Browse > Article
http://dx.doi.org/10.5423/PPJ.OA.10.2016.0219

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)
Publication Information
The Plant Pathology Journal / v.33, no.3, 2017 , pp. 296-306 More about this Journal
Abstract
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.
Keywords
coat protein gene; genetic diversity; Iran; population structure; Sugarcane mosaic virus;
Citations & Related Records
연도 인용수 순위
  • Reference
1 McDonald, J. H. and Kreitman, M. 1991. Adaptive protein evolution at the Adh locus in Drosophila. Nature 351:652-654.   DOI
2 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.   DOI
3 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.   DOI
4 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.   DOI
5 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.
6 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.   DOI
7 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).
8 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.   DOI
9 Biswas, S. and Akey, J. M. 2006. Genomic insights into positive selection. Trends Genet. 22:437-446.   DOI
10 Chare, E. R. and Holmes, E. C. 2006. A phylogenetic survey of recombination frequency in plant RNA viruses. Arch. Virol. 151:933-946.   DOI
11 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.   DOI
12 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.   DOI
13 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.   DOI
14 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.   DOI
15 Padhi, A. and Ramu, K. 2011. Genomic evidence of intraspecific recombination in Sugarcane mosaic virus. Virus Genes 42:282-285.   DOI
16 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.
17 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.   DOI
18 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.   DOI
19 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.   DOI
20 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.   DOI
21 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.   DOI
22 Tajima, F. 1989. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123:585-595.
23 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.   DOI
24 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.
25 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.   DOI
26 Urcuqui-Inchima, S., Haenni, A. L. and Bernardi, F. 2001. Potyvirus proteins: a wealth of functions. Virus Res. 74:157-175.   DOI
27 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.   DOI
28 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.   DOI
29 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.   DOI
30 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.   DOI
31 Fu, Y. X. and Li, W. H. 1993. Statistical tests of neutrality of mutations. Genetics 133:693-709.
32 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.   DOI
33 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.   DOI
34 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.   DOI
35 Gibbs, A. and Ohshima, K. 2010. Potyviruses and the digital revolution. Annu. Rev. Phytopathol. 48:205-223.   DOI
36 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.   DOI
37 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.   DOI
38 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.   DOI
39 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.   DOI
40 Hudson, R. R. 2000. A new statistic for detecting genetic differentiation. Genetics 155:2011-2014.
41 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.   DOI
42 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.
43 Li, Y., Liu, R., Zhou, T. and Fan, Z. 2013. Genetic diversity and population structure of Sugarcane mosaic virus. Virus Res. 171:242-246.   DOI
44 Librado, P. and Rozas, J. 2009. DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics 25:1451-1452.   DOI
45 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.   DOI
46 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.   DOI
47 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.
48 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.
49 Wright, S. 1951. The genetical structure of populations. Ann. Eugen. 15:323-354.
50 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.   DOI
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.   DOI
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.   DOI