Complete genome sequence of ornithogalum virus 3


Ornithogalum thyrsoides, a widely cultivated bulbous ornamental plant endemic to South Africa, has significant commercial value as a pot plant and for the production of cut flowers. However, infection by viruses threatens the success of commercial cultivation, as symptoms negatively affect the appearance of the plant and flowers. To date, four Ornithogalum-infecting viruses have been reported. Complete genome sequence data are available for three of these viruses, but the genome of the potyvirus ornithogalum virus 3 (OV3) has not been fully sequenced. In this study, the complete sequence of OV3 was determined by high-throughput sequencing (HTS) and validated by Sanger sequencing. Based on recognition of protease cleavage patterns and multiple sequence alignments with closely related viruses, the polyprotein of OV3 was predicted to be proteolytically cleaved to produce 10 mature peptides containing domains conserved in members of the genus Potyvirus. Phylogenetic analysis and species demarcation criteria confirm the previous classification of OV3 as a member of a separate species in this genus. This is the first report of a complete genome sequence of OV3.

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  1. 1.

    Bodkin F (1986) Encyclopaedia botanica: the essential reference guide to native and exotic plants in Australia. Angus & Robertson, Sydney

    Google Scholar 

  2. 2.

    Mostert I, Visser M, Gazendam I et al (2020) Complete genome sequence of a novel polerovirus in Ornithogalum thyrsoides from South Africa. Arch Virol 165:483–486.

    CAS  Article  PubMed  Google Scholar 

  3. 3.

    Burger JT, von Wechmar MB (1989) Purification and some properties of South African isolates of Ornithogalum mosaic virus. Phytopathology 79:385–391.

    Article  Google Scholar 

  4. 4.

    Matsumoto T, Yamamoto H, Fuji S, Inoue M (2007) Isolation and characterization of a novel potyvirus tentatively named Ornithogalum virus 2. J Gen Plant Pathol 73:222–224.

    CAS  Article  Google Scholar 

  5. 5.

    Matsumoto T, Yamamoto H, Fuji S, Inoue M (2008) Characterization of a novel potyvirus tentatively named Ornithogalum virus 3, successfully isolated from O. thyrsoides co-infected with two other potyviruses by single-aphid inoculation. J Gen Plant Pathol 74:76–80.

    CAS  Article  Google Scholar 

  6. 6.

    Adams M, Antoniw J, Beaudoin F (2005) Overview and analysis of the polyprotein cleavage sites in the family Potyviridae. Mol Plant Pathol 6:471–487.

    CAS  Article  PubMed  Google Scholar 

  7. 7.

    Chung BYW, Miller WA, Atkins JF, Firth AE (2008) An overlapping essential gene in the Potyviridae. Proc Natl Acad Sci USA 105:5897–5902.

    CAS  Article  PubMed  Google Scholar 

  8. 8.

    Shiboleth YM, Haronsky E, Leibman D et al (2007) The conserved FRNK box in HC-Pro, a plant viral suppressor of gene silencing, is required for small RNA binding and mediates symptom development. J Virol 81:13135–13148.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  9. 9.

    Revers F, García JA (2015) Chapter three—molecular biology of potyviruses. In: Maramorosch K, Mettenleiter TC (eds) Advances in virus research. Academic Press, pp 101–199

  10. 10.

    Atreya CD, Raccah B, Pirone TP (1990) A point mutation in the coat protein abolishes aphid transmissibility of a potyvirus. Virology 178:161–165.

    CAS  Article  PubMed  Google Scholar 

  11. 11.

    Katoh K, Standley DM (2013) MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol 30:772–780.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  12. 12.

    Kumar S, Stecher G, Li M et al (2018) MEGA X: molecular evolutionary genetics analysis across computing platforms. MolBiolEvol 35:1547–1549.

    CAS  Article  Google Scholar 

  13. 13.

    Adams MJ, Antoniw JF, Fauquet CM (2005) Molecular criteria for genus and species discrimination within the family Potyviridae. Arch Virol 150:459–479.

    CAS  Article  PubMed  Google Scholar 

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All authors contributed to the study conception and design. Material preparation, data collection and analysis were performed by Rachelle Bester, Ilani Mostert, Dirk Aldrich, and Marike Visser. The first draft of the manuscript was written by Ilani Mostert, and all authors commented on previous versions of the manuscript. All authors read and approved the final manuscript.

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Correspondence to H. J. Maree.

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Mostert, I., Bester, R., Aldrich, D. et al. Complete genome sequence of ornithogalum virus 3. Arch Virol 166, 1213–1216 (2021).

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