The global distribution of Banana bunchy top virus reveals little evidence for frequent recent, human-mediated long distance dispersal events

Virus Evolution

Volumn 1, Issue 1, 2015, Pages

  Stainton, Daisy ^a   Martin, Darren P ^b   Muhire, Brejnev M ^b   Lolohea, Samiuela ^c   Halafihi, Mana'ia ^d   Lepoint, Pascale ^e   Blomme, Guy ^e   Crew, Kathleen S ^f   Sharman, Murray ^f   Kraberger, Simona ^a   Dayaram, Anisha ^a   Walters, Matthew ^a   Collings, David A ^a   Mabvakure, Batsirai ^g   Lemey, Philippe ^h   Harkins, Gordon W ^g   Thomas, John E ⁱ   Varsani, Arvind ^a,b,j  

^a UNIVERSITY OF CANTERBURY   (New Zealand)

^b UNIVERSITY OF CAPE TOWN   (South Africa)

^c Tonga College   (Tonga)

^d Forests and Fisheries   (Japan)

^e BIOVERSITY INTERNATIONAL   (Italy)

^f DEPARTMENT OF AGRICULTURE AND FISHERIES   (Australia)

^g UNIVERSITY OF THE WESTERN CAPE   (South Africa)

^h UNIVERSITY OF LEUVEN   (Belgium)

ⁱ UNIVERSITY OF QUEENSLAND   (Australia)

^j UNIVERSITY OF FLORIDA   (United States)

more..

Author keywords

Babuvirus; Banana bunchy top virus; Nanoviridae; Phylogeography; Reassortment; Recombination

Indexed keywords

EID: 84958196932     PISSN: None     EISSN: 20571577     Source Type: Journal    
DOI: 10.1093/ve/vev009     Document Type: Article

References (78)

1. Almeida, R. P. et al. (2009) 'Spread of an Introduced Vector-Borne Banana Virus in Hawaii', Molecular Ecology, 18: 136-46.
2. Altschul, S. F. et al. (1990) 'Basic Local Alignment Search Tool', Journal of Molecular Biology, 215: 403-10.
3. Aronson, M. N. et al. (2000) 'Clink, a Nanovirus-Encoded Protein, Binds Both pRB and SKP1', Journal of Virology, 74: 2967-72.
4. Banerjee, A. et al. (2014) 'Identification and Characterization of a Distinct Banana Bunchy Top Virus Isolate of Pacific-Indian Oceans Group from North-East India', Virus Research, 183: 41-9.
5. Bielejec, F. et al. (2011) 'SPREAD: Spatial Phylogenetic Reconstruction of Evolutionary Dynamics', Bioinformatics, 27: 2910-12.
6. Boni, M. F., Posada D., and Feldman M. W. (2007) 'An Exact Nonparametric Method for Inferring Mosaic Structure in Sequence Triplets', Genetics, 176: 1035-47.
7. Burns, T. M., Harding R. M., and Dale J. L. (1994) 'Evidence that Banana Bunchy Top Virus has a Multiple Component Genome', Archives of Virology, 137: 371-80.
8. Burns, T. M., Harding R. M., and Dale J. L. (1995) 'The Genome Organisation of Banana Bunchy Top Virus: Analysis of Six ssDNA Components', Journal of General Virology, 76: 1471-82.
9. Dale, J. L. (1987) 'Banana Bunchy Top-An Economically Important Tropical Plant-Virus Disease', Advances in Virus Research, 33: 301-25.
10. Denham, T. P. et al. (2003) 'Origins of Agriculture at Kuk Swamp in the Highlands of New Guinea', Science, 301: 189-93.
11. Drummond, A. J., and Rambaut A. (2007) 'BEAST: Bayesian Evolutionary Analysis by Sampling Trees', BMC Evolutionary Biology 7: 214.
12. Duay, J. A. M. et al. (2014) 'Pentalonia Nigronervosa Coquerel and Pentalonia caladii van der Goot (Hemiptera: Aphididae) and Their Relationship to Banana Bunchy Top Virus in Micronesia', Pacific Science, 68: 359-64.
13. Duffy, S., and Holmes E. C. (2008) 'Phylogenetic Evidence for Rapid Rates of Molecular Evolution in the Single-Stranded DNA Begomovirus Tomato Yellow Leaf Curl Virus', Journal of Virology, 82: 957-65.
14. Duffy, S., and Holmes E. C. (2008) 'Rates of Evolutionary Change in Viruses: Patterns and Determinants', Nature Reviews Genetics, 9: 267-76.
15. Edgar, R. C. (2004) 'MUSCLE: Multiple Sequence Alignment with High Accuracy and High Throughput', Nucleic Acids Research, 32: 1792-7.
16. Firth, C. et al. (2009) 'Insights into the Evolutionary History of an Emerging Livestock Pathogen: Porcine Circovirus 2', Journal of Virology, 83: 12813-21.
17. Foottit, R. G. et al. (2010) 'The Identity of Pentalonia Nigronervosa Coquerel and P. caladii van der Goot (Hemiptera: Aphididae) Based on Molecular and Morphometric Analysis', Zootaxa, 2358: 25-38.
18. Fu, H. C. et al. (2009) 'Unusual Events Involved in Banana Bunchy Top Virus Strain Evolution', Phytopathology, 99: 812-22.
19. Geering, A. D. W., and Thomas J. E. (1997) 'Search for Alternative Hosts of Banana Bunchy Top Virus in Australia', Australasian Plant Pathology, 26: 250-4.
20. 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: 573-82.
21. Grigoras, I. et al. (2010) 'High Variability and Rapid Evolution of a Nanovirus', Journal of Virology, 84: 9105-17.
22. Grigoras, I. et al. (2014) 'Genome Diversity and Evidence of Recombination and Reassortment in Nanoviruses from Europe', Journal of General Virology, 95: 1178-91.
23. Guindon, S. et al. (2010) 'New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0', Systematic Biology, 59: 307-21.
24. Hafner, G. J., Harding R. M., and Dale J. L. (1997) 'A DNA Primer Associated with Banana Bunchy Top Virus', Journal of General Virology, 78: 479-86.
25. Hafner, G. J., Harding R. M., and Dale J. L. (1997) 'Nicking and Joining Activity of Banana Bunchy Top Virus Replication Protein in vitro', Journal of General Virology, 78: 1795-9.
26. Harding, R. M., Burns T. M., and Dale J. L. (1991) 'Virus-Like Particles Associated with Banana Bunchy Top Disease Contain Small Single-Stranded DNA', Journal of General Virology, 72: 225-30.
27. Harding, R. M., Burns T. M., and Dale J. L. (1993) 'Nucleotide Sequence of One Component of the Banana Bunchy Top Virus Genome Contains a Putative Replicase Gene', Journal of General Virology, 74: 323-8.
28. Harkins, G. W. et al. (2009) 'Experimental Evidence Indicating that Mastreviruses Probably did not Co-Diverge with Their Hosts', Virology Journal, 6: 104.
29. Harkins, G. W. et al. (2014) 'Towards Inferring the Global Movement of Beak and Feather Disease Virus', Virology, 450-451: 24-33.
30. Herrera-Valencia, V. A. et al. (2006) 'An Iterated Sequence in the Genome of Banana Bunchy Top Virus is Essential for Efficient Replication', Journal of General Virology, 87: 3409-12.
31. Hooks, C. R. R. et al. (2008) 'Effect of Banana Bunchy Top Virus Infection on Morphology and Growth Characteristics of Banana', Annuals of Applied Biology, 153: 1-9.
32. Hu, J. M. et al. (2007) 'Reassortment and Concerted Evolution in Banana Bunchy Top Virus Genomes', Journal of Virology, 81: 1746-61.
33. Hu, J. S. et al. (1996) 'Use of Polymerase Chain Reaction (PCR) to Study Transmission of Banana Bunchy Top Virus by the Banana Aphid (Pentalonia nigronervosa)', Annals of Applied Biology, 128: 55-64.
34. Hyder, M. Z. et al. (2011) 'Evidence of Recombination in the Banana Bunchy Top Virus Genome', Infection Genetics and Evolution, 11: 1293-300.
35. Islam, M. N. et al. (2010) 'Genetic Diversity and Possible Evidence of Recombination among Banana Bunchy Top Virus (BBTV) Isolates', International Research Journal of Microbiology, 1: 001-12.
36. Izquierdo-Carrasco, F., Smith S. A., and Stamatakis A. (2011) 'Algorithms, Data Structures, and Numerics for Likelihood-Based Phylogenetic Inference of Huge Trees', BMC Bioinformatics, 12: 470.
37. Karan, M., Harding R. M., and Dale J. L. (1994) 'Evidence for Two Groups of Banana Bunchy Top Virus Isolates', Journal of General Virology, 75: 3541-6.
38. Kass, R. E., and Raftery A. E. (1995) 'Bayes Factors', Journal of American Statistical Association, 90: 773-95.
39. King, A. M. et al. (2012) Virus Taxonomy: Ninth Report of the International Committee on Taxonomy of Viruses. Burlington: Elsevier Science.
40. Kraberger, S. et al. (2013) 'Evidence that Dicot-Infecting Mastreviruses are Particularly Prone to Inter-Species Recombination and have Likely been Circulating in Australia for Longer than in Africa and the Middle East. Virology, 444: 282-91.
41. Lefeuvre, P. et al. (2009) 'Widely Conserved Recombination Patterns among Single-Stranded DNA Viruses', Journal of Virology, 83: 2697-707.
42. Lejju, B. J., Robertshaw P., and Taylor D. (2006) 'Africa's Earliest Bananas?', Journal of Archaeological Science, 33: 102-13.
43. Lemey, P. et al. (2009) 'Bayesian Phylogeography Finds Its Roots', PLoS Computational Biology, 5: e1000520.
44. Magee, C. J. P. (1927) 'Investigation on the Bunchy Top Disease of the Banana', Bulletin of the Council for Scientific and Industrial Research in Australia, 30.
45. Magee, C. J. P. (1940) 'Transmission Studies on the Banana Bunchy-Top Virus', Journal of the Australian Institute of Agricultural Science, 6: 109-10.
46. Mandal, B. et al. (2013) 'Nine Novel DNA Components Associated with the Foorkey Disease of Large Cardamom: Evidence of a Distinct Babuvirus Species in Nanoviridae', Virus Research, 178: 297-305.
47. Manickam, K. et al. (2002) 'Early Detection of Banana Bunchy Top Virus in India Using Polymerase Chain Reaction', Acta Phytopathologica et Entomologica Hungarica, 37: 9-16.
48. Martin, D., and Rybicki E. (2000) 'RDP: Detection of Recombination amongst Aligned Sequences', Bioinformatics, 16: 562-3.
49. Martin, D. P. et al. (2005) 'A Modified Bootscan Algorithm for Automated Identification of Recombinant Sequences and Recombination Breakpoints', Aids Research and Human Retroviruses, 21: 98-102.
50. Martin, D. P. et al. (2010) 'RDP3: A Flexible and Fast Computer Program for Analyzing Recombination', Bioinformatics, 26: 2462-3.
51. Muhire, B. M., Varsani A., and Martin D. P. (2014) 'SDT: A Virus Classification Tool Based on Pairwise Sequence Alignment and Identity Calculation', PLoS One, 9: e108277.
52. Owor, B. E. et al. (2007) 'Successful Application of FTAVR Classic Card Technology and Use of Bacteriophage Phi 29 DNA Polymerase for Large-Scale Field Sampling and Cloning of Complete Maize Streak Virus Genomes', Journal of Virological Methods, 140: 100-5.
53. Padidam, M., Sawyer S., and Fauquet C. M. (1999) 'Possible Emergence of New Geminiviruses by Frequent Recombination', Virology, 265: 218-25.
54. Perrier, X. et al. (2011) 'Multidisciplinary Perspectives on Banana (Musa spp.) Domestication', Proceedings of the National Academy of Sciences of the United States of America, 108: 11311-8.
55. Pinili, M. S. et al. (2013) 'Cross-Transmission and New Alternate Hosts of Banana Bunchy Top Virus', Tropical Agriculture and Development, 57: 1-7.
56. Posada, D. (2008) 'jModelTest: Phylogenetic Model Averaging', Molecular Biology and Evolution, 25: 1253-6.
57. Posada, D. (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: 13757-62.
58. Posada, D. (2002) 'The Effect of Recombination on the Accuracy of Phylogeny Estimation', Journal of Molecular Evolution, 54: 396-402.
59. Ram, R. D., and Summanwar A. S. (1984) 'Colocasia esculenta (L.) schott. A Reservoir of Bunchy Top Disease of Banana', Current Science, 53: 145-6.
60. Randrianja, S., and Ellis S. (2009) Madagascar: A Short History. Chicago, IL: University of Chicago Press.
61. Rybicki, E. P. (2015) 'A Top Ten List for Economically Important Plant Viruses', Archives of Virology, 160: 17-20.
62. Rybicki, E. P. (1999) 'Plant Virus Disease Problems in the Developing World', Advances in Virus Research, 53: 127-75.
63. Savory, F. R., and Ramakrishnan U. (2014) 'Asymmetric Patterns of Reassortment and Concerted Evolution in Cardamom Bushy Dwarf Virus', Infection, Genetics and Evolution, 24: 15-24.
64. Schierup, M. H., and Hein J. (2000) 'Consequences of Recombination on Traditional Phylogenetic Analysis', Genetics, 156: 879-91.
65. Sharman, M. et al. (2008) 'Abaca Bunchy Top Virus, a New Member of the Genus Babuvirus (family Nanoviridae)', Archives of Virology, 153: 135-47.
66. Shepherd, D. N. et al. (2008) 'A Protocol for the Rapid Isolation of Full Geminivirus Genomes from Dried Plant Tissue', Journal of Virological Methods, 149: 97-102.
67. Smith, J. M. (1992) 'Analyzing the Mosaic Structure of Genes', Journal of Molecular Evolution, 34: 126-9.
68. Stainton, D. et al. (2012) 'Evidence of Inter-Component Recombination, Intra-Component Recombination and Reassortment in Banana Bunchy Top Virus', Journal of General Virology, 93: 1103-19.
69. Stamatakis, A. (2014) 'RAxML Version 8: A Tool for Phylogenetic Analysis and Post-Analysis of Large Phylogenies', Bioinformatics, 30: 1312-3.
70. Su, H.-J., Wu R.-Y., and Tsao L.-Y. (1992) 'Ecology of Banana Bunchy-Top Virus Disease', in Proceedings of the International Symposium on Recent Developments in Banana Cultivation Technology, Los Ban os, Philippines: INIBAP-ASPNET, pp. 308-12.
71. Tamura, K. et al. (2011) 'MEGA5: Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods', Molecular Biology and Evolution, 28: 2731-9.
72. Thomas, J. E., and Dietzgen R. G. (1991) 'Purification, Characterization and Serological Detection of Virus-Like Particles Associated with Banana Bunchy Top Disease in Australia', Journal of General Virology, 72: 217-24.
73. van der Walt, E. et al. (2008) 'Experimental Observations of Rapid Maize Streak Virus Evolution Reveal a Strand-Specific Nucleotide Substitution Bias', Virology Journal, 5: 104.
74. Varsani, A. et al. (2014) 'Establishment of Three New Genera in the Family Geminiviridae: Becurtovirus, Eragrovirus and Turncurtovirus', Archives of Virology, 159: 2193-203.
75. Wang, H. I. et al. (2013) 'Application of Motif-Based Tools on Evolutionary Analysis of Multipartite Single-Stranded DNA Viruses', PLoS One, 8: e71565.
76. Wanitchakorn, R., Harding R. M., and Dale J. L. (2000) 'Sequence Variability in the Coat Protein Gene of Two Groups of Banana Bunchy Top Isolates', Archives of Virology, 145: 593-602.
77. Wanitchakorn, R., Harding R. M., and Dale J. L. (2000) 'Functional Analysis of Proteins Encoded by Banana Bunchy Top Virus DNA-4 to-6', Journal of General Virology, 81: 299-306.
78. Yu, N. T. et al. (2012) 'Cloning and Sequence Analysis of Two Banana Bunchy Top Virus Genomes in Hainan', Virus Genes, 44: 488-94.