The population genomics of begomoviruses: global scale population structure and gene flow

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dc.contributor.authorPrasanna, HCen_ZA
dc.contributor.authorSinha, Den_ZA
dc.contributor.authorVerma, Ajayen_ZA
dc.contributor.authorSingh, Majoren_ZA
dc.contributor.authorSingh, Bijendraen_ZA
dc.contributor.authorRai, Mathuraen_ZA
dc.contributor.authorMartin, Darrenen_ZA
dc.date.accessioned2015-11-11T11:57:27Z
dc.date.available2015-11-11T11:57:27Z
dc.date.issued2010en_ZA
dc.description.abstractBACKGROUND: The rapidly growing availability of diverse full genome sequences from across the world is increasing the feasibility of studying the large-scale population processes that underly observable pattern of virus diversity. In particular, characterizing the genetic structure of virus populations could potentially reveal much about how factors such as geographical distributions, host ranges and gene flow between populations combine to produce the discontinuous patterns of genetic diversity that we perceive as distinct virus species. Among the richest and most diverse full genome datasets that are available is that for the dicotyledonous plant infecting genus, Begomovirus, in the Family Geminiviridae. The begomoviruses all share the same whitefly vector, are highly recombinogenic and are distributed throughout tropical and subtropical regions where they seriously threaten the food security of the world's poorest people. RESULTS: We focus here on using a model-based population genetic approach to identify the genetically distinct sub-populations within the global begomovirus meta-population. We demonstrate the existence of at least seven major sub-populations that can further be sub-divided into as many as thirty four significantly differentiated and genetically cohesive minor sub-populations. Using the population structure framework revealed in the present study, we further explored the extent of gene flow and recombination between genetic populations. CONCLUSIONS: Although geographical barriers are apparently the most significant underlying cause of the seven major population sub-divisions, within the framework of these sub-divisions, we explore patterns of gene flow to reveal that both host range differences and genetic barriers to recombination have probably been major contributors to the minor population sub-divisions that we have identified. We believe that the global Begomovirus population structure revealed here could facilitate population genetics studies into how central parameters of population genetics namely selection, recombination, mutation, gene flow, and genetic drift shape the global begomovirus diversity.en_ZA
dc.identifier.apacitationPrasanna, H., Sinha, D., Verma, A., Singh, M., Singh, B., Rai, M., & Martin, D. (2010). The population genomics of begomoviruses: global scale population structure and gene flow. <i>Virology Journal</i>, http://hdl.handle.net/11427/14877en_ZA
dc.identifier.chicagocitationPrasanna, HC, D Sinha, Ajay Verma, Major Singh, Bijendra Singh, Mathura Rai, and Darren Martin "The population genomics of begomoviruses: global scale population structure and gene flow." <i>Virology Journal</i> (2010) http://hdl.handle.net/11427/14877en_ZA
dc.identifier.citationPrasanna, H. C., Sinha, D. P., Verma, A., Singh, M., Singh, B., Rai, M., & Martin, D. P. (2010). The population genomics of begomoviruses: global scale population structure and gene flow. Virology journal, 7(1), 1-12.en_ZA
dc.identifier.ris TY - Journal Article AU - Prasanna, HC AU - Sinha, D AU - Verma, Ajay AU - Singh, Major AU - Singh, Bijendra AU - Rai, Mathura AU - Martin, Darren AB - BACKGROUND: The rapidly growing availability of diverse full genome sequences from across the world is increasing the feasibility of studying the large-scale population processes that underly observable pattern of virus diversity. In particular, characterizing the genetic structure of virus populations could potentially reveal much about how factors such as geographical distributions, host ranges and gene flow between populations combine to produce the discontinuous patterns of genetic diversity that we perceive as distinct virus species. Among the richest and most diverse full genome datasets that are available is that for the dicotyledonous plant infecting genus, Begomovirus, in the Family Geminiviridae. The begomoviruses all share the same whitefly vector, are highly recombinogenic and are distributed throughout tropical and subtropical regions where they seriously threaten the food security of the world's poorest people. RESULTS: We focus here on using a model-based population genetic approach to identify the genetically distinct sub-populations within the global begomovirus meta-population. We demonstrate the existence of at least seven major sub-populations that can further be sub-divided into as many as thirty four significantly differentiated and genetically cohesive minor sub-populations. Using the population structure framework revealed in the present study, we further explored the extent of gene flow and recombination between genetic populations. CONCLUSIONS: Although geographical barriers are apparently the most significant underlying cause of the seven major population sub-divisions, within the framework of these sub-divisions, we explore patterns of gene flow to reveal that both host range differences and genetic barriers to recombination have probably been major contributors to the minor population sub-divisions that we have identified. We believe that the global Begomovirus population structure revealed here could facilitate population genetics studies into how central parameters of population genetics namely selection, recombination, mutation, gene flow, and genetic drift shape the global begomovirus diversity. DA - 2010 DB - OpenUCT DO - 10.1186/1743-422X-7-220 DP - University of Cape Town J1 - Virology Journal LK - https://open.uct.ac.za PB - University of Cape Town PY - 2010 T1 - The population genomics of begomoviruses: global scale population structure and gene flow TI - The population genomics of begomoviruses: global scale population structure and gene flow UR - http://hdl.handle.net/11427/14877 ER - en_ZA
dc.identifier.urihttp://hdl.handle.net/11427/14877
dc.identifier.urihttp://dx.doi.org/10.1186/1743-422X-7-220
dc.identifier.vancouvercitationPrasanna H, Sinha D, Verma A, Singh M, Singh B, Rai M, et al. The population genomics of begomoviruses: global scale population structure and gene flow. Virology Journal. 2010; http://hdl.handle.net/11427/14877.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.holder2010 Prasanna 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.otherCassava Mosaic Virusen_ZA
dc.subject.otherAfrican Cassava Mosaicen_ZA
dc.subject.otherPepper Golden Mosaic Virusen_ZA
dc.subject.otherFull Genome Dataseten_ZA
dc.subject.otherRelative Membershipen_ZA
dc.titleThe population genomics of begomoviruses: global scale population structure and gene flowen_ZA
dc.typeJournal Articleen_ZA
uct.type.filetypeText
uct.type.filetypeImage
uct.type.publicationResearchen_ZA
uct.type.resourceArticleen_ZA
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