Genomic analysis of Sweet potato feathery mottle virus from East Africa
Sweet potato feathery mottle virus is a potyvirus that infect sweet potato. The genome of the virus was analysed to understand genetic diversity, evolution and gene flow. Motifs, nucleotide identity and a phylogenetic tree were used to determine phylogroup of the isolates. Gene flow and genetic dive...
| Main Authors: | , , , , , , , , |
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| Format: | Journal Article |
| Language: | Inglés |
| Published: |
Elsevier
2020
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| Subjects: | |
| Online Access: | https://hdl.handle.net/10568/110641 |
| _version_ | 1855522534307397632 |
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| author | Wokorach, G. Otim, G. Njuguna, Joyce N. Edema, H. Njung'e, V. Machuka, Eunice M. Yao, Nasser Stomeo, Francesca Echodua, R. |
| author_browse | Echodua, R. Edema, H. Machuka, Eunice M. Njuguna, Joyce N. Njung'e, V. Otim, G. Stomeo, Francesca Wokorach, G. Yao, Nasser |
| author_facet | Wokorach, G. Otim, G. Njuguna, Joyce N. Edema, H. Njung'e, V. Machuka, Eunice M. Yao, Nasser Stomeo, Francesca Echodua, R. |
| author_sort | Wokorach, G. |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | Sweet potato feathery mottle virus is a potyvirus that infect sweet potato. The genome of the virus was analysed to understand genetic diversity, evolution and gene flow. Motifs, nucleotide identity and a phylogenetic tree were used to determine phylogroup of the isolates. Gene flow and genetic diversity were tested using DnaSP v.5. Codons evolution were tested using three methods embedded in Datamonkey. The results indicate occurrence of an isolate of phylogroup B within East Africa. Low genetic differentiation was observed between isolates from Kenya and Uganda indicating evidence of gene flow between the two countries. Four genes were found to have positively selected codons bordering or occurring within functional motifs. A motif within P1 gene evolved differently between phylogroup A and B. The evidence of gene flow indicates frequent exchange of the virus between the two countries and P1 gene motif provide a possible marker that can be used for mapping the distribution of the phylogroups. |
| format | Journal Article |
| id | CGSpace110641 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2020 |
| publishDateRange | 2020 |
| publishDateSort | 2020 |
| publisher | Elsevier |
| publisherStr | Elsevier |
| record_format | dspace |
| spelling | CGSpace1106412025-12-02T10:59:51Z Genomic analysis of Sweet potato feathery mottle virus from East Africa Wokorach, G. Otim, G. Njuguna, Joyce N. Edema, H. Njung'e, V. Machuka, Eunice M. Yao, Nasser Stomeo, Francesca Echodua, R. crops sweet potatoes genomes Sweet potato feathery mottle virus is a potyvirus that infect sweet potato. The genome of the virus was analysed to understand genetic diversity, evolution and gene flow. Motifs, nucleotide identity and a phylogenetic tree were used to determine phylogroup of the isolates. Gene flow and genetic diversity were tested using DnaSP v.5. Codons evolution were tested using three methods embedded in Datamonkey. The results indicate occurrence of an isolate of phylogroup B within East Africa. Low genetic differentiation was observed between isolates from Kenya and Uganda indicating evidence of gene flow between the two countries. Four genes were found to have positively selected codons bordering or occurring within functional motifs. A motif within P1 gene evolved differently between phylogroup A and B. The evidence of gene flow indicates frequent exchange of the virus between the two countries and P1 gene motif provide a possible marker that can be used for mapping the distribution of the phylogroups. 2020-04-15 2020-12-27T14:22:40Z 2020-12-27T14:22:40Z Journal Article https://hdl.handle.net/10568/110641 en Open Access Elsevier Wokorach, G., Otim, G., Njuguna, J., Edema, H., Njung'e, V., Machuka, E.M., Yao, N., Stomeo, F. and Echodua, R. 2020. Genomic analysis of Sweet potato feathery mottle virus from East Africa. Physiological and Molecular Plant Pathology 110:101473. |
| spellingShingle | crops sweet potatoes genomes Wokorach, G. Otim, G. Njuguna, Joyce N. Edema, H. Njung'e, V. Machuka, Eunice M. Yao, Nasser Stomeo, Francesca Echodua, R. Genomic analysis of Sweet potato feathery mottle virus from East Africa |
| title | Genomic analysis of Sweet potato feathery mottle virus from East Africa |
| title_full | Genomic analysis of Sweet potato feathery mottle virus from East Africa |
| title_fullStr | Genomic analysis of Sweet potato feathery mottle virus from East Africa |
| title_full_unstemmed | Genomic analysis of Sweet potato feathery mottle virus from East Africa |
| title_short | Genomic analysis of Sweet potato feathery mottle virus from East Africa |
| title_sort | genomic analysis of sweet potato feathery mottle virus from east africa |
| topic | crops sweet potatoes genomes |
| url | https://hdl.handle.net/10568/110641 |
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