Metagenomic analyses and genetic diversity of Tomato leaf curl Arusha virus affecting tomato plants in Kenya

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.

Integrated Potential of Microbial, Botanical, and Chemical Pesticides for the Control of Viral Disease Vector Whiteflies (Hemiptera: Aleyrodidae) on Tomato under Greenhouse and Field Perspectives

“…ese polyphagous pests cause direct damage to tomato by feeding on plant sap, opening up to secondary infection by sooty molds which reduces photosynthesis and decrease plant vigor [11], and transmitting different tomato viral diseases [12] caused by Begomovirus, Crinivirus, Ipomovirus, Carlavirus, and Torradovirus [13]. According to [14], tomato production is threatened worldwide by the occurrence of whitefly-transmitted Begomoviruses, which are associated with tomato leaf curl diseases.…”