Archives of Virology

, Volume 163, Issue 3, pp 695–700 | Cite as

Nanovirus-alphasatellite complex identified in Vicia cracca in the Rhône delta region of France

  • Romain Gallet
  • Simona Kraberger
  • Denis Filloux
  • Serge Galzi
  • Hugo Fontes
  • Darren P. Martin
  • Arvind Varsani
  • Philippe Roumagnac
Brief Report

Abstract

Nanoviruses are multi-component plant-infecting single-stranded DNA viruses. Using a viral metagenomics-informed approach, a new nanovirus and two associated alphasatellite molecules have been identified in an uncultivated asymptomatic Vicia cracca plant in the Rhône region of France. This novel nanovirus genome includes eight genomic components (named DNA-R, DNA-S, DNA-M, DNA-C, DNA-N, DNA-U1, DNA-U2 and DNA-U4) and, across all components, shares < 66% pairwise sequence identity with other nanovirus genomes. The two associated alphasatellites share 62% identity with each other and < 81% identity will all other nanovirus-associated alphasatellites.

Keywords

Nanoviridae ssDNA virus cow vetch 

Notes

Compliance with ethical standards

Conflict of interest

Authors DPM and AV have received research grants from the National Research Foundation of South Africa. Author PR has received an EU grant FP7-PEOPLE-2013-IOF (N° PIOF-GA-2013-622571). Authors DPM, AV and PR declare that they have no conflict of interest.

Ethical approval

This article does not contain any studies with human participants or animals performed by any of the authors.

Supplementary material

705_2017_3634_MOESM1_ESM.pdf (228 kb)
Supplementary Figure 1 Alignment of the CR-I (A) and CR-II (B) regions identified in the CvLV sequences. The iterated triplet sequences and the presumed virion strand-origin of replication nonanucleotide sequence and a highly conserved motif in CR-II are highlighted in grey boxes. (PDF 227 kb)
705_2017_3634_MOESM2_ESM.docx (14 kb)
Supplementary Table 1 Details of primer pairs used to recover the DNA-R, DNA-S, DNA-C, DNA-M, DNA-N, DNA-U1, DNA-U2 and DNA-U4 molecules and the alphasatellite molecules from cow vetch. (DOCX 14 kb)
705_2017_3634_MOESM3_ESM.xlsx (107 kb)
Supplementary Data 1 Pairwise identity matrix of nanovirus DNA-R, DNA-S, DNA-C, DNA-M, DNA-N, DNA-U1, DNA-U2, and DNA-U4 components and nanovirus-associated alphasatellite molecules (XLSX 107 kb)

References

  1. 1.
    Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215:403–410CrossRefPubMedGoogle Scholar
  2. 2.
    Aronson MN, Meyer AD, Gyorgyey J, Katul L, Vetten HJ, Gronenborn B, Timchenko T (2000) Clink, a nanovirus-encoded protein, binds both pRB and SKP1. J Virol 74:2967–2972CrossRefPubMedPubMedCentralGoogle Scholar
  3. 3.
    Bernardo P, Golden M, Akram M, Naimuddin Nadarajan N, Fernandez E, Granier M, Rebelo AG, Peterschmitt M, Martin DP, Roumagnac P (2013) Identification and characterisation of a highly divergent geminivirus: evolutionary and taxonomic implications. Virus Res 177:35–45CrossRefPubMedGoogle Scholar
  4. 4.
    Bernardo P, Charles-Dominique T, Barakat M, Ortet P, Fernandez E, Filloux D, Hartnady P, Rebelo TA, Cousins SL, Mesleard F, Cohez D, Yavercovski N, Varsani A, Harkins GW, Peterschmitt M, Malmstrom CM, Martin DP, Roumagnac P (2017) Geometagenomics illuminates the impact of agriculture on the distribution and prevalence of plant viruses at the ecosystem scale. ISME J.  https://doi.org/10.1038/ismej.2017.155
  5. 5.
    Darriba D, Taboada GL, Doallo R, Posada D (2012) jModelTest 2: more models, new heuristics and parallel computing. Nat Methods 9:772CrossRefPubMedPubMedCentralGoogle Scholar
  6. 6.
    Edgar RC (2004) MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinform 5:113CrossRefGoogle Scholar
  7. 7.
    Guindon S, Dufayard JF, Lefort V, Anisimova M, Hordijk W, Gascuel O (2010) New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst Biol 59:307–321CrossRefPubMedGoogle Scholar
  8. 8.
    Haible D, Kober S, Jeske H (2006) Rolling circle amplification revolutionizes diagnosis and genomics of geminiviruses. J Virol Methods 135:9–16CrossRefPubMedGoogle Scholar
  9. 9.
    Heydarnejad J, Kamali M, Massumi H, Kvarnheden A, Male MF, Kraberger S, Stainton D, Martin DP, Varsani A (2017) Identification of a nanovirus-alphasatellite complex in Sophora alopecuroides. Virus Res 235:24–32CrossRefPubMedGoogle Scholar
  10. 10.
    Huang XQ, Madan A (1999) CAP3: a DNA sequence assembly program. Genome Res 9:868–877CrossRefPubMedPubMedCentralGoogle Scholar
  11. 11.
    Inoue-Nagata AK, Albuquerque LC, Rocha WB, Nagata T (2004) A simple method for cloning the complete begomovirus genome using the bacteriophage phi 29 DNA polymerase. J Virol Methods 116:209–211CrossRefPubMedGoogle Scholar
  12. 12.
    Kraberger S, Farkas K, Bernardo P, Booker C, Arguello-Astorga GR, Mesleard F, Martin DP, Roumagnac P, Varsani A (2015) Identification of novel Bromus- and Trifolium-associated circular DNA viruses. Arch Virol 160:1303–1311CrossRefPubMedGoogle Scholar
  13. 13.
    Muhire BM, Varsani A, Martin DP (2014) SDT: a virus classification tool based on pairwise sequence alignment and identity calculation. PLoS One 9:e108277CrossRefPubMedPubMedCentralGoogle Scholar
  14. 14.
    Palanga E, Filloux D, Martin DP, Fernandes E, Gargani D, Ferdinand R, Zabre J, Bouda Z, Neya JB, Sawadogo M, Traore O, Peterschmitt M, Roumagnac P (2016) Metagenomic-based screening and molecular characterization of cowpea-infecting viruses in Burkina Faso. PLoS One 11:e0165188CrossRefPubMedPubMedCentralGoogle Scholar
  15. 15.
    Roossinck MJ, Martin DP, Roumagnac P (2015) Plant virus metagenomics: advances in virus discovery. Phytopathology 105:716–727CrossRefPubMedGoogle Scholar
  16. 16.
    Shepherd DN, Martin DP, Lefeuvre P, Monjane AL, Owor BE, Rybicki EP, Varsani A (2008) A protocol for the rapid isolation of full geminivirus genomes from dried plant tissue. J Virol Methods 149:97–102CrossRefPubMedGoogle Scholar
  17. 17.
    Stover BC, Muller KF (2010) TreeGraph 2: combining and visualizing evidence from different phylogenetic analyses. BMC Bioinform 11:7CrossRefGoogle Scholar
  18. 18.
    Susi H, Laine AL, Filloux D, Kraberger S, Farkas K, Bernardo P, Frilander MJ, Martin DP, Varsani A, Roumagnac P (2017) Genome sequences of a capulavirus infecting Plantago lanceolata in the Aland archipelago of Finland. Arch Virol 162:2041–2045CrossRefPubMedGoogle Scholar
  19. 19.
    Vetten HJ, Dale JL, Grigoras I, Gronenborn B, Harding R, Randles JW, Sano Y, Thomas JE, Timchenko T, Yeh HH (2012) Nanoviridae. In: King AMQ, Adams MJ, Carstens EB, Lefkowitz EJ (eds) Virus taxonomy: ninth report of the international committee on taxonomy of viruses. Elsevier, Academic Press, AmsterdamGoogle Scholar

Copyright information

© Springer-Verlag GmbH Austria 2017

Authors and Affiliations

  • Romain Gallet
    • 1
  • Simona Kraberger
    • 2
  • Denis Filloux
    • 1
  • Serge Galzi
    • 1
  • Hugo Fontes
    • 3
  • Darren P. Martin
    • 4
  • Arvind Varsani
    • 2
    • 5
  • Philippe Roumagnac
    • 1
  1. 1.BGPI, CIRAD, INRA, Montpellier SupAgro, Univ MontpellierMontpellierFrance
  2. 2.The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life SciencesArizona State UniversityTempeUSA
  3. 3.Tour du Valat, Institut de recherche pour la conservation des zones humides méditerranéennesArlesFrance
  4. 4.Computational Biology Division, Department of Integrative Biomedical SciencesInstitute of Infectious Diseases and Molecular Medicine, University of Cape TownCape TownSouth Africa
  5. 5.Structural Biology Research Unit, Department of Clinical Laboratory SciencesUniversity of Cape TownCape TownSouth Africa

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