Complete Genome Sequence of a New
            <i>Chickpea Chlorotic Dwarf Virus</i>
            Strain Isolated from Tomato in Kenya, Obtained from Illumina Sequencing

Avedi, Edith Khamonya; Kilalo, C. D.; Olubayo, Florence; Macharia, Isaac; Adediji, Adedapo Olutola; Ateka, Elijah; Machuka, Eunice; Mutuku, J. Musembi

doi:10.1128/mra.01344-19

Cited by 5 publications

(4 citation statements)

References 17 publications

(19 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The presence of beta-satellites was not evaluated in this study. However, a sample (Tom54) produced the full-length genome of a separate begomovirus, Chickpea chlorotic dwarf virus , which we recently described [ 43 ]. The PCR primers designed from the full begomovirus genomes produced the expected 530 bp amplicons from the genomic DNA of infected tomato plants.…”

Section: Resultsmentioning

confidence: 99%

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

Avedi

Adediji

Kilalo

et al. 2021

Virol J

View full text Add to dashboard Cite

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.

show abstract

Section: Resultsmentioning

confidence: 99%

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

Avedi

Adediji

Kilalo

et al. 2021

Virol J

View full text Add to dashboard Cite

show abstract

“…Recombination has been shown to crucially contribute to the evolution of tomato-infecting begomoviruses [17,20,22,74] with far-reaching implications. A distinct begomovirus has recently been identi ed from tomato plants in Kenya [53]. Thus, the existence of these naturally-occurring recombinant isolates could evolve into the existence of virus complexes with signi cant effect on disease development, and evolution of virus populations.…”

Section: Discussionmentioning

confidence: 99%

Section: Sequence Data and De Novo Assembly Of Dna Virusesmentioning

confidence: 99%

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

Avedi

Adediji

Kilalo

et al. 2020

Preprint

View full text Add to dashboard Cite

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 In 2018, we obtained tomato leaf samples with virus-like symptoms from farmers’ fields across Kenya and used Illumina sequencing to identify associated begomoviruses. Using the sequences, we determined the genetic diversity of begomoviruses. Additionally, selection pressure and recombinant isolates within the population were 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. When we analyzed the amino acid sequences, we detected the highest identities in the regions coding for the coat protein gene (98.5–100%) within the isolates, and with the C4 gene of ToLCArV (97.1–100%). Phylogenetic algorithms clustered all Kenyan isolates in the same clades with ToLCArV, thus confirming the isolates to be a variant of the virus. Recombination analyses identified four putative events (P ≤ 0.05) among the 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. Conclusions The begomovirus associated with tomato leaf curl diseases in Kenya is a variant of ToLCArV possibly originating from Tanzania. Recombinant virus strains were detected within the population and there are divergence evolutionary events within the coding regions of the virus in Kenya. This information is useful in the development of appropriate management strategies for the disease.

show abstract

“…( 2000 ) Kenya Avedi et al. ( 2020 ) Morocco Radouane et al. ( 2019 ) Nigeria Present Fiallo‐Olivé et al.…”

Section: Appendix B – Distribution Of Chickpea Chlorotic Dwarf Virusmentioning

confidence: 99%

Pest categorisation of chickpea chlorotic dwarf virus

Bragard¹,

Baptista²,

Chatzivassiliou³

et al. 2022

EFS2

View full text Add to dashboard Cite

The EFSA Panel on Plant Health conducted a pest categorisation of chickpea chlorotic dwarf virus (CpCDV) for the EU territory. The identity of CpCDV, a member of the genus Mastrevirus (family Geminiviridae ) is established. Reliable detection and identification methods are available. The pathogen is not included in the EU Commission Implementing Regulation 2019/2072. CpCDV has been reported in Africa, Asia and Oceania. It has not been reported in the EU. CpCDV infects plant species in the family Fabaceae and several species of other families (Amaranthaceae, Brassicaceae, Caricaceae, Cucurbitaceae, Malvaceae and Solanaceae), including weeds. It may induce symptoms on its hosts, causing severe yield reduction. The virus is transmitted in a persistent, circulative and non‐propagative manner by the leafhopper species Orosius orientalis and O. albicinctus , which are not regulated. O. orientalis is known to be present in some EU member states. Plants for planting (other than seeds), parts of plants and cut flowers of CpCDV hosts and viruliferous leafhoppers were identified as the most relevant pathways for the entry of CpCDV into the EU. Cultivated and wild hosts of CpCDV are distributed across the EU. Would the pest enter and establish in the EU territory, impact on the production of cultivated hosts is expected. Phytosanitary measures are available to prevent entry and spread of the virus in the EU. CpCDV fulfils the criteria that are within the remit of EFSA to assess for it to be regarded as a potential Union quarantine pest.

show abstract

Complete Genome Sequence of a New Chickpea Chlorotic Dwarf Virus Strain Isolated from Tomato in Kenya, Obtained from Illumina Sequencing

Cited by 5 publications

References 17 publications

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

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

Pest categorisation of chickpea chlorotic dwarf virus

Contact Info

Product

Resources

About