Experimental observations of rapid Maize streak virus evolution reveal a strand-specific nucleotide substitution bias

 

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dc.contributor.author van der Walt, Eric
dc.contributor.author Martin, Darren P A
dc.contributor.author Varsani, Arvind
dc.contributor.author Polston, Jane E
dc.contributor.author Rybicki, Edward P
dc.date.accessioned 2016-07-26T10:29:59Z
dc.date.available 2016-07-26T10:29:59Z
dc.date.issued 2008
dc.identifier http://dx.doi.org/10.1186/1743-422X-5-104
dc.identifier.citation van der Walt, E., Martin, D. P., Varsani, A., Polston, J. E., & Rybicki, E. P. (2008). Experimental observations of rapid Maize streak virus evolution reveal a strand-specific nucleotide substitution bias. Virology journal, 5(1), 104. en_ZA
dc.identifier.issn 1743-422X en_ZA
dc.identifier.uri http://hdl.handle.net/11427/20755
dc.description.abstract Background: Recent reports have indicated that single-stranded DNA (ssDNA) viruses in the taxonomic families Geminiviridae, Parvoviridae and Anellovirus may be evolving at rates of ~10-4 substitutions per site per year (subs/site/year). These evolution rates are similar to those of RNA viruses and are surprisingly high given that ssDNA virus replication involves host DNA polymerases with fidelities approximately 10 000 times greater than those of error-prone viral RNA polymerases. Although high ssDNA virus evolution rates were first suggested in evolution experiments involving the geminivirus maize streak virus (MSV), the evolution rate of this virus has never been accurately measured. Also, questions regarding both the mechanistic basis and adaptive value of high geminivirus mutation rates remain unanswered. Results: We determined the short-term evolution rate of MSV using full genome analysis of virus populations initiated from cloned genomes. Three wild type viruses and three defective artificial chimaeric viruses were maintained in planta for up to five years and displayed evolution rates of between 7.4 × 10-4 and 7.9 × 10-4 subs/site/year. Conclusion: These MSV evolution rates are within the ranges observed for other ssDNA viruses and RNA viruses. Although no obvious evidence of positive selection was detected, the uneven distribution of mutations within the defective virus genomes suggests that some of the changes may have been adaptive. We also observed inter-strand nucleotide substitution imbalances that are consistent with a recent proposal that high mutation rates in geminiviruses (and possibly ssDNA viruses in general) may be due to mutagenic processes acting specifically on ssDNA molecules. en_ZA
dc.language eng en_ZA
dc.publisher BioMed Central en_ZA
dc.rights Creative Commons Attribution 4.0 International (CC BY 4.0) *
dc.rights.uri http://creativecommons.org/licenses/by/4.0/ en_ZA
dc.source Virology Journal en_ZA
dc.source.uri https://virologyj.biomedcentral.com/
dc.title Experimental observations of rapid Maize streak virus evolution reveal a strand-specific nucleotide substitution bias en_ZA
dc.type Journal Article en_ZA
dc.date.updated 2016-07-13T09:50:34Z
uct.type.publication Research en_ZA
uct.type.resource Article en_ZA
dc.publisher.institution University of Cape Town
uct.type.filetype Text
uct.type.filetype Image
dc.identifier.apacitation van der Walt, E., Martin, D. P. A., Varsani, A., Polston, J. E., & Rybicki, E. P. (2008). Experimental observations of rapid Maize streak virus evolution reveal a strand-specific nucleotide substitution bias. <i>Virology Journal</i>, http://hdl.handle.net/11427/20755 en_ZA
dc.identifier.chicagocitation van der Walt, Eric, Darren P A Martin, Arvind Varsani, Jane E Polston, and Edward P Rybicki "Experimental observations of rapid Maize streak virus evolution reveal a strand-specific nucleotide substitution bias." <i>Virology Journal</i> (2008) http://hdl.handle.net/11427/20755 en_ZA
dc.identifier.vancouvercitation van der Walt E, Martin DPA, Varsani A, Polston JE, Rybicki EP. Experimental observations of rapid Maize streak virus evolution reveal a strand-specific nucleotide substitution bias. Virology Journal. 2008; http://hdl.handle.net/11427/20755. en_ZA
dc.identifier.ris TY - Journal Article AU - van der Walt, Eric AU - Martin, Darren P A AU - Varsani, Arvind AU - Polston, Jane E AU - Rybicki, Edward P AB - Background: Recent reports have indicated that single-stranded DNA (ssDNA) viruses in the taxonomic families Geminiviridae, Parvoviridae and Anellovirus may be evolving at rates of ~10-4 substitutions per site per year (subs/site/year). These evolution rates are similar to those of RNA viruses and are surprisingly high given that ssDNA virus replication involves host DNA polymerases with fidelities approximately 10 000 times greater than those of error-prone viral RNA polymerases. Although high ssDNA virus evolution rates were first suggested in evolution experiments involving the geminivirus maize streak virus (MSV), the evolution rate of this virus has never been accurately measured. Also, questions regarding both the mechanistic basis and adaptive value of high geminivirus mutation rates remain unanswered. Results: We determined the short-term evolution rate of MSV using full genome analysis of virus populations initiated from cloned genomes. Three wild type viruses and three defective artificial chimaeric viruses were maintained in planta for up to five years and displayed evolution rates of between 7.4 × 10-4 and 7.9 × 10-4 subs/site/year. Conclusion: These MSV evolution rates are within the ranges observed for other ssDNA viruses and RNA viruses. Although no obvious evidence of positive selection was detected, the uneven distribution of mutations within the defective virus genomes suggests that some of the changes may have been adaptive. We also observed inter-strand nucleotide substitution imbalances that are consistent with a recent proposal that high mutation rates in geminiviruses (and possibly ssDNA viruses in general) may be due to mutagenic processes acting specifically on ssDNA molecules. DA - 2008 DB - OpenUCT DP - University of Cape Town J1 - Virology Journal LK - https://open.uct.ac.za PB - University of Cape Town PY - 2008 SM - 1743-422X T1 - Experimental observations of rapid Maize streak virus evolution reveal a strand-specific nucleotide substitution bias TI - Experimental observations of rapid Maize streak virus evolution reveal a strand-specific nucleotide substitution bias UR - http://hdl.handle.net/11427/20755 ER - en_ZA


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