Genetic diversity and Phylogenetic analyses of cucumber mosaic virus strains in Iran

Document Type : Research Article

Authors

Assis. Prof. of the Dept. of Plant Protection, Shahrekord University, Sahrekord, Iran

Abstract

Cucumber mosaic virus (CMV) belongs to the genus Cucumovirus of the family Bromoviridae. Compared to other plant viruses, it has the broadest host range, and is reported from different regions of Iran. In the present study, the genetic diversity of Iranian CMV isolates was estimated through the sequence analysis of all the CMV genes and compared to those in other countries. To this purpose we report the genome sequence of two CMV strains isolated from squash (SqSh) and melon (MeEs) in Shiraz and Esfahan. The two isolates were closely related based on the analysis of all gene sequences. Phylogenetic analysis revealed that most of the Iranian CMV isolates belonged to the subgroup IA, however, they did not share a most recent common ancestor based on RNAs 2 and 3. The reassortment type of IA-IA-IB was fount to have played a very important role in the evolution and genetic diversity of CMV population in Iran. 1a and CP ORFs had the lowest and highest genetic diversity among Iranian CMV population of the subgroup I, respectively. We suggested that migration in long and short distances have played a role in evolution and genetic structure of CMV strains in Iran.

Keywords


Andika I.B. Wei S. Cao C. Salaipeth L. Kondo H. and Sun L. 2017. Phytopathogenic fungus hosts a plant virus: A naturally occurring cross-kingdom viral infection. PNAS, 114: 12267-12272.
Ben Tamarzizt H., Montarry J., Girardot G., Fakhfakh H., Tepfer M. and Jacquemond M. 2013. Cucumber mosaic virus populations in Tunisian pepper crops are mainly composed of virus reassortants with resistance‐breaking properties. Plant Pathology 62:1415-1428.
Bolou B.A., Moury B., Abo K., Sorho F., Cherif M., Girardot G., Kouassi N.P., and Kone D. 2018. Survey of viruses infecting open‐field pepper crops in Côte d'Ivoire and diversity of Pepper veinal mottle virus and Cucumber mosaic virus. Plant Pathology 67: 1416-1425
Bonnet J., Fraile A., Sacristán S., Malpica J.M. and García-Arenal F. 2005. Role of recombination in the evolution of natural populations of Cucumber mosaic virus, a tripartite RNA plant virus. Virology 332: 359-368.
Davies C. and Symons R. H. 1988. Further implications for the evolutionary relationships between tripartite plant viruses based on cucumber mosaic virus RNA 3. Virology 165: 216-224.
Davino S., Panno S., Rangel E.A., Davino M., Bellardi M.G., and Rubio L. 2012. Population genetics of Cucumber mosaic virus infecting medicinal, aromatic and ornamental plants from northern Italy. Archives of virology 157: 739-745.
Doolittle S. P., 1916. A new infectious mosaic disease of cucumber. Phytopathology 6: 145-147
Gambino G., Perrone I. and Gribaudo I. 2008. A rapid and effective method for RNA extraction from different tissues of grapevine and other woody plants. Phytochemical Analysis, 19, 520-525.
Gibbs M.J., Armstrong J.S. and Gibbs A.J. 2000. Sister-scanning: a Monte Carlo procedure for assessing signals in recombinant sequences. Bioinformatics 16: 573-582.
Guindon S., Dufayard J.F., Lefort V., Anisimova M., Hordijk W. and Gascuel O. 2010. New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Systematic biology 59: 307-21
Haase A., Richter J. and Rabenstein F. 1989. Monoclonal antibodies for detection and serotyping of cucumber mosaic virus. Journal of Phytopathology 127: 129-136.
Jacquemond M. 2012. Cucumber mosaic virus, pp. 439-504. In: Loebenstein G. and Lecoq H. (Eds.). Advances in Virus Research. Academic Press.
Kim M.K., Seo J.K., Kwak H.R., Kim J.S., Kim K.H., Cha B.J. and Choi H.S. 2014. Molecular genetic analysis of cucumber mosaic virus populations infecting pepper suggests unique patterns of evolution in Korea. Phytopathology 104: 993-1000.
Lin H.X., Rubio L., Smythe A.B. and Falk B.W. 2004. Molecular population genetics of Cucumber mosaic virus in California: evidence for founder effects and reassortment. Journal of virology 78: 6666-6675
Liu YY., Yu SL., Lan YF., Zhang CL., Hou SS., Li XD., Chen XZ. and Zhu XP.  2009. Molecular variability of five Cucumber mosaic virus isolates from China. Acta virologica 53: 89-97
Martin D. and Rybicki E. 2000 RDP: detection of recombination amongst aligned sequences. Bioinformatics 16: 562–563.
Martin D.P., Murrell B., Golden M., Khoosal A. and Muhire B. 2015. RDP4: Detection and analysis of recombination patterns in virus genomes. Virus evolution 1: 1-5
Maynard Smith S. J.1992. Analyzing the mosaic structure of genes. Journal of Molecular Evolution .34: 126–129.
Nematollahi S., Sokhandan-Bashir N., Rakhshandehroo F. and Zamanizadeh H.R. 2012. Phylogenetic analysis of new isolates of Cucumber mosaic virus from Iran on the basis of different genomic regions. The Plant Pathology Journal 28: 381-389.
Nouri S., Arevalo R., Falk B.W. and Groves R.L. 2014. Genetic structure and molecular variability of cucumber mosaic virus isolates in the United States. PLoS ONE 9: e96582.
Ohshima K., Matsumoto K., Yasaka R., Nishiyama M., Soejima K., Korkmaz S., Ho S.Y.W., Gibbs A.J. and Takeshita M. 2016. Temporal analysis of reassortment and molecular evolution of Cucumber mosaic virus: Extra clues from its segmented genome. Virology 487: 188–197.
Palukaitis P. and Zaitlin M. 1997. Replicase-mediated resistance to plant virus disease, pp. 349-377. In: K. Maramorosch, F. A. Murphy, A. J. Shatkin (Eds) Advances in Virus Research. Vol.48.
Palukaitis P., and Garcı´a-Arenal F. 2003. Cucumoviruses. Advances in Virus Research 62:242–323.
Pressing J. and D. C. Reaney. 1984. Divided genomes and intrinsic noise. Molecular Evolution 20:135–146
Rasoulpour R. and Izadpanah K. 2008. Properties and taxonomic position of hoary cress strain of cucumber mosaic virus. Journal of Plant Pathology 90:97–102.
Rasoulpour R., Afsharifar A. and Izadpanah K. 2016. Partial biological and molecular characterization of a Cucumber mosaic virus isolate naturally infecting Cucumis melo in Iran. Virus Disease 27:193-197.
Roossinck M. J. 2001. Cucumber mosaic virus as a model for RNA virus evolution. Molecular Plant Pathology 2:59−63.
Roossinck M. J., Zhang L. and Hellwald K.-H. 1999. Rearrangements in the 50 nontranslated evolution region and phylogenetic analyses of Cucumber mosaic virus RNA3 indicate radial of three subgroups. Journal of Virology 73:6752
Roossinck M.J. 2002 Evolutionary history of Cucumber mosaic virus deduced by phylogenetic analyses. Journal of Virology 76:3382–338
Roossinck MJ. 2012.  Persistent Plant Viruses: Molecular Hitchhikers or Epigenetic Elements? Viruses: Essential Agents of Life (Springer, Dordrecht, The Netherlands), pp 177–186.
Salminen M.O., Carr J.K., Burke D.S. and McCutchan F.E. 1995.Identification of breakpoints inintergenotypic recombinants of HIV type1 by Bootscanning. AIDS Research and Human Retroviruses 11: 1423–1425.
Sawyer S.A. 1999. GENECONV: A Computer Package for the Statistical Detection of Gene Conversion. Washigton University in St Louis, USA, Distributed by the author. Department of Mathematics. Available at: ⟨http://www.math.wustl.edu/ _sawyer⟩.
Sokhandan-Bashir N., Kalhor M. and Zarghani S. 2006. Detection, differentiation and phylogenetic analysis of Cucumber mosaic virus isolates from cucurbits in the northwest region of Iran. Virus Genes 32: 277–88.