Archives of Virology

, Volume 162, Issue 2, pp 555–559 | Cite as

Identification of a novel mycovirus isolated from Rhizoctonia solani (AG 2-2 IV) provides further information about genome plasticity within the order Tymovirales

  • Anika Bartholomäus
  • Daniel Wibberg
  • Anika Winkler
  • Alfred Pühler
  • Andreas Schlüter
  • Mark Varrelmann
Annotated Sequence Record


The complete genome of a novel mycovirus, named Rhizoctonia solani flexivirus 1 (RsFV-1), which infects an avirulent strain of Rhizoctonia solani AG 2-2 IV, was sequenced and analyzed. Its RNA genome consists of 10,621 nucleotides, excluding the poly-A tail, and encodes a single protein of 3477 amino acids. The identification of conserved motifs of methyltransferase, helicase and RNA-dependent RNA polymerase revealed its relatedness to members of the alphavirus-like superfamily of positive-strand RNA viruses. Phylogenetic analysis of these fused domains suggested that this virus should be assigned to the order Tymovirales. The recently described Fusarium graminearum deltaflexivirus 1 was found to be its closest relative. However, the whole genome, as well as the encoded protein of RsFV-1, is larger than that of other known members of the order Tymovirales, and unlike all other viruses belonging to this order, its methyltransferase domain is not located at the N-terminus of the replicase. Although genome diversity, as a result of recombination and gene loss, is a well-documented trait in members of the order Tymovirales, no related virus with a comparable genome alteration has been reported before. For these reasons, RsFV-1 broadens our perception about genome plasticity and diversity within the order Tymovirales.


Sugar Beet Herpes Simplex Virus Type Graminearum Helicase Domain Genome Plasticity 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.


Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

This study did not include experiments with human participants or animals performed by any of the authors.

Supplementary material

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Supplementary material 1 (PDF 177 kb)
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Supplementary material 2 (PDF 183 kb)
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Supplementary material 3 (PDF 103 kb)
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Supplementary material 4 (PDF 16 kb)
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Supplementary material 5 (PDF 24 kb)


  1. 1.
    Cubeta MA, Vilgalys R (1997) Population biology of the Rhizoctonia solani complex. Phytopathol 87:480–484CrossRefGoogle Scholar
  2. 2.
    Bharathan N, Tavantzis SM (1990) Genetic diversity of double-stranded RNA from Rhizoctonia solani. Phytopathol 80:631–635CrossRefGoogle Scholar
  3. 3.
    Bharathan N et al (2005) Double-stranded RNA: distribution and analysis among isolates of Rhizoctonia solani AG-2 to-13. Plant Pathol 54:196–203CrossRefGoogle Scholar
  4. 4.
    Zanzinger DH, Bandy BP, Tavantzis SM (1984) High frequency of finding double-stranded RNA in naturally occurring isolates of Rhizoctonia solani. J Gen Virol 65:1601–1605CrossRefGoogle Scholar
  5. 5.
    Lakshman DK, Jian J, Tavantzis SM (1998) A double-stranded RNA element from a hypovirulent strain of Rhizoctonia solani occurs in DNA form and is genetically related to the pentafunctional AROM protein of the shikimate pathway. Microbiol 95:6425–6429Google Scholar
  6. 6.
    Strauss EE, Lakshman DK, Tavantzis SM (2000) Molecular characterization of the genome of a partitivirus from the basidiomycete Rhizoctonia solani. J Gen Virol 81:549–555CrossRefPubMedGoogle Scholar
  7. 7.
    Li et al (2014) Complete genome sequence of a novel endornavirus in the wheat sharp eyespot pathogen Rhizoctonia cerealis. Arch Virol 159:1213–1216CrossRefPubMedGoogle Scholar
  8. 8.
    Zheng et al (2014) A novel mycovirus closely related to viruses in the genus Alphapartitivirus confers hypovirulence in the phytopathogenic fungus Rhizoctonia solani. Virol 456:220–226CrossRefGoogle Scholar
  9. 9.
    Zheng et al (2013) The complete genomic sequence of a novel mycovirus from Rhizoctonia solani AG-1 IA strain B275. Arch Virol 158:1609–1612CrossRefPubMedGoogle Scholar
  10. 10.
    Li et al (2015) Molecular characterization of a novel mycovirus from Rhizoctonia fumigata AG-Ba isolate C-314 Baishi. Arch Virology 160:2371–2374CrossRefGoogle Scholar
  11. 11.
    Zhong J, Chen CY, Gao BD (2015) Genome sequence of a novel mycovirus of Rhizoctonia solani, a plant pathogenic fungus. Virus Genes 51:167–170CrossRefPubMedGoogle Scholar
  12. 12.
    Marzano et al (2016) Identification of diverse mycoviruses through metatranscriptomics characterization of the viromes of five major fungal plant pathogens. J Virol. doi: 10.1128/JVI.00357-16 PubMedPubMedCentralGoogle Scholar
  13. 13.
    King AMQ, Adams MJ, Carstens EB, Lefkowitz EJ (2012) Virus taxonomy: classification and nomenclature of viruses. 9th report of the international committee of taxonomy of viruses. Elsevier Academic Press, San Diego, pp 920–941Google Scholar
  14. 14.
    Howitt RL, Beever RE, Pearson MN, Forster RL (2001) Genome characterization of Botrytis virus F, a flexuous rod-shaped mycovirus resembling plant ‘potex-like’viruses. J Gen Virol 82:67–78CrossRefPubMedGoogle Scholar
  15. 15.
    Howitt RL, Beever RE, Pearson MN, Forster RL (2006) Genome characterization of a flexuous rod-shaped mycovirus, Botrytis virus X, reveals high amino acid identity to genes from plant ‘potex-like’viruses. Arch Virol 151:563–579CrossRefPubMedGoogle Scholar
  16. 16.
    Xie et al (2006) Characterization of debilitation-associated mycovirus infecting the plant-pathogenic fungus Sclerotinia sclerotiorum. J Gen Virol 87:241–249CrossRefPubMedGoogle Scholar
  17. 17.
    Valverde RA, Nameth ST, Jordan RL (1990) Analysis of double-stranded RNA for plant virus diagnosis. Plant Dis 74:255–258CrossRefGoogle Scholar
  18. 18.
    Froussard P (1992) A random-PCR method (rPCR) to construct whole cDNA library from low amounts of RNA. Nucleic Acids Res 20:2900CrossRefPubMedPubMedCentralGoogle Scholar
  19. 19.
    Wibberg D et al (2011) Complete genome sequencing of Agrobacterium sp. H13-3, the former Rhizobium lupini H13-3, reveals a tripartite genome consisting of a circular and a linear chromosome and an accessory plasmid but lacking a tumor-inducing Ti-plasmid. J Biotechnol 155:50–62CrossRefPubMedGoogle Scholar
  20. 20.
    Tamura et al (2013) MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 30:2725–2729CrossRefPubMedPubMedCentralGoogle Scholar
  21. 21.
    Martelli GP, Adams MJ, Kreuze JF, Dolja VV (2007) Family Flexiviridae: a case study in virion and genome plasticity. Phytopathol 45:73–100CrossRefGoogle Scholar
  22. 22.
    Balance DJ (1990) Transformation systems for filamentous fungi and an overview of fungal gene structure. Molecular industrial mycology. Dekker, New York, pp 1–29Google Scholar
  23. 23.
    Van der Heijden MW, Bol JF (2002) Composition of alphavirus-like replication complexes: involvement of virus and host encoded proteins. Arch Virol 147:875–898CrossRefPubMedGoogle Scholar
  24. 24.
    Koonin EV, Dolja VV, Morris TJ (1993) Evolution and taxonomy of positive-strand RNA viruses: implications of comparative analysis of amino acid sequences. Critical Rev Biochem Mol Biol 28:375–430CrossRefGoogle Scholar
  25. 25.
    Dolja VV, Koonin EV (2012) Capsid-Less RNA Viruses. eLS. doi: 10.1002/9780470015902.a0023269 Google Scholar
  26. 26.
    Dolja VV, Kreuze JF, Valkonen JP (2006) Comparative and functional genomics of closteroviruses. Virus Res 117:38–51CrossRefPubMedGoogle Scholar
  27. 27.
    Lombardi C et al (2013) A compact viral processing proteinase/ubiquitin hydrolase from the OTU family. PLoS Pathog 9:e1003560CrossRefPubMedPubMedCentralGoogle Scholar
  28. 28.
    Lawrence DM, Rozanov MN, Hillman BI (1995) Autocatalytic processing of the 223-kDa protein of blueberry scorch carlavirus by a papain-like proteinase. Virol 207:127–135CrossRefGoogle Scholar
  29. 29.
    Fan WH et al (2015) The large tegument protein pUL36 is essential for formation of the capsid vertex-specific component at the capsid-tegument interface of herpes simplex virus 1. J Virol 89:1502–1511CrossRefPubMedGoogle Scholar
  30. 30.
    Schipke J et al (2012) The C terminus of the large tegument protein pUL36 contains multiple capsid binding sites that function differently during assembly and cell entry of herpes simplex virus. J Virol 86:3682–3700CrossRefPubMedPubMedCentralGoogle Scholar
  31. 31.
    Li K et al (2015) Characterization of a novel Sclerotinia sclerotiorum RNA virus as the prototype of a new proposed family within the order Tymovirales. Virus Res 219:92–99CrossRefPubMedGoogle Scholar

Copyright information

© Springer-Verlag Wien 2016

Authors and Affiliations

  1. 1.Institute of Sugar Beet ResearchGöttingenGermany
  2. 2.Institute for Genome Research and Systems Biology, CeBiTec, Bielefeld UniversityBielefeldGermany

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