Metagenomic-based screening and molecular characterization of cowpea-infecting viruses in Burkina Faso

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dc.contributor.authorPalanga, Essowèen_ZA
dc.contributor.authorFilloux, Denisen_ZA
dc.contributor.authorMartin, Darren Pen_ZA
dc.contributor.authorFernandez, Emmanuelen_ZA
dc.contributor.authorGargani, Danielen_ZA
dc.contributor.authorFerdinand, Romainen_ZA
dc.contributor.authorZabré, Jeanen_ZA
dc.contributor.authorBouda, Zakariaen_ZA
dc.contributor.authorNeya, James Boumaen_ZA
dc.contributor.authorSawadogo, Mahamadouen_ZA
dc.contributor.authorTraore, Oumaren_ZA
dc.contributor.authorPeterschmitt, Michelen_ZA
dc.contributor.authorRoumagnac, Philippeen_ZA
dc.date.accessioned2016-10-31T07:38:00Z
dc.date.available2016-10-31T07:38:00Z
dc.date.issued2016en_ZA
dc.description.abstractCowpea, ( Vigna unguiculata L. (Walp)) is an annual tropical grain legume. Often referred to as "poor man's meat", cowpea is one of the most important subsistence legumes cultivated in West Africa due to the high protein content of its seeds. However, African cowpea production can be seriously constrained by viral diseases that reduce yields. While twelve cowpea-infecting viruses have been reported from Africa, only three of these have so-far been reported from Burkina Faso. Here we use a virion-associated nucleic acids (VANA)-based metagenomics method to screen for the presence of cowpea viruses from plants collected from the three agro-climatic zones of Burkina Faso. Besides the three cowpea-infecting virus species which have previously been reported from Burkina Faso (Cowpea aphid borne mosaic virus [Family Potyviridae ], the Blackeye cowpea mosaic virus--a strain of Bean common mosaic virus--[Family Potyviridae ] and Cowpea mottle virus [Family Tombusviridae ]) five additional viruses were identified: Southern cowpea mosaic virus (Sobemovirus genus), two previously uncharacterised polerovirus-like species (Family Luteoviridae ), a previously uncharacterised tombusvirus-like species (Family Tombusviridae ) and a previously uncharacterised mycotymovirus-like species (Family Tymoviridae ). Overall, potyviruses were the most prevalent cowpea viruses (detected in 65.5% of samples) and the Southern Sudan zone of Burkina Faso was found to harbour the greatest degrees of viral diversity and viral prevalence. Partial genome sequences of the two novel polerovirus-like and tombusvirus-like species were determined and RT-PCR primers were designed for use in Burkina Faso to routinely detect all of these cowpea-associated viruses.en_ZA
dc.identifier.apacitationPalanga, E., Filloux, D., Martin, D. P., Fernandez, E., Gargani, D., Ferdinand, R., ... Roumagnac, P. (2016). Metagenomic-based screening and molecular characterization of cowpea-infecting viruses in Burkina Faso. <i>PLoS One</i>, http://hdl.handle.net/11427/22351en_ZA
dc.identifier.chicagocitationPalanga, Essowè, Denis Filloux, Darren P Martin, Emmanuel Fernandez, Daniel Gargani, Romain Ferdinand, Jean Zabré, et al "Metagenomic-based screening and molecular characterization of cowpea-infecting viruses in Burkina Faso." <i>PLoS One</i> (2016) http://hdl.handle.net/11427/22351en_ZA
dc.identifier.citationPalanga, E., Filloux, D., Martin, D. P., Fernandez, E., Gargani, D., Ferdinand, R., ... & Traore, O. (2016). Metagenomic-based screening and molecular characterization of cowpea-infecting viruses in Burkina Faso. PloS one, 11(10), e0165188. doi:10.1371/journal.pone.0165188en_ZA
dc.identifier.ris TY - Journal Article AU - Palanga, Essowè AU - Filloux, Denis AU - Martin, Darren P AU - Fernandez, Emmanuel AU - Gargani, Daniel AU - Ferdinand, Romain AU - Zabré, Jean AU - Bouda, Zakaria AU - Neya, James Bouma AU - Sawadogo, Mahamadou AU - Traore, Oumar AU - Peterschmitt, Michel AU - Roumagnac, Philippe AB - Cowpea, ( Vigna unguiculata L. (Walp)) is an annual tropical grain legume. Often referred to as "poor man's meat", cowpea is one of the most important subsistence legumes cultivated in West Africa due to the high protein content of its seeds. However, African cowpea production can be seriously constrained by viral diseases that reduce yields. While twelve cowpea-infecting viruses have been reported from Africa, only three of these have so-far been reported from Burkina Faso. Here we use a virion-associated nucleic acids (VANA)-based metagenomics method to screen for the presence of cowpea viruses from plants collected from the three agro-climatic zones of Burkina Faso. Besides the three cowpea-infecting virus species which have previously been reported from Burkina Faso (Cowpea aphid borne mosaic virus [Family Potyviridae ], the Blackeye cowpea mosaic virus--a strain of Bean common mosaic virus--[Family Potyviridae ] and Cowpea mottle virus [Family Tombusviridae ]) five additional viruses were identified: Southern cowpea mosaic virus (Sobemovirus genus), two previously uncharacterised polerovirus-like species (Family Luteoviridae ), a previously uncharacterised tombusvirus-like species (Family Tombusviridae ) and a previously uncharacterised mycotymovirus-like species (Family Tymoviridae ). Overall, potyviruses were the most prevalent cowpea viruses (detected in 65.5% of samples) and the Southern Sudan zone of Burkina Faso was found to harbour the greatest degrees of viral diversity and viral prevalence. Partial genome sequences of the two novel polerovirus-like and tombusvirus-like species were determined and RT-PCR primers were designed for use in Burkina Faso to routinely detect all of these cowpea-associated viruses. DA - 2016 DB - OpenUCT DO - 10.1371/journal.pone.0165188 DP - University of Cape Town J1 - PLoS One LK - https://open.uct.ac.za PB - University of Cape Town PY - 2016 T1 - Metagenomic-based screening and molecular characterization of cowpea-infecting viruses in Burkina Faso TI - Metagenomic-based screening and molecular characterization of cowpea-infecting viruses in Burkina Faso UR - http://hdl.handle.net/11427/22351 ER - en_ZA
dc.identifier.urihttp://dx.doi.org/10.1371/journal.pone.0165188en_ZA
dc.identifier.urihttp://hdl.handle.net/11427/22351
dc.identifier.vancouvercitationPalanga E, Filloux D, Martin DP, Fernandez E, Gargani D, Ferdinand R, et al. Metagenomic-based screening and molecular characterization of cowpea-infecting viruses in Burkina Faso. PLoS One. 2016; http://hdl.handle.net/11427/22351.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© 2016 Palanga 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.otherPlant viral pathogensen_ZA
dc.subject.otherReverse transcriptase-polymerase chain reactionen_ZA
dc.subject.otherPotyvirusen_ZA
dc.subject.otherEcosystemsen_ZA
dc.subject.otherMutant genotypesen_ZA
dc.subject.otherPhylogenetic analysisen_ZA
dc.subject.otherMetagenomicsen_ZA
dc.subject.otherBurkina Fasoen_ZA
dc.titleMetagenomic-based screening and molecular characterization of cowpea-infecting viruses in Burkina Fasoen_ZA
dc.typeJournal Articleen_ZA
uct.type.filetypeText
uct.type.filetypeImage
uct.type.publicationResearchen_ZA
uct.type.resourceArticleen_ZA
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