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Dilemmas caused by endogenous pararetroviruses regarding the taxonomy and diagnosis of yam (Dioscorea spp.) badnaviruses: analyses to support safe germplasm movement

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Abstract

The discovery of endogenous pararetroviral sequences (EPRVs) has had a deep impact on the approaches needed for diagnosis, taxonomy, safe movement of germplasm and management of diseases caused by pararetroviruses. In this article, we illustrate this through the example of yam (Dioscorea spp.) badnaviruses. To enable progress, it is first necessary to clarify the taxonomical status of yam badnavirus sequences. Phylogeny and pairwise sequence comparison of 121 yam partial reverse transcriptase sequences provided strong support for the identification of 12 yam badnavirus species, of which ten have not been previously named. Virus prevalence data were obtained, and they support the presence of EPRVs in D. rotundata, but not in D. praehensilis, D. abyssinica, D. alata or D. trifida. Five yam badnavirus species characterised by a wide host range seem to be of African origin. Seven other yam badnavirus species with a limited host range are probably of Asian-Pacific origin. Recombination under natural circumstances appears to be rare. Average values of nucleotide intra-species genetic distances are comparable to data obtained for other RNA and DNA virus families. The dispersion scenarios proposed here, combined with the fact that host-switching events appear common for some yam badnaviruses, suggest that the risks linked to introduction via international plant material exchanges are high.

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Acknowledgments

The authors would like to thank Camara Fadjimba for granting access to his Guinean yam collection, and the many other people who provided samples. We wish also to express a special gratitude to the local guides, farmers and smallholders who so willingly offered tuber samples from their fields and for the information they supplied. The authors gratefully acknowledge the technical assistance of Rose-Marie Gomez, Lassaad Belbahri, Gautier Calmin and Chanban Black.

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Authors and Affiliations

  1. INRA-URPV, Domaine Duclos, Prise d’Eau, 9170, Petit-Bourg, Guadeloupe, France

    Mustapha Bousalem & O. Durand

  2. Plants and Pathogens Group, Research Institute Earth Nature and Landscape, School of Engineering of Lullier, University of Applied Sciences of Western Switzerland, 150 Route de Presinge, 1254, Jussy, Switzerland

    O. Durand & F. Lefort

  3. Equipe DYNADIV, UMR 1097 Diversité et Génomes des Plantes Cultivées, Institut de Recherche pour le Développement (IRD), BP 64501, 34394, Montpellier Cedex 5, France

    N. Scarcelli

  4. Natural Resources Institute, University of Greenwich at Medway, Central Avenue, Chatham Maritime, Kent, ME4 4TB, UK

    B. S. M. Lebas, L. Kenyon & S. E. Seal

  5. UPR 75, CIRAD, 73 rue Jean-Francois Breton-TA 70/16, 34398, Montpellier Cedex 5, France

    J.-L. Marchand

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  1. Mustapha Bousalem
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Bousalem, M., Durand, O., Scarcelli, N. et al. Dilemmas caused by endogenous pararetroviruses regarding the taxonomy and diagnosis of yam (Dioscorea spp.) badnaviruses: analyses to support safe germplasm movement. Arch Virol 154, 297–314 (2009). https://doi.org/10.1007/s00705-009-0311-2

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