Edith Khamonya Avedi1,2,3, Adedapo Olutola Adediji4, Dora Chao Kilalo5, Florence Mmogi Olubayo5, Isaac Macharia6, Elijah Miinda Ateka7, Eunice Magoma Machuka8, Josiah Musembi Mutuku8,9,10. 1. Department of Phytosanitary Services and Biosafety, Kenya Plant Health Inspectorate Service, Nairobi, Kenya. E.Aved@kephis.org. 2. Department of Plant Science and Crop Protection, University of Nairobi, Nairobi, Kenya. E.Aved@kephis.org. 3. Biosciences Eastern and Central Africa, International Livestock Research Institute, Nairobi, Kenya. E.Aved@kephis.org. 4. Department of Crop Protection and Environmental Biology, Faculty of Agriculture, University of Ibadan, Ibadan, Nigeria. adedapo.adediji@gmail.com. 5. Department of Plant Science and Crop Protection, University of Nairobi, Nairobi, Kenya. 6. Department of Phytosanitary Services and Biosafety, Kenya Plant Health Inspectorate Service, Nairobi, Kenya. 7. Department of Horticulture and Food Security, Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya. 8. Biosciences Eastern and Central Africa, International Livestock Research Institute, Nairobi, Kenya. 9. Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, UK. 10. The Central and West African Virus Epidemiology (WAVE), Pôle Scientifique et d'Innovation de Bingerville, Université Félix Houphouët-Boigny, Abidjan, Côte d'Ivoire.
Abstract
BACKGROUND: Tomato production is threatened worldwide by the occurrence of begomoviruses which are associated with tomato leaf curl diseases. There is little information on the molecular properties of tomato begomoviruses in Kenya, hence we investigated the population and genetic diversity of begomoviruses associated with tomato leaf curl in Kenya. METHODS: Tomato leaf samples with virus-like symptoms were obtained from farmers' field across the country in 2018 and Illumina sequencing undertaken to determine the genetic diversity of associated begomoviruses. Additionally, the occurrence of selection pressure and recombinant isolates within the population were also evaluated. RESULTS: Twelve complete begomovirus genomes were obtained from our samples with an average coverage of 99.9%. The sequences showed 95.7-99.7% identity among each other and 95.9-98.9% similarities with a Tomato leaf curl virus Arusha virus (ToLCArV) isolate from Tanzania. Analysis of amino acid sequences showed the highest identities in the regions coding for the coat protein gene (98.5-100%) within the isolates, and 97.1-100% identity with the C4 gene of ToLCArV. Phylogenetic algorithms clustered all Kenyan isolates in the same clades with ToLCArV, thus confirming the isolates to be a variant of the virus. There was no evidence of recombination within our isolates. Estimation of selection pressure within the virus population revealed the occurrence of negative or purifying selection in five out of the six coding regions of the sequences. CONCLUSIONS: The begomovirus associated with tomato leaf curl diseases of tomato in Kenya is a variant of ToLCArV, possibly originating from Tanzania. There is low genetic diversity within the virus population and this information is useful in the development of appropriate management strategies for the disease in the country.
BACKGROUND:Tomato production is threatened worldwide by the occurrence of begomoviruses which are associated with tomato leaf curl diseases. There is little information on the molecular properties of tomato begomoviruses in Kenya, hence we investigated the population and genetic diversity of begomoviruses associated with tomato leaf curl in Kenya. METHODS:Tomato leaf samples with virus-like symptoms were obtained from farmers' field across the country in 2018 and Illumina sequencing undertaken to determine the genetic diversity of associated begomoviruses. Additionally, the occurrence of selection pressure and recombinant isolates within the population were also evaluated. RESULTS: Twelve complete begomovirus genomes were obtained from our samples with an average coverage of 99.9%. The sequences showed 95.7-99.7% identity among each other and 95.9-98.9% similarities with a Tomato leaf curl virus Arusha virus (ToLCArV) isolate from Tanzania. Analysis of amino acid sequences showed the highest identities in the regions coding for the coat protein gene (98.5-100%) within the isolates, and 97.1-100% identity with the C4 gene of ToLCArV. Phylogenetic algorithms clustered all Kenyan isolates in the same clades with ToLCArV, thus confirming the isolates to be a variant of the virus. There was no evidence of recombination within our isolates. Estimation of selection pressure within the virus population revealed the occurrence of negative or purifying selection in five out of the six coding regions of the sequences. CONCLUSIONS: The begomovirus associated with tomato leaf curl diseases of tomato in Kenya is a variant of ToLCArV, possibly originating from Tanzania. There is low genetic diversity within the virus population and this information is useful in the development of appropriate management strategies for the disease in the country.
Entities:
Keywords:
Begomovirus; Haplotype diversity; Phylogeny; Solanum lycopersicum; Tajima’s D
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