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Novel circular DNA viruses associated with Apiaceae and Poaceae from South Africa and New Zealand

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Abstract

Advances in molecular techniques used in viral metagenomics coupled with high throughput sequencing is rapidly expanding our knowledge of plant-associated virus diversity. Applying such approaches, we have identified five novel circular replication-associated protein (Rep)-encoding single-stranded (CRESS) DNA viruses from Poaceae and Apiaceae plant from South Africa and New Zealand. These viruses have a simple genomic organization, including two open reading frames that likely encode a Rep and a capsid protein (CP), a conserved nonanucleotide motif on the apex of a putative stem loop structure, and conserved rolling-circle replication and helicase motifs within their likely Rep: all suggesting that they replicate through rolling-circle replication. The Reps and the CPs putatively encoded by these five novel viruses share low to moderate degrees of similarity (22.1 - 44.6%) with other CRESS DNA viruses.

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Acknowledgements

D.P.M., G.W.H. and A.V. have received research Grants from the National Research Foundation of South Africa. P.R. has received an EU Grant FP7-PEOPLE-2013-IOF (No. PIOF-GA-2013-622571). This work was supported by Direction Générale de l’Armement, MEM INRA Metaprogram, the Fondation pour la Recherche. GenBank Accession Numbers: MH425569–MH425573.

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Authors and Affiliations

  1. CIRAD, BGPI, Montpellier, France

    Cécile Richet, Denis Filloux, Pauline Bernardo & Philippe Roumagnac

  2. BGPI, INRA, CIRAD, SupAgro, Univ Montpellier, Montpellier, France

    Cécile Richet, Denis Filloux, Pauline Bernardo & Philippe Roumagnac

  3. The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine and School of Life Sciences, Arizona State University, Tempe, AZ, 85287-5001, USA

    Cécile Richet, Simona Kraberger & Arvind Varsani

  4. Department of Plant Pathology, Ohio State University, OARDC, Wooster, OH, USA

    Pauline Bernardo

  5. South African Medical Research Council Bioinformatics Unit, South African National Bioinformatics Institute, University of the Western Cape, Cape Town, South Africa

    Gordon W. Harkins

  6. Computational Biology Division, Department of Integrative Biomedical Sciences, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Observatory, Cape Town, 7925, South Africa

    Darren P. Martin

  7. School of Biological Sciences and Biomolecular Interaction Centre, University of Canterbury, Christchurch, New Zealand

    Arvind Varsani

  8. Structural Biology Research Unit, Department of Clinical Laboratory Sciences, University of Cape Town, Observatory, Cape Town, 7925, South Africa

    Arvind Varsani

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  1. Cécile Richet
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  2. Simona Kraberger
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  8. Arvind Varsani
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Correspondence to Philippe Roumagnac or Arvind Varsani.

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Handling Editor: Elvira Fiallo-Olivé.

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Supplementary Table 1:

Details of primers used to recover the circular genomic DNA molecules of AeaV, HlaV, LpaV, PeaV and SaV (DOCX 12 kb)

Supplementary Table 2:

Summary of the CRESS DNA viruses which have Rep sequences that are most closely related to those of AeaV, HlaV, LpaV, PeaV and SaV (Hit-CRESS dataset) and which were used to construct the phylogenetic trees presented in Figure 1 (DOCX 19 kb)

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Richet, C., Kraberger, S., Filloux, D. et al. Novel circular DNA viruses associated with Apiaceae and Poaceae from South Africa and New Zealand. Arch Virol 164, 237–242 (2019). https://doi.org/10.1007/s00705-018-4031-3

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