DOI QR코드

DOI QR Code

Occurrence and Evolutionary Analysis of Coat Protein Gene Sequences of Iranian Isolates of Sugarcane mosaic virus

  • Moradi, Zohreh (Department of Plant Pathology, Faculty of Agriculture, Ferdowsi University of Mashhad) ;
  • Nazifi, Ehsan (Department of Biology, Faculty of Basic Sciences, University of Mazandaran) ;
  • Mehrvar, Mohsen (Department of Plant Pathology, Faculty of Agriculture, Ferdowsi University of Mashhad)
  • 투고 : 2016.10.30
  • 심사 : 2017.03.11
  • 발행 : 2017.06.01

초록

Sugarcane mosaic virus (SCMV) is one of the most damaging viruses infecting sugarcane, maize and some other graminaceous species around the world. To investigate the genetic diversity of SCMV in Iran, the coat protein (CP) gene sequences of 23 SCMV isolates from different hosts were determined. The nucleotide sequence identity among Iranian isolates was more than 96%. They shared nucleotide identities of 75.5-99.9% with those of other SCMV isolates available in GenBank, the highest with the Egyptian isolate EGY7-1 (97.5-99.9%). The results of phylogenetic analysis suggested five divergent evolutionary lineages that did not completely reflect the geographical origin or host plant of the isolates. Population genetic analysis revealed greater between-group than within-group evolutionary divergence values, further supporting the results of the phylogenetic analysis. Our results indicated that natural selection might have contributed to the evolution of isolates belonging to the five identified SCMV groups, with infrequent genetic exchanges occurring between them. Phylogenetic analyses and the estimation of genetic distance indicated that Iranian isolates have low genetic diversity. No recombination was found in the CP cistron of Iranian isolates and the CP gene was under negative selection. These findings provide a comprehensive analysis of the population structure and driving forces for the evolution of SCMV with implications for global exchange of sugarcane germplasm. Gene flow, selection and somehow homologous recombination were found to be the important evolutionary factors shaping the genetic structure of SCMV populations.

키워드

참고문헌

  1. Achon, M. A., Serrano, L., Alonso-Duenas, N. and Porta, C. 2007. Complete genome sequences of Maize dwarf mosaic and Sugarcane mosaic virus isolates coinfecting maize in Spain. Arch. Virol. 152:2073-2078. https://doi.org/10.1007/s00705-007-1042-x
  2. Adams, M. J., Zerbini, F. M., French, R., Rabenstein, F., Stenger, D. C. and Valkonen, J. P. T. 2012. Family Potyviridae. In: Virus taxonomy: classification and nomenclature of viruses: ninth report of the International Committee on Taxonomy of Viruses, eds. by A. M. Q. King, M. J. Adams, E. B. Carstens and E. J. Lefkowitz, pp. 1069-1089. Elsevier Academic Press, San Diego, CA, USA.
  3. Alegria, O. M., Royer, M., Bousalem, M., Chatenet, M., Peterschmitt, M., Girard, J. C. and Rott, P. 2003. Genetic diversity in the coat protein coding region of eighty-six Sugarcane mosaic virus isolates from eight countries, particularly from Cameroon and Congo. Arch. Virol. 148:357-372. https://doi.org/10.1007/s00705-002-0916-1
  4. Amiri, F. and Izadpanah, K. 1993. Purification, serology and transmission of Sugarcane mosaic virus in Khuzestan. Proc. 11th Iran. Plant Protec. Cong., Rasht, Iran. p. 126 (in Persian).
  5. Atreya, P. L., Lopez-Moya, J. J., Chu, M., Atreya, C. D. and Pirone, T. P. 1995. Mutational analysis of the coat protein Nterminal amino acids involved in potyvirus transmission by aphids. J. Gen. Virol. 76:265-270. https://doi.org/10.1099/0022-1317-76-2-265
  6. Biswas, S. and Akey, J. M. 2006. Genomic insights into positive selection. Trends Genet. 22:437-446. https://doi.org/10.1016/j.tig.2006.06.005
  7. Chare, E. R. and Holmes, E. C. 2006. A phylogenetic survey of recombination frequency in plant RNA viruses. Arch. Virol. 151:933-946. https://doi.org/10.1007/s00705-005-0675-x
  8. Dolja, V. V., Haldeman-Cahill, R., Montgomery, A. E., Vandenbosch, K. A. and, Carrington, J. C. 1995. Capsid protein determinants involved in cell-to-cell and long distance movement of tobacco etch potyvirus. Virology 206:1007-1016. https://doi.org/10.1006/viro.1995.1023
  9. Dujovny, G., Sasaya, T., Koganesawa, H., Usugi, T., Shohara, K. and Lenardon, S. L. 2000. Molecular characterization of a new potyvirus infecting sunflower. Arch. Virol. 145:2249-2258. https://doi.org/10.1007/s007050070018
  10. Dussle, M., Quint, M., Xu, L., Melchinger, E. and Lubberstedt, T. 2002. Conversion of AFLP fragments tightly linked to SCMV resistance genes Scmv1 and Scmv2 into simple PCRbased markers. Theor. Appl. Genet. 105:1190-1195. https://doi.org/10.1007/s00122-002-0964-7
  11. Elena, S. F., Bedhomme, S., Carrasco, P., Cuevas, J. M., de la Iglesia, F., Lafforgue, G., Lalic, J., Prosper, A., Tromas, N. and Zwart, M. P. 2011. The evolutionary genetics of emerging plant RNA viruses. Mol. Plant-Microbe Interact. 24:287-293. https://doi.org/10.1094/MPMI-09-10-0214
  12. Fu, Y. X. and Li, W. H. 1993. Statistical tests of neutrality of mutations. Genetics 133:693-709.
  13. Gao, B., Cui, X. W., Li, X. D., Zhang, C. Q. and Miao, H. Q. 2011. Complete genomic sequence analysis of a highly virulent isolate revealed a novel strain of Sugarcane mosaic virus. Virus Genes 43:390. https://doi.org/10.1007/s11262-011-0644-2
  14. Gell, G., Sebestyen, E. and Balazs, E. 2015. Recombination analysis of Maize dwarf mosaic virus (MDMV) in the Sugarcane mosaic virus (SCMV) subgroup of potyviruses. Virus Genes 50:79-86. https://doi.org/10.1007/s11262-014-1142-0
  15. Gemechu, A. L., Chiemsombat, P., Attathom, S., Reanwarakorn, K. and Lersrutaiyotin, R. 2006. Cloning and sequence analysis of coat protein gene for characterization of Sugarcane mosaic virus isolated from sugarcane and maize in Thailand. Arch. Virol. 151:167-172. https://doi.org/10.1007/s00705-005-0643-5
  16. Gibbs, A. and Ohshima, K. 2010. Potyviruses and the digital revolution. Annu. Rev. Phytopathol. 48:205-223. https://doi.org/10.1146/annurev-phyto-073009-114404
  17. Ha, C., Revill, P., Harding, R. M., Vu, M. and Dale, J. L. 2008. Identification and sequence analysis of potyviruses infecting crops in Vietnam. Arch. Virol. 153:45-60. https://doi.org/10.1007/s00705-007-1067-1
  18. Handley, J. A., Smith, G. R., Dale, J. L. and Harding, R. M. 1998. Sequence diversity in the coat protein coding region of twelve sugarcane mosaic potyvirus isolates from Australia, USA and South Africa. Arch. Virol. 143:1145-1153. https://doi.org/10.1007/s007050050362
  19. He, Z., Yasaka, R., Li, W., Li, S. and Ohshima, K. 2016. Genetic structure of populations of Sugarcane streak mosaic virus in China: comparison with the populations in India. Virus Res. 211:103-116. https://doi.org/10.1016/j.virusres.2015.09.020
  20. Hudson, R. R. 2000. A new statistic for detecting genetic differentiation. Genetics 155:2011-2014.
  21. Jones, R. A. 2009. Plant virus emergence and evolution: origins, new encounter scenarios, factors driving emergence, effects of changing world conditions, and prospects for control. Virus Res. 141:113-130. https://doi.org/10.1016/j.virusres.2008.07.028
  22. Kimura, M. 1980. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J. Mol. Evol. 16:111-120. https://doi.org/10.1007/BF01731581
  23. Koike, H. and Gillaspie, A. G., Jr. 1989. Mosaic. In: Diseases of sugarcane: major diseases, eds. by C. Ricaud, B. T. Egan, A. G. Gillaspie and C. G. Hughes, pp. 301-322. Elsevier, Amsterdam, Netherlands.
  24. Li, Y., Liu, R., Zhou, T. and Fan, Z. 2013. Genetic diversity and population structure of Sugarcane mosaic virus. Virus Res. 171:242-246. https://doi.org/10.1016/j.virusres.2012.10.024
  25. Librado, P. and Rozas, J. 2009. DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics 25:1451-1452. https://doi.org/10.1093/bioinformatics/btp187
  26. Mangrauthia, S. K., Parameswari, B., Jain, R. K. and Praveen, S. 2008. Role of genetic recombination in the molecular architecture of Papaya ringspot virus. Biochem. Genet. 46:835-846. https://doi.org/10.1007/s10528-008-9198-y
  27. Martin, D. P., Murrell, B., Golden, M., Khoosal, A. and Muhire, B. 2015. RDP4: detection and analysis of recombination patterns in virus genomes. Virus Evol. 1:vev003.
  28. McDonald, J. H. and Kreitman, M. 1991. Adaptive protein evolution at the Adh locus in Drosophila. Nature 351:652-654. https://doi.org/10.1038/351652a0
  29. Moradi, Z., Mehrvar, M., Nazifi, E. and Zakiaghl, M. 2016. The complete genome sequences of two naturally occurring recombinant isolates of Sugarcane mosaic virus from Iran. Virus Genes 52:270-280. https://doi.org/10.1007/s11262-016-1302-5
  30. Moreno, I. M., Malpica, J. M., Diaz-Pendon, J. A., Moriones, E., Fraile, A. and Garcia-Arenal, F. 2004. Variability and genetic structure of the population of Watermelon mosaic virus infecting melon in Spain. Virology 318:451-460. https://doi.org/10.1016/j.virol.2003.10.002
  31. Moury, B., Morel, C., Johansen, E. and Jacquemond, M. 2002. Evidence for diversifying selection in Potato virus Y and in the coat protein of other potyviruses. J. Gen. Virol. 83:2563-2573. https://doi.org/10.1099/0022-1317-83-10-2563
  32. Muhire, B., Martin, D. P., Brown, J. K., Navas-Castillo, J., Moriones, E., Zerbini, F. M., Rivera-Bustamante, R., Malathi, V. G., Briddon, R. W. and Varsani, A. 2013. A genome-wide pairwise-identity-based proposal for the classification of viruses in the genus Mastrevirus (family Geminiviridae). Arch. Virol. 158:1411-1424. https://doi.org/10.1007/s00705-012-1601-7
  33. Padhi, A. and Ramu, K. 2011. Genomic evidence of intraspecific recombination in Sugarcane mosaic virus. Virus Genes 42:282-285. https://doi.org/10.1007/s11262-010-0564-6
  34. Perera, M. F., Filippone, M. P., Ramallo, C. J., Cuenya, M. I., García, M. L., Ploper, L. D. and Castagnaro, A. P. 2009. Genetic diversity among viruses associated with sugarcane mosaic disease in Tucuman, Argentina. Phytopathology 99:38-49. https://doi.org/10.1094/PHYTO-99-1-0038
  35. Perez-Losada, M., Porter, M. and Crandall, K. A. 2008. Methods for analyzing viral evolution. In: Plant virus evolution, ed. by M. J. Roossinck, pp. 165-204. Springer, Berlin, Germany.
  36. Revers, F., Le Gall, O., Candresse, T., Le Romancer, M. and Dunez, J. 1996. Frequent occurrence of recombinant potyvirus isolates. J. Gen. Virol. 77:1953-1965. https://doi.org/10.1099/0022-1317-77-8-1953
  37. Rozas, J., Sanchez-DelBarrio, J. C., Messeguer, X. and Rozas, R. 2003. DnaSP, DNA polymorphism analyses by the coalescent and other methods. Bioinformatics 19:2496-2497. https://doi.org/10.1093/bioinformatics/btg359
  38. Shukla, D. D., Frenkel, M. J. and Ward, C. W. 1991. Structure and function of the potyvirus genome with special reference to the coat protein coding region. Can. J. Plant Pathol. 13:178-191. https://doi.org/10.1080/07060669109500953
  39. Shukla, D. D. and Ward, C. W. 1989. Identification and classification of potyviruses on the basis of coat protein sequence data and serology. Brief review. Arch. Virol. 106:171-200. https://doi.org/10.1007/BF01313952
  40. Sztuba-Solinska, J., Urbanowicz, A., Figlerowicz, M. and Bujarski, J. J. 2011. RNA-RNA recombination in plant virus replication and evolution. Annu. Rev. Phytopathol. 49:415-443. https://doi.org/10.1146/annurev-phyto-072910-095351
  41. Tajima, F. 1989. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123:585-595.
  42. Tamura, K., Stecher, G., Peterson, D., Filipski, A. and Kumar, S. 2013. MEGA6: molecular evolutionary genetics analysis version 6.0. Mol. Biol. Evol. 30:2725-2729. https://doi.org/10.1093/molbev/mst197
  43. Tsompana, M., Abad, J., Purugganan, M. and Moyer, J. W. 2005. The molecular population genetics of the Tomato spotted wilt virus (TSWV) genome. Mol. Ecol. 14:53-66.
  44. Ullah, Z., Chai, B., Hammar, S., Raccah, B., Gal-On, A. and Grumat, R. 2003. Effect of substitution of the amino termini of coat proteins of distinct potyvirus species on viral infectivity and host specificity. Physiol. Mol. Plant Pathol. 63:129-139. https://doi.org/10.1016/j.pmpp.2003.11.001
  45. Urcuqui-Inchima, S., Haenni, A. L. and Bernardi, F. 2001. Potyvirus proteins: a wealth of functions. Virus Res. 74:157-175. https://doi.org/10.1016/S0168-1702(01)00220-9
  46. Valli, A., Lopez-Moya, J. J. and Garcia, J. A. 2007. Recombination and gene duplication in the evolutionary diversification of P1 proteins in the family Potyviridae. J. Gen. Virol. 88:1016-1028. https://doi.org/10.1099/vir.0.82402-0
  47. Wang, J. G., Zheng, H. Y., Chen, H. R., Adams, M. J. and Chen, J. P. 2010. Molecular diversities of Sugarcane mosaic virus and Sorghum mosaic virus isolated from Yunnan province, China. J. Phytopathol. 158:427-432.
  48. Wright, S. 1951. The genetical structure of populations. Ann. Eugen. 15:323-354.
  49. Xie, X., Chen, W., Fu, Q., Zhang, P., An, T., Cui, A. and An, D. 2016. Molecular variability and distribution of Sugarcane mosaic virus in Shanxi, China. PLoS One 11:e0151549. https://doi.org/10.1371/journal.pone.0151549
  50. Xu, D. L., Park, J. W., Mirkov, T. E. and Zhou, G. H. 2008. Viruses causing mosaic disease in sugarcane and their genetic diversity in southern China. Arch. Virol. 153:1031-1039. https://doi.org/10.1007/s00705-008-0072-3
  51. Xu, D. L., Zhou, G. H., Xie, Y. J., Mock, R. and 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. https://doi.org/10.1007/s11262-010-0457-8
  52. Zhong, Y., Guo, A., Li, C., Zhuang, B., Lai, M., Wei, C., Luo, J. and Li, Y. 2005. Identification of a naturally occurring recombinant isolate of Sugarcane mosaic virus causing maize dwarf mosaic disease. Virus Genes 30:75-83. https://doi.org/10.1007/s11262-004-4584-y

피인용 문헌

  1. Genetic diversity and biological characterization of sugarcane streak mosaic virus isolates from Iran vol.29, pp.3, 2018, https://doi.org/10.1007/s13337-018-0461-5