Genetic Diversity Analysis of Badnaviruses Infecting Banana in Burkina Faso — Oak Academic Publishing
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Genetic Diversity Analysis of Badnaviruses Infecting Banana in Burkina Faso
Laboratoire de Protection et Défense des Cultures, Institut de l’Environnement et de Recherches Agricoles (INERA), Centre National de Recherche Scientifique et Technologique (CNRST), Ouagadougou, Burkina Faso
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Laboratoire de Protection et Défense des Cultures, Institut de l’Environnement et de Recherches Agricoles (INERA), Centre National de Recherche Scientifique et Technologique (CNRST), Ouagadougou, Burkina Faso
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Laboratoire de Protection et Défense des Cultures, Institut de l’Environnement et de Recherches Agricoles (INERA), Centre National de Recherche Scientifique et Technologique (CNRST), Ouagadougou, Burkina Faso
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Laboratoire Central d’Horticulture, Institut de l’Environnement et de Recherches Agricoles (INERA), Centre National de Recherche Scientifique et Technologique (CNRST), Bobo Dioulasso, Burkina Faso
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Laboratoire de Biosciences, Université Joseph KI-ZERBO, Ouagadougou, Burkina Faso
1 Laboratoire de Protection et Défense des Cultures, Institut de l’Environnement et de Recherches Agricoles (INERA), Centre National de Recherche Scientifique et Technologique (CNRST), Ouagadougou, Burkina Faso
2 Laboratoire de Protection et Défense des Cultures, Institut de l’Environnement et de Recherches Agricoles (INERA), Centre National de Recherche Scientifique et Technologique (CNRST), Ouagadougou, Burkina Faso
3 Laboratoire de Protection et Défense des Cultures, Institut de l’Environnement et de Recherches Agricoles (INERA), Centre National de Recherche Scientifique et Technologique (CNRST), Ouagadougou, Burkina Faso
4 Laboratoire Central d’Horticulture, Institut de l’Environnement et de Recherches Agricoles (INERA), Centre National de Recherche Scientifique et Technologique (CNRST), Bobo Dioulasso, Burkina Faso
5 Laboratoire de Biosciences, Université Joseph KI-ZERBO, Ouagadougou, Burkina Faso
Badnaviruses are serious plant pararetroviruses affecting banana and causes serious economic losses to banana production worldwide. This study aims to examine the variability of BSV and SCBV nature infecting banana in Burkina Faso. Polymerase Chain Reaction (PCR) used the Badna FP/RP specific primers for the RT/RNase H regions present in badnaviruses. The PCR yielded about 579 bp amplicons from banana infected by BSV and SCBV. The 38 BSV isolates recorded low nucleotide identity ranging from 58.9% - 98.1%. Based on percentage nucleotide sequence identity and phylogenetic analyse, BSV isolates were categorized into four groups: 1, 2, 3 and 4. Group 4 shared 76.9% - 100% identity with BSOL species. However, Groups 1 and 3 rec orded a low identity ranging, from 76.8% - 79.2%, 68.8% - 79.7% with BSCV, and 72.8% - 79.0% between Group 2 and BSOLV. Groups 1, 2 and 3 were as signed to a potentially new BSV species. The two SCBV isolates recorded a low nucleotide identity of 68% among themselves indicating high diversity. In addi tion, SCBV_Cd and SCBV_CE showed high nucleotide identity 91.3% and 58.7% with SCBV_C and SCBV, when they were compared to all published SCBV genotypes. In addition, phylogenetic analysis revealed the segregation of SCBV isolates into two genotypes, SCBV_Cd in C and SCBV_CE segregated in a new genotype namely Z. Recombination analyses showed weak signa tures of recombination among some of the BSV and SCBV sequences.
Vo, J.N., Campbell, P.R. and Mahfuzc, N.N. (2016) Characterization of the Banana Streak Virus Capsid Protein and Mapping of the Immunodominant Continuous B-Cell Epitopes to the Surface-Exposed N-Terminus. Journal of General Virology, 97, 3446-3457. https://doi.org/10.1099/jgv.0.000643
Iskra-Caruana, M.-L., Chabannes, M., Duroy, P.-O. and Muller, E. (2014) A Possible Scenario for the Evolution of Banana Streak Virus in Banana. Virus Research, 186, 155-162. https://doi.org/10.1016/j.virusres.2014.01.005
Alangar, B., Thomas, H. and Ramasamy, S. (2016) Badnaviruses: The Current Global Scenario. Viruses, 8, Article 177. https://doi.org/10.3390/v8060177
Harper, G., Hart, D., Moult, S. and Hull, R. (2002) Detection of Banana Streak Virus in Field Samples of Bananas from Uganda. Annals of Applied Biology, 141, 247-257. https://doi.org/10.1111/j.1744-7348.2002.tb00216.x
Yot-Dauthy, D. and Bové, J.-M. (1966) Mosaïque du bananier. Identification et purification de diverses souches du virus. Fruits, 21, 449-466.
Dallot, S., Acuna, P., Rivera, C., Ramirez, P., Cote, F., Lockhart, B.E.L. and Iskra-Caruana, M.-L. (2001) Evidence That the Proliferation Stage of Micro Propagation Procedure Is Determinant in the Expression of Banana Streak Virus Integrated into the Genome of the FHIA21 Hybrid (Musa AAAB). Archive of Virology, 146, 2179-2190. https://doi.org/10.1007/s007050170028
Geering, A.D., Maumus, F., Copetti, D., Choisne, N., Zwickl, D.J., Zytnicki, M., McTaggart, A.R., Scalabrin, S., Vezzulli, S., Wing, R.A., Quesneville, H. and Teycheney, P.Y. (2014) Endogenous Florendoviruses Are Major Components of Plant Genomes and Hallmarks of Virus Evolution. Nature Communications, 5, Article No. 5269. https://doi.org/10.1038/ncomms6269
Gayral, P., Carlos, J., Noa-Carrazana, N., Lescot, M., Lheureux, F., Lockhart, E.L.B., Mutsumoto, Piffanelli, P. and Iscra-Caruana, M.-L. (2008) A Single Banana Streak Virus Integration Event in the Banana Genome as the Origin of Infectious Endogenous Pararetrovirus. Journal of Virology, 82, 6697-6710. https://doi.org/10.1128/JVI.00212-08
Cote, F.-X., Galzi, S., Folliot, M., Lamagnere, Y., Teycheney, P.-Y. and Iskra-Caruana, M.-L. (2010) Micropropagation by Tissue Culture Triggers Differential Expression of Endogenous Banana Streak Virus (eBSV) in the B Genome of Natural and Synthetic Interspecific Banana Plantain. Molecular Plant Pathology, 11, 137-144. https://doi.org/10.1111/j.1364-3703.2009.00583.x
Harper, G., Dahal, G., Thottapilly, G. and Hull, R. (1999) Detection of Episomal Banana Streak Badnavirus by IC-PCR. Journal of Virological Methods, 79, 1-8. https://doi.org/10.1016/S0166-0934(98)00158-X
Geering, A.D.W., Olszewski, N.E., Harper, G., Lockhart, B.E.L., Hull, R. and Thomas, J.E. (2005) Banana Contains a Diverse Array of Endogenous Badnaviruses. Journal of General Virology, 86, 511-520. https://doi.org/10.1099/vir.0.80261-0
Hohn, T. and Rothnie, H. (2013) Plant Pararetroviruses: Replication and Expression. Current Opinion in Virology, 3, Article ID: 621628. https://doi.org/10.1016/j.coviro.2013.08.013
Bouhida, M., Lockhart, B.E.L. and Olszewski, N.E. (1993) An Analysis of the Complete Sequence of a Sugarcane Bacilliform Virus Genome Infectious to Banana and Rice. Journal of General Virology, 74, 15-22. https://doi.org/10.1099/0022-1317-74-1-15
Frison, E.A. and Putter, C.A. (1993) FAO/IBPGR Technical Guidelines for the Safe Movement of Sugarcane Germplasm. FAO/IBPGR.
Abdel-Salam, A.M., Dawoud, R.A., Aly, A.M.E. and El Saghir, S.M. (2014) The Detection and Diversity of Banana Streak Virus Isolates in Egypt. Egyptian Journal of Virology, 11, 136-149.
Rao, X.-Q., Wu, Z.-L., Wang, W., Zhou, L., Sun, J. and Li, H.-P. (2020) Genetic Diversity Analysis Reveals New Badnaviruses Infecting Banana in South China. Journal of Plant Pathology, 102, 1065-1075. https://doi.org/10.1007/s42161-020-00646-8
Ouattara, B., Sérémé, D., Koala, M., Nitiema, L., Koïta, K., Kaboré, E. and Wonni, I. (2023) Prevalence and Spatial Distribution of Badnavirus in the Banana (Musa spp.) Major Growing Areas in Burkina Faso. In Press.
Geijskes, R.J., Braithwaite, K.S., Dale, J.L., Harding, R.M. and Smith, G.R. (2002) Sequence Analysis of an Australian Isolate of Sugarcane Bacilliform Badnavirus. Archives of Virology, 147, 2393-2404. https://doi.org/10.1007/s00705-002-0879-2
Adams, M.J. and Carstens, E.B. (2012) Ratification Vote on Taxonomic Proposals to the International Committee on Taxonomy of Viruses. Archives of Virology, 157, 1411-1422. https://doi.org/10.1007/s00705-012-1299-6
Karuppaiah, R., Viswanathan, R. and Kumar, V.G. (2013) Genetic Diversity of Sugarcane Bacilliform Virus Isolates Infecting Saccharum spp. in India. Virus Genes, 46, 505-516. https://doi.org/10.1007/s11262-013-0890-6
Muller, E., Dupuy, V., Blondin, L., Bauffe, F., Daugrois, J., Nathalie, L. and Iskra-Caruana, M. (2011) High Molecular Variability of Sugarcane Bacilliform Viruses in Guadeloupe Implying the Existence of at Least Three New Species. Virus Research, 160, 414-419. https://doi.org/10.1016/j.virusres.2011.06.016
Wu, X.-B., Alabi, O.J., Damaj, M.B., Sun, S.-R., Mirkov, T.E., Fu, H.-Y., Chen, R.-K. and Gao, S.-J. (2016) Prevalence and RT/RNase H Genealogy of Sugarcane Bacilliform Virus Isolates from China. Journal of Phytopathology, 164, 595-607. https://doi.org/10.1111/jph.12483
Ahmad, K., Sun, S.-R., Chen, J.-L., Huang, M.-T., Fu, H.-Y. and Gao, S.-J. (2019) Presence of Diverse Sugarcane Bacilliform Viruses Infecting Sugarcane in China Revealed by Pairwise Sequence Comparisons and Phylogenetic Analysis. The Plant Pathology Journal, 35, 41-50. https://doi.org/10.5423/PPJ.OA.08.2018.0156
Janiga, P.K., Nithya, K. and Viswanathan, R. (2021) Dynamics of Genetic Diversity among Indian Sugarcane Bacilliform Virus Species and Implications of Associated Recombination Events in the Virus. Research Square. https://doi.org/10.21203/rs.3.rs-713719/v2
Lockhart, B.E.L. and Autrey, L.J.C. (1988) Occurrence in Sugarcane of a Bacilliform Virus Related Serologically to Banana Streak Virus. Plant Disease, 72, 230-233. https://doi.org/10.1094/PD-72-0230
Harper, G., Hart, D., Moult, S., Hull, R., Geering, A. and Thomas, J. (2005) The Diversity of Banana Streak Virus in Uganda. Archives of Virology, 150, 2407-2420. https://doi.org/10.1007/s00705-005-0610-1
Gayral, P. and Iskra-Caruana, M.L. (2009) Phylogeny of Banana Streak Virus Reveals Recent and Repetitive Endogenization in the Genome of Its Banana Host (Musa sp.). Journal of Molecular Evolution, 69, 65-80. https://doi.org/10.1007/s00239-009-9253-2
Mukwa, F.T.L. (2016) Les virus du bananier et plantain (Musa spp.) en République démocratique du Congo: Occurrence, identification de nouveaux virus et diversité génétique. Thèse de Doctorat, Université Catholique de Louvain, Belgique, 257 p.
James, A.P., Geijskes, R.J., Dale, J.L. and Harding, R.M. (2011) Development of a Novel Rolling Circle Amplification Technique to Detect Banana Streak Virus That Also Discriminates between Integrated and Episomal Virus Sequences. Plant Disease, 95, 57-62. https://doi.org/10.1094/PDIS-07-10-0519
Permingeat, H.R., Romagnoli, M.V. and Vallejos, R.H. (1998) A Simple Method for Isolating High Yield and Quality DNA from (Gossypium hirsutum L.) Leaves. Plant Molecular Biology Reporter, 16, 1-6.
Yang, I.C., Hafner, G.J., Revill, P.A., Dale, J.L. and Harding, R.M. (2003) Sequence Diversity of South Pacific Isolates of Taro Bacilliform Virus and the Development of a PCR Based Diagnostic Test. Archives of Virology, 148, 1957-1968. https://doi.org/10.1007/s00705-003-0163-0
Muhire, B., Varsani, A. and Martin, D.P. (2014) SDT: A Virus Classification Tool Based on Pairwise Sequence Alignment and Identity Calculation. PLOS ONE, 9, e108277. https://doi.org/10.1371/journal.pone.0108277
Tamura, K., Stecher, G., Peterson, D., Filipski, A. and Kumar, S. (2013) MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0. Molecular Biology and Evolution, 30, 2725-2729. https://doi.org/10.1093/molbev/mst197
Martin, D.P., Williamson, C. and Posada, D. (2005) RDP2: Recombination Detection and Analysis from Sequence Alignments. Bioinformatics, 21, 260-262. https://doi.org/10.1093/bioinformatics/bth490
Martin, D.P., Lemey, P. and Posada, D. (2011) Analysing Recombination in Nucleotide Sequences. Molecular Ecology Resources, 11, 943-955. https://doi.org/10.1111/j.1755-0998.2011.03026.x
Padidam, M., Beachy, R. and Fauquet, C.M. (1995) Classification and Identification of Geminiviruses Using Sequence Comparisons. Journal of Virology, 76, 249-263. https://doi.org/10.1099/0022-1317-76-2-249
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 of the United States of America, 98, 13757-13762. https://doi.org/10.1073/pnas.241370698
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
Boni, M.F., Posada, D. and Feldman, M.W. (2007) An Exact Nonparametric Method for Inferring Mosaic Structure in Sequence Triplets. Genetics, 176, 1035-1047. https://doi.org/10.1534/genetics.106.068874
Bousalem, M., Douzery, E.J. and Seal, S.E. (2008) Taxonomy, Molecular Phylogeny and Evolution of Plant Reverse Transcribing Viruses (Family Caulimoviridae) Inferred from Full-Length Genome and Reverse Transcriptase Sequences. Archives of Virology, 153, 1085-1102. https://doi.org/10.1007/s00705-008-0095-9
Gayral, P., Blondin, L., Guidolin, O., Carreel, F., Hippolyte, I., Perrier, X., et al. (2010) Evolution of Endogenous Sequences of Banana Streak Virus: What Can We Learn from Banana (Musa sp.) Evolution? Journal of Virology, 84, 7346-7359. https://doi.org/10.1128/JVI.00401-10
Iskra-Caruana, M.-L., Baurens, F.-C., Gayral, P. and Chabannes, M. (2010) A Four-Partner Plant-Virus Interaction: Enemies Can Also Come from Within. Molecular Plant-Microbe Interaction, 23, 1394-1402. https://doi.org/10.1094/MPMI-05-10-0107
Ferreira, C.H.L.H., Jordäo, L.J., Ramos-Sobrinho, R., Ferro, M.M.M., Cavalcanti da Silva, S.J. and Assunçäo Lima, G.S.A. (2019) Diversification into Genus Badnavirus: Phylogeny and Population Genetic Variability. Ciência Agricola, 17, 59-72. https://doi.org/10.28998/rca.v17i2.6286
Lheureux, F., Laboureau, N., Muller, E., Lochart, E.L. and Iskra-Caruana, M.L. (2007) Molecular Characterization of Banana Streak Acuminata Vietnam Virus Isolated from Musa acuminata Siamea (Banana Cultivar). Archive of Virology, 152, 1409-1416. https://doi.org/10.1007/s00705-007-0946-9
King, M.Q., Adams, M.J., Carstens, E.B. and Lefkowitz, E.J. (2012) Virus Taxonomy: Classification and Nomenclature of Viruses. 9th Report of International Committee on Taxonomy of Viruses. Elsevier, San Diego.
Ermini, J.L., Tenaglia, G.C. and Pratta, G.R. (2018) Molecular Diversity in Selected Banana Clones (Musa AAA “Cavendish”) Adapted to the Subtropical Environment of Formosa Province (Argentina). American Journal of Plant Sciences, 9, 2504-2513. https://doi.org/10.4236/ajps.2018.912181
Chabannes, M., Gabriel, M., Aksa, A., Galzi, S., Dufayard, Iskra-Caruana, M.-L. and Muller, E. (2020) Badnaviruses and Banana Genomes: A Long Association Sheds Light on Musa Phylogeny and Origin. Molecular Plant Pathology, 22, 216-230. https://doi.org/10.1111/mpp.13019
Geering, A.D.W., McMichael, L.A., Dietzgen, R.G. and Thomas, J.E. (2000) Genetic Diversity among Banana Streak Virus Isolates from Australia. Phytopathology, 90, 921-927. https://doi.org/10.1094/PHYTO.2000.90.8.921
Zhuang, J., Wang, J.-H., Zhang, X. and Liu, Z.-X. (2011) Molecular Characterization of Banana Streak Virus Isolate from Musa acuminata in China. Virologica Sinica, 26, 393-402. https://doi.org/10.1007/s12250-011-3212-y
Geering, A.D.W. and Hull, R. (2012) Family Caulimoviridae. In: King, A.M.Q., Adams, M.J., Carestens, E.B. and Lefkowitz, E.J., Eds., Virus Taxonomy Classification and Nomenclature of Viruses Ninth Report of the International Committee on Taxonomy of Viruses, Elsevier, San Diego, 424-443.
Banerjee, A., Roy, S., Behere, G.T., Roy, S.S., Duttad, S.K. and Ngachan, S.V. (2014) Identification and Characterization of a Distinct Banana Bunchy Top Virus Isolate of Pacific-Indian Oceans Group from North-East India. Virus Research, 183, 41-49. https://doi.org/10.1016/j.virusres.2014.01.017
Fox, M.J. and Erill, I. (2010) Relative Codon Adaptation: A Generic Codon Bias Index for Prediction of Gene Expression. DNA Research, 17, 185-196. https://doi.org/10.1093/dnares/dsq012
Zongo, A.E., Neya, B.J., Palanga, E., Sereme, D., Koala, M., Longue, R.D.S., Zabre, J., Bouda, Z., Barro, N. and Traore, O. (2019) Molecular Characterization of a Large Diversity of Bambara Groundnut Potyviruses (Vigna subterranea (L.) Verdc.) in Burkina Faso. Advances in Bioscience and Biotechnology, 10, 270-281. https://doi.org/10.4236/abb.2019.109021
Harper, G., Hart, D., Moult, S. and Hull, R. (2004) Banana Streak Virus Is Very Diverse in Uganda. Virus Research, 100, 51-56. https://doi.org/10.1016/j.virusres.2003.12.024
Iskra-Caruana, M.-L., Duroy, P.-O., Chabannes, M. and Muller, E. (2013) The Common Evolutionary History of Badnaviruses and Banana. Infection, Genetics and Evolution, 21, 83-89. https://doi.org/10.1016/j.meegid.2013.10.013
James, A.P., Geijskes, R.J., Dale, J.L. and Harding, R.M. (2011) Molecular Characterisation of Six Badnavirus Species Associated with Leaf Streak Disease of Banana in East Africa. Annals of Applied Biology, 158, 346-353. https://doi.org/10.1111/j.1744-7348.2011.00466.x
Jaufeerally-Fakim, Y., Khorugdharry, A. and Harper, G. (2006) Genetic Variants of Banana Streak Virus in Mauritius. Virus Research, 115, 91-98. https://doi.org/10.1016/j.virusres.2005.06.015
Lockhart, B.E.L. and Jones, D.R. (2000) Banana Streak. In: Jones, D.R., Ed., Diseases of Banana, Abaca and Enset, CAB International, Wallingford, 263-274.
Sharma, S.K., Vignesh, K.P., Geetanjali, A.S., Pun, K.B. and Baranwal, V.K. (2015) Subpopulation Level Variation of Banana Streak Viruses in India and Common Evolution of Banana and Sugarcane Badnaviruses. Virus Genes, 50, 450-465. https://doi.org/10.1007/s11262-015-1179-8
Geering, A.D.W., McMichael, L.A., Dietzgen, R.G. and Lockhart, B.E.L. (2001) Analysis of the Distribution and Structure of Integrated Banana Streak Virus DNA in a Range of Musa Cultivars. Molecular Plant Pathology, 2, 207-213. https://doi.org/10.1046/j.1464-6722.2001.00071.x