Skip to main content
SpringerLink
Log in

The complete genome sequences of two naturally occurring recombinant isolates of Sugarcane mosaic virus from Iran

  • Published:
Virus Genes Aims and scope Submit manuscript

Abstract

Sugarcane mosaic virus (SCMV) is the most prevalent virus causing sugarcane mosaic and maize dwarf mosaic diseases. Here, we presented the first two complete genomic sequences of Iranian SCMV isolates, NRA and ZRA from sugarcane and maize. The complete genome sequences of NRA and ZRA were, respectively, 9571 and 9572 nucleotides (nt) in length, excluding the 3′-terminal poly(A) tail. Both isolates contained a 5′-untranslated region (UTR) of 149 nt, an open reading frame of 9192 nt encoding a polyprotein of 3063 amino acids (aa), and 3′-UTR of 230 nt for NRA and 231 nt for ZRA. SCMV-NRA and -ZRA genome nucleotide sequences were 97.3 % identical and shared nt identities of 79.1–92 % with those of other 21 SCMV isolates available in the GenBank, highest with the isolate Bris-A (AJ278405) (92 and 91.7 %) from Australia. When compared for separate genes, most of their genes shared the highest identities with Australian and Argentinean isolates. Phylogenetic analysis of the complete genomic sequences reveals that SCMV can be clustered to three groups. Both NRA and ZRA were clustered with sugarcane isolates from Australia and Argentina in group III but formed a separate sublineage. Recombination analysis showed that both isolates were intraspecific recombinants, and represented two novel recombination patterns of SCMV (in the P1 coding region). NRA had six recombination sites within the P1, HC-Pro, CI, NIa-Vpg, and NIa-pro coding regions, while ZRA had four within the P1, HC-Pro, NIa-Pro, and NIb coding regions.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2

Similar content being viewed by others

References

  1. M.J. Adams, F.M. Zerbini, R. French, F. Rabenstein, D.C. Stenger, J.P.T. Valkonen, in Virus Taxonomy: 9th Report of the International Committee on the Taxonomy of Viruses, ed. by A.M.Q. King, M.J. Adams, E.B. Carstens (Elsevier Academic Press, San Diego, 2012), pp. 1069–1089

    Google Scholar 

  2. H. Koike, A.G. Gillaspie, in Diseases of Sugarcane: Major Diseases, ed. by C. Ricaud, B.T. Egan, A.G. Gillaspie, G.G. Hughes (Elsevier, Amsterdam, 1989), pp. 301–322

    Chapter  Google Scholar 

  3. B.F. Janson, C.W. Ellett, Plant Dis. Rep. 47, 1107–1108 (1963)

    Google Scholar 

  4. D.D. Shukla, M.J. Frenkel, N.M. Mckern, C.W. Ward, J. Jilka, M. Tosic, R.E. Ford, Arch. Virol. 5, 363–373 (1992)

    Article  CAS  Google Scholar 

  5. D.L. Seifers, R. Salomon, V. Marie-Jeanne, B. Alliot, P. Signoret, S. Haber, A. Loboda, W. Ens, Y.M. She, K.G. Standing, Phytopathology 90, 505–513 (2000)

    Article  CAS  PubMed  Google Scholar 

  6. R. Gotz, E. Maiss, Arch. Virol. 147, 1573–1583 (2002)

    Article  CAS  PubMed  Google Scholar 

  7. Z.F. Fan, W.J. Wang, X. Jiang, X.M. Liang, F.R. Wang, H.F. Li, Plant Pathol. 53, 796 (2004)

    Article  Google Scholar 

  8. J. Chen, J.P. Chen, M.J. Adams, Arch. Virol. 147, 1237–1246 (2002)

    Article  CAS  PubMed  Google Scholar 

  9. M.P. Grisham, in A Guide to Sugarcane Diseases, ed. by P. Rott, R.A. Bailey, J.C. Comstock, B.J. Croft, A.S. Saumtally (Cirad/Issct, Montpellier, 2000), pp. 249–254

    Google Scholar 

  10. S. Urcuqui-Inchima, A.L. Haenni, F. Bernardi, Virus Res. 74, 157–175 (2001)

    Article  CAS  PubMed  Google Scholar 

  11. B.Y. Chung, W.A. Miller, J.F. Atkins, A.E. Firth, Proc. Natl Acad. Sci. USA 105, 5897–5902 (2008)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. L. Wu, X. Zu, S. Wang, Y. Chen, Crop Prot. 42, 74–78 (2012)

    Article  Google Scholar 

  13. F. Amiri, K. Izadpanah, in Proceedings of the 11th Plant Protection Congress, Iran, 1993, p. 126

  14. K. Izadpanah, R. Kamran, in Proceedings of the 12th Plant Protection Congress, Iran, 1995, p. 94

  15. M.R. Mohammadi, M. Koohi-Habibi, G. Mosahebi, B. Hajieghrari, Commun. Agric. Appl. Biol. Sci. 71, 1311–1319 (2006)

    CAS  PubMed  Google Scholar 

  16. M. Masumi, A. Zare, K. Izadpanah, Iran. J. Plant Pathol. 43, 1–16 (2007)

    Google Scholar 

  17. M.M.C. Lai, Microbiol. Rev. 56, 61–79 (1992)

    CAS  PubMed  PubMed Central  Google Scholar 

  18. E.R. Chare, E.C. Holmes, Arch. Virol. 151, 933–946 (2006)

    Article  CAS  PubMed  Google Scholar 

  19. P. Nagy, in Plant Virus Evolution, ed. by M.J. Roossinck (Springer, Berlin, 2008), pp. 133–156

    Chapter  Google Scholar 

  20. F. Garcia-Arenal, A. Fraile, J.M. Malpica, Int. Microbiol. 6, 225–232 (2003)

    Article  PubMed  Google Scholar 

  21. T. Ogawa, Y. Tomitaka, A. Nakagawa, K. Ohshima, Virus Res. 131, 199–212 (2008)

    Article  CAS  PubMed  Google Scholar 

  22. A. Padhi, K. Ramu, Virus Genes 42, 282–285 (2011)

    Article  CAS  PubMed  Google Scholar 

  23. M.A. Achon, L. Serrano, N. Alonso-Duenas, C. Porta, Arch. Virol. 152, 2073–2078 (2007)

    Article  CAS  PubMed  Google Scholar 

  24. Y. Cheng, J. Chen, J.P. Chen, Sci. China, Ser. C 45, 322–330 (2002)

    Article  CAS  Google Scholar 

  25. Z.F. Fan, H.Y. Cheng, X.M. Liang, H.F. Li, Arch. Virol. 148, 773–782 (2003)

    Article  CAS  PubMed  Google Scholar 

  26. Y.W. Zhong, A.Y. Guo, C.B. Li, B.Q. Zhuang, M. Lai, C.H. Wei, J.C. Luo, Y. Li, Virus Genes 30, 75–83 (2005)

    Article  CAS  PubMed  Google Scholar 

  27. B. Gao, X.W. Cui, X.D. Li, C.Q. Zhang, H.Q. Miao, Virus Genes 43, 390–397 (2011)

    Article  CAS  PubMed  Google Scholar 

  28. G. Mahuku, A.W. Wangai, K. Sadessa, A. Teklewold, D. Ayalneh, I. Adams, J. Smith, E. Bottomley, S. Bryce, B. Feyissa, Plant Dis. (2015). doi:10.1094/PDIS-04-15-0373-PDN

    Google Scholar 

  29. C. Ha, P. Revill, R.M. Harding, M. Vu, J.L. Dale, Arch. Virol. 153, 45–60 (2008)

    Article  CAS  PubMed  Google Scholar 

  30. M.F. Perera, M.P. Filippone, C.J. Ramallo, M.I. Cuenya, M.L. García, L.D. Ploper, A.P. Castagnaro, Phytopathology 99, 38–49 (2009)

    Article  CAS  PubMed  Google Scholar 

  31. R. Viswanathan, R. Karuppaiah, M. Balamuralikrishnan, Virus Genes 39, 375–386 (2009)

    Article  CAS  PubMed  Google Scholar 

  32. O.M. Alegria, M. Royer, M. Bousalem, M. Chatenet, M. Peterschmitt, J.C. Girard, P. Rott, Arch. Virol. 148, 357–372 (2003)

    Article  CAS  PubMed  Google Scholar 

  33. A. Meunier, J.F. Schmit, A. Stas, N. Kutluk, C. Bragard, Appl. Environ. Microbiol. 69, 2356–2360 (2003)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  34. K. Tamura, D. Peterson, N. Peterson, G. Stecher, M. Nei, S. Kumar, Mol. Biol. Evol. 28, 2731–2739 (2011)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  35. D.P. Martin, P. Lemey, M. Lott, V. Moulton, V.D. Posada, P. Lefeuvre, Bioinformatics 26, 2462–2463 (2010)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  36. D. Martin, E. Rybicki, Bioinformatics 16, 562–563 (2000)

    Article  CAS  PubMed  Google Scholar 

  37. M. Padidam, S. Sawyer, C.M. Fauquet, Virology 265, 218–225 (1999)

    Article  CAS  PubMed  Google Scholar 

  38. D. Posada, K.A. Crandall, Proc. Natl Acad. Sci. USA 98, 13757–13762 (2001)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  39. M.J. Gibbs, J.S. Armstrong, A.J. Gibbs, Bioinformatics 16, 573–582 (2000)

    Article  CAS  PubMed  Google Scholar 

  40. J. Maynard Smith, J. Mol. Evol. 34, 126–129 (1992)

    Google Scholar 

  41. M.F. Boni, D. Posada, M.W. Feldman, Genetics 176, 1035–1047 (2007)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  42. D.P. Martin, D. Posada, K.A. Crandall, C. Williamson, AIDS Res. Hum. Retroviruses 21, 98–102 (2005)

    Article  CAS  PubMed  Google Scholar 

  43. U. Puurand, K. Makinen, L. Paulin, M. Saarma, J. Gen. Virol. 75, 457–461 (1994)

    Article  CAS  PubMed  Google Scholar 

  44. H.A. Lütcke, K.C. Chow, F.S. Mickel, K.A. Moss, H.F. Kern, G.A. Scheele, EMBO J. 6, 43–48 (1987)

    PubMed  PubMed Central  Google Scholar 

  45. D.R. Gallie, V. Walbot, Nucleic Acids Res. 20, 4631–4638 (1992)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  46. T. Turpen, J. Gen. Virol. 70, 1951–1960 (1989)

    Article  CAS  PubMed  Google Scholar 

  47. J. Basso, P. Dallaire, P.J. Charest, Y. Devantier, J.-F. Laliberté, J. Gen. Virol. 75, 3157–3165 (1994)

    Article  CAS  PubMed  Google Scholar 

  48. R. Haldeman-Cahill, J.A. Daros, J.C. Carrington, J. Virol. 72, 4072–4079 (1998)

    CAS  PubMed  PubMed Central  Google Scholar 

  49. P. Kong, H.H. Steinbiss, Arch. Virol. 143, 1791-1799 (1998)

  50. M.J. Adams, J.F. Antoniw, F. Beaudoin, Mol. Plant Pathol. 6, 471–487 (2005)

    Article  CAS  PubMed  Google Scholar 

  51. W.G. Dougherty, B.L. Semler, Microbiol. Rev. 57, 781–822 (1993)

    CAS  PubMed  PubMed Central  Google Scholar 

  52. C. Robaglia, M. Durand-Tardif, M. Tronchet, G. Boudazin, S. Astier-Manifacier, F. Casse-Delbart, J. Gen. Virol. 70, 935–947 (1989)

    Article  CAS  PubMed  Google Scholar 

  53. J. Chen, M.J. Adams, H.Y. Zheng, J.P. Chen, Arch. Virol. 148, 1165–1173 (2003)

    Article  CAS  PubMed  Google Scholar 

  54. C. Plisson, M. Drucker, S. Blanc, S. German-Retana, O. Le Gall, D. Thomas, P. Bron, J. Biol. Chem. 278, 23753–23761 (2003)

    Article  CAS  PubMed  Google Scholar 

  55. S. Blanc, E.D. Ammar, S. Garcia-Lampasona, V.V. Dolja, C. Llave, J. Baker, T.P. Pirone, J. Gen. Virol. 79, 3119–3122 (1998)

    Article  CAS  PubMed  Google Scholar 

  56. A. Gal-On, Phytopathology 90, 467–473 (2000)

    Article  CAS  PubMed  Google Scholar 

  57. Y.M. Shiboleth, E. Haronsky, D. Leibman, T. Arazi, M. Wassenegger, S.A. Whitham, V. Gaba, A. Gal-On, J. Virol. 81, 13135–13148 (2007)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  58. S. Cronin, J. Verchot, R. Haldeman-Cahill, M.C. Schaad, J.C. Carrington, Plant Cell 7, 549–559 (1995)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  59. V.V. Dolja, R. Haldeman, N.L. Robertson, W.G. Dougherty, J.C. Carrington, EMBO J. 13, 1482–1491 (1994)

    CAS  PubMed  PubMed Central  Google Scholar 

  60. J.L. Riechmann, S. Lain, J.A. Garcia, J. Gen. Virol. 73, 1–16 (1992)

    Article  CAS  PubMed  Google Scholar 

  61. G. Kadare, A.-L. Haenni, J. Virol. 71, 2583–2590 (1997)

    CAS  PubMed  PubMed Central  Google Scholar 

  62. J. Jiang, C. Patarroyo, D. Garcia Cabanillas, H. Zheng, J.F. Laliberté, J. Virol. 89, 6695–6710 (2015)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  63. J.F. Murphy, P.G. Klein, A.G. Hunt, J.G. Shaw, Virology 220, 535–538 (1996)

    Article  CAS  PubMed  Google Scholar 

  64. V.V. Dolja, R. Halderman-Cahill, A.E. Montgomery, K.A. Vandenbosch, J.C. Carrington, Virology 206, 1007–1016 (1995)

    Article  CAS  PubMed  Google Scholar 

  65. G. Dujovny, T. Sasaya, H. Koganezawa, T. Usugi, K. Shohara, S. Lenardon, Arch. Virol. 145, 2249–2258 (2000)

    Article  CAS  PubMed  Google Scholar 

  66. G. Gell, E. Sebestyén, E. Balázs, Virus Genes 50, 79–86 (2014)

    Article  PubMed  Google Scholar 

  67. Y. Li, R. Liu, T. Zhou, Z. Fan, Virus Res. 177, 242–246 (2013)

    Article  Google Scholar 

  68. L. Li, X. Wang, G. Zhou, Plant Sci. 172, 131–138 (2007)

    Article  CAS  Google Scholar 

  69. M. Black, J.D. Bewley, P. Halmer (eds.), The Encyclopedia of Seeds: Science, Technology and Uses (CAB International, Wallingford, 2006), p. 828

    Google Scholar 

  70. D. O’Brien, World Corn Market Supply Demand Trends. (Kansas State University, 2011), http://www.agmanager.info/marketing/outlook/newletters/archives/grain-outlook_05-03-11.pdf. Accessed 11 Oct 2015

  71. M. Barat Shooshtari, S. Ahmadian, G.H. Asfia, in Sugarcane in Iran ed. (Aeej Press, Tehran, 2008), 337 p (In Persian)

  72. F. Revers, O. LeGall, T. Candresse, M. LeRomancer, J. Dunez, J. Gen. Virol. 77, 1953–1965 (1996)

    Article  CAS  PubMed  Google Scholar 

  73. X.C. Xia, A.E. Melchinger, L. Kuntze, T. Lübberstedt, Phytopathology 89, 660–667 (1999)

    Article  CAS  PubMed  Google Scholar 

  74. C. Ingvardsen, Y. Xing, L. Xu, T. Lubberstedt, Parasitica 61, 61–67 (2005)

    Google Scholar 

  75. B.J. Croft, C.M. Piggin, E.S. Wallis, D.M. Hogarth, in: Sugarcane Germplasm Conservation and Exchange, ed. Proc ACIAR, vol. 67 (1996), 134p

Download references

Acknowledgments

The author Zohreh Moradi has received research Grant from Ministry of Science, Research and Technology of Iran.

Author information

Authors and Affiliations

  1. Department of Plant Pathology, Faculty of Agriculture, Ferdowsi University of Mashhad, 1163, 91779-48974, Mashhad, Iran

    Zohreh Moradi, Mohsen Mehrvar & Mohammad Zakiaghl

  2. Department of Biology, Faculty of Basic Sciences, University of Mazandaran, 47416-95447, 47416-13534, Babolsar, Iran

    Ehsan Nazifi

Authors
  1. Zohreh Moradi
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Mohsen Mehrvar
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Ehsan Nazifi
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Mohammad Zakiaghl
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Mohsen Mehrvar.

Ethics declarations

Funding

This study was funded by Iran’s Ministry of Science, Research, and Technology (Grant Number 33375).

Conflict of Interest

The authors declare that they have no conflict of interest.

Ethical approval

This article does not contain any studies with human participants or animals performed by any of the authors.

Additional information

Edited by Seung-Kook Choi.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary material 1 (DOCX 81 kb)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Moradi, Z., Mehrvar, M., Nazifi, E. et al. The complete genome sequences of two naturally occurring recombinant isolates of Sugarcane mosaic virus from Iran. Virus Genes 52, 270–280 (2016). https://doi.org/10.1007/s11262-016-1302-5

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s11262-016-1302-5

Keywords

Search

Navigation