterization of potyviruses. Archives of Virology, 153, 25-36.
  13. Hammond, J. & Hammond, R. W. (2003). The complete nucleotide sequence of isolate BYMV-GDD of Bean yellow mosaic virus, and comparison to other potyviruses. Archives of Virology, 148(12), 2461-2470.
  14. Kaur, C., Raj, R., Srivastava, A., Kumar, S. & Raj, S.K. (2018). Sequence analysis of six full-length bean yellow mosaic virus genomes reveals phylogenetic diversity in India strains, suggesting subdivision of phylogenetic group-IV. Archives of Virology, 163, 235-242.
  15. Kehoe, M. A., Coutts, B. A., Buirchell, B. J. & Jones, R. A. (2014). Plant virology and next generation sequencing: experiences with a Potyvirus. PLoS ONE, 9(8), e104580.
  16. Parrella, G. & Lanave, C. (2009). Identification of a new pathotype of Bean yellow mosaic virus (BYMV) infecting blue passion flower and some evolutionary characteristics of BYMV. Archives of Virology, 154, 1689-1694.
  17. Rabiee, S. (2013). Distribution and characterization of most prevalent potyviruses in sunflower fields of Isfahan province. M.Sc. Thesis in Plant Pathology, Faculty of Agriculture, Vali-e-Asr University of Rafsanjan, Rafsanjan, Iran (in Farsi with English abstract).
  18. Riechmann, J.L., Lain, S. & Garcia, J.A. (1992). Highlights and prospects of potyvirus molecular biology. Journal of General Virology, 73, 1-16.
  19. Sasaya, T., Shimizu, T., Nozu, Y., Nishiguchi, M., Inouye, N. & Koganezawa, H. (1997). Biological, serological, and molecular variabilities of clover yellow vein virus. Phytopathology, 87(10), 1014-1019.
  20. Shukla, D. D., Ward, C. W. & Brunt, A. A. (1994). The Potyviridae. Wallingford, UK, CAB International.
  21. Wylie, S., Coutts, B., Jones, M. & Jones, R. (2008). Phylogenetic analysis of Bean yellow mosaic virus isolates from four continents: relationship between the seven groups found and their hosts and origins. Plant Disease, 92, 1596-1603.
  22. Wylie, S. & Jones, R. (2009). Role of recombination in the evolution of host specialization within Bean yellow mosaic virus. Phytopathology, 99, 512-518.
  23. Xu, D. L., Zhou, G. H., Xie, Y. J., Mock, R. & Li, R. (2010). Complete nucleotide sequence and taxonomy of Sugarcane streak mosaic virus, member of a novel genus in the family Potyviridae. Virus Genes, 40, 432-439.
  24. Zhou, Y., Mammen, M.P., Klungthong, C., Chinnawirotpisan, P., Vaughn, D.W., Nimmannitya, S., Kalayanarooj, S., Holmes, E.C. & Zhang, C. (2006). Comparative analysis reveals no consistent association between the secondary structure of the 3'-untranslated region of dengue viruses and disease syndrome. Journal of General Virology, 87, 2595-2603.

    

Iranian Journal of Plant Protection Science
Volume 50, Issue 2
February 2020
Pages 261-276

  • Receive Date 18 August 2019
  • Revise Date 03 December 2019
  • Accept Date 08 December 2019