Possible emergence of new geminiviruses by frequent recombination.
Abstract:Although exchange of genetic information by recombination plays a role in the evolution of viruses, the extent to which it generates diversity is not clear. We analyzed genomes of geminiviruses for recombination using a new statistical procedure developed to detect gene conversions. Geminiviruses (family, Geminiviridae) are a group of plant viruses characterized by a genome of circular single-stranded DNA (approximately 2700 nucleotides in length) encapsidated in twinned quasi-isometric particles. Complete nucleotide sequences of geminiviruses were aligned, and recombination events were detected by searching pairs of viruses for sequences that are significantly more similar than expected based on random distribution of polymorphic sites. The analyses revealed that recombination is very frequent and occurs between species and within and across genera. Tests identified 420 statistically significant recombinant fragments distributed across the genome. The results suggest that recombination is a significant contributor to geminivirus evolution. The high rate of recombination may be contributing to the recent emergence of new geminivirus diseases.
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[1] M. Witty,et al. Integration of multiple repeats of geminiviral DNA into the nuclear genome of tobacco during evolution. , 1996, Proceedings of the National Academy of Sciences of the United States of America.
[2] M. Lai. RNA recombination in animal and plant viruses. , 1992, Microbiological reviews.
[3] J. Messing,et al. Geminiviruses and their uses as extrachromosomal replicons , 1994 .
[4] Rupert G. Miller. Simultaneous Statistical Inference , 1966 .
[5] D. Hartl,et al. Genetic exchange among natural isolates of bacteria: recombination within the phoA gene of Escherichia coli. , 1988, Proceedings of the National Academy of Sciences of the United States of America.
[6] S. Khalid,et al. Cotton leaf curl disease in Pakistan caused by a whitefly-transmitted geminivirus , 1994 .
[7] Stephen S. Morse,et al. The Evolutionary biology of viruses , 1994 .
[8] X. Zhou,et al. Four DNA-A variants among Pakistani isolates of cotton leaf curl virus and their affinities to DNA-A of geminivirus isolates from okra. , 1998, The Journal of general virology.
[9] S. Karlin,et al. Methods for assessing the statistical significance of molecular sequence features by using general scoring schemes. , 1990, Proceedings of the National Academy of Sciences of the United States of America.
[10] S. Sawyer. Statistical tests for detecting gene conversion. , 1989, Molecular biology and evolution.
[11] J. Stephens,et al. Statistical methods of DNA sequence analysis: detection of intragenic recombination or gene conversion. , 1985, Molecular biology and evolution.
[12] D. Bois,et al. First report of a tomato yellow leaf curl-like geminivirus in the Western Hemisphere. , 1994 .
[13] R. Hudson,et al. Statistical properties of the number of recombination events in the history of a sample of DNA sequences. , 1985, Genetics.
[14] S. Lazarowitz,et al. Geminiviruses: Genome structure and gene function , 1992 .
[15] P. Fultz,et al. Human immunodeficiency virus type 1 intersubtype (B/E) recombination in a superinfected chimpanzee , 1997, Journal of virology.
[16] J. Bujarski,et al. RNA-RNA Recombination and Evolution in Virus-Infected Plants , 1994 .
[17] S. Karlin,et al. Applications and statistics for multiple high-scoring segments in molecular sequences. , 1993, Proceedings of the National Academy of Sciences of the United States of America.
[18] Yule Liu,et al. Evidence that DNA-A of a geminivirus associated with severe cassava mosaic disease in Uganda has arisen by interspecific recombination. , 1997, The Journal of general virology.
[19] S. Easteal,et al. The partition matrix: exploring variable phylogenetic signals along nucleotide sequence alignments. , 1997, Molecular biology and evolution.
[20] J. Drake. Rates of spontaneous mutation among RNA viruses. , 1993, Proceedings of the National Academy of Sciences of the United States of America.
[21] C. Fauquet,et al. Tomato leaf curl geminivirus from India has a bipartite genome and coat protein is not essential for infectivity. , 1995, The Journal of general virology.
[22] E. Holmes,et al. A likelihood method for the detection of selection and recombination using nucleotide sequences. , 1997, Molecular biology and evolution.
[23] S. Khalid,et al. Detection and relationships of cotton leaf curl virus and allied whitefly-transmitted geminiviruses occurring in Pakistan , 1997 .
[24] N. Saitou,et al. The neighbor-joining method: a new method for reconstructing phylogenetic trees. , 1987, Molecular biology and evolution.
[25] T. Candresse,et al. Frequent occurrence of recombinant potyvirus isolates. , 1996, The Journal of general virology.
[26] M. Mayo,et al. Guidelines to the demarcation of virus species , 1997, Archives of Virology.
[27] C. Fauquet,et al. A proposal for naming geminiviruses. , 1997, Archives of virology.
[28] J. Bujarski. Introduction: Experimental systems of genetic recombination and defective RNA formation in RNA viruses , 1996 .
[29] J. M. Smith,et al. Detecting recombination from gene trees. , 1998, Molecular biology and evolution.
[30] D. Burke,et al. Recombination in HIV: an important viral evolutionary strategy. , 1997, Emerging infectious diseases.
[31] C. Fauquet,et al. Presence of a new virus closely related to East African cassava mosaic geminivirus, associated with cassava mosaic outbreak in Uganda. , 1997 .
[32] M. Roossinck. Mechanisms of plant virus evolution. , 1997, Annual review of phytopathology.
[33] D. Bisaro. Recombination in the Geminiviruses: Mechanisms for Maintaining Genome Size and Generating Genomic Diversity , 1994 .
[34] G. Weiller. Phylogenetic profiles: a graphical method for detecting genetic recombinations in homologous sequences. , 1998, Molecular biology and evolution.
[35] J. Paszkowski. Homologous Recombination and Gene Silencing in Plants , 2012, Springer Netherlands.
[36] E. Myers,et al. Basic local alignment search tool. , 1990, Journal of molecular biology.
[37] G. Sunter,et al. Tobacco lines with high copy number of replicating recombinant geminivirus vectors after biolistic DNA delivery , 1992 .
[38] A. Gibbs,et al. Plant viruses: master explorers of evolutionary space. , 1993, Current opinion in genetics & development.
[39] C. Fauquet,et al. Distribution and diversity of geminiviruses in trinidad and tobago. , 1998, Phytopathology.
[40] G. McGuire,et al. A graphical method for detecting recombination in phylogenetic data sets. , 1997, Molecular biology and evolution.
[41] L. Herrera-Estrella,et al. Complete nucleotide sequence of pepper huasteco virus: analysis and comparison with bipartite geminiviruses. , 1993, The Journal of general virology.
[42] R. Rosell,et al. Geminivirus transmission and biological characterisation of Bemisia tabaci (Gennadius) biotypes from different geographic regions , 1994 .
[43] R. Callis,et al. The nucleotide sequence of an infectious clone of the geminivirus beet curly top virus , 1986, The EMBO journal.
[44] Desmond G. Higgins,et al. Fast and sensitive multiple sequence alignments on a microcomputer , 1989, Comput. Appl. Biosci..