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

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.

Effect of bean common mosaic virus on seed germination and yield of cowpea (Vigna unguiculata [L.] Walp.) breeding lines and characterisation of virus strains.

The study was conducted to characterise bean common mosaic virus strain Blackeye (BCMV-BICM) and determine the likelihood of seed transmission in cowpea breeding lines. F6 cowpea lines obtained from crosses between 'Ife-Brown' and 'IT-95 K-193-12' were planted at five locations in Southwest Nigeria for multilocational evaluation. Virus symptoms were observed on leaves of the breeding lines planted in Ibadan at eight weeks after planting. Enzyme-linked immunosorbent assay (ELISA) was used to determine the presence of six viruses: BCMV-BICM, cowpea aphid-borne mosaic virus, cucumber mosaic virus, cowpea mottle virus, southern bean mosaic virus and cowpea mild mottle virus. Seed transmission tests were carried out to determine virus transmission by seeds while growth and yield components of the cowpea lines were obtained. Reverse transcription polymerase chain reaction, sequencing and phylogenetic analyses were also used to characterise the BCMV-BICM isolates. The observed symptoms, leaf curling and mosaics, were typical of BCMV-BICM infection and ELISA results confirmed the presence of only BCMV-BICM. Line 'L-22-B' had the highest yield of 1653.9 kgha-1 followed by 'L-43-A' (1072 kgha-1). A non-significant relationship existed between the virus and germination parameters and similarly, the relationship between virus titres and yield parameters was not significant. Sequence analysis of the virus coat protein (CP) gene revealed the presence of three isolates with 96.87-97.47% nucleotide and 98.2-98.65% amino acid similarities and a 99.10-99.55% match with BCMV-BICM CP genes in GenBank. The deduced CP gene sequences showed unique changes at specific sites, while phylogenetic inferences revealed at least two separate origins for the isolates. Seed transmission is evident in all the cowpea breeding lines and 'L-22-B' and 'L-43-A' showed significant tolerance to BCMV-BICM. Thus, it is recommended that seeds from infected fields should not be used for further planting to prevent the introduction of viruses into new areas where their effect could be devastating in susceptible lines. Supplementary Information: The online version contains supplementary material available at 10.1007/s13337-023-00812-3.