DIVERSIFICATION INTO THE GENUS Badnavirus: PHYLOGENY AND POPULATION GENETIC VARIABILITY
DOI:
https://doi.org/10.28998/rca.v17i2.6286Keywords:
Evolution, recombination, species demarcation.Abstract
Badnaviruses (family Caulimoviridae) have semicircular dsDNA genomes encapsidated into bacilliform particles. The genus Badnavirus is the most important due to its high number of species reported infecting cultivated plants worldwide. This study aimed to evaluate the phylogenetic positioning and population genetic variability into Badnavirus. Data sets comprising the badnavirus complete genome and partial sequences of the RT and RNaseH genes were obtained from the GenBank database. Multiple nucleotide sequence alignments from complete genome, ORFIII, complete genomic domain RT/RNaseH (1020pb) and partial (579pb) were performed. A total of 127 genomes were obtained, representing 53 species of badnavirus. Nucleotide sequence comparisons for the RT/RNaseH domain showed only a few isolates reported as distinct species shared ≥80% identity, the current threshold used for species demarcation into this genus. Phylogenetic trees for the complete genome and for ORFIII showed four well supported clusters (badnavirus groups 1-4), with clusters 1 and 3 being sister groups comprising predominantly sugarcane- and banana-infecting species. Non-tree-like evolution analysis evidenced putative recombination events among badnaviruses, and at least 23 independent events were detected. High levels of nucleotide diversity were observed for the partial RT/RNaseH region in isolates of 11 badnavirus species. These results showed that mutation and recombination are important mechanisms that acting on badnavirus diversification.Downloads
References
Bhat, A.I.; Hohn, T.; Selvarajan, R. Badnaviruses: The Current Global Scenario. Viruses, 2016, 177, 1-29.
Bouhida, M.L.; Lockhart, B.E.; Olszewski, N.E. An analysis of the complete sequence of a sugarcane bacilliform virus genome infectious to banana and rice. Journal of General Virology, 1993, 74, 15-22.
Bousalem, M.; Douzery, E.J.P.; Seal, S.E. Molecular taxonomy, phylogeny, and evolution of plant reverse transcribing viruses (Caulimoviridae) inferred from the reverse transcriptase sequences. Archives of Virology, 2008, 153, 1085-1102.
Cheng, C.P.; Lockhart, B.E.; Olszewski, N.E. The ORF I and II Proteins of Commelina yellow mottle virus are virion-associated. Virology, 1996, 223, 263-271.
Côte, F.X.; Galzi, S.; Folliot, M.; Lamagnère, Y.; Teycheney, P.Y.; Iskra-Caruana, M.L. Micropropagation by tissue culture triggers differential expression of infectious endogenous Banana streak virus sequences (eBSV) present in the B genome of natural and synthetic interspecific banana plantains. Molecular Plant Pathology, 2010, 11, 137-144.
Dahal, G.; Ortiz, R.; Tenkouano, A.; Hughes, Jd’A.; Thottappilly, G.; Vuylsteke, D.; Lockhart, B.E.L. Relationship between natural occurrence of banana streak badnavirus and symptom expression, relative concentration of viral antigen, and yield characteristics of some micropropagated Musa spp. Plant Pathology, 2000, 49, 68-79.
Dallot, S.; Accuna, P.; Rivera, C.; Ramirez, P.; Cote, F.; Lockhart, B.E.L.; Caruana, M.L. Evidence that the proliferation stage of micropropagation procedure is determinant in the expression of Banana streak virus integrated into the genome of the FHIA21 hybrid (Musa AAAB). Archives of Virology, 2001, 146, 2179-2190.
Daniells, J.W.; Geering, A.D.W.; Bride, N.J.; Thomas, J.E. The effect of banana streak virus on the growth andyield of dessert bananas in tropical Australia. Annals of Applied Biology, 2001, 139, 51-60.
Deeshma, K.P.; Bhat, A.I. Complete genome sequencing of Piper yellow mottle virus infecting black pepper, betelvine, and Indian long pepper. Virus Genes, 2015, 50, 172–175.
Edgar R.C. MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics, 2004, 5, 1–19.
Eni, A.O.; Hughes, Jd.; Asiedu, R.; Rey, M.E. Sequence diversity among Badnavirus isolates infecting yam (Dioscorea spp.) in Ghana, Togo, Benin and Nigeria. Archives of Virology, 2008, 153, 2263-2272.
García-Andrés, S.; Monci, F.; Navas-Castillo, J.; Moriones, E. Begomovirus genetic diversity in the native plant reservoir Solanum nigrum: Evidence for the presence of a new virus species of recombinant nature. Virology, 2006, 350, 433-442.
Gayral, P.; Iskra-Caruana, M. Phylogeny of Banana Streak Virus Reveals Recent and Repetitive Endogenization in the Genome of Its Banana Host (Musa sp.). Journal of Molecular Evolution, 2009, 69, 65-80.
Graham, A.P.; Martin, D.P.; Roye, M.E. Molecular characterization and phylogeny of two begomoviruses infecting Malvastrum americanum in Jamaica: Evidence of the contribution of inter-species recombination to the evolution of malvaceous weed-associated begomoviruses from the Northern Carribbean. Virus Genes, 2010, 40, 256-266.
Geering, A.D.W.; Hull, R. Family Caulimoviridae. In: King AMQ, Adams MJ, Carstens EB, Lefkowitz EJ (Eds.). Virus Taxonomy. 9th Report of the International Committee on Taxonomy of Viruses. London, UK. Elsevier Academic Press. 2012, pp. 429-443.
Geering, A.D.W.; Mcmichael, L.A.; Dietzgen, R.G.; Thomas, J.E. Genetic diversity among Banana streak virus isolates from Australia. Phytopathology, 2000, 90, 921-927.
Geijskes, R.J.; Braithwaite, K.S.; Dale, J.L.; Harding, R.M.; Smith, G.R. Sequence analysis of an Australian isolate of sugarcane bacilliform badnavirus. Archives of Virology, 2002, 147, 2393-2404.
Govind, P.R.; Susheel, K.S.; Deepti, S.; Meenakshi, A.; Priyanka, S.; Virendra, K.B. Genetically Diverse Variants of Sugarcane bacilliform virus Infecting Sugarcane in India and Evidence of a Novel Recombinant Badnavirus Variant. Journal of Phytopathology, 2014, 162, 779–787.
Guimarães, K.M.; Silva, S.J.C.; Melo, A.M.; Ramos-Sobrinho, R.; Lima, J.S.; Zerbini, F.M.; Assunção, I.P.; Lima, G.S.A. Genetic variability of badnaviruses infecting yam (Dioscorea spp.) in northeastern Brazil. Tropical Plant Pathology, 2015, 40, 111-118.
Hagen, L.S.; Jacquemond, M.; Lepingle, A.; Lot, H.; Tepfer, M. Nucleotide sequence and genomic organisation of cacao swollen shoot virus. Virology, 1993, 196, 619-628.
Harper, G.; Hart, D.; Moult, S.; Hull, R.; Geering, A.; Thomas, J. Diversity of banana streak virus isolates in Uganda. Archives of Virology, 2005, 150, 2407-2420.
Harper, G.; Hull, R. Cloning and sequence analysis of Banana Streak Virus DNA. Virus Genes, 1998, 17, 271-278.
Hohn, T.; Richert-Poggeler, K.R.; Harper, G.; Schawarzacher, T.; Teo, C.; Teycheney, P.Y.; Iskra-Caruana, M.L.; Hull, R. Evolution of integrated plant viruses. In: Roosinck M (Eds.) Plant Virus Evolution. Heidelberg, Germany. Academic Springer. 2008, pp. 54–76.
Huson, D.H.; Bryant, D. Application of phylogenetic networks in evolutionary studies. Molecular Biology and Evolution, 2006, 23, 254–267.
Jacquot, E.; Hagen, L.S.; Jacquemond, M.; Yot, P. The open reading frame 2 product of cacao swollen shoot badnavirus is a nucleic acid-binding protein. Virology, 1996, 225, 191-195.
James, A.P.; Geijskes, R.J.; Dale, J.L.; Harding, R.M. Molecular characterization of six badnavirus species associated with leaf streak disease of banana in East Africa. Annals of Applied Biology, 2011, 158, 346-353.
Johnson, A.M.; Borah, B.K.; Sai Gopal, D.V.; Dasgupta, I. Analysis of full-length sequences of two Citrus yellow mosaic badnavirus isolates infecting Citrus jambhiri (Rough Lemon) and Citrus sinensis L. Osbeck (Sweet Orange) from a nursery in India. Virus Genes, 2012, 45, 600–605.
Jones, D.R.; Lockhart, B.E.L. Banana streak disease. Musa fact sheet No. 1, International network for improvement of banana and plantain, Montpellier, France. 1993.
Karuppaiah, R.; Viswanathan, R.; Kumar, V.G. Genetic diversity of Sugarcane bacilliform virus isolates infecting Saccharum spp. in India. Virus Genes, 2013, 46, 505–516.
Kouakou, K.; Kébé, B.I.; Kouassi, N.; Muller, E. Geographical distribution of Cacao swollen shoot virus molecular variability in Côte d’Ivoire. Plant Disease, 2012, 96, 1445-1450.
Kumar, S.; Stecher, G.; Tamura, K. MEGA7: Molecular Evolutionary Genetics Analysis version 7.0 for Bigger Datasets. Molecular Biology and Evolution, 2016, 33, 1870-1874.
Lheureux, F.; Carreel, F.; Jenny, C.; Lockhart, B.E.L.; Iskra-Caruana, M.L. Identification of genetic markers linked to banana streak disease expression in inter-specific Musa hybrids. Theoretical and Applied Genetics, 2003, 106, 594-598.
Lockhart, B.E.L.; Autrey, L.J.C. Occurrence in sugarcane of a bacilliform virus related serologically to banana streak virus. Plant Disease, 1988, 72, 230-233.
Martin, D.P.; Murrell, B.; Golden, M.; Khoosal, A.; Muhire, B. RDP4: Detection and analysis of recombination patterns in virus genomes. Virus Evolution, 2015, 1, 1-5.
Medberry, S.L.; Lockhart, B.E.L.; Olszewski, N.E. Properties of Commelina yellow mottle virus complete DNA sequence, genomic discontinuities and transcript suggest that it is a pararetrovirus. Nucleic Acids Research, 1990, 18, 5505-5513.
Miller, M.A.; Holder, M.T.; Vos, R.; Midford, P.E.; Liebowitz, T.; Chan, L.; Hoover, P.; Warnow, T. (2010) The CIPRES portals. CIPRES. http://www.phylo.org/sub-sections/portal (Accessed 15 Aug 2016).
Muller, E.; Dupuy, V.; Blondin, L.; Bauffe, F.; Daugrois, J.H.; Laboureau, N.; Iskra Caruana, M.L. High molecular variability of sugarcane bacilliform viruses in Guadeloupe implying the existence of at least three new species. Virus Reseach, 2011, 160, 414-419.
Muhire, B.; Martin, D.P.; Brown, J.K.; Navas-Castillo, J.; Moriones, E.; Zerbini, F.M.; Rivera-Bustamante, R.; Malathi, V.G.; Briddon, R.W.; Varsani, A. A genome-wide pairwise-identity-based proposal for the classification of viruses in the genus Mastrevirus (family Geminiviridae). Archives of Virology, 2013, 158, 1411-1424.
Rannala, B.; Yang, Z. Probability distribution of molecular evolutionary trees: a new method of phylogenetic inference. Journal of Molecular Evolution, 1996, 43, 304-311.
Ronquist, F.; Teslenko, M.; van der Mark, P.; Ayres, D.L.; Darling, A.; Hohna, S.; Larget, B.; Liu, L.; Suchard, M.A.; Huelsenbeck, J.P. MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice across a Large Model Space. Systematic Biology Advance Access, 2012, 61, 539-42.
Rozas, J.; Ferrer-Mata, A.; Sánchez-DelBarrio, J.C.; Guirao-Rico, S.; Librado, P.; Ramos-Orsins, S.E.; Sánchez-Gracia, A. DnaSP v6: DNA Sequence Polymorphism Analysis of Large Datasets. Molecular Biology and Evolution, 2017, 34, 3299-3302.
Sharma, S.K.; Kumar, P.V.; Geetanjali, A.S.; Pun, K.B.; Baranwal, V.K. Subpopulation level variation of banana streak viruses in India and common evolution of banana and sugarcane badnaviruses. Virus genes, 2015, 50, 450-465.
Silva, J.M.; Jobim, L.J.; Ramos-Sobrinho, R.; Lima, J.S.; Assunção, I.P.; Cruz, M.M.; Lima, G.S.A. Incidence and species diversity of badnaviruses infecting sugarcane from a germplasm collection in Brazil. Tropical Plant Pathology, 2015, 40, 212-217.
Staginnus, C.; Iskra-Caruana, M.; Lockhart, B.; Hohn, T.; Richert-Pöggeler, K.R. Suggestions for a nomenclature of endogenous pararetroviral sequences in plants. Archives of Virology, 2009, 154, 1189-1193.
Svarovskaia, E.S.; Cheslock, S.R.; Zhang, W.H.; Hu, W.S.; Pathak, V.K. Retroviral mutation rates and reverse transcriptase fidelity. Fronties in Bioscience. 2003, 8, 117–134.
Yang, I.C.; Hafner, G.J.; Dale, J.L.; Harding, R.M. Genomic characterization of taro bacilliform virus. Archives of Virology, 2003, 148, 937-949.
Zhou, X.; Liu, Y.; Calvert, L.; Munoz, C.; Otim-Nape, G.W.; Robinson, D.J.; Harrison, B.D. Evidence that DNA-A of a geminivirus associated with severe cassava mosaic disease in Uganda has arisen by interspecific recombination. Journal of General Virology, 1997, 78, 2101-2111.
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