Advertisement

Archives of Virology

, Volume 163, Issue 3, pp 771–776 | Cite as

Characterization of a novel single-stranded RNA mycovirus related to invertebrate viruses from the plant pathogen Verticillium dahliae

  • M. Carmen Cañizares
  • Francisco J. López-Escudero
  • Encarnación Pérez-Artés
  • María D. García-Pedrajas
Annotated Sequence Record

Abstract

Fungal viruses, also known as mycoviruses, are widespread in all major groups of fungi. Mycoviruses from plant pathogens can reduce the virulence of their host fungus and have therefore potential as biological control agents. This has spurred the identification of novel mycoviruses in plant pathogens, research which is greatly contributing to our understanding of these organisms. In this work, we report the characterization of a novel monopartite mycovirus from Verticillium dahliae, the main causal agent of Verticillium wilt. This novel mycovirus, which we termed Verticillium dahliae RNA virus 1 (VdRV1), was identified in three different isolates of V. dahliae collected in olive growing areas of the Guadalquivir valley, southern Spain. We determined that the VdRV1 genome is a positive (+) single-stranded (ss) RNA, 2631 nucleotides in length, containing two open reading frames. VdRV1 showed few similarities with known mycoviruses, only with a group of unassigned (+) ssRNA mycoviruses which are related to plant viruses classified within the family Tombusviridae. However, phylogenetic analysis revealed that VdRV1 and the unassigned (+) ssRNA mycoviruses have a closer relationship with recently reported invertebrate viruses. This result indicates that as more viral sequences become available, the relationships of mycoviruses with viruses from other hosts should be reexamined. Additionally, the work supports the hypothesis of a heterogeneous origin for mycoviruses.

Notes

Acknowledgements

This research was supported by Grants AGL2013-48980-R and AGL2016-80048-R from the Spanish Ministry of Economy and Competitiveness, co-funded by the European Union (FEDER funds). The authors would like to thank Dr Scott E. Gold for his editorial review of this manuscript.

Compliance with ethical standards

Funding

Financial support for this study was provided by the Spanish Ministry of Economy and Competitiveness through Grants AGL2013-48980-R and AGL2016-80048-R, co-funded by the European Union (FEDER funds).

Conflict of interest

The authors declare no conflict of interest.

Ethical approval

This article does not contain any studies of animals performed by any of the authors.

Supplementary material

705_2017_3644_MOESM1_ESM.pptx (48 kb)
Supplementary Figure 1: Identification of two putative transmembrane domains at the N-terminus of the VdRV1 ORF1-encoded protein using the TMHMM Server v. 2.0 program. (PPTX 47 kb)
705_2017_3644_MOESM2_ESM.pptx (209 kb)
Supplementary Figure 2: Multiple amino acid sequence alignment of the RdRp encoded by the three variants of VdVR1 and similar RdRps from other viruses. The horizontal lines above the amino acid areas define the conserved motifs. The red square box highlights a GDN domain which is unusual in other RdRps from (+) ssRNA viruses but rather found in non-segmented (-) stranded RNA viruses. Black shading indicates identical or similar amino acid residues in all RdRp sequences included, dark grey shading indicates a conservation of residues below 100% and above 80%, and light grey below 80% and above 60%. Numbers in brackets correspond to the number of amino acid residues separating the motifs. The abbreviations of the virus names are as follows: DaRV1, Diaporthe ambigua RNA virus 1; MoVA, Magnaporthe oryzae virus A; MpSRV3, Macrophomina phaseolina single-stranded RNA virus 3; SLaSSRV1, Soybean leaf-associated ssRNA virus 1; SLaSSRV2, soybean leaf-associated ssRNA virus 2; SLaSSRV3, soybean leaf-associated ssRNA virus; SsULV1, Sclerotinia sclerotiorum umbra-like virus 1; TBSV, tomato bushy stunt virus; VdRV1, Verticillium dahliae RNA virus 1. (PPTX 209 kb)
705_2017_3644_MOESM3_ESM.pptx (90 kb)
Supplementary Figure 3: The RdRps of VdVR1 and related mycoviruses and invertebrate viruses contain unique motifs highly conserved in the RdRps of the plant tombusviruses. Black shading indicates identical or similar amino acid residues in all RdRp sequences included, dark grey shading indicates a conservation of residues below 100% and above 80%, and light grey shading indicates below 80% and above 60%. (PPTX 90 kb)
705_2017_3644_MOESM4_ESM.pptx (42 kb)
Supplementary Figure 4: Predicted secondary structure of the VdVR1 5’ and 3’ UTRs. Secondary structures of the 29 nucleotide 5’ UTR and the 181 nucleotide 3’ UTR were predicted using the mfold program. (PPTX 42 kb)
705_2017_3644_MOESM5_ESM.docx (14 kb)
Supplementary material 5 (DOCX 14 kb)

References

  1. 1.
    Ghabrial SA, Suzuki N (2009) Viruses of plant pathogenic fungi. Annu Rev Phytopathol 47:353–384CrossRefPubMedGoogle Scholar
  2. 2.
    Pearson MN, Beever RF, Boine B, Arthur K (2009) Mycoviruses of filamentous fungi and their relevance to plant pathology. Mol Plant Pathol 10:115–128CrossRefPubMedGoogle Scholar
  3. 3.
    Donaire L, Pagán I, Ayllón MA (2016) Characterization of Botrytis cinerea negative-stranded RNA virus 1, a new mycovirus related to plant viruses, and a reconstruction of host pattern evolution in negative-sense ssRNA viruses. Virology 499:212–218CrossRefPubMedGoogle Scholar
  4. 4.
    Du Z, Tang Y, Zhang S, Xhe X, Lan G, Varsani A, He Z (2014) Identification and molecular characterization of a single-stranded circular DNA virus with similarities to Sclerotinia sclerotiorum hypovirulence-associated DNA virus 1. Arch Virol 159:1527–1531CrossRefPubMedGoogle Scholar
  5. 5.
    Kondo H, Chiba S, Toyoda K, Suzuki N (2013) Evidence for negative-strand RNA virus infection in fungi. Virology 435:201–209CrossRefPubMedGoogle Scholar
  6. 6.
    Liu L, Xie J, Cheng J, Fu Y, Li G, Yi X, Jiang D (2014) Fungal negative-stranded RNA virus that is related to bornaviruses and nyaviruses. Proc Natl Acad Sci USA 111:12205–12210CrossRefPubMedPubMedCentralGoogle Scholar
  7. 7.
    Marzano S-YL, Dormier LL (2016) Novel mycoviruses discovered from metatranscriptomics survey of soybean phyllosphere phytobiomas. Virus Res 213:332–342CrossRefPubMedGoogle Scholar
  8. 8.
    Marzano S-YL, Nelson BD, Ajayi-Oyetunde O, Bradley CA, Hughes TH, Hartman GL, Eastburn DM, Dormier LL (2016) Identification of diverse mycoviruses through metatranscriptomics characterization of the viromes of five major fungal plant pathogens. J Virol 90:6846–6863CrossRefPubMedPubMedCentralGoogle Scholar
  9. 9.
    Yu X, Li B, Fu Y, Jian D, Ghabrial SA, Li G, Peng Y, Xie J, Cheng J, Huang J, Yi X (2010) A geminivirus-related DNA mycovirus that confers hypovirulence to a plant pathogenic fungus. Proc Natl Acad Sci USA 107:8387–8392CrossRefPubMedPubMedCentralGoogle Scholar
  10. 10.
    Mokili JL, Rohwer F, Dutilh BE (2012) Metagenomics and future perspectives in virus discovery. Curr Opin Virol 2:63–77CrossRefPubMedGoogle Scholar
  11. 11.
    Li C-X, Shi M, Tian J-H, Lin X-D, Kang Y-J, Chen L-J, Qin X-C, Xu J, Holmes EC, Zhang Y-Z (2015) Unprecedent genomic diversity of RNA viruses in arthropods reveals the ancestry of negative-sense RNA viruses. eLIFE 4:e05378PubMedCentralGoogle Scholar
  12. 12.
    Shi M, Lin X-D, Tian J-H, Chen L-J, Chen X, Li C-X, Qin X-C, Li J, Cao J-P, Eden J-S, Buchmann J, Wang W, Xu J, Holmes EC, Zhang Y-Z (2016) Redefining the invertebrate RNA virosphere. Nature 540:539–543CrossRefGoogle Scholar
  13. 13.
    Xie J, Jiang D (2014) New insights into the mycoviruses and exploration for the biological control of crop fungal diseases. Annu Rev Phytopathol 52:45–68CrossRefPubMedGoogle Scholar
  14. 14.
    Klosterman SJ, Atallah ZK, Vallad GE, Subbarao KV (2009) Diversity, pathogenicity, and management of Verticillium species. Annu Rev Phytopathol 47:39–62CrossRefPubMedGoogle Scholar
  15. 15.
    Pegg GF, Brady BI (2002) Verticillium wilts. C.A.B. International, OxfordCrossRefGoogle Scholar
  16. 16.
    Cao Y-F, Zhu X-W, Xiang Y, Li D-G, Yang J-R, Mao Q-Z, Chen J-S (2011) Genomic characterization of a novel dsRNA virus detected in the phytopathogenic fungus Verticillium dahliae Kleb. Virus Res 159:73–78CrossRefPubMedGoogle Scholar
  17. 17.
    Feng Z, Zhu H, Li Z, Shi Y, Zhao L, Liu L, Jiang D (2013) Complete genome sequence of a novel dsRNA mycovirus isolated from the phytopathogenic fungus Verticillium dahliae Kleb. Arch Virol 158:2621–2623CrossRefPubMedGoogle Scholar
  18. 18.
    Cañizares MC, Pérez-Artés E, García-Pedrajas NE, García-Pedrajas MD (2015) Characterization of a new partitivirus strain in Verticillium dahliae provides further evidence of the spread of the highly virulent defoliating pathotype through new introductions. Phytopathol Mediterr 54:423–516Google Scholar
  19. 19.
    Pérez-Artés E, García-Pedrajas MD, Bejarano-Alcázar J, Jiménez-Díaz RM (2000) Differentiation of cotton-defoliating and nondefoliating pathotypes of Verticillium dahliae by RAPD and specific PCR analysis. Eur J Plant Pathol 106:507–517CrossRefGoogle Scholar
  20. 20.
    López-Escudero FJ, Blanco-López MA (2005) Isolation and morphologic characterization of microsclerotia of Verticillium dahliae isolates from soil. Biotechnology 4:296–304CrossRefGoogle Scholar
  21. 21.
    Morris TJ, Dodds JA (1979) Isolation and analysis of double-stranded RNA from virus-infected plant and fungal tissue. Phytopathology 69:855–858CrossRefGoogle Scholar
  22. 22.
    Cañizares MC, Pérez-Artés E, García-Pedrajas MD (2014) The complete nucleotide sequence of a novel partitivirus isolated from the plant pathogenic fungus Verticillium albo-atrum. Arch Virol 159:3141–3144CrossRefPubMedGoogle Scholar
  23. 23.
    Xie J, Wei D, Jiang D, Fu Y, Li G, Ghabrial S, Peng Y (2006) Characterization of debilitation-associated mycovirus infecting the plant-pathogenic fungus Sclerotinia sclerotiorum. J Gen Virol 87:241–249CrossRefPubMedGoogle Scholar
  24. 24.
    Ai Y-P, Zhong J, Chen C-Y, Zhu H-J, Gao B-D (2016) A novel single-stranded RNA virus isolated from the rice pathogenic fungus Magnaporthe oryzae with similarity to members of the family Tombusviridae. Arch Virol 161:725–729CrossRefPubMedGoogle Scholar
  25. 25.
    Preisig O, Moleleki N, Smit WA, Wingfield BD, Wingfield MJ (2000) A novel RNA mycovirus in a hypovirulent isolate of the plant pathogen Diaporthe ambigua. J Gen Virol 81:3107–3114CrossRefPubMedGoogle Scholar
  26. 26.
    Gunawardene CD, Donaldson LW, White KA (2017) Tombusvirus polymerase: structure and function. Virus Res 234:74–86CrossRefPubMedGoogle Scholar
  27. 27.
    Bruenn JA (2003) A structural and primary sequence comparison of the viral RNA-dependent RNA polymerases. Nucleic Acids Res 31(7):1821–1829CrossRefPubMedPubMedCentralGoogle Scholar
  28. 28.
    Zuker M (2003) Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res 31:3406–3415CrossRefPubMedPubMedCentralGoogle Scholar
  29. 29.
    Edgar R (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32:1792–1797CrossRefPubMedPubMedCentralGoogle Scholar
  30. 30.
    Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28:2731–2739CrossRefPubMedPubMedCentralGoogle Scholar
  31. 31.
    Ghabrial SA (1998) Origin, adaptation and evolutionary pathways of fungal viruses. Virus Genes 16:119–131CrossRefPubMedGoogle Scholar

Copyright information

© Springer-Verlag GmbH Austria, part of Springer Nature 2017

Authors and Affiliations

  1. 1.Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”-Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Estación Experimental “La Mayora”Algarrobo-CostaSpain
  2. 2.Departamento de AgronomíaUniversidad de CórdobaCórdobaSpain
  3. 3.Department of Crop ProtectionInstituto de Agricultura Sostenible, IAS-CSICCórdobaSpain

Personalised recommendations