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http://dx.doi.org/10.5423/PPJ.OA.04.2018.0062

A New Distinct Clade for Iranian Tomato spotted wilt virus Isolates Based on the Polymerase, Nucleocapsid, and Non-structural Genes  

Abadkhah, Mahsa (Department of Plant Protection, Faculty of Agriculture, University of Zanjan)
Koolivand, Davoud (Department of Plant Protection, Faculty of Agriculture, University of Zanjan)
Eini, Omid (Department of Plant Protection, Faculty of Agriculture, University of Zanjan)
Publication Information
The Plant Pathology Journal / v.34, no.6, 2018 , pp. 514-531 More about this Journal
Abstract
Tomato spotted wilt virus (TSWV; Genus Orthotospovirus: Family Tospoviridae) is one of the most destructive viruses affecting a wide range of horticultural crops on a worldwide basis. In 2015 and 2016, 171 leaf and fruit samples from tomato (Solanum lycopersicum) plants with viral symptoms were collected from the fields in various regions of Iran. ELISA test revealed that the samples were infected by TSWV. The results of RT-PCR showed that the expected DNA fragments of about 819 bp in length were amplified using a pair of universal primer corresponding to the RNA polymerase gene and DNA fragments of ca 777 bp and 724 bp in length were amplified using specific primers that have been designed based on the nucleocapsid (N) and non-structural (NSs) genes, respectively. The amplified fragments were cloned into pTG19-T and sequenced. Sequence comparisons with those available in the GenBank showed that the sequences belong to TSWV. The high nucleotide identity and similarities of new sequences based on the L, N, and NSs genes showed that minor evolutionary differences exist amongst the isolates. The phylogenetic tree grouped all isolates six clades based on N and NSs genes. Phylogenetic analysis showed that the Iranian isolates were composed a new distinct clade based on a part of polymerase, N and NSs genes. To our knowledge, this is the first detailed study on molecular characterization and genetic diversity of TSWV isolates from tomato in Iran that could be known as new clade of TSWV isolates.
Keywords
Neighbor-Joining; Orthotospovirus; phylogenetic analysis; Tomato spotted wilt virus;
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1 Bananej, K., Ahoonmanesh, A., Shahraeen, N. and Lesemann, D. 1996. Identification of Tomato spotted wilt virus from tomato fields in Varamin area. Iran. J. Plant Pathol. 32:29-30.
2 Bashir, N. S., Kalhor, M. R. and Zarghani, S. N. 2006. Detection, differentiation and phylogenetic analysis of Cucumber mosaic virus isolates from cucurbits in the northwest region of Iran. Virus Genes 32:277-288.   DOI
3 Brittlebank, C. 1919. Tomato diseases. J. Agric. Victoria 17:231-235.
4 Chen, T. C., Huang, C. W., Kuo, Y. W., Liu, F. L., Yuan, C. H., Hsu, H. T. and Yeh, S. D. 2006. Identification of common epitopes on a conserved region of NSs proteins among tospoviruses of Watermelon silver mottle virus serogroup. Phytopathology 96:1296-1304.   DOI
5 Chen, T. C., Tsai, W. T., Kang, Y. C., Wang, Y. C. and Yeh, S. D. 2016. Using monoclonal antibodies against the common epitopes of NSs proteins for the prompt detection and differentiation of tospoviruses prevalent in Euro-America and Asia regions. Eur. J. Plant Pathol. 144:509-524.   DOI
6 Chiemsombat, P., Gajanandana, O., Warin, N., Hongprayoon, R., Bhunchoth, A. and Pongsapich, P. 2008. Biological and molecular characterization of tospoviruses in Thailand. Arch. Virol. 153:571-577.   DOI
7 Chu, F. H., Chao, C. H., Chung, M. H., Chen, C. C. and Yeh, S. D. 2001. Completion of the genome sequence of Watermelon silver mottle virus and utilization of degenerate primers for detecting tospoviruses in five serogroups. Phytopathology 91:361-368.   DOI
8 Fu, Y. X. and Li, W. H. 1993. Statistical tests of neutrality of mutations. Genetics 133:693-709.
9 Chung, C. T., Niemela, S. L. and Miller, R. H. 1989. One-step preparation of competent Escherichia coli: transformation and storage of bacterial cells in the same solution. Proc. Natl. Acad. Sci. U.S.A. 86:2172-2175.   DOI
10 Escriu, F., Fraile, A. and Garcia-Arenal, F. 2003. The evolution of virulence in a plant virus. Evolution 57:755-765.   DOI
11 Gao, F., Lin, W., Shen, J. and Liao, F. 2016. Genetic diversity and molecular evolution of Arabis mosaic virus based on the CP gene sequence. Arch. Virol. 161:1047-1051.   DOI
12 Ghotbi, T. and Shahraeen, N. 2012. Incidence and distribution of viruses infecting propagated ornamentals in Northern Iran. Int. Res. J. Microbiol. 3:373-381.
13 Golnaraghi, A. R., Shahraeen, N., Pourrahim, R., Ghorbani, S. and Farzadfar, S. 2001a. First report of a Tospovirus infection of peanuts in Iran. Plant Dis. 85:1286.
14 Golnaraghi, A. R., Shahraeen, N., Pourrahim, R., Ghorbani, S. and Farzadfar, S. 2001b. First report of Tomato spotted wilt virus on soybean in Iran. Plant Dis. 85:1290.
15 Hudson, R. R. 2000. A new statistic for detecting genetic differentiation. Genetics 155:2011-2014.
16 Golnaraghi, A. R., Shahraeen, N., Pourrahim, R., Farzadfar, S. and Ghasemi, A. 2004. Occurrence and relative incidence of viruses infecting soybeans in Iran. Plant Dis. 88:1069-1074.   DOI
17 Golnaraghi, A. R., Pourrahim, R., Farzadfar, S. and Ahoonmanesh, A. 2007. Identification and partial characterization of a Tospovirus causing leaf and stem necrosis on potato. Plant Pathol. J. 6:227-234.   DOI
18 Hajiabadi, A. M., Asaei, F., Abdollahi Mandoulakani, B. and Rastgou, M. 2012. Natural incidence of tomato viruses in the North of Iran. Phytopathol. Mediterr. 51:390-396.
19 Hanssen, I. M. and Lapidot, M. 2012. Major tomato viruses in the Mediterranean Basin. Adv. Virus Res. 84:31-66.
20 Harrison, B. D. 2002. Virus variation in relation to resistancebreaking in plants. Euphytica 124:181-192.   DOI
21 Hudson, R. R., Boos, D. D. and Kaplan, N. L. 1992. A statistical test for detecting geographic subdivision. Mol. Biol. Evol. 9:138-151.
22 Jones, D. R. 2005. Plant viruses transmitted by thrips. Eur. J. Plant Pathol. 113:119-157.   DOI
23 Kaye, A. C., Moyer, J. W., Parks, E. J., Carbone, I. and Cubeta, M. A. 2011. Population genetic analysis of Tomato spotted wilt virus on peanut in North Carolina and Virginia. Phytopathology 101:147-153.   DOI
24 Kimura, S. and Sinha, N. 2008. Tomato (Solanum lycopersicum): a model fruit-bearing crop. Cold Spring Harb. Protoc. 2008:pdb.emo105.
25 King, A. M. Q., Adams, M. J., Carstens, E. B. and Lefkowitz, E. J. 2011. Virus taxonomy: Ninth Report of the International Committee on Taxonomy of Viruses. 9th ed. Elsevier, Cambridge, MA, USA, 1327 pp.
26 Pang, S. Z., Bock, J. H., Gonsalves, C., Slightom, J. L. and Gonsalves, D. 1994. Resistance of transgenic Nicotiana benthamiana plants to Tomato spotted wilt and Impatiens necrotic spot tospoviruses: evidence of involvement of the N protein and N gene RNA in resistance. Phytopathology 84:243-249.   DOI
27 Lian, S., Lee, J. S., Cho, W. K., Yu, J., Kim, M. K., Choi, H. S. and Kim, K. H. 2013. Phylogenetic and recombination analysis of Tomato spotted wilt virus. PloS One 8:e63380.   DOI
28 Margaria, P., Miozzi, L., Ciuffo, M., Pappu, H. and Turina, M. 2015. The first complete genome sequences of two distinct European Tomato spotted wilt virus isolates. Arch. Virol. 160:591-595.   DOI
29 Muhire, B. M., Varsani, A. and Martin, D. P. 2014. SDT: a virus classification tool based on pairwise sequence alignment and identity calculation. PloS One 9:e108277.   DOI
30 Nischwitz, C., Pappu, H., Mullis, S., Sparks, A., Langston, D., Csinos, A. and Gitaitis, R. 2007. Phylogenetic analysis of Iris yellow spot virus isolates from onion (Allium cepa) in Georgia (USA) and Peru. J. Phytopathol. 155:531-535.   DOI
31 Pappu, H., Du Toit, L., Schwartz, H. and Mohan, S. 2006. Sequence diversity of the nucleoprotein gene of Iris yellow spot virus (genus Tospovirus, family Bunyaviridae) isolates from the western region of the United States. Arch. Virol. 151:1015-1023.   DOI
32 Pappu, H., Jones, R. and Jain, R. 2009. Global status of tospovirus epidemics in diverse cropping systems: successes achieved and challenges ahead. Virus Res. 141:219-236.   DOI
33 Parrella, G., Gognalons, P., Gebre-Selassie, K., Vovlas, C. and Marchoux, G. 2003. An update of the host range of Tomato spotted wilt virus. J. Plant Pathol. 85:227-264.
34 Pond, S. L. K. and Muse, S. V. 2005. HyPhy: hypothesis testing using phylogenies. In: Statistical methods in molecular evolution, pp. 125-181. Springer, New York, USA.
35 Saitou, N. and Nei, M. 1987. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4:406-425.
36 Pourrahim, R., Farzadfar, S., Moini, A., Shahraeen, N. and Ahoonmanesh, A. 2001. First report of Tomato spotted wilt virus on potatoes in Iran. Plant Dis. 85:442.
37 Rosenberg, N. A. and Nordborg, M. 2002. Genealogical trees, coalescent theory and the analysis of genetic polymorphisms. Nat. Rev. Genet. 3:380-390.   DOI
38 Rozas, J., Ferrer-Mata, A., Sanchez-DelBarrio, J. C., Guirao-Rico, S., Librado, P., Ramos-Onsins, S. E. and Sanchez-Garcia, A. 2017. DnaSP 6: DNA Sequence Polymorphism Analysis of Large Data Sets. Mol. Biol. Evol. 34:3299-3302.   DOI
39 Samuel, G., Bald, J. G. and Pittman, H. A. 1930. Investigations on "Spotted Wilt" of Tomatoes. H. J. Green, Government Printer, Melbourne, Australia. 120 pp.
40 Sherwood, J., German, T., Moyer, J. and Ullman, D. 2003. Tomato spotted wilt. The Plant Health Instructor. doi:10.1094/PHI-1-2003-0613-02.
41 Sokhandan, B. N., Nematollahi, S. and Torabi, E. 2008. Cucumber mosaic virus subgroup IA frequently occurs in the northwest Iran. Acta Virol. 52:237-242.
42 Tajima, F. 1989. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123:585-595.
43 Takeda, A., Sugiyama, K., Nagano, H., Mori, M., Kaido, M., Mise, K., Tsuda, S. and Okuno, T. 2002. Identification of a novel RNA silencing suppressor, NSs protein of Tomato spotted wilt virus. FEBS Lett. 532:75-79.   DOI
44 Zhang, Z., Wang, D., Yu, C., Wang, Z., Dong, J., Shi, K. and Yuan, X. 2016. Identification of three new isolates of Tomato spotted wilt virus from different hosts in China: molecular diversity, phylogenetic and recombination analyses. Virol. J. 13:8.   DOI
45 Timmerman-Vaughan, G. M., Lister, R., Cooper, R. and Tang, J. 2014. Phylogenetic analysis of New Zealand Tomato spotted wilt virus isolates suggests likely incursion history scenarios and mechanisms for population evolution. Arch. Virol. 159:993-1003.   DOI
46 Tripathi, D., Raikhy, G. and Pappu, H. R. 2015. Movement and nucleocapsid proteins coded by two tospovirus species interact through multiple binding regions in mixed infections. Virology 478:137-147.   DOI
47 Tsompana, M., Abad, J., Purugganan, M. and Moyer, J. 2005. The molecular population genetics of the Tomato spotted wilt virus (TSWV) genome. Mol. Ecol. 14:53-66.
48 Valizadeh, M., Valizadeh, J. and Jafari, M. 2011. Identification, distribution and incidence of important tomato and cucurbits viruses in the southeast of Iran. Am. J. Plant Physiol. 6:242-251.   DOI
49 Whitfield, A. E., Ullman, D. E. and German, T. L. 2005. Tospovirus-thrips interactions. Annu. Rev. Phytopathol. 43:459-489.   DOI
50 Zheng, Y. X., Chen, C. C., Yang, C. J., Yeh, S. D. and Jan, F. J. 2008. Identification and characterization of a tospovirus causing chlorotic ringspots on Phalaenopsis orchids. Eur. J. Plant Pathol. 120:199-209.   DOI
51 Zindovic, J., Ciuffo, M. and Turina, M. 2014. Molecular characterization of Tomato spotted wilt virus in Montenegro. J. Plant Pathol. 96:201-205.