Archives of Virology

, Volume 154, Issue 2, pp 297–314 | Cite as

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

  • Mustapha Bousalem
  • O. Durand
  • N. Scarcelli
  • B. S. M. Lebas
  • L. Kenyon
  • J.-L. Marchand
  • F. Lefort
  • S. E. Seal
Original Article


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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Copyright information

© Springer-Verlag 2009

Authors and Affiliations

  • Mustapha Bousalem
    • 1
  • O. Durand
    • 1
    • 2
  • N. Scarcelli
    • 3
  • B. S. M. Lebas
    • 4
  • L. Kenyon
    • 4
  • J.-L. Marchand
    • 5
  • F. Lefort
    • 2
  • S. E. Seal
    • 4
  1. 1.INRA-URPVPetit-BourgFrance
  2. 2.Plants and Pathogens Group, Research Institute Earth Nature and Landscape, School of Engineering of LullierUniversity of Applied Sciences of Western SwitzerlandJussySwitzerland
  3. 3.Equipe DYNADIV, UMR 1097 Diversité et Génomes des Plantes CultivéesInstitut de Recherche pour le Développement (IRD)Montpellier Cedex 5France
  4. 4.Natural Resources InstituteUniversity of Greenwich at MedwayKentUK
  5. 5.UPR 75CIRADMontpellier Cedex 5France

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