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

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dc.contributor.authorvan der Walt, Ericen_ZA
dc.contributor.authorMartin, Darrenen_ZA
dc.contributor.authorVarsani, Arvinden_ZA
dc.contributor.authorPolston, Janeen_ZA
dc.contributor.authorRybicki, Edwarden_ZA
dc.date.accessioned2015-10-28T07:03:38Z
dc.date.available2015-10-28T07:03:38Z
dc.date.issued2008en_ZA
dc.description.abstractBACKGROUND: 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 x 10-4 and 7.9 x 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.identifier.apacitationvan der Walt, E., Martin, D., Varsani, A., Polston, J., & Rybicki, E. (2008). Experimental observations of rapid Maize streak virus evolution reveal a strand-specific nucleotide substitution bias. <i>Virology Journal</i>, http://hdl.handle.net/11427/14463en_ZA
dc.identifier.chicagocitationvan der Walt, Eric, Darren Martin, Arvind Varsani, Jane Polston, and Edward 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/11427/14463en_ZA
dc.identifier.citationvan 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.ris TY - Journal Article AU - van der Walt, Eric AU - Martin, Darren AU - Varsani, Arvind AU - Polston, Jane AU - Rybicki, Edward 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 x 10-4 and 7.9 x 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 DO - 10.1186/1743-422X-5-104 DP - University of Cape Town J1 - Virology Journal LK - https://open.uct.ac.za PB - University of Cape Town PY - 2008 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/11427/14463 ER - en_ZA
dc.identifier.urihttp://hdl.handle.net/11427/14463
dc.identifier.urihttp://dx.doi.org/10.1186/1743-422X-5-104
dc.identifier.vancouvercitationvan der Walt E, Martin D, Varsani A, Polston J, Rybicki E. Experimental observations of rapid Maize streak virus evolution reveal a strand-specific nucleotide substitution bias. Virology Journal. 2008; http://hdl.handle.net/11427/14463.en_ZA
dc.language.isoengen_ZA
dc.publisherBioMed Central Ltden_ZA
dc.publisher.departmentDepartment of Molecular and Cell Biologyen_ZA
dc.publisher.facultyFaculty of Scienceen_ZA
dc.publisher.institutionUniversity of Cape Town
dc.rightsThis is an Open Access article distributed under the terms of the Creative Commons Attribution Licenseen_ZA
dc.rights.holder2008 Walt et al; licensee BioMed Central Ltd.en_ZA
dc.rights.urihttp://creativecommons.org/licenses/by/2.0en_ZA
dc.sourceVirology Journalen_ZA
dc.source.urihttp://www.virologyj.com/en_ZA
dc.subject.otherMaize streak virusen_ZA
dc.subject.otherPlant Diseasesen_ZA
dc.titleExperimental observations of rapid Maize streak virus evolution reveal a strand-specific nucleotide substitution biasen_ZA
dc.typeJournal Articleen_ZA
uct.type.filetypeText
uct.type.filetypeImage
uct.type.publicationResearchen_ZA
uct.type.resourceArticleen_ZA
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