Complete genome sequence of rose virus A, the first carlavirus identified in rose

  • Alfredo Diaz-Lara
  • Dimitre Mollov
  • Deborah Golino
  • Maher Al RwahnihEmail author
Annotated Sequence Record


A novel virus was discovered in a Rosa wichuraiana Crep. by high-throughput sequencing and tentatively named “rose virus A” (RVA). Based on sequence identity and phylogenetic analysis, RVA represents a new member of the genus Carlavirus (family Betaflexiviridae). The genome of RVA is 8,849 nucleotides long excluding the poly(A) tail and contains six open reading frames (ORFs). The predicted ORFs code for a replicase, triple gene block (TGB), coat protein, and nucleic acid binding protein, as in a typical carlavirus. RVA is the first carlavirus identified in rose and has the highest nucleotide sequence similarity to poplar mosaic virus. Reverse transcription-PCR-based assays were developed to confirm the presence of RVA in the original source and to screen additional rose plants.



Many thanks to Min Sook Hwang and Kristian Stevens (UC-Davis, Foundation Plant Services) for technical assistance.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Ethical approval

This article does not contain any studies with human participants or animal performed by any of the authors.


  1. 1.
    Goody J (1993) The culture of flowers. Cambridge University Press Archive, Cambridge, pp 462Google Scholar
  2. 2.
    Heinrichs F (2008) International statistics flowers and plants. Institut für Gartenbauökonomie der Universität Hannover, vol 57Google Scholar
  3. 3.
    Mollov D, Lockhart B, Zlesak D (2013) Complete nucleotide sequence of rose yellow mosaic virus, a novel member of the family Potyviridae. Arch Virol 158:1917–1923. CrossRefPubMedGoogle Scholar
  4. 4.
    Lockhart B, Zlesak D, Fetzer J (2008) Identification and partial characterization of six new viruses of cultivated roses in the USA. In: XII International symposium on virus diseases of ornamental plants, vol 901, pp 139–147Google Scholar
  5. 5.
    Adams MJ, Antoniw JF, Bar-Joseph M et al (2004) Virology Division News: the new plant virus family Flexiviridae and assessment of molecular criteria for species demarcation. Arch Virol 149:1045–1060. CrossRefPubMedGoogle Scholar
  6. 6.
    Naidu RA, Gowda S, Satyanarayana T et al (1998) Evidence that whitefly-transmitted cowpea mild mottle virus belongs to the genus Carlavirus. Arch Virol 143:769–780. CrossRefPubMedGoogle Scholar
  7. 7.
    Bristow PR, Martin RR, Windom GE (2000) Transmission, field spread, cultivar response, and impact on yield in highbush blueberry infected with blueberry scorch virus. Phytopathology 90:474–479. CrossRefPubMedGoogle Scholar
  8. 8.
    Bankevich A, Nurk S, Antipov D et al (2012) SPAdes: a new genome assembly algorithm and Its applications to single-cell sequencing. J Comput Biol 19:455–477. CrossRefPubMedPubMedCentralGoogle Scholar
  9. 9.
    Stothard P (2000) The sequence manipulation suite: JavaScript programs for analyzing and formatting protein and DNA sequences. BioTechniques 28(6):1102–1104CrossRefGoogle Scholar
  10. 10.
    Marchler-Bauer A, Bo Y, Han L et al (2016) CDD/SPARCLE: functional classification of proteins via subfamily domain architectures. Nucleic Acids Res 45:D200–D203CrossRefGoogle Scholar
  11. 11.
    Gasteiger E, Hoogland C, Gattiker A et al (2005) Protein identification and analysis tools on the ExPASy server. The proteomics protocols handbook. Springer, New York, pp 571–607CrossRefGoogle Scholar
  12. 12.
    Kumar S, Stecher G, Li M et al (2018) MEGA X: molecular evolutionary genetics analysis across computing platforms. Mol Biol Evol 35:1547–1549. CrossRefPubMedPubMedCentralGoogle Scholar
  13. 13.
    King AM, Lefkowitz E, Adams MJ, Carstens EB (2011) Virus taxonomy: ninth report of the international committee on taxonomy of viruses. Elsevier, AmsterdamGoogle Scholar
  14. 14.
    Wang R, Dong J, Wang Z et al (2018) Complete nucleotide sequence of a new carlavirus in chrysanthemums in China. Arch Virol 163:1973–1976. CrossRefPubMedGoogle Scholar
  15. 15.
    Zhao X, Liu X, Ge B et al (2015) A multiplex RT-PCR for simultaneous detection and identification of five viruses and two viroids infecting chrysanthemum. Arch Virol 160:1145–1152. CrossRefPubMedGoogle Scholar
  16. 16.
    Choi SA, Ryu KH (2003) The complete nucleotide sequence of the genome RNA of lily symptomless virus and its comparison with that of other carlaviruses. Arch Virol 148:1943–1955. CrossRefPubMedGoogle Scholar
  17. 17.
    Cohen J, Zeidan M, Feigelson L et al (2003) Characterization of a distinct carlavirus isolated from Verbena. Arch Virol 148:1007–1015. CrossRefPubMedGoogle Scholar

Copyright information

© Springer-Verlag GmbH Austria, part of Springer Nature 2019

Authors and Affiliations

  1. 1.Department of Plant PathologyUniversity of California-DavisDavisUSA
  2. 2.USDA-ARS, National Germplasm Resources LaboratoryBeltsvilleUSA

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