Abstract
Cucumber mosaic virus (CMV) is a geographically widespread plant virus with a very broad host range. The virus has been detected in diverse crops all over Iran. In this study, we estimated the timescale of the evolution of CMV subgroup I and the geographical movement of the virus with a focus on Iranian strains. Analyses using the MP and CP genes and their concatenation revealed that the CMV population within subgroup I had a single ancestor dating back to about 450-550 years ago. The Iranian strains formed three clusters in a maximum-clade-credibility phylogenetic tree. It was found that the most recent common ancestor of the Iranian strains within each cluster dates back to less than 100 years ago. Our results also suggest that both short- and long-distance migration of Iranian CMV strains has occurred in the last 100 years.
References
Bielejec F, Baele G, Vrancken B, Suchard MA, Rambaut A, Lemey P (2016) SpreaD3: interactive visualisation of spatiotemporal history and trait evolutionary processes. Mol Biol Evol 33:2167–2169
Brigneti G, Voinnet O, Li WX, Ji LH, Ding SW, Baulcombe DC (1998) Viral pathogenicity determinants are suppressors of transgene silencing in Nicotiana benthamiana. EMBO J 17:6739–6746
Canto T, Prior DA, Hellwald MKH, Oparka KJ, Palukaitis P (1997) Characterization of cucumber mosaic virus. IV. Movement protein and coat protein are both essential for cell-to-cell movement of cucumber mosaic virus. Virology 237:237–248
Danesh D (1969) Studies of the different strains of cucumber mosaic virus in Iran. Regional pulse improvement project. In: Proceedings of the 2nd plant medicine congress of Iran (PMCI’69), Tehran Iran, pp 45–57
Davino S, Panno S, Rangel EA, Davino M, Bellardi MG, Rubio L (2012) Population genetics of cucumber mosaic virus infecting medicinal, aromatic and ornamental plants from northern Italy. Arch Virol 157:739–745
Ding SW, Anderson BJ, Haase HR, Symons RH (1994) New overlapping gene encoded by the cucumber mosaic virus genome. Virology 198:593–601
Domingo E, Holland JJ (1997) RNA virus mutations and fitness for survival. Annu Rev Microbiol 51:151–178
Drummond AJ, Bouckaert RR (2015) Bayesian evolutionary analysis with BEAST. Cambridge University Press, Cambridge, UK
Drummond AJ, Ho SYW, Phillips MJ, Rambaut A (2006) Relaxed phylogenetics and dating with confidence. PLoS Biol 4:e88
Drummond AJ, Suchard MA, Xie D, Rambaut A (2012) Bayesian phylogenetics with BEAUti and the BEAST 1.7. Mol Biol Evol 29:1969–1973
Duchêne S, Holmes EC, Ho SY (2014) Analyses of evolutionary dynamics in viruses are hindered by a time-dependent bias in rate estimates. Proc Biol Sci 281(2014):0732
Duffy S, Holmes EC (2009) Validation of high rates of nucleotide substitution in geminiviruses: phylogenetic evidence from East African cassava mosaic viruses. J Gen Virol 90:1539–1547
Firth C, Kitchen A, Shapiro B, Suchard MA, Holmes EC, Rambaut A (2010) Using time-structured data to estimate evolutionary rates of double-stranded DNA viruses. Mol Biol Evol 27:2038–2051
Hanada K, Suzuki Y, Gojobori T (2004) A large variation in the rates of synonymous substitution for RNA viruses and its relationship to a diversity of viral infection and transmission modes. Mol Biol Evol 21:1074–1080
Hayes RJ, Buck KW (1990) Complete replication of a eukaryotic virus RNA in vitro by a purified RNA-dependent RNA polymerase. Cell 63:363–368
Holmes EC (2003) Molecular clocks and the puzzle of RNA virus origins. J Virol 77:3893–3897
Holmes EC (2003) Patterns of intra- and inter host nonsynonymous variation reveal strong purifying selection in dengue virus. J Virol 77:11296–11298
Kim JI, Park S, Lee I, Park KS, Kwak EJ, Moon KM, Lee CK, Bae JY, Park MS, Song KJ (2016) Genome-wide analysis of human metapneumovirus evolution. PloS One 11:e0152962
Lefeuvre P, Martin DP, Harkins G, Lemey P, Gray AJ, Meredith S, Lakay F, Monjane A, Lett JM, Varsani A, Heydarnejad J (2010) The spread of tomato yellow leaf curl virus from the Middle East to the world. PLoS Pathog 6:e1001164
MaturanaRussel P, Brewer BJ, Klaere S, Bouckaert R (2018) Model selection and parameter inference in phylogenetics using nested sampling. Syst Biol 2:219–233
Ohshima K, Matsumoto K, Yasaka R, Nishiyama M, Soejima K, Korkmaz S, Ho SY, Gibbs AJ, Takeshita M (2016) Temporal analysis of reassortment and molecular evolution of Cucumber mosaic virus: extra clues from its segmented genome. Virology 487:188–197
Ohshima K, Yamaguchi Y, Hirota R, Hamamoto T, Tomimura K, Tan Z, Sano T, Azuhata F, Walsh JA, Fletcher J, Chen J (2002) Molecular evolution of Turnip mosaic virus: evidence of host adaptation, genetic recombination and geographical spread. J Gen Virol 83:1511–1521
Pagán I, Firth C, Holmes EC (2010) Phylogenetic analysis reveals rapid evolutionary dynamics in the plant RNA virus genus Tobamovirus. J Mol Evol 71:298–307
Perry K, Zhang LL, Shintaku MH, Palukaitis P (1994) Mapping determinants in cucumber mosaic virus for transmission by Aphis gossypii. Virology 205:591–595
Pond SLK, Frost SD (2005) Datamonkey: rapid detection of selective pressure on individual sites of codon alignments. Bioinformatics 21:2531–2533
Siampour M, Shirvani M (2019) Genetic diversity and phylogenetic analyses of cucumber mosaic virus strains in Iran. Iran J Plant Pathol 54:231–253
Visser JC, Bellstedt DU, Pirie MD (2012) The recent recombinant evolution of a major crop pathogen, Potato virus Y. PLoS One 7:e50631
Xia X (2009) Assessing substitution saturation with DAMBE. In: Lemey P, Salemi M, Vandamme AM (eds) The phylogenetic handbook: a practical approach to phylogenetic analysis and hypothesis testing. Cambridge University Press, UK, pp 615–630
Xia X (2013) DAMBE5: a comprehensive software package for data analysis in molecular biology and evolution. Mol Biol Evol 30:1720–1728
Yasaka R, Fukagawa H, Ikematsu M, Soda H, Korkmaz S, Golnaraghi A, Katis N, Ho SY, Gibbs AJ, Ohshima K (2017) The timescale of emergence and spread of Turnip mosaic potyvirus. Sci Rep 7(1):4240
Yasaka R, Nguyen HD, Ho SY, Duchêne S, Korkmaz S, Katis N, Takahashi H, Gibbs AJ, Ohshima K (2014) The temporal evolution and global spread of Cauliflower mosaic virus, a plant pararetrovirus. PLoS One 9(1):e85641
Funding
This study was supported by a grant from Shahrekord University.
Author information
Authors and Affiliations
Corresponding author
Additional information
Handling Editor: Sead Sabanadzovic.
Publisher's Note
Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Rights and permissions
About this article
Cite this article
Siampour, M., Izadpanah, K. Evolutionary timescale and geographical movement of cucumber mosaic virus, with focus on Iranian strains. Arch Virol 165, 185–192 (2020). https://doi.org/10.1007/s00705-019-04439-y
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s00705-019-04439-y