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

  • Cécile Richet
  • Simona Kraberger
  • Denis Filloux
  • Pauline Bernardo
  • Gordon W. Harkins
  • Darren P. Martin
  • Philippe Roumagnac
  • Arvind Varsani
Brief Report

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.

Notes

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.

Compliance with ethical standards

Disclosure of potential conflicts of interest

The authors declare there are no conflicts of interest.

Research involving human participants and/or animals

The research did not involve human participants or animals.

Informed consent

The research did not involve human participants or animals.

Supplementary material

705_2018_4031_MOESM1_ESM.docx (13 kb)
Supplementary Table 1: Details of primers used to recover the circular genomic DNA molecules of AeaV, HlaV, LpaV, PeaV and SaV (DOCX 12 kb)
705_2018_4031_MOESM2_ESM.docx (19 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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Copyright information

© Springer-Verlag GmbH Austria, part of Springer Nature 2018

Authors and Affiliations

  1. 1.CIRAD, BGPIMontpellierFrance
  2. 2.BGPI, INRA, CIRAD, SupAgro, Univ MontpellierMontpellierFrance
  3. 3.The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine and School of Life SciencesArizona State UniversityTempeUSA
  4. 4.Department of Plant PathologyOhio State University, OARDCWoosterUSA
  5. 5.South African Medical Research Council Bioinformatics Unit, South African National Bioinformatics InstituteUniversity of the Western CapeCape TownSouth Africa
  6. 6.Computational Biology Division, Department of Integrative Biomedical Sciences, Institute of Infectious Diseases and Molecular MedicineUniversity of Cape TownCape TownSouth Africa
  7. 7.School of Biological Sciences and Biomolecular Interaction CentreUniversity of CanterburyChristchurchNew Zealand
  8. 8.Structural Biology Research Unit, Department of Clinical Laboratory SciencesUniversity of Cape TownCape TownSouth Africa

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