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Molecular characterization of Cordyline virus 1 isolates infecting yam (Dioscorea spp)

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Abstract

Cordyline virus 1 (CoV1) is a velarivirus that has so far only been reported in ornamental Ti plants (Cordyline fruticosa). Using high-throughput sequencing, we identified CoV1 infection in yam accessions from Vanuatu. Using a specific RT-PCR assay, we found that CoV1 is also present and highly prevalent in Dioscorea alata, D. cayenensis, and D. trifida in Guadeloupe. Phylogenetic analysis showed that CoV1 isolates infecting yam in Guadeloupe display a low level of molecular diversity. These data provide insights into the transmission of CoV1 in yam in Guadeloupe.

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Fig. 1

Availability of data and material

The nucleotide sequences reported in this work have been deposited in the GenBank database under accession numbers MZ648045 to MZ648087 and OM471839.

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Acknowledgements

The authors wish to thank Eric Francius, Lévy Laurent, and Lucien Montpierre for assistance with sampling, and Léa Zozo, Alisson Abadie, and Nolan Pellecuier for technical help.

Funding

This work was funded by the Agence Nationale de la Recherche (ANR) and the Guadeloupe Region through the NetBiome program under project SafePGR (ANR-11-EBIM-0002-06) and by the European Commission and the Guadeloupe Region through the Malin project (2018-FED-1088) under the EU’s Seventh Framework Programme.

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Authors and Affiliations

  1. INRAE, UR ASTRO, 97170, Petit‑Bourg, Guadeloupe, France

    Mame Boucar Diouf, Olyvia Gaspard, Rose‑Marie Gomez & Marie Umber

  2. CIRAD, UMR AGAP Institut, 97130, Capesterre Belle Eau, France

    Mame Boucar Diouf

  3. UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, 97130, Capesterre Belle Eau, France

    Mame Boucar Diouf

  4. INRAE, Univ. Bordeaux, UMR BFP, CS20032, 33882, Villenave d’Ornon Cedex, France

    Armelle Marais, Chantal Faure, Thierry Candresse, Sébastien Theil & Sandy Contreras

  5. CIRAD, UMR PHIM, 34090, Montpellier, France

    Denis Filloux & Philippe Roumagnac

  6. PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, 34090, Montpellier, France

    Denis Filloux & Philippe Roumagnac

  7. CIRAD, UMR PVBMT, 97410, Saint-Pierre, La Réunion, France

    Pierre‑Yves Teycheney

  8. UMR PVBMT, Université de la Réunion, 97410, Saint-Pierre, La Réunion, France

    Pierre‑Yves Teycheney

Authors
  1. Mame Boucar Diouf
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  2. Olyvia Gaspard
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  3. Armelle Marais
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  4. Denis Filloux
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  9. Sébastien Theil
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  11. Pierre‑Yves Teycheney
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  12. Marie Umber
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Correspondence to Marie Umber.

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Supplementary Information

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705_2022_5535_MOESM1_ESM.pptx

Supplementary file1 (PPTX 44 KB) Supplementary Fig. S1 Schematic representation of the genome of CoV1-VU567Da (A) and CoV1-Kahaluu (B). Boxes represent the putative open reading frames (ORFs). RdRp, RNA-dependent RNA polymerase; HSP70h, heat shock protein 70 homolog; CP, coat protein; CPm, minor coat protein. A size scale is provided in the upper part of the figure.

705_2022_5535_MOESM2_ESM.xlsx

Supplementary file2 (XLSX 14 KB) Supplementary Table S1 Position and size of the ORFs and conceptually translated proteins of CoV1-VU567Da and CoV1-Kahaluu

705_2022_5535_MOESM3_ESM.xlsx

Supplementary file3 (XLSX 13 KB) Supplementary Table S2 Prevalence of CoV1 in yam accessions maintained under field conditions and collected in 2019

705_2022_5535_MOESM4_ESM.xlsx

Supplementary file4 (XLSX 14 KB) Supplementary Table S3 Prevalence of CoV1 in yam accessions maintained under field conditions and collected in 2020

705_2022_5535_MOESM5_ESM.xlsx

Supplementary file5 (XLSX 31 KB) Supplementary Table S4 Prevalence of CoV1 in yam accessions from the BRC-TP in vitro collection collected between 2014 and 2019. CoV1-VU567Da: complete sequence VU567Da CoV1 isolate. YamCoV1 diversity: RdRp sequences of CoV1 yam isolates used for diversity analysis

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Diouf, M.B., Gaspard, O., Marais, A. et al. Molecular characterization of Cordyline virus 1 isolates infecting yam (Dioscorea spp). Arch Virol 167, 2275–2280 (2022). https://doi.org/10.1007/s00705-022-05535-2

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