Identification of a novel polerovirus in cocoa (Theobroma cacao) germplasm and development of molecular methods for use in diagnostics

Download

Preview

Text (Open Access) - Published Version
· Available under License Creative Commons Attribution.
· Please see our End User Agreement before downloading. | Preview

Available under license: Creative Commons Attribution

Advice

Please see our End User Agreement.

It is advisable to refer to the publisher's version if you intend to cite from this work. See Guidance on citing.

Tools

Lists

Ullah, I. ORCID: https://orcid.org/0000-0002-9367-6741, Kamran, M. and Dunwell, J. M. ORCID: https://orcid.org/0000-0003-2147-665X (2023) Identification of a novel polerovirus in cocoa (Theobroma cacao) germplasm and development of molecular methods for use in diagnostics. Pathogens, 12 (11). 1284. ISSN 2076-0817 doi: 10.3390/pathogens12111284

Abstract/Summary

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.

Altmetric Badge

Item Type	Article
URI	https://reading-clone.eprints-hosting.org/id/eprint/113813
Identification Number/DOI	10.3390/pathogens12111284
Refereed	Yes
Divisions	Life Sciences > School of Agriculture, Policy and Development > Department of Crop Science
Uncontrolled Keywords	cacao; polerovirus; genome; RT-PCR; NGS; ORF
Publisher	MDPI
Download/View statistics	View download statistics for this item

Download Statistics

Downloads

Downloads per month over past year

Deposit Details

Date Deposited:	07 Nov 2023 09:47	Date item deposited into CentAUR
Last Modified:	23 Jun 2024 05:44	Date item last modified

References

1. Statista. Revenue of the Confectionery MarketWorldwide from 2016 to 2027, by Segment. Available online: https://www.statista. com/forecasts/1309970/worldwide-confectionery-market-size-by-category (accessed on 20 September 2023). 2. Muller, E.; Ravel, S.; Agret, C.; Abrokwah, F.; Dzahini-Obiatey, H.; Galyuon, I.; Kouakou, K.; Jeyaseelan, E.C.; Allainguillaume, J.; Wetten, A. Next Generation Sequencing Elucidates Cacao Badnavirus Diversity and Reveals the Existence of More than Ten Viral Species. Virus Res. 2018, 244, 235–251. [CrossRef] 3. ICCO. Quarterly Bulletin of Cocoa Statistics, Vol. XLIX, No.2, Cocoa Year 2022/23. Available online: https://www.icco.org/wpcontent/ uploads/Production_QBCS-XLIX-No.-2.pdf (accessed on 20 September 2023). 4. Chingandu, N.; Zia-Ur-Rehman, M.; Sreenivasan, T.N.; Surujdeo-Maharaj, S.; Umaharan, P.; Gutierrez, O.A.; Brown, J.K. Molecular Characterization of Previously Elusive Badnaviruses Associated with Symptomatic Cacao in the NewWorld. Arch. Virol. 2017, 162, 1363–1371. [CrossRef] [PubMed] 5. Puig, A.S.; Ramos-Sobrinho, R.; Keith, C.; Kitchen, N.; Gutierrez, O.A.; Goenaga, R.J. First Report of Cacao Mild Mosaic Virus (CaMMV) Associated with Symptomatic Commercial Cacao (Theobroma cacao L.) trees in Puerto Rico. Plant Dis. 2020, 104, 3089. [CrossRef] 6. Puig, A.S. Detection of Cacao Mild Mosaic Virus (CaMMV) Using Nested PCR and Evidence of Uneven Distribution in Leaf Tissue. Agronomy 2021, 11, 1842. [CrossRef] 7. Ullah, I.; Daymond, A.J.; Hadley, P.; End, M.J.; Umaharan, P.; Dunwell, J.M. Identification of Cacao Mild Mosaic Virus (CaMMV) and Cacao Yellow Vein-Banding Virus (CYVBV) in Cocoa (Theobroma cacao) Germplasm. Viruses 2021, 13, 2152. [CrossRef] [PubMed] 8. Kandito, A.; Hartono, S.; Trisyono, Y.A.; Somowiyarjo, S. First Report of Cacao Mild Mosaic Virus Associated with Cacao Mosaic Disease in Indonesia. New Dis. Rep. 2022, 45, e12071. [CrossRef] 9. Muller, E.; Ullah, I.; Dunwell, J.M.; Daymond, A.J.; Richardson, M.; Allainguillaume, J.; Wetten, A. Identification and Distribution of Novel Badnaviral Sequences Integrated in the Genome of Cacao (Theobroma cacao). Sci. Rep. 2021, 11, 8270. [CrossRef] 10. Ullah, I.; Dunwell, J.M. Bioinformatic, Genetic and Molecular Analysis of Several Badnavirus Sequences Integrated in the Genomes of Diverse Cocoa (Theobroma cacao L.) Germplasm. Saudi J. Biol. Sci. 2023, 30, 103648. [CrossRef] 11. Edula, S.R.; Bag, S.; Milner, H.; Kumar, M.; Suassuna, N.D.; Chee, P.W.; Kemerait, R.C.; Hand, L.C.; Snider, J.L.; Srinivasan, R.; et al. Cotton Leafroll Dwarf Disease: An Enigmatic Viral Disease in Cotton. Mol. Plant Pathol. 2023, 24, 513–526. [CrossRef] 12. Walker, P.J.; Siddell, S.G.; Lefkowitz, E.J.; Mushegian, A.R.; Adriaenssens, E.M.; Alfenas-Zerbini, P.; Davison, A.J.; Dempsey, D.M.; Dutilh, B.E.; García, M.L.; et al. Changes to Virus Taxonomy and to the International Code of Virus Classification and Nomenclature Ratified by the International Committee on Taxonomy of Viruses (2021). Arch. Virol. 2021, 166, 2633–2648. [CrossRef] 13. Osman, T.A.; Coutts, R.H.; Buck, K.W. In Vitro Synthesis of Minus-Strand RNA by an Isolated Cereal Yellow Dwarf Virus RNADependent RNA Polymerase Requires VPg and a Stem-Loop Structure at the 3’ End of the Virus RNA. J. Virol. 2006, 80, 10743–10751. [CrossRef] [PubMed] 14. Delfosse, V.C.; Barrios-Barón, M.P.; Distéfano, A.J. What we Know about Poleroviruses: Advances in Understanding the Functions of Polerovirus Proteins. Plant Pathol. 2021, 70, 1047–1061. [CrossRef] 15. Silva, J.M.F.; Al Rwahnih, M.; Blawid, R.; Nagata, T.; Fajardo, T.V.M. Discovery and Molecular Characterization of a Novel Enamovirus, Grapevine Enamovirus-1. Virus Genes 2017, 53, 667–671. [CrossRef] [PubMed] 16. Adegbola, R.O.; Keith, C.V.; Gutierrez, O.A.; Goenaga, R.J.; Brown, J.K. A Previously Undescribed Polerovirus (Solemoviridae) Infecting Theobroma cacao Germplasm. Plant Dis. 2023, 107, 975. [CrossRef] 17. Ramos-Sobrinho, R.; Ferro, M.M.M.; Lima, G.S.A.; Nagata, T. First Report of Cotton Leafroll Dwarf Virus Infecting Cacao (Theobroma cacao L.) Trees in Brazil. Plant Dis. 2022, 107, 1251. [CrossRef] 18. Csorba, T.; Kontra, L.; Burgyán, J. Viral Silencing Suppressors: Tools Forged to Fine-Tune Host-Pathogen Coexistence. Virology 2015, 479–480, 85–103. [CrossRef] 19. Sivakumaran, K.; Fowler, B.C.; Hacker, D.L. Identification of Viral Genes Required for Cell-to-Cell Movement of Southern Bean Mosaic Virus. Virology 1998, 252, 376–386. [CrossRef] 20. Prüfer, D.; Tacke, E.; Schmitz, J.; Kull, B.; Kaufmann, A.; Rohde, W. Ribosomal Frameshifting in Plants: A Novel Signal Directs the

University Staff: Request a correction | Centaur Editors: Update this record

Search Google Scholar