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Molecular Variability and Genetic Structure of IYMV in Burkina Faso

DOI: 10.4236/ajps.2018.92025, PP. 311-324

Keywords: Imperata yellow mottle virus (IYMV), Coat Protein (CP), Genetic Var-iability, Phylogenetic Analysis

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Abstract:

Imperata yellow mottle virus (IYMV, Sobemovirus) was first described in 2008 in the south-western region of Burkina Faso (West Africa). The genetic diversity of IYMV was not documented up to day. In this study, the variability of CP of IYMV was evaluated through the molecular characterization of 38 isolates collected in the western part of Burkina Faso. Comparison of sequences of these new isolates and one IYMV sequence available in GenBank revealed that the average nucleotide diversity was low. The ratio of non-synonymous over synonymous nucleotide substitutions per site was low, indicating a CP diversification under strong purifying selection. Despite of the low nucleotide diversity, phylogenetic analyses revealed segregation of IYMV isolates into six major clades. There was no correlation of phylogenetic grouping of isolates based on geographical location. This is the first study of the genetic diversity of IYMV.

References

[1]  Ntume, R. and Anywar, G. (2015) Ethnopharmacological Survey of Medicinal Plants Used in the Treatment of Snakebites in Central Uganda. Current Life Siences, 1, 6-14.
[2]  Tsobou, R., Mapongmetsem, P.M. and Van Damme, P. (2013) Medicinal Plants Used against Typhoid Fever in Bamboutos Division, Western Cameroon. Ethnobotany Research & Applications, 11, 163-174.
[3]  Mak-Mensah, E.E., Komlaga, G. and Terlabi, E.O. (2010) Antiypertensive Action of Ethanolic Extract of Imperata Cylindrica Leaves in Animal Models. Journal of Medicinal Plants Research, 4, 1486-1491.
[4]  Sérémé, D., Lacombe, S., Konaté, M., Pinel-Galzi, A., Traoré, V.S.E., Hébrard, E., Traoré, O., Brugidou, C., Fargette, D. and Konaté, G. (2008) Biological and Molecular Characterization of a Putative New Sobemovirus Infecting Imperata Cylindrica and Maize in Africa. Archives of Virology, 153, 1813-1820.
https://doi.org/10.1007/s00705-008-0190-y
[5]  Koala, M., Traoré, V.S.E., Sérémé, D., Neya, B.J., Brugidou, C., Barro, N. and Traoré, O. (2017) Imperata Yellow Mottle Virus an Emerging Threat to Maize, Sorghum and Pearl Millet in Burkina Faso. Agricultural Sciences, 8, 397-408.
https://doi.org/10.4236/as.2017.85030
[6]  Ling, R., Pate, A.E., Carr, J.P. and Firth, A.E. (2013) An Essential Fifth Coding ORF in the Sobemoviruses. Virology, 446, 397-408.
https://doi.org/10.1016/j.virol.2013.05.033
[7]  Bonneau, C., Brugidou, C., Chen, L., Beachy, R.N. and Fauquet, C. (1998) Expression of the Rice Yellow Mottle Virus P1 Protein in Vitro and in Vivo and Its Involvement in Virus Spread. Virology, 244, 79-86.
https://doi.org/10.1006/viro.1998.9100
[8]  Vigne, E., Bergdoll, M., Guyader, S. and Fuchs, M. (2004) Population Structure and Genetic Variability within Isolates of Grapevine Fanleaf Virus from a Naturally Infected Vineyard in France: Evidence for Mixed Infection and Recombination. Journal of General Virology, 85, 2435-2445.
https://doi.org/10.1099/vir.0.79904-0
[9]  Cuevas, J.M., Delaunay, A., Rupar, M., Jacquot, E. and Elena, S.F. (2012) Molecular Evolution and Phylogeography of Potato Virus Y Based on the CP Gene. Journal of General Virology, 93, 2496-2501.
https://doi.org/10.1099/vir.0.044347-0
[10]  Neeraj, V., Mahinghara, B.K., Ram, R. and Zaidi, A.A. (2006) Coat Protein Sequence Shows That Cucumber Mosaic Virus Isolate from Geraniums (Pelargonium spp.) Belongs to Subgroup II. Journal of Biosciences, 31, 47-54.
https://doi.org/10.1007/BF02705234
[11]  Thompson, J.D., Higgins, D.G. and Gibson, T.J. (1994) CLUSTAL W: Improving the Sensitivity of Progressive Multiple Sequence Alignment through Sequence Weighting, Position-Specific Gap Penalties and Weight Matrix Choice. Nucleic Acids Research, 22, 4673-4680.
https://doi.org/10.1093/nar/22.22.4673
[12]  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, vev003.
[13]  Martin, D. (2000) RDP: Detection of Recombination amongst Aligned Sequences. Bioinformatics, 16, 562-563.
https://doi.org/10.1093/bioinformatics/16.6.562
[14]  Padidam, M., Sawyer, S. and Fauquet, C.M. (1999) Possible Emergence of New Geminiviruses by Frequent Recombination. Virology, 265, 218-225.
https://doi.org/10.1006/viro.1999.0056
[15]  Martin, D.P., Posada, D., Candall, K.A. and Williamson, C. (2005) A Modified Bootscan Algorithm for Automated Identification of Recombinant Sequences and Recombination Breakpoints. AIDS Research and Human Retroviruses, 21, 98-102.
[16]  Smith, J.M. (1992) Analyzing the Mosaic Structure of Genes. Journal of Molecular Evolution, 34, 126-129.
https://doi.org/10.1007/BF00182389
[17]  Posada, D. and Crandall, K.A. (2001) Evaluation of Methods for Detecting Recombination from DNA Sequences: Computer Simulations. Proceedings of the National Academy of Sciences, 98, 13757-13762.
https://doi.org/10.1073/pnas.241370698
[18]  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.
https://doi.org/10.1093/bioinformatics/16.7.573
[19]  Kimura, M. (1980) A Simple Method for Estimating Evolutionary Rates of Base Substitutions through Comparative Studies of Nucleotide Sequences. Journal of Molecular Evolution, 16, 111-120.
https://doi.org/10.1007/BF01731581
[20]  Koichiro, T., Glen, S., Daniel, P., Alan, F. and Sudhir, K. (2013) MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0. Molecular Biology and Evolution, 30, 2725-2729.
https://doi.org/10.1093/molbev/mst197
[21]  Garcia-Arenal, F., Fraile, A. and Malpica, J.M. (2001) Variability and Genetic Structure of Plant Virus Populations. Annual Review of Phytopathology, 39, 157-186.
https://doi.org/10.1146/annurev.phyto.39.1.157
[22]  Varanda, C.M.R., Nolasco, G., Clara, M.I. and Félix, M.R. (2013) Genetic Diversity of the Coat Protein of Olive Latent Virus 1 Isolates. Archives of Virology, 13, 1953-1957.
[23]  Rubio, L., Ayllon, M.A., Kong, P., Fernandez, A., Polek, M., Guerri, J., Moreno, P. and Falk, B.W. (2001) Genetic Variation of Citrus Tristeza Virus Isolates from California and Spain: Evidence for Mixed Infections and Recombination. Journal of virology, 75, 8054-8062.
https://doi.org/10.1128/JVI.75.17.8054-8062.2001
[24]  Fraile, A., Malpica, J.M., Aranda, M.A., Rodriguez-Cerezo, E. and Garcia-Arenal, F. (1996) Genetic Diversity in Tobacco Mild Green Mosaic Tobamovirus Infecting the Wild Plant Nicotiana glauca. Virology, 223, 148-155.
https://doi.org/10.1006/viro.1996.0463
[25]  Yager, L.Y., Miller, D.L. and Jones, J. (2011) Woody Shrubs as a Barrier to Invasion by Cogongrass (Imperata cylindrica). Invasive Plant Science and Management, 4, 207-211.
https://doi.org/10.1614/IPSM-D-10-00052.1
[26]  Chiang, Y.C., Tsai, C.C., Hsu, T.W. and Chou, C.H. (2012) Characterization of 21 Microsatellite Markers from Cogongrass, Imperata cylindrica (Poaceae), a Weed Species Distributed Worldwide. American Journal of Botany, 99, e428-e430.
https://doi.org/10.3732/ajb.1200152
[27]  Somera, M., Sarmiento, C. and Truve, E. (2015) Overview on Sobemoviruses and a Proposal for the Creation of the Family Sobemoviridae. Viruses, 7, 3076-3115.
https://doi.org/10.3390/v7062761
[28]  Dingwall, C. and Laskey, R.A. (1991) Nuclear Targeting Sequences—A Consensus? Trends Biochemical Sciences, 16, 478-481.
https://doi.org/10.1016/0968-0004(91)90184-W
[29]  Sérémé, D., Séverine, L., Konaté, M., Bangratz, M., Pinel-Galzi, A., Fargette, D., Traoré, A.S., Konaté, G. and Brugidou, C. (2014) Sites under Positive Selection Modulate the RNA Silencing Suppressor Activity of Rice Yellow Mottle Virus Movement Protein P1. Journal of General Virology, 95, 213-218.
https://doi.org/10.1099/vir.0.057026-0
[30]  Traoré, O., Pinel-galzi, A., Issaka, S., Poulicard, N., Aribi, J., Aké, S., Ghesquière, A., Séré, Y., Konaté, G., Hébrard, E. and Fargette, D. (2010) The Adaptation of Rice Yellow Mottle Virus to the eIF (iso) 4G-Mediated Rice Resistance. Virology, 408, 103-108.
https://doi.org/10.1016/j.virol.2010.09.007

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