Evolutionary time-scale of the begomoviruses: evidence from integrated sequences in the Nicotiana genome

dc.contributor.authorLefeuvre, Pierreen_ZA
dc.contributor.authorHarkins, Gordon Wen_ZA
dc.contributor.authorLett, Jean-Michelen_ZA
dc.contributor.authorBriddon, Rob Wen_ZA
dc.contributor.authorChase, Mark Wen_ZA
dc.contributor.authorMoury, Benoiten_ZA
dc.contributor.authorMartin, Darren Pen_ZA
dc.date.accessioned2015-12-28T06:47:45Z
dc.date.available2015-12-28T06:47:45Z
dc.date.issued2011en_ZA
dc.description.abstractDespite having single stranded DNA genomes that are replicated by host DNA polymerases, viruses in the family Geminiviridae are apparently evolving as rapidly as some RNA viruses. The observed substitution rates of geminiviruses in the genera Begomovirus and Mastrevirus are so high that the entire family could conceivably have originated less than a million years ago (MYA). However, the existence of geminivirus related DNA (GRD) integrated within the genomes of various Nicotiana species suggests that the geminiviruses probably originated >10 MYA. Some have even suggested that a distinct New-World (NW) lineage of begomoviruses may have arisen following the separation by continental drift of African and American proto-begomoviruses ∼110 MYA. We evaluate these various geminivirus origin hypotheses using Bayesian coalescent-based approaches to date firstly the Nicotiana GRD integration events, and then the divergence of the NW and Old-World (OW) begomoviruses. Besides rejecting the possibility of a<2 MYA OW-NW begomovirus split, we could also discount that it may have occurred concomitantly with the breakup of Gondwanaland 110 MYA. Although we could only confidently narrow the date of the split down to between 2 and 80 MYA, the most plausible (and best supported) date for the split is between 20 and 30 MYA - a time when global cooling ended the dispersal of temperate species between Asia and North America via the Beringian land bridge.en_ZA
dc.identifier.apacitationLefeuvre, P., Harkins, G. W., Lett, J., Briddon, R. W., Chase, M. W., Moury, B., & Martin, D. P. (2011). Evolutionary time-scale of the begomoviruses: evidence from integrated sequences in the Nicotiana genome. <i>PLoS One</i>, http://hdl.handle.net/11427/16047en_ZA
dc.identifier.chicagocitationLefeuvre, Pierre, Gordon W Harkins, Jean-Michel Lett, Rob W Briddon, Mark W Chase, Benoit Moury, and Darren P Martin "Evolutionary time-scale of the begomoviruses: evidence from integrated sequences in the Nicotiana genome." <i>PLoS One</i> (2011) http://hdl.handle.net/11427/16047en_ZA
dc.identifier.citationLefeuvre, P., Harkins, G. W., Lett, J. M., Briddon, R. W., Chase, M. W., Moury, B., & Martin, D. P. (2011). Evolutionary time-scale of the begomoviruses: evidence from integrated sequences in the Nicotiana genome. PLoS One, 6(5), e19193-e19193. doi:10.1371/journal.pone.0019193en_ZA
dc.identifier.ris TY - Journal Article AU - Lefeuvre, Pierre AU - Harkins, Gordon W AU - Lett, Jean-Michel AU - Briddon, Rob W AU - Chase, Mark W AU - Moury, Benoit AU - Martin, Darren P AB - Despite having single stranded DNA genomes that are replicated by host DNA polymerases, viruses in the family Geminiviridae are apparently evolving as rapidly as some RNA viruses. The observed substitution rates of geminiviruses in the genera Begomovirus and Mastrevirus are so high that the entire family could conceivably have originated less than a million years ago (MYA). However, the existence of geminivirus related DNA (GRD) integrated within the genomes of various Nicotiana species suggests that the geminiviruses probably originated >10 MYA. Some have even suggested that a distinct New-World (NW) lineage of begomoviruses may have arisen following the separation by continental drift of African and American proto-begomoviruses ∼110 MYA. We evaluate these various geminivirus origin hypotheses using Bayesian coalescent-based approaches to date firstly the Nicotiana GRD integration events, and then the divergence of the NW and Old-World (OW) begomoviruses. Besides rejecting the possibility of a<2 MYA OW-NW begomovirus split, we could also discount that it may have occurred concomitantly with the breakup of Gondwanaland 110 MYA. Although we could only confidently narrow the date of the split down to between 2 and 80 MYA, the most plausible (and best supported) date for the split is between 20 and 30 MYA - a time when global cooling ended the dispersal of temperate species between Asia and North America via the Beringian land bridge. DA - 2011 DB - OpenUCT DO - 10.1371/journal.pone.0019193 DP - University of Cape Town J1 - PLoS One LK - https://open.uct.ac.za PB - University of Cape Town PY - 2011 T1 - Evolutionary time-scale of the begomoviruses: evidence from integrated sequences in the Nicotiana genome TI - Evolutionary time-scale of the begomoviruses: evidence from integrated sequences in the Nicotiana genome UR - http://hdl.handle.net/11427/16047 ER - en_ZA
dc.identifier.urihttp://hdl.handle.net/11427/16047
dc.identifier.urihttp://dx.doi.org/10.1371/journal.pone.0019193
dc.identifier.vancouvercitationLefeuvre P, Harkins GW, Lett J, Briddon RW, Chase MW, Moury B, et al. Evolutionary time-scale of the begomoviruses: evidence from integrated sequences in the Nicotiana genome. PLoS One. 2011; http://hdl.handle.net/11427/16047.en_ZA
dc.language.isoengen_ZA
dc.publisherPublic Library of Scienceen_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 License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.en_ZA
dc.rights.holder© 2011 Lefeuvre et alen_ZA
dc.rights.urihttp://creativecommons.org/licenses/by/4.0en_ZA
dc.sourcePLoS Oneen_ZA
dc.source.urihttp://journals.plos.org/plosoneen_ZA
dc.subject.otherNicotianaen_ZA
dc.subject.otherSequence analysisen_ZA
dc.subject.otherDNA sequence analysisen_ZA
dc.subject.otherPhylogenetic analysisen_ZA
dc.subject.otherViral evolutionen_ZA
dc.subject.otherSequence alignmenten_ZA
dc.subject.otherPaleogeneticsen_ZA
dc.subject.otherPhylogeneticsen_ZA
dc.titleEvolutionary time-scale of the begomoviruses: evidence from integrated sequences in the Nicotiana genomeen_ZA
dc.typeJournal Articleen_ZA
uct.type.filetypeText
uct.type.filetypeImage
uct.type.publicationResearchen_ZA
uct.type.resourceArticleen_ZA
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