Metagenomic analyses and genetic diversity of Tomato leaf curl Arusha virus affecting tomato plants in Kenya.
Authors
Kilalo, Dora Chao
Olubayo, Florence Mmogi
Macharia, Isaac
Ateka, Elijah Miinda
Machuka, Eunice Magoma
Mutuku, Josiah Musembi
Publication Date
2021-01-06Journal Title
Virol J
ISSN
1743-422X
Publisher
Springer Science and Business Media LLC
Volume
18
Issue
1
Language
en
Type
Article
This Version
VoR
Metadata
Show full item recordCitation
Avedi, E. K., Adediji, A. O., Kilalo, D. C., Olubayo, F. M., Macharia, I., Ateka, E. M., Machuka, E. M., & et al. (2021). Metagenomic analyses and genetic diversity of Tomato leaf curl Arusha virus affecting tomato plants in Kenya.. Virol J, 18 (1) https://doi.org/10.1186/s12985-020-01466-z
Description
Funder: Bill and Melinda Gates Foundation; doi: http://dx.doi.org/10.13039/100000865
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.
Keywords
Research, Plant viruses, Solanum lycopersicum, Begomovirus, Phylogeny, Haplotype diversity, Tajima’s D
Sponsorship
UK Biotechnological and Biological Sciences Research Council GCRF (BB/P023223/1.)
Identifiers
s12985-020-01466-z, 1466
External DOI: https://doi.org/10.1186/s12985-020-01466-z
This record's URL: https://www.repository.cam.ac.uk/handle/1810/315841
Rights
Attribution 4.0 International (CC BY 4.0)
Licence URL: https://creativecommons.org/licenses/by/4.0/
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