Evolutionary insights of Bean common mosaic necrosis virus and Cowpea aphid-borne mosaic virus
Plant viral diseases are one of the major limitations in legume production within sub-Saharan Africa (SSA), as they account for up to 100% in production losses within smallholder farms. In this study, field surveys were conducted in the western highlands of Kenya with viral symptomatic leaf samples...
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PeerJ Inc.
2019-02-01
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| Serija: | PeerJ |
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| Online dostop: | https://peerj.com/articles/6297.pdf |
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| author | James M. Wainaina Laura Kubatko Jagger Harvey Elijah Ateka Timothy Makori David Karanja Laura M. Boykin Monica A. Kehoe |
| author_facet | James M. Wainaina Laura Kubatko Jagger Harvey Elijah Ateka Timothy Makori David Karanja Laura M. Boykin Monica A. Kehoe |
| author_sort | James M. Wainaina |
| collection | DOAJ |
| description | Plant viral diseases are one of the major limitations in legume production within sub-Saharan Africa (SSA), as they account for up to 100% in production losses within smallholder farms. In this study, field surveys were conducted in the western highlands of Kenya with viral symptomatic leaf samples collected. Subsequently, next-generation sequencing was carried out to gain insights into the molecular evolution and evolutionary relationships of Bean common mosaic necrosis virus (BCMNV) and Cowpea aphid-borne mosaic virus (CABMV) present within symptomatic common bean and cowpea. Eleven near-complete genomes of BCMNV and two for CABMV were obtained from western Kenya. Bayesian phylogenomic analysis and tests for differential selection pressure within sites and across tree branches of the viral genomes were carried out. Three well–supported clades in BCMNV and one supported clade for CABMNV were resolved and in agreement with individual gene trees. Selection pressure analysis within sites and across phylogenetic branches suggested both viruses were evolving independently, but under strong purifying selection, with a slow evolutionary rate. These findings provide valuable insights on the evolution of BCMNV and CABMV genomes and their relationship to other viral genomes globally. The results will contribute greatly to the knowledge gap involving the phylogenomic relationship of these viruses, particularly for CABMV, for which there are few genome sequences available, and inform the current breeding efforts towards resistance for BCMNV and CABMV. |
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| institution | Directory Open Access Journal |
| issn | 2167-8359 |
| language | English |
| last_indexed | 2024-03-09T06:26:28Z |
| publishDate | 2019-02-01 |
| publisher | PeerJ Inc. |
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| spelling | doaj.art-fca4a9a7c9c544bf8eed9b18de0681c92023-12-03T11:19:38ZengPeerJ Inc.PeerJ2167-83592019-02-017e629710.7717/peerj.6297Evolutionary insights of Bean common mosaic necrosis virus and Cowpea aphid-borne mosaic virusJames M. Wainaina0Laura Kubatko1Jagger Harvey2Elijah Ateka3Timothy Makori4David Karanja5Laura M. Boykin6Monica A. Kehoe7School of Molecular Sciences and Australian Research Council Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley, Western Australia, AustraliaOhio State University, Columbus, OH, United States of AmericaFeed the Future Innovation Lab for the Reduction of Post-Harvest Loss, Kansas State University, Manhattan, KS, United States of AmericaDepartment of Horticulture, Jomo Kenyatta University of Agriculture and Technology, Nairobi, KenyaDepartment of Horticulture, Jomo Kenyatta University of Agriculture and Technology, Nairobi, KenyaKenya Agricultural and Livestock Research Organization (KARLO), Machakos, KenyaSchool of Molecular Sciences and Australian Research Council Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley, Western Australia, AustraliaPlant Pathology, Department of Primary Industries and Regional Development Diagnostic Laboratory Service, South Perth, AustraliaPlant viral diseases are one of the major limitations in legume production within sub-Saharan Africa (SSA), as they account for up to 100% in production losses within smallholder farms. In this study, field surveys were conducted in the western highlands of Kenya with viral symptomatic leaf samples collected. Subsequently, next-generation sequencing was carried out to gain insights into the molecular evolution and evolutionary relationships of Bean common mosaic necrosis virus (BCMNV) and Cowpea aphid-borne mosaic virus (CABMV) present within symptomatic common bean and cowpea. Eleven near-complete genomes of BCMNV and two for CABMV were obtained from western Kenya. Bayesian phylogenomic analysis and tests for differential selection pressure within sites and across tree branches of the viral genomes were carried out. Three well–supported clades in BCMNV and one supported clade for CABMNV were resolved and in agreement with individual gene trees. Selection pressure analysis within sites and across phylogenetic branches suggested both viruses were evolving independently, but under strong purifying selection, with a slow evolutionary rate. These findings provide valuable insights on the evolution of BCMNV and CABMV genomes and their relationship to other viral genomes globally. The results will contribute greatly to the knowledge gap involving the phylogenomic relationship of these viruses, particularly for CABMV, for which there are few genome sequences available, and inform the current breeding efforts towards resistance for BCMNV and CABMV.https://peerj.com/articles/6297.pdfPhylogenomics of BCMNV and CABMVVirus evolutionGenomicsNext-generation sequencing (NGS)KenyaSmallholder farmer |
| spellingShingle | James M. Wainaina Laura Kubatko Jagger Harvey Elijah Ateka Timothy Makori David Karanja Laura M. Boykin Monica A. Kehoe Evolutionary insights of Bean common mosaic necrosis virus and Cowpea aphid-borne mosaic virus PeerJ Phylogenomics of BCMNV and CABMV Virus evolution Genomics Next-generation sequencing (NGS) Kenya Smallholder farmer |
| title | Evolutionary insights of Bean common mosaic necrosis virus and Cowpea aphid-borne mosaic virus |
| title_full | Evolutionary insights of Bean common mosaic necrosis virus and Cowpea aphid-borne mosaic virus |
| title_fullStr | Evolutionary insights of Bean common mosaic necrosis virus and Cowpea aphid-borne mosaic virus |
| title_full_unstemmed | Evolutionary insights of Bean common mosaic necrosis virus and Cowpea aphid-borne mosaic virus |
| title_short | Evolutionary insights of Bean common mosaic necrosis virus and Cowpea aphid-borne mosaic virus |
| title_sort | evolutionary insights of bean common mosaic necrosis virus and cowpea aphid borne mosaic virus |
| topic | Phylogenomics of BCMNV and CABMV Virus evolution Genomics Next-generation sequencing (NGS) Kenya Smallholder farmer |
| url | https://peerj.com/articles/6297.pdf |
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