ORIGINAL ARTICLE
Phylogenetic analysis and genetic structure of new isolates of Tomato mosaic virus in Iran
 
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Department of Plant Pathology, College of Agriculture and Natural Resources, Science and Research Branch, Islamic Azad University, Tehran, Iran
CORRESPONDING AUTHOR
Farshad Rakhshandehroo
Department of Plant Pathology, College of Agriculture and Natural Resources, Science and Research Branch, Islamic Azad University, Tehran, Iran
Submission date: 2017-10-09
Acceptance date: 2018-02-12
 
Journal of Plant Protection Research 2018;58(1):25–35
KEYWORDS
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ABSTRACT
The present report describes the new occurrence of Tomato mosaic virus (ToMV) in cabbage, bean and Malva neglecta plants in Iran. In this study, sequence analyses of a partial RNA dependent RNA polymerases (RdRp) and complete movement protein (MP) and the coat protein (CP) nucleotide sequences of three new ToMV isolates collected from major crop fields in Iran revealed low genetic variation of RdRp gene compared to the CP and MP genes. The different topologies of the phylogenetic trees constructed, using available open reading frame (ORF1), ORF2 and ORF3 sequences from ToMV isolates, indicated different evolutionary constraints in these genomic regions. Statistical analysis also revealed that with the exception of CP other tested ToMV genes were under negative selection and the RdRp gene was under the strongest constraints. According to the phylogenetic tree it can be inferred from the nucleotide sequences of the complete CP and MP genes, that isolates from Iran and Egypt formed separate groups, irrespective of host origin. However, isolates clustered into groups with correlation to geographic origin but not the host. Analysis of the Ks*, Z* and Snn values also indicated genetic differentiation between ToMV populations. The Tajima’s D, Fu and Li’s statistical values were significantly negative for the RdRp gene of the Asian population which suggests the sudden expansion of ToMV in Asia. Taken together, the results indicate that negative selection and genetic drift were important evolutionary factors driving the genetic diversification of ToMV.
CONFLICT OF INTEREST
The authors have declared that no conflict of interests exist.
 
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