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Complete genome sequence of a novel cytorhabdovirus infecting elderberry (Sambucus nigra L.) in the Czech Republic

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Abstract

The genus Cytorhabdovirus includes plant viruses with an unsegmented, single-stranded, negative-sense RNA genome that infect various plant hosts. In this work, we report the detection of a new cytorhabdovirus infecting elderberry (Sambucus nigra L.). Total RNA was purified from infected leaves and, after ribodepletion, sequenced using an Illumina system. The RNA genome of viral isolate B15 is 12,622 nucleotides (nt) long, and that of isolate B42 is 12,621 nt long. A nearly complete sequence (12,592 nt) was also obtained for a third isolate (B160). The RNA genomes of all three isolates showed an organisation typical of cytorhabdoviruses, harbouring all six of the expected genes (3´ N-P-P3-M-G-L 5´), separated by intergenic regions. These isolates were closely related to each other (99.5–99.6% nt sequence identity) and showed the highest overall similarity to trichosanthes associated rhabdovirus 1 (63.5% identity) and Wuhan insect virus 5 (58% identity), and similar results were obtained when comparing individual coding sequences or proteins. Phylogenetic analysis confirmed that this elderberry virus, for which we propose the name "sambucus virus 1" belongs to the genus Cytorhabdovirus and fulfils the criteria to represent a novel species.

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Data availability

The virus genome sequences were deposited in the GenBank database. The datasets generated during and/or analysed during the current study are available from the corresponding author on reasonable request.

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Funding

This work was supported by projects FA1407 (DIVAS) of European Cooperation in Science and Technology and LD15048 of the Ministry of Education, Youth and Sports (CZ).

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Authors and Affiliations

  1. Department of Cell Biology and Genetics, Faculty of Science, Palacký University Olomouc, Šlechtitelů 27, 783 71, Olomouc-Holice, Czech Republic

    Dana Šafářová & Milan Navrátil

  2. Univ. Bordeaux, INRAE, UMR 1332 Biologie du Fruit et Pathologie, CS20032, 33882, Villenave d’Ornon Cedex, France

    Thierry Candresse

Authors
  1. Dana Šafářová
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  2. Thierry Candresse
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  3. Milan Navrátil
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Contributions

DS and MN contributed to the study conception and design, material preparation, and data collection. Data analysis was performed by DS and TC. The first draft of the manuscript was written by DS, and all authors commented and reviewed the manuscript. All authors read and approved the final manuscript.

Corresponding author

Correspondence to Dana Šafářová.

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Conflict of interest

The authors have no relevant financial or non-financial interests to disclose.

Ethical approval

This study was performed on plants and did not require ethical approval.

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Handling Editor: Ralf Georg Dietzgen.

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Šafářová, D., Candresse, T. & Navrátil, M. Complete genome sequence of a novel cytorhabdovirus infecting elderberry (Sambucus nigra L.) in the Czech Republic. Arch Virol 167, 1589–1592 (2022). https://doi.org/10.1007/s00705-022-05444-4

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  • DOI: https://doi.org/10.1007/s00705-022-05444-4

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