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.

Keywords: Begomovirus; Haplotype diversity; Phylogeny; Solanum lycopersicum; Tajima’s D.

Fig. 1

a The map of Kenya showing counties where tomato fields were sampled for this study. b Photograph of symptomatic tomato plants showing leaf curl from farmer fields

Fig. 1

a The map of Kenya showing counties where tomato fields were sampled for this study. b Photograph of symptomatic tomato plants showing leaf curl from farmer fields

Fig. 2

Phylogenetic analyses of tomato leaf curl virus from Kenya (n = 12) with selected worldwide begomoviruses based on alignment of complete DNA-A nucleotide sequences. The tree was generated using the maximum likelihood inference based on the Jukes-Cantor model as implemented in MEGA v.6.06 [37]. Percentage bootstrap support values (1,000 iterations) are indicated at the branch nodes. The tree is rooted with Tomato leaf curl purple vein virus (accession number KY196216) as an outgroup. The scale bar shows the number of nucleotide substitutions power site. Details of all the isolates are provided in Additional file 2: Table S1