Adaptive evolution by recombination is not associated with increased mutation rates in Maize streak virus

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dc.contributor.authorMonjane, Aderitoen_ZA
dc.contributor.authorPande, Danielen_ZA
dc.contributor.authorLakay, Franciscoen_ZA
dc.contributor.authorShepherd, Dionneen_ZA
dc.contributor.authorvan der Walt, Ericen_ZA
dc.contributor.authorLefeuvre, Pierreen_ZA
dc.contributor.authorLett, Jean-Michelen_ZA
dc.contributor.authorVarsani, Arvinden_ZA
dc.contributor.authorRybicki, Edwarden_ZA
dc.contributor.authorMartin, Darrenen_ZA
dc.date.accessioned2015-11-18T03:58:33Z
dc.date.available2015-11-18T03:58:33Z
dc.date.issued2012en_ZA
dc.description.abstractBACKGROUND: Single-stranded (ss) DNA viruses in the family Geminiviridae are proving to be very useful in real-time evolution studies. The high mutation rate of geminiviruses and other ssDNA viruses is somewhat mysterious in that their DNA genomes are replicated in host nuclei by high fidelity host polymerases. Although strand specific mutation biases observed in virus species from the geminivirus genus Mastrevirus indicate that the high mutation rates in viruses in this genus may be due to mutational processes that operate specifically on ssDNA, it is currently unknown whether viruses from other genera display similar strand specific mutation biases. Also, geminivirus genomes frequently recombine with one another and an alternative cause of their high mutation rates could be that the recombination process is either directly mutagenic or produces a selective environment in which the survival of mutants is favoured. To investigate whether there is an association between recombination and increased basal mutation rates or increased degrees of selection favoring the survival of mutations, we compared the mutation dynamics of the MSV-MatA and MSV-VW field isolates of Maize streak virus (MSV; Mastrevirus), with both a laboratory constructed MSV recombinant, and MSV recombinants closely resembling MSV-MatA. To determine whether strand specific mutation biases are a general characteristic of geminivirus evolution we compared mutation spectra arising during these MSV experiments with those arising during similar experiments involving the geminivirus Tomato yellow leaf curl virus (Begomovirus genus). RESULTS: Although both the genomic distribution of mutations and the occurrence of various convergent mutations at specific genomic sites indicated that either mutation hotspots or selection for adaptive mutations might elevate observed mutation rates in MSV, we found no association between recombination and mutation rates. Importantly, when comparing the mutation spectra of MSV and TYLCV we observed similar strand specific mutation biases arising predominantly from imbalances in the complementary mutations G->T: C->A. CONCLUSIONS: While our results suggest that recombination does not strongly influence mutation rates in MSV, they indicate that high geminivirus mutation rates are at least partially attributable to increased susceptibility of all geminivirus genomes to oxidative damage while in a single stranded state.en_ZA
dc.identifier.apacitationMonjane, A., Pande, D., Lakay, F., Shepherd, D., van der Walt, E., Lefeuvre, P., ... Martin, D. (2012). Adaptive evolution by recombination is not associated with increased mutation rates in Maize streak virus. <i>BMC Evolutionary Biology</i>, http://hdl.handle.net/11427/15074en_ZA
dc.identifier.chicagocitationMonjane, Aderito, Daniel Pande, Francisco Lakay, Dionne Shepherd, Eric van der Walt, Pierre Lefeuvre, Jean-Michel Lett, Arvind Varsani, Edward Rybicki, and Darren Martin "Adaptive evolution by recombination is not associated with increased mutation rates in Maize streak virus." <i>BMC Evolutionary Biology</i> (2012) http://hdl.handle.net/11427/15074en_ZA
dc.identifier.citationMonjane, A. L., Pande, D., Lakay, F., Shepherd, D. N., van der Walt, E., Lefeuvre, P., ... & Martin, D. P. (2012). Adaptive evolution by recombination is not associated with increased mutation rates in Maize streak virus. BMC evolutionary biology, 12(1), 252.en_ZA
dc.identifier.ris TY - Journal Article AU - Monjane, Aderito AU - Pande, Daniel AU - Lakay, Francisco AU - Shepherd, Dionne AU - van der Walt, Eric AU - Lefeuvre, Pierre AU - Lett, Jean-Michel AU - Varsani, Arvind AU - Rybicki, Edward AU - Martin, Darren AB - BACKGROUND: Single-stranded (ss) DNA viruses in the family Geminiviridae are proving to be very useful in real-time evolution studies. The high mutation rate of geminiviruses and other ssDNA viruses is somewhat mysterious in that their DNA genomes are replicated in host nuclei by high fidelity host polymerases. Although strand specific mutation biases observed in virus species from the geminivirus genus Mastrevirus indicate that the high mutation rates in viruses in this genus may be due to mutational processes that operate specifically on ssDNA, it is currently unknown whether viruses from other genera display similar strand specific mutation biases. Also, geminivirus genomes frequently recombine with one another and an alternative cause of their high mutation rates could be that the recombination process is either directly mutagenic or produces a selective environment in which the survival of mutants is favoured. To investigate whether there is an association between recombination and increased basal mutation rates or increased degrees of selection favoring the survival of mutations, we compared the mutation dynamics of the MSV-MatA and MSV-VW field isolates of Maize streak virus (MSV; Mastrevirus), with both a laboratory constructed MSV recombinant, and MSV recombinants closely resembling MSV-MatA. To determine whether strand specific mutation biases are a general characteristic of geminivirus evolution we compared mutation spectra arising during these MSV experiments with those arising during similar experiments involving the geminivirus Tomato yellow leaf curl virus (Begomovirus genus). RESULTS: Although both the genomic distribution of mutations and the occurrence of various convergent mutations at specific genomic sites indicated that either mutation hotspots or selection for adaptive mutations might elevate observed mutation rates in MSV, we found no association between recombination and mutation rates. Importantly, when comparing the mutation spectra of MSV and TYLCV we observed similar strand specific mutation biases arising predominantly from imbalances in the complementary mutations G->T: C->A. CONCLUSIONS: While our results suggest that recombination does not strongly influence mutation rates in MSV, they indicate that high geminivirus mutation rates are at least partially attributable to increased susceptibility of all geminivirus genomes to oxidative damage while in a single stranded state. DA - 2012 DB - OpenUCT DO - 10.1186/1471-2148-12-252 DP - University of Cape Town J1 - BMC Evolutionary Biology LK - https://open.uct.ac.za PB - University of Cape Town PY - 2012 T1 - Adaptive evolution by recombination is not associated with increased mutation rates in Maize streak virus TI - Adaptive evolution by recombination is not associated with increased mutation rates in Maize streak virus UR - http://hdl.handle.net/11427/15074 ER - en_ZA
dc.identifier.urihttp://hdl.handle.net/11427/15074
dc.identifier.urihttp://dx.doi.org/10.1186/1471-2148-12-252
dc.identifier.vancouvercitationMonjane A, Pande D, Lakay F, Shepherd D, van der Walt E, Lefeuvre P, et al. Adaptive evolution by recombination is not associated with increased mutation rates in Maize streak virus. BMC Evolutionary Biology. 2012; http://hdl.handle.net/11427/15074.en_ZA
dc.language.isoengen_ZA
dc.publisherBioMed Central Ltden_ZA
dc.publisher.departmentInstitute of Infectious Disease and Molecular Medicineen_ZA
dc.publisher.facultyFaculty of Health Sciencesen_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.holder2012 Monjane et al.; licensee BioMed Central Ltd.en_ZA
dc.rights.urihttp://creativecommons.org/licenses/by/2.0en_ZA
dc.sourceBMC Evolutionary Biologyen_ZA
dc.source.urihttp://www.biomedcentral.com/bmcevolbiol/en_ZA
dc.subject.otherSingle-stranded (ss) DNA virusesen_ZA
dc.subject.othergeminivirus genus Mastrevirusen_ZA
dc.titleAdaptive evolution by recombination is not associated with increased mutation rates in Maize streak virusen_ZA
dc.typeJournal Articleen_ZA
uct.type.filetypeText
uct.type.filetypeImage
uct.type.publicationResearchen_ZA
uct.type.resourceArticleen_ZA
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