A virome from ornamental flowers in an Australian rural town


Samples of leaves exhibiting symptoms resembling those caused by virus infection were collected from ornamental street flowers in a rural town in Western Australia. Thirty-seven leaf samples were collected from plants of iris, tulip, lily, daffodil, stock and grape hyacinth. Shotgun sequencing of cDNA derived from leaf samples was done, and analysis showed that about 6% of the sequences obtained were of viral origin. Assembly of virus-like sequences revealed complete or partial genome sequences of 13 virus isolates representing 11 virus species. Eight of the isolates were of potyviruses, one was of a macluravirus, three were of potexviruses, and one was of a bunya-like virus. The complete genome of an isolate originally classified as ornithogalum mosaic virus was genetically divergent and differed in polyprotein cleavage motifs, and we propose that this isolate represents a distinct species. The implications of importing to Australia live plant propagules infected with viruses are discussed.

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  1. 1.

    Morris TJ, Dodds JA (1979) Isolation and analysis of double-stranded RNA from virus-infected plant and fungal tissue. Phytopathol 69:854–858

    Article  CAS  Google Scholar 

  2. 2.

    Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215:403–410

    Article  CAS  Google Scholar 

  3. 3.

    Marchler-Bauer A, Bryant SH (2004) CD-Search: protein domain annotations on the fly. Nuc Acids Res 32(suppl2):327–331

    Article  CAS  Google Scholar 

  4. 4.

    Xin M, Cao M, Liu W, Ren Y, Zhou X, Wang X (2017) Two negative-strand RNA viruses identified in watermelon represent a novel clade in the order Bunyavirales. Front Microbiol 8:1

    Article  Google Scholar 

  5. 5.

    Navarro B, Minutolo M, De Stradis A, Palmisano F, Alioto D, Di Serio F (2018) The first phlebo-like virus infecting plants: a case study on the adaptation of negative-stranded RNA viruses to new hosts. Mol Plant Pathol 19:1075–1089

    Article  CAS  PubMed  Google Scholar 

  6. 6.

    Navarro B, Zicca S, Minutolo M, Saponari M, Alioto D, Di Serio F (2018) A negative-stranded RNA virus infecting citrus trees: the second member of a new genus within the order Bunyavirales. Front Microbiol 9:2340

    Article  PubMed Central  PubMed  Google Scholar 

  7. 7.

    Alexandre MAV, Duarte LM, Rodrigues LK, Ramos AF, Harakava R (2017) Hyacinth mosaic virus infecting Hyacinthus sp. plants in Brazil. Trop Plant Pathol 42:51–54

    Article  Google Scholar 

  8. 8.

    Pearson MN, Cohen D, Cowell SJ, Jones D, Blouin A, Lebas BSM et al (2009) A survey of viruses of flower bulbs in New Zealand. Aust Plant Pathol 38:305–309

    Article  Google Scholar 

  9. 9.

    Wylie SJ, Nouri S, Coutts BA, Jones MGK (2010) Narcissus late season yellows virus and Vallota speciosa virus found infecting domestic and wild populations of Narcissus species in Australia. Arch Virol 155:1171–1174

    Article  CAS  PubMed  Google Scholar 

  10. 10.

    Wylie SJ, Li H, Sivasithamparam K, Jones MGK (2014) Complete genome analysis of three isolates of narcissus late season yellows virus and two of narcissus yellow stripe virus: three species or one? Arch Virol 159:1521–1525

    Article  CAS  PubMed  Google Scholar 

  11. 11.

    Lin SQ, Shen JG, Gao FL, Cai W, Huang Z, Xie LY, Wu ZJ (2012) Complete genome sequence of narcissus late season yellows virus infecting Chinese narcissus in China. Arch Virol 157:1821–1824

    Article  CAS  PubMed  Google Scholar 

  12. 12.

    Wylie SJ, Luo H, Li H, Jones MGK (2012) Multiple polyadenylated RNA viruses detected in pooled cultivated and wild plant samples. Arch Virol 157:271–284

    Article  CAS  PubMed  Google Scholar 

  13. 13.

    Wylie SJ, Li H, Dixon KW, Richards H, Jones MGK (2013) Exotic and indigenous viruses infect wild populations and captive collections of temperate terrestrial orchids (Diuris species) in Australia. Virus Res 171:22–32

    Article  CAS  PubMed  Google Scholar 

  14. 14.

    Wylie SJ, Adams M, Chalam C, Kreuze J, López-Moya JJ, Ohshima K et al (2017) ICTV virus taxonomy profile: Potyviridae. J Gen Virol 98:352–354

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  15. 15.

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

    Article  CAS  PubMed  Google Scholar 

  16. 16.

    King AM, Lefkowitz E, Adams MJ, Carstens EB (2011) Virus taxonomy: ninth report of the international committee on taxonomy of viruses. Elsevier, Oxford

    Google Scholar 

  17. 17.

    Adams IP, Glover RH, Monger WA, Mumford R, Jackeviciene E, Navalinskiene M et al (2009) Next-generation sequencing and metagenomic analysis: a universal diagnostic tool in plant virology. Mol Plant Pathol 10:537–545

    Article  CAS  PubMed  Google Scholar 

  18. 18.

    Pecman A, Kutnjak D, Gutiérrez-Aguirre I, Adams I, Fox A, Boonham N et al (2017) Next generation sequencing for detection and discovery of plant viruses and viroids: comparison of two approaches. Front Microbiol 8:1998

    Article  PubMed Central  PubMed  Google Scholar 

  19. 19.

    Myers N, Mittermeier RA, Mittermeier CG, Da Fonseca GA, Kent J (2000) Biodiversity hotspots for conservation priorities. Nature 403:853

    Article  CAS  PubMed  Google Scholar 

  20. 20.

    Cho SY, Lim S, Kim H, Yi SI, Moon JS (2016) Complete genome sequence of Ornithogalum mosaic virus infecting Gladiolus spp. in South Korea. Genome Announc 4:e00816-16

    Article  PubMed Central  PubMed  Google Scholar 

  21. 21.

    Rott ME, Kesanakurti P, Berwarth C, Rast H, Boyes I, Phelan J et al (2018) Discovery of negative-sense RNA viruses in trees infected with apple rubbery wood disease by next-generation sequencing. Plant Dis 102:1254–1263

    Article  CAS  PubMed  Google Scholar 

  22. 22.

    Wright AA, Szostek SA, Beaver-Kanuya E, Harper SJ (2018) Diversity of three bunya-like viruses infecting apple. Arch Virolm 163:3339–3343

    Article  CAS  Google Scholar 

  23. 23.

    Briese T, Alkhovsky S, Beer M, Calisher CH, Charrel R, Ebihara H, et al (2017) ICTV taxonomic proposal 2016.030 a-vM. A. v6. Bunyavirales. Create the order Bunyavirales, including eight new families, and one renamed family. https://talk.ictvonline.org/ICTV/proposals/2016.030a-vM.A.v6.Bunyavirales.pdf (accessed 10 Jan 2019)

  24. 24.

    Clarke SF, Burritt DJ, Jameson PE, Guy PL (1998) Influence of plant hormones on virus replication and pathogenesis-related proteins in Phaseolus vulgaris L. infected with white clover mosaic potexvirus. Physiol Mol Plant Pathol 53:195–207

    Article  CAS  Google Scholar 

  25. 25.

    Ellis MH, Rebetzke GJ, Mago R, Chu P (2003) First report of wheat streak mosaic virus in Australia. Austral Plant Pathol 32:551–553

    Article  Google Scholar 

  26. 26.

    Hailstones DL, Tesoriero LA, Terras MA, Dephoff C (2003) Detection and eradication of potato spindle tuber viroid in tomatoes in commercial production in New South Wales, Australia. Austral Plant Pathol 32:317–318

    Article  Google Scholar 

  27. 27.

    Rodoni B (2009) The role of plant biosecurity in preventing and controlling emerging plant virus disease epidemics. Virus Res 141:150–157

    Article  CAS  PubMed  Google Scholar 

  28. 28.

    Wylie SJ, Li H, Saqib M, Jones MGK (2014) The global trade in fresh produce and the vagility of plant viruses: a case study in garlic. PloS One 9:p.e105044

    Article  CAS  Google Scholar 

  29. 29.

    Koh SH, Li H, Admiraal R, Jones MGK, Wylie SJ (2015) Catharanthus mosaic virus: A potyvirus from a gymnosperm, Welwitschia mirabilis. Virus Res 203:41–46

    Article  CAS  PubMed  Google Scholar 

  30. 30.

    Tesoriero LA, Chambers G, Srivastava M, Smith S, Conde B, Tran-Nguyen LTT (2016) First report of cucumber green mottle mosaic virus in Australia. Austral Plant Dis Note 11:1

    Article  Google Scholar 

  31. 31.

    Koh SH, Li H, Sivasithamparam K, Admiraal R, Jones MGK, Wylie SJ (2017) Evolution of a wild-plant tobamovirus passaged through an exotic host: Fixation of mutations and increased replication. Virus Evolution 3:p.vex001. https://doi.org/10.1093/ve/vex001

    Article  Google Scholar 

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We acknowledge Mr. Steve Winfield, Head Gardener of the Shire of Nannup, Western Australia, for his assistance. Tran TT and Nguyen DQ each received a scholarship provided jointly by Vietnam International Education Development (VIED) and Murdoch University. Xu W received a scholarship provided jointly by Jiangsu Academy of Agricultural Sciences (JAAS) and Murdoch University.

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Wylie, S.J., Tran, T.T., Nguyen, D.Q. et al. A virome from ornamental flowers in an Australian rural town. Arch Virol 164, 2255–2263 (2019). https://doi.org/10.1007/s00705-019-04317-7

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