Genome wide molecular evolution analysis of begomoviruses reveals unique diversification pattern in coat protein gene of Old World and New World viruses

Mondal, Debayan; Mandal, Somnath; Shil, Sandip; Sahana, Nandita; Pandit, Goutam K.; Choudhury, Ashok

doi:10.1007/s13337-019-00524-7

Cited by 20 publications

(10 citation statements)

References 60 publications

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“…The CPs of all the whitefly-transmitted geminiviruses have one or more antigenic epitopes in common, suggesting that these could be determinants of vector specificity and that they play a leading role in virus transmission [ 66 , 67 ]. Recently, an in silico study showed a higher mean diversity in the cp gene of OW BGVs compared to the NW [ 68 ]. However, highly mutable amino acids have been identified in the CP of Squash leaf curl China virus (SLCCNV) [ 69 ], which did not alter their fitness in the host plant but rendered the virus more competitive for certain species of whiteflies.…”

Section: Introductionmentioning

confidence: 99%

Genomic Variation and Diversification in Begomovirus Genome in Implication to Host and Vector Adaptation

Nigam

2021

Plants

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Begomoviruses (family Geminiviridae, genus Begomovirus) are DNA viruses transmitted in a circulative, persistent manner by the whitefly Bemisia tabaci (Gennadius). As revealed by their wide host range (more than 420 plant species), worldwide distribution, and effective vector transmission, begomoviruses are highly adaptive. Still, the genetic factors that facilitate their adaptation to a diverse array of hosts and vectors remain poorly understood. Mutations in the virus genome may confer a selective advantage for essential functions, such as transmission, replication, evading host responses, and movement within the host. Therefore, genetic variation is vital to virus evolution and, in response to selection pressure, is demonstrated as the emergence of new strains and species adapted to diverse hosts or with unique pathogenicity. The combination of variation and selection forms a genetic imprint on the genome. This review focuses on factors that contribute to the evolution of Begomovirus and their global spread, for which an unforeseen diversity and dispersal has been recognized and continues to expand.

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Section: Introductionmentioning

confidence: 99%

Genomic Variation and Diversification in Begomovirus Genome in Implication to Host and Vector Adaptation

Nigam

2021

Plants

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“…This is probably why this phenomenon is more in the CP region with the lowest mean dN/dS values, indicating that it is undergoing a stronger purifying selection. Other studies have also indicated similar patterns within begomoviruses, with the CP gene having the strongest evolutionary constraint [ 66 – 68 ]. dN/dS ratios are estimators of evolutionary bottlenecks imposed on a coding region at intra-specific levels.…”

Section: Discussionmentioning

confidence: 63%

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

Avedi

Adediji

Kilalo

et al. 2021

Virol J

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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.

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“…This is probably why this phenomenon is more in the CP region with the lowest mean dN/dS values, indicating that it is undergoing a stronger purifying selection. Other studies have also indicated similar patterns within begomoviruses, with the CP gene having the strongest evolutionary constraint [66][67][68]. dN/dS ratios are estimators of evolutionary bottlenecks imposed on a coding region at intra-speci c levels.…”

Section: Discussionmentioning

confidence: 67%

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

Avedi

Adediji

Kilalo

et al. 2020

Preprint

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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 5 out of the 6 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.

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Genome wide molecular evolution analysis of begomoviruses reveals unique diversification pattern in coat protein gene of Old World and New World viruses

Cited by 20 publications

References 60 publications

Genomic Variation and Diversification in Begomovirus Genome in Implication to Host and Vector Adaptation

Genomic Variation and Diversification in Begomovirus Genome in Implication to Host and Vector Adaptation

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

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

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