Abstract
A novel virus infecting yams (Dioscorea spp.), tentatively named “yam asymptomatic virus 1” (YaV1), was characterized and sequenced from an asymptomatic D. alata plant from Vanuatu. Sequence comparisons and phylogenetic analysis showed that YaV1 is a novel ampelovirus and has the smallest genome among “subgroup 1” members. RT-PCR-based screening of a yam germplasm collection conserved in Guadeloupe showed that YaV1 is prevalent in D. alata, D. bulbifera, D. cayennensis subsp. rotundata, D. esculenta and D. trifida accessions but causes no apparent symptoms. Additional phylogenetic analysis revealed a low variability of YaV1 in Guadeloupe in a limited part of the genome, and suggested the occurrence of plant-to-plant transmission.
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Acknowledgements
This work was funded by the European Regional Development Fund, the Guadeloupe Region, and the Agence Nationale de la Recherche through project SafePGR (ANR-11-EBIM-0002-06). The authors wish to thank Nadia Adjano-Lubin and Eric Bandou for technical help, David Lange for assistance with sampling, Roger Malapa (Vanuatu Agricultural Research and Technical Centre (VARTC) for sampling, and the GenomEast Platform (IGBMC, Illkirch) for Illumina sequencing.
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The nucleotide sequences reported in this work have been deposited in the GenBank database under accession numbers MT409627 and MT409662-MT409682.
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Supplementary file1 Supplementary Table 1 Percent amino acid sequence identity of ampeloviruses HSP70 (A) and CP (B) and sequences from an ampelovirus, a closterovirus, a crinivirus, and a velavirus (XLS 38 kb)
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Supplementary file2 Supplementary Table 2 Results of the yam asymptomatic virus 1 indexing of accessions from the BRC-PT germplasm collection (XLSX 19 kb)
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Supplementary file3 Supplementary Table 3 Percent nucleotide sequence identity for yam asymptomatic virus 1 isolate sequences corresponding to positions 14555 to 14764 in the YaV1 genome (XLSX 22 kb)
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Supplementary Figure 1 Absence of symptoms in yam asymptomatic virus 1-infected D. alataplants from the BRC-TP germplasm collection. A, cultivar (cv) Ti Joseph 1; B, cv MP1 16H56;C, cv Vino purple forme; D, cv Tana; E, cv Toro; F, cv A 6; G, cv Fafadro bis; H, cv Wabé; I, cvKL 21; J, cv Saine Anne; K, cv Pakutrany (uninfected control) (PPTX 743 kb)
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Marais, A., Umber, M., Filloux, D. et al. Yam asymptomatic virus 1, a novel virus infecting yams (Dioscorea spp.) with significant prevalence in a germplasm collection. Arch Virol 165, 2653–2657 (2020). https://doi.org/10.1007/s00705-020-04787-0
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DOI: https://doi.org/10.1007/s00705-020-04787-0