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Archives of Virology

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01.04.2024 | Annotated Sequence Record

Complete genome characterization of cacao leafroll virus, a newly described cacao-infecting polerovirus

verfasst von: Raphael O. Adegbola, Cory V. Keith, Osman Gutierrez, Ricardo Goenaga, Judith K. Brown

Erschienen in: Archives of Virology | Ausgabe 4/2024

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Abstract

The complete genome sequence of cacao leafroll virus (CaLRV; family Solemoviridae, genus Polerovirus) was determined by high-throughput sequencing of total RNA isolated from symptomatic cacao Theobroma cacao L. plants (n = 4). The CaLRV genome sequences ranged from 5,976 to 5,997 nucleotides (nt) in length and contained seven open reading frames (ORFs). Nucleotide and amino acid (aa) sequence comparisons showed that, among selected well-characterized poleroviruses, the CaLRV genome shared the highest nt sequence identity of 62% with that of potato leafroll virus (PLRV, NC_076505). A comparison of the predicted aa sequence of the CaLRV coat protein indicated that cotton leafroll dwarf virus (CLRDV, NC_014545) and melon aphid-borne yellows virus (MABYV, NC_010809) were the closest relatives, sharing 57% aa sequence identity. Bayesian phylogenetic analysis based on complete genome sequences showed that CaLRV grouped with well-characterized poleroviruses that cause diseases of cereal and vegetable crops. During the course of publishing this work, the nearly complete genome sequence of a member of the same polerovirus species, referred to as “cacao polerovirus” (OR605721), with which CaLRV shares 99% nt sequence identity, was reported.

Nur mit Berechtigung zugänglich

de Souza PA, Moreira LF, Sarmento DH, da Costa FB (2018) Cacao-Theobroma cacao. In: Rodrigues S, de Oliveira Silva E, de Brito ES (eds) Exotic Fruits. Academic Press, pp 69–76. https://doi.org/10.1016/B978-0-12-803138-4.00010-1

Kandito A, Hartono S, Trisyono YA, Somowiyarjo S (2022) First Report of Cacao Mild Mosaic Virus Associated with Cacao Mosaic Disease in Indonesia. New Dis Rep 45:e12071. https://doi.org/10.1002/ndr2.12071CrossRef

Ramos-Sobrinho R, Ferro MMM, Lima GSA, Nagata T (2022) First report of cotton leafroll dwarf virus infecting cacao (Theobroma cacao) trees in Brazil. Plant Dis 107:1251. https://doi.org/10.1094/PDIS-07-22-1570-PDNCrossRef

Ramos-Sobrinho R, Ferro MMM, Nagata T, Puig AS, Keith CV, Britto DS, Gutierrez OA, Marelli J-P, Brown JK (2021) Complete genome sequences of three newly discovered cacao mild mosaic virus isolates from Theobroma cacao L. in Brazil and Puerto Rico and evidence for recombination. Arch Virol 166:2027–2031. https://doi.org/10.1007/s00705-021-05063-5CrossRefPubMed

Ullah I, Daymond AJ, Hadley P, End MJ, Umaharan P, Dunwell JM (2021) Identification of cacao mild mosaic virus (CaMMV) and cacao yellow vein-banding virus (CYVBV) in cocoa (Theobroma cacao) Germplasm. Viruses 13:2152CrossRefPubMedPubMedCentral

Ramos-Sobrinho R, Chingandu N, Gutierrez OA, Marelli J-P, Brown JK (2020) A complex of badnavirus species infecting cacao reveals mixed infections, extensive genomic variability, and interspecific recombination. Viruses 12:443. https://doi.org/10.3390/v12040443CrossRefPubMedPubMedCentral

Muller E, Ravel S, Agret C, Abrokwah F, Dzahini-Obiatey H, Galyuon I, Kouakou K, Jeyaseelan EC, Allainguillaume J, Wetten A (2018) Next generation sequencing elucidates cacao badnavirus diversity and reveals the existence of more than ten viral species. Virus Res 244:235–251. https://doi.org/10.1016/j.virusres.2017.11.019CrossRefPubMed

Sõmera M, Fargette D, Hébrard E, Sarmiento C (2021) ICTV Report Consortium. ICTV virus taxonomy profile: Solemoviridae 2021. J Gen Virol 102:12. https://doi.org/10.1099/jgv.0.001707CrossRef

Brault V, Bergdoll M, Mutterer J, Prasad V, Pfeffer S, Erdinger M, Richards KE, Ziegler-Graff V (2003) Effects of point mutations in the major capsid protein of beet western yellows virus on capsid formation, virus accumulation, and aphid transmission. J Virol 77:3247–3256. https://doi.org/10.1128/jvi.77.5.3247-3256.2003CrossRefPubMedPubMedCentral

10.

Delfosse VC, Barrios Barón MP, Distéfano AJ (2021) What we know about poleroviruses: Advances in understanding the functions of polerovirus proteins. Plant Pathol 70:1047–1061. https://doi.org/10.1111/ppa.1336CrossRef

11.

Adegbola RO, Keith CV, Gutierrez OA, Goenaga R, Brown JK (2022) A Previously undescribed polerovirus (Solemoviridae) Infecting Theobroma cacao germplasm. Plant Dis 107:975. https://doi.org/10.1094/PDIS-06-22-1449-PDNCrossRef

12.

Turnbull CJ, Hadley P (2021) International Cocoa Germplasm Database (ICGD). CRA Ltd./ICE Futures Europe/University of Reading, UK

13.

Rott ME, Jelkmann W (2001) Characterization and detection of several filamentous viruses of cherry: Adaptation of an alternative cloning method (DOP-PCR), and modification of an RNA extraction protocol. Eur J Plant Pathol 107:411–420. https://doi.org/10.1023/A:1011264400482CrossRef

14.

Prjibelski A, Antipov D, Meleshko D, Lapidus A, Korobeynikov A (2020) Using SPAdes de novo assembler. Curr Protocols Bioinformat 70:e102. https://doi.org/10.1002/cpbi.102CrossRef

15.

Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215:403–410. https://doi.org/10.1016/S0022-2836(05)80360-2CrossRefPubMed

16.

Edgar RC (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32:1792–1797. https://doi.org/10.1093/nar/gkh340CrossRefPubMedPubMedCentral

17.

Muhire BM, Varsani A, Martin DP (2014) SDT: a virus classification tool based on pairwise sequence alignment and identity calculation. PLoS ONE 9:e108277. https://doi.org/10.1371/journal.pone.0108277CrossRefPubMedPubMedCentral

18.

Ronquist F, Teslenko M, Van Der Mark P, Ayres DL, Darling A, Höhna S, Larget B, Liu L, Suchard MA, Huelsenbeck JP (2012) MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space. Syst Biol 61:539–542. https://doi.org/10.1093/sysbio/sys029CrossRefPubMedPubMedCentral

19.

Paysan-Lafosse T, Blum M, Chuguransky S, Grego T, Pinto BL et al (2023) InterPro in 2022. Nucleic Acids Res 51:D418–D427. https://doi.org/10.1093/nar/gkac993CrossRefPubMed

20.

Theis C, Reeder J, Giegerich R (2008) KnotInFrame: prediction of -1 ribosomal frameshift events. Nucleic Acids Res 36:6013–6020. https://doi.org/10.1093/nar/gkn578CrossRefPubMedPubMedCentral

21.

Knierim D, Tsai WS, Deng TC, Green SK, Kenyon L (2013) Full-length genome sequences of four polerovirus isolates infecting cucurbits in Taiwan determined from total RNA extracted from field samples. Plant Pathol 62:633–641. https://doi.org/10.1111/j.1365-3059.2012.02653.xCrossRef

22.

Bergkessel M, Guthrie C (2013) Colony PCR. Methods in enzymology, vol 529. Academic, Cambridge, MA, pp 299–309CrossRef

23.

Pazhouhandeh M, Dieterle M, Marrocco K, Lechner E, Berry B, Brault V, Hemmer O, Kretsch T, Richards KE, Genschik P, Ziegler-Graff V (2006) F-box-like domain in the polerovirus protein P0 is required for silencing suppressor function. P Natl Acad Sci USA 103:1994–1999. https://doi.org/10.1073/pnas.0510784103CrossRef

24.

Pfeffer S, Dunoyer P, Heim F, Richards KE, Jonard G, Ziegler-Graff V (2002) P0 of beet Western yellows virus is a suppressor of posttranscriptional gene silencing. J Virol 76:6815–6824. https://doi.org/10.1128/jvi.76.13.6815-6824.2002CrossRefPubMedPubMedCentral

25.

Nickel H, Kawchuk L, Twyman RM, Zimmermann S, Junghans H, Winter S, Fischer R, Prüfer D (2008) Plantibody-mediated inhibition of the Potato leafroll virus P1 protein reduces virus accumulation. Virus Res 136:140–145. https://doi.org/10.1016/j.virusres.2008.05.001CrossRefPubMed

26.

Miller WA, Liu S, Beckett R (2002) Barley yellow dwarf virus: Luteoviridae or Tombusviridae? Mol Plant Pathol 3:177–183. https://doi.org/10.1046/j.1364-3703.2002.00112.xCrossRefPubMed

27.

Miller WA, Dinesh-Kumar SP, Paul CP (1995) Luteovirus gene expression. CRC Crit Rev Plant Sci 14:179–211. https://doi.org/10.1080/07352689509701926CrossRef

28.

Kamer G, Argos P (1984) Primary structural comparison of RNA-dependent polymerases from plant, animal and bacterial viruses. Nucleic Acids Res 12:7269–7282. https://doi.org/10.1093/nar/12.18.7269CrossRefPubMedPubMedCentral

29.

Smirnova E, Firth AE, Miller WA, Scheidecker D, Brault V, Reinbold C, Rakotondrafara AM, Chung BY, Ziegler-Graff V (2015) Discovery of a small non-AUG-initiated ORF in poleroviruses and luteoviruses that is required for long-distance movement. PLoS Pathog 11:e1004868. https://doi.org/10.1371/journal.ppat.1004868CrossRefPubMedPubMedCentral

30.

Tacke E, Schmitz J, Prüfer D, Rohde W (1993) Mutational analysis of the nucleic acid- binding 17 kDa phosphoprotein of potato leaf- roll luteovirus identifies an amphipathic alpha- helix as the domain for protein/protein interactions. Virology 197:274–282. https://doi.org/10.1006/viro.1993.1588CrossRefPubMed

31.

Hwang YT, Kalischuk M, Fusaro AF, Waterhouse PM, Kawchuk L (2013) Small RNA sequencing of Potato leafroll virus-infected plants reveals an additional subgenomic RNA encoding a sequence-specific RNA-binding protein. Virology 438:61–69. https://doi.org/10.1016/j.virol.2012.12.012CrossRefPubMed

32.

Domier LL (2012) Family Luteoviridae. In: King AMQ, Adams MJ, Carstens EB, Lefkowitz EJ (eds) Virus taxonomy, ninth report of the international committee on taxonomy of viruses. Elsevier/Academic, London, pp 1045–1053

33.

Ullah I, Kamran M, Dunwell JM (2023) Identification of a novel polerovirus in cocoa (Theobroma cacao) germplasm and development of molecular methods for use in diagnostics. Pathogens 12:1284. https://doi.org/10.3390/pathogens12111284CrossRefPubMedPubMedCentral

Titel: Complete genome characterization of cacao leafroll virus, a newly described cacao-infecting polerovirus
verfasst von: Raphael O. Adegbola
Cory V. Keith
Osman Gutierrez
Ricardo Goenaga
Judith K. Brown
Publikationsdatum: 01.04.2024
Verlag: Springer Vienna
Erschienen in: Archives of Virology / Ausgabe 4/2024
Print ISSN: 0304-8608
Elektronische ISSN: 1432-8798
DOI: https://doi.org/10.1007/s00705-024-06013-7

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Complete genome characterization of cacao leafroll virus, a newly described cacao-infecting polerovirus

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