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

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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.

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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.

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Authors and Affiliations

  1. Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”-Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Estación Experimental “La Mayora”, 29750, Algarrobo-Costa, Málaga, Spain

    M. Carmen Cañizares & María D. García-Pedrajas

  2. Departamento de Agronomía, Universidad de Córdoba, Campus Universitario de Rabanales, Edificio Celestino Mutis (C4), 14071, Córdoba, Spain

    Francisco J. López-Escudero

  3. Department of Crop Protection, Instituto de Agricultura Sostenible, IAS-CSIC, Alameda del Obispo s/n. Apdo 4084, 14080, Córdoba, Spain

    Encarnación Pérez-Artés

Authors
  1. M. Carmen Cañizares
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  2. Francisco J. López-Escudero
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  3. Encarnación Pérez-Artés
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  4. María D. García-Pedrajas
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Corresponding authors

Correspondence to M. Carmen Cañizares or María D. García-Pedrajas.

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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.

Additional information

Handling Editor: Robert H.A. Coutts.

Electronic supplementary material

Below is the link to the electronic supplementary material.

705_2017_3644_MOESM1_ESM.pptx

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

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

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

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)

Supplementary material 5 (DOCX 14 kb)

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Cañizares, M.C., López-Escudero, F.J., Pérez-Artés, E. et al. Characterization of a novel single-stranded RNA mycovirus related to invertebrate viruses from the plant pathogen Verticillium dahliae . Arch Virol 163, 771–776 (2018). https://doi.org/10.1007/s00705-017-3644-2

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  • DOI: https://doi.org/10.1007/s00705-017-3644-2

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