Viral metagenomics of aphids present in bean and maize plots on mixed-use farms in Kenya reveals the presence of three dicistroviruses including a novel Big Sioux River virus-like dicistrovirus
Abstract Background Aphids are major vectors of plant viruses. Common bean (Phaseolus vulgaris L.) and maize (Zea mays L.) are important crops that are vulnerable to aphid herbivory and aphid-transmitted viruses. In East and Central Africa, common bean is frequently intercropped by smallholder farme...
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doaj-54f008045d30417f895d1f8d112bac7a2020-11-24T22:31:24ZengBMCVirology Journal1743-422X2017-10-0114111310.1186/s12985-017-0854-xViral metagenomics of aphids present in bean and maize plots on mixed-use farms in Kenya reveals the presence of three dicistroviruses including a novel Big Sioux River virus-like dicistrovirusFrancis O. Wamonje0George N. Michuki1Luke A. Braidwood2Joyce N. Njuguna3J. Musembi Mutuku4Appolinaire Djikeng5Jagger J. W. Harvey6John P. Carr7Department of Plant Sciences, University of CambridgeInternational Livestock Research InstituteDepartment of Plant Sciences, University of CambridgeBiosciences eastern and central Africa-International Livestock Research Institute (BecA-ILRI) HubBiosciences eastern and central Africa-International Livestock Research Institute (BecA-ILRI) HubBiosciences eastern and central Africa-International Livestock Research Institute (BecA-ILRI) HubBiosciences eastern and central Africa-International Livestock Research Institute (BecA-ILRI) HubDepartment of Plant Sciences, University of CambridgeAbstract Background Aphids are major vectors of plant viruses. Common bean (Phaseolus vulgaris L.) and maize (Zea mays L.) are important crops that are vulnerable to aphid herbivory and aphid-transmitted viruses. In East and Central Africa, common bean is frequently intercropped by smallholder farmers to provide fixed nitrogen for cultivation of starch crops such as maize. We used a PCR-based technique to identify aphids prevalent in smallholder bean farms and next generation sequencing shotgun metagenomics to examine the diversity of viruses present in aphids and in maize leaf samples. Samples were collected from farms in Kenya in a range of agro-ecological zones. Results Cytochrome oxidase 1 (CO1) gene sequencing showed that Aphis fabae was the sole aphid species present in bean plots in the farms visited. Sequencing of total RNA from aphids using the Illumina platform detected three dicistroviruses. Maize leaf RNA was also analysed. Identification of Aphid lethal paralysis virus (ALPV), Rhopalosiphum padi virus (RhPV), and a novel Big Sioux River virus (BSRV)-like dicistrovirus in aphid and maize samples was confirmed using reverse transcription-polymerase chain reactions and sequencing of amplified DNA products. Phylogenetic, nucleotide and protein sequence analyses of eight ALPV genomes revealed evidence of intra-species recombination, with the data suggesting there may be two ALPV lineages. Analysis of BSRV-like virus genomic RNA sequences revealed features that are consistent with other dicistroviruses and that it is phylogenetically closely related to dicistroviruses of the genus Cripavirus. Conclusions The discovery of ALPV and RhPV in aphids and maize further demonstrates the broad occurrence of these dicistroviruses. Dicistroviruses are remarkable in that they use plants as reservoirs that facilitate infection of their insect replicative hosts, such as aphids. This is the first report of these viruses being isolated from either organism. The BSRV-like sequences represent a potentially novel dicistrovirus infecting A. fabae.http://link.springer.com/article/10.1186/s12985-017-0854-xMetagenomicsPhylogeneticsRecombinationDicistrovirusPotyvirusVector |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Francis O. Wamonje George N. Michuki Luke A. Braidwood Joyce N. Njuguna J. Musembi Mutuku Appolinaire Djikeng Jagger J. W. Harvey John P. Carr |
spellingShingle |
Francis O. Wamonje George N. Michuki Luke A. Braidwood Joyce N. Njuguna J. Musembi Mutuku Appolinaire Djikeng Jagger J. W. Harvey John P. Carr Viral metagenomics of aphids present in bean and maize plots on mixed-use farms in Kenya reveals the presence of three dicistroviruses including a novel Big Sioux River virus-like dicistrovirus Virology Journal Metagenomics Phylogenetics Recombination Dicistrovirus Potyvirus Vector |
author_facet |
Francis O. Wamonje George N. Michuki Luke A. Braidwood Joyce N. Njuguna J. Musembi Mutuku Appolinaire Djikeng Jagger J. W. Harvey John P. Carr |
author_sort |
Francis O. Wamonje |
title |
Viral metagenomics of aphids present in bean and maize plots on mixed-use farms in Kenya reveals the presence of three dicistroviruses including a novel Big Sioux River virus-like dicistrovirus |
title_short |
Viral metagenomics of aphids present in bean and maize plots on mixed-use farms in Kenya reveals the presence of three dicistroviruses including a novel Big Sioux River virus-like dicistrovirus |
title_full |
Viral metagenomics of aphids present in bean and maize plots on mixed-use farms in Kenya reveals the presence of three dicistroviruses including a novel Big Sioux River virus-like dicistrovirus |
title_fullStr |
Viral metagenomics of aphids present in bean and maize plots on mixed-use farms in Kenya reveals the presence of three dicistroviruses including a novel Big Sioux River virus-like dicistrovirus |
title_full_unstemmed |
Viral metagenomics of aphids present in bean and maize plots on mixed-use farms in Kenya reveals the presence of three dicistroviruses including a novel Big Sioux River virus-like dicistrovirus |
title_sort |
viral metagenomics of aphids present in bean and maize plots on mixed-use farms in kenya reveals the presence of three dicistroviruses including a novel big sioux river virus-like dicistrovirus |
publisher |
BMC |
series |
Virology Journal |
issn |
1743-422X |
publishDate |
2017-10-01 |
description |
Abstract Background Aphids are major vectors of plant viruses. Common bean (Phaseolus vulgaris L.) and maize (Zea mays L.) are important crops that are vulnerable to aphid herbivory and aphid-transmitted viruses. In East and Central Africa, common bean is frequently intercropped by smallholder farmers to provide fixed nitrogen for cultivation of starch crops such as maize. We used a PCR-based technique to identify aphids prevalent in smallholder bean farms and next generation sequencing shotgun metagenomics to examine the diversity of viruses present in aphids and in maize leaf samples. Samples were collected from farms in Kenya in a range of agro-ecological zones. Results Cytochrome oxidase 1 (CO1) gene sequencing showed that Aphis fabae was the sole aphid species present in bean plots in the farms visited. Sequencing of total RNA from aphids using the Illumina platform detected three dicistroviruses. Maize leaf RNA was also analysed. Identification of Aphid lethal paralysis virus (ALPV), Rhopalosiphum padi virus (RhPV), and a novel Big Sioux River virus (BSRV)-like dicistrovirus in aphid and maize samples was confirmed using reverse transcription-polymerase chain reactions and sequencing of amplified DNA products. Phylogenetic, nucleotide and protein sequence analyses of eight ALPV genomes revealed evidence of intra-species recombination, with the data suggesting there may be two ALPV lineages. Analysis of BSRV-like virus genomic RNA sequences revealed features that are consistent with other dicistroviruses and that it is phylogenetically closely related to dicistroviruses of the genus Cripavirus. Conclusions The discovery of ALPV and RhPV in aphids and maize further demonstrates the broad occurrence of these dicistroviruses. Dicistroviruses are remarkable in that they use plants as reservoirs that facilitate infection of their insect replicative hosts, such as aphids. This is the first report of these viruses being isolated from either organism. The BSRV-like sequences represent a potentially novel dicistrovirus infecting A. fabae. |
topic |
Metagenomics Phylogenetics Recombination Dicistrovirus Potyvirus Vector |
url |
http://link.springer.com/article/10.1186/s12985-017-0854-x |
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