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Complete genomic sequence of Raphanus sativus cryptic virus 4 (RsCV4), a novel alphapartitivirus from radish

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Abstract

The present work reports the discovery and complete genome sequencing of a virus from symptomless radish seedlings, classifiable as a novel member of the genus Alphapartitivirus, family Partitiviridae. Total RNA extracted from germinating seedlings was sequenced using Illumina technology. Bioinformatic analysis of the RNA-seq data revealed two contigs representing the near full-length genomic sequences of two genomic RNAs representing a new virus. Analysis of the genome sequence (excluding the polyA tail, RNA1: 1976 nt and RNA2: 1751 nt, respectively) showed a genomic organization typical of viruses classed within the Partitiviridae, with each genomic RNA encoding a single open reading frame (ORF). Phylogenetic analysis of the RNA dependent RNA polymerase (RNA1 ORF) and of the capsid protein (RNA2 ORF) clearly showed the new virus can be classified within the genus Alphapartitivirus, but sequence divergence establishes it as a new species, for which the name “Raphanus sativus cryptic virus 4” is proposed.

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Acknowledgements

This work was supported in part by the MetaT Project of the Meta-omics and microbial ecosystems (MEM) INRA Metaprogram. The authors want to thank Catherine Zanchetta and Olivier Bouchez from the GeT core facility (Toulouse, France, http://get.genotoul.fr) for their help in the sequencing experiments.

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Authors and Affiliations

  1. UMR 1332 Biologie du Fruit et Pathologie, INRA, Univ. Bordeaux, CS 20032, 33882, Villenave d’Ornon Cedex, France

    Laurence Svanella-Dumas, Sébastien Theil & Thierry Candresse

  2. IRHS, INRA, University of Angers, 42 rue Georges Morel, 49071, Beaucouzé, France

    Matthieu Barret

Authors
  1. Laurence Svanella-Dumas
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  2. Sébastien Theil
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  3. Matthieu Barret
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  4. Thierry Candresse
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Correspondence to Thierry Candresse.

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All authors (LS, ST, MB and TC) declare they have no conflict of interest.

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

Additional information

Handling Editor: Ioannis E. Tzanetakis.

The nucleotide sequence reported in this work has been deposited in the GenBank database under accession numbers MF686921 and MF686922.

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Svanella-Dumas, L., Theil, S., Barret, M. et al. Complete genomic sequence of Raphanus sativus cryptic virus 4 (RsCV4), a novel alphapartitivirus from radish. Arch Virol 163, 1097–1100 (2018). https://doi.org/10.1007/s00705-017-3693-6

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  • DOI: https://doi.org/10.1007/s00705-017-3693-6

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