Bioinformatic, genetic and molecular analysis of several badnavirus sequences integrated in the genomes of diverse cocoa (Theobroma cacao L.) germplasm

Ullah, Ihsan; Dunwell, Jim M.

doi:10.1016/j.sjbs.2023.103648

Cited by 4 publications

(3 citation statements)

References 36 publications

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“…Recent studies showed badnaviruses on cacao could also integrate to the host genome as endogenous pararetrovirus (EPRV) and be inherited to the progenies (Muller et al, 2021;Ullah & Dunwell, 2023). EPRV is known abundant in plants and present in several species including banana, tomato, and cacao (de Tomás & Vicient, 2022;Furuya et al, 2012;Muller et al, 2021;Staginnus et al, 2007).…”

Section: Re Sults and Discussionmentioning

confidence: 99%

Geographical distribution of emerging cacao mosaic disease caused by cacao mild mosaic virus (Badnavirus tesellotheobromae) in Indonesia

Kandito,

Hartono,

Trisyono

et al. 2024

Journal of Phytopathology

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Indonesia is the third largest cocoa producer in the world with annual export value of more than 1.2 million USD. However, cacao production in Indonesia has decreased by approximately 50% in the last decade due to socioeconomic issues and the high prevalence of pests and diseases. Cacao mosaic disease caused by cacao mild mosaic virus (Badnavirus teselotheobromae, CMMV) is currently emerging in Indonesia. This study aims to map the distribution of CMMV in cacao‐growing areas in Indonesia. Samples were collected in 2021–2023 in Java, Sumatera, Bali, and Sulawesi, which represent major cacao‐growing areas in Indonesia. We successfully detected CMMV from all samples, indicating CMMV is already distributed widely in Indonesia. Sequencing data suggests the Indonesian isolates have a common ancestor with American isolates. These findings provide new information for the quarantine board, government, and industry to arrange the policy to control the emerging CMMV.

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Section: Re Sults and Discussionmentioning

confidence: 99%

Geographical distribution of emerging cacao mosaic disease caused by cacao mild mosaic virus (Badnavirus tesellotheobromae) in Indonesia

Kandito,

Hartono,

Trisyono

et al. 2024

Journal of Phytopathology

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“…Endogenous viral elements (EVEs) are viral sequences (whole or partial) that have become integrated into the host genome; subsequent replication of the host genome fixes these EVEs such that daughter cells now carry the entire complement of the host genome with EVE elements [ 112 ]. The integration of functional full-length viral sequences into host genomes can trigger a response to systemic virus infection and affect the expression of specific host genes, e.g., the banana streak virus ( Badnavirus ) in bananas [ 113 ].…”

Section: Endemic and Potential Re-emerging Threatsmentioning

confidence: 99%

Viral Threats to Fruit and Vegetable Crops in the Caribbean

Tennant,

Rampersad,

Alleyne

et al. 2024

Viruses

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Viruses pose major global challenges to crop production as infections reduce the yield and quality of harvested products, hinder germplasm exchange, increase financial inputs, and threaten food security. Small island or archipelago habitat conditions such as those in the Caribbean are particularly susceptible as the region is characterized by high rainfall and uniform, warm temperatures throughout the year. Moreover, Caribbean islands are continuously exposed to disease risks because of their location at the intersection of transcontinental trade between North and South America and their role as central hubs for regional and global agricultural commodity trade. This review provides a summary of virus disease epidemics that originated in the Caribbean and those that were introduced and spread throughout the islands. Epidemic-associated factors that impact disease development are also discussed. Understanding virus disease epidemiology, adoption of new diagnostic technologies, implementation of biosafety protocols, and widespread acceptance of biotechnology solutions to counter the effects of cultivar susceptibility remain important challenges to the region. Effective integrated disease management requires a comprehensive approach that should include upgraded phytosanitary measures and continuous surveillance with rapid and appropriate responses.

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“…To date, none of these infections have been associated with any effect on plant growth or productivity. Badnaviruses have also been reported as endogenized in the cacao genome [9,10].…”

Section: Introductionmentioning

confidence: 99%

Identification of a Novel Polerovirus in Cocoa (Theobroma cacao) Germplasm and Development of Molecular Methods for Use in Diagnostics

Ullah,

Kamran,

Dunwell

2023

Pathogens

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The cocoa crop (Theobroma cacao L.) is known to be a host for several badnaviruses, some of which cause severe disease, while others are asymptomatic. Recently, the first preliminary evidence has been published concerning the occurrence of a polerovirus in cacao. We report here the first near-complete genome sequence of cacao polerovirus (CaPV) by combining bioinformatic searches of cacao transcript databases, with cloning from the infected germplasm. The reported novel genome has all the genome features known for poleroviruses from other species. Pairwise identity analyses of RNA-dependent RNA polymerase and coat protein indicates < 60% similarity of CaPV with any reported poleroviruses; hence, we propose that the polerovirus isolate reported in this study is a novel polerovirus. The genome sequence information was also used to develop a multiplex RT-PCR assay, which was applied to screen a selected range of germplasms and to identify several infected clones. Although there is no evidence that this virus causes any severe disease, this new information, together with a robust diagnostic assay, are of strategic importance in developing protocols for the safe international transfer of cacao germplasms.

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Bioinformatic, genetic and molecular analysis of several badnavirus sequences integrated in the genomes of diverse cocoa (Theobroma cacao L.) germplasm

Cited by 4 publications

References 36 publications

Geographical distribution of emerging cacao mosaic disease caused by cacao mild mosaic virus (Badnavirus tesellotheobromae) in Indonesia

Geographical distribution of emerging cacao mosaic disease caused by cacao mild mosaic virus (Badnavirus tesellotheobromae) in Indonesia

Viral Threats to Fruit and Vegetable Crops in the Caribbean

Identification of a Novel Polerovirus in Cocoa (Theobroma cacao) Germplasm and Development of Molecular Methods for Use in Diagnostics

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