Archives of Virology

, Volume 153, Issue 5, pp 877–889 | Cite as

Yams (Dioscorea spp.) from the South Pacific Islands contain many novel badnaviruses: implications for international movement of yam germplasm

  • Lawrence KenyonEmail author
  • B. S. M. Lebas
  • S. E. Seal
Original Article


Yam (Dioscorea spp.) samples (n = 690) from seven South Pacific Islands were screened for badnavirus infection by ELISA using two antisera to African badnaviruses. Positive readings were obtained for 26.4–34.6% of samples representing both known (D. bulbifera, D. nummularia and D. pentaphylla) and unreported host species (D. alata, D. esculenta, D. rotundata and D. trifida) in this region. Total DNAs were extracted from 25 ELISA-positive plants and 4 ELISA-negative controls and subjected to PCR amplification with badnavirus-specific primers targeting the reverse transcriptase (RT)–RNaseH genes. All 29 samples yielded the expected size PCR-product for badnaviruses, which were cloned and sequenced. Phylogenetic analyses of the resulting 45 partial (500–527 bp) RT–RNaseH sequences revealed 11 new sequence groups with <79% nucleotide identity to each other or any EMBL sequence. Three sequences (two groups) were highly divergent to the other nine new South Pacific yam badnavirus groups (47.9–57.2% identity) and probably represent either new Caulimoviridae genera or endogenous pararetrovirus sequences. Some sequence groups appeared specific to particular Dioscorea host species. Four 99.9% identical RT–RNaseH sequences possessing nine amino acid deletions from D. esculenta from three islands represent a putative integrated sequence group. The distribution of sequence groups across the islands indicates that badnaviruses have spread extensively between islands and continents through infected germplasm.


Nucleotide Identity Solomon Island Sequence Group Amino Acid Deletion Rice Tungro Bacilliform Virus 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.



The first two authors contributed equally to this work, which formed part of the European Commission-funded South Pacific Yam Network (SPYN) project for the selection of yam cultivars for disease resistance and commercial potential in the Pacific Islands. The authors would like to thank Vincent Lebot and Grahame Jackson for all their guidance through the SPYN project and Godwin Ala (Vanuatu), Moti Lala Autar (Fiji), Tolo Iosefa (Samoa), Siosiua Halavatau (Tonga), Tony Gunua (PNG) and Jean Galo (Solomon Islands) for assisting in collecting the leaf samples. Benedicte Lebas was funded by the Higher Education Funding Council through the Natural Resources Institute (NRI) of the University of Greenwich.


  1. 1.
    Barrau J (1956) Les ignames alimentaires des îles du Pacifique Sud. J Agric Trop Bot Appl 8:385–401Google Scholar
  2. 2.
    Bouhida M, Lockhart BEL, Olszewski NE (1993) An analysis of the complete sequence of a sugarcane bacilliform virus genome infectious to banana and rice. J Gen Virol 74:15–22PubMedGoogle Scholar
  3. 3.
    Bousalem M, Dallot S, Fuji S, Natsuaki KT (2003) Origin, world-wide dispersion, bio-geographical diversification, radiation and recombination: an evolutionary history of Yam mild mosaic virus. Infect Genet Evol 3:189–206PubMedCrossRefGoogle Scholar
  4. 4.
    Bousalem M, Dallot S, Guyader S (2000) Using phylogenetic data to develop molecular tools for the detection and genotyping of Yam mosaic virus. Potential application in molecular epidemiology. J Virol Methods 90:25–36PubMedCrossRefGoogle Scholar
  5. 5.
    Briddon RW, Phillips S, Brunt A, Hull R (1999) Analysis of the sequence of Dioscorea alata bacilliform virus; comparison to other members of the badnavirus group. Virus Genes 18:277–283PubMedCrossRefGoogle Scholar
  6. 6.
    Fuji S, Nakamae H (1999) Complete nucleotide sequence of the genomic RNA of a Japanese yam mosaic virus, a new potyvirus in Japan. Arch Virol 144:231–240PubMedCrossRefGoogle Scholar
  7. 7.
    Fuji S, Mitobe I, Nakamae H, Natsuaki KT (1999) Nucleotide sequence of coat protein gene of yam mild mosaic virus, isolated in Papua New Guinea. Arch Virol 144:1415–1419PubMedCrossRefGoogle Scholar
  8. 8.
    Geering ADW, McMichael LA, Dietzgen RG, Thomas JE (2000) Genetic diversity among banana streak virus isolates from Australia. Phytopathology 90:921–927CrossRefPubMedGoogle Scholar
  9. 9.
    Geering ADW, Olszewski NE, Harper G, Lockhart BEL, Hull R, Thomas JE (2005) Banana contains a diverse array of endogenous badnaviruses. J Gen Virol 86:511–520PubMedCrossRefGoogle Scholar
  10. 10.
    Geijskes RJ, Braithwaite KS, Dale JL, Harding RM, Smith GR (2002) Sequence analysis of an Australian isolate of sugarcane bacilliform badnavirus. Arch Virol 147:2393–2404PubMedCrossRefGoogle Scholar
  11. 11.
    Hagen LS, Jacquemond M, Lepingle A, Lot H, Tepfer M (1993) Nucleotide sequence and genomic organization of cacao swollen shoot virus. Virology 196:619–628PubMedCrossRefGoogle Scholar
  12. 12.
    Harper G, Hart D, Moult S, Hull R, Geering A, Thomas J (2005) The diversity of Banana streak virus isolates in Uganda. Arch Virol 150:2407–2420PubMedCrossRefGoogle Scholar
  13. 13.
    Harper G, Hull R (1998) Cloning and sequence analysis of banana streak virus DNA. Virus Genes 17:271–278PubMedCrossRefGoogle Scholar
  14. 14.
    Harper G, Osuji J, Heslop-Harrison JS, Hull R (1999) Integration of banana streak badnavirus in the Musa genome: molecular and cytogenetic evidence. Virology 255:207–213PubMedCrossRefGoogle Scholar
  15. 15.
    Harrison BD, Roberts IM (1973) Association of virus-like particles with internal brown spot of yam (Dioscorea alata). Tropical Agriculture, University of West Indies, Published by IPC, vol 50, pp 335–340Google Scholar
  16. 16.
    Hughes Jd’A (1986) Viruses of the Araceae and Dioscorea species: their isolation, characterisation and detection. Ph D Thesis, Reading University, ReadingGoogle Scholar
  17. 17.
    Hull R, Geering A, Harper G, Lockhart BEL, Schoelz JE (2005) Caulimoviridae. In: Fauquet CM, Mayo MA, Maniloff J, Desselberger U, Ball LA (eds) Virus taxonomy, 8th report of the international committee on taxonomy of viruses. Elsevier Academic Press, Amsterdam, pp 385–396Google Scholar
  18. 18.
    Kaper JM, Waterworth HE (1981) Cucumoviruses. In: Kurstak E (ed) Handbook of plant virus infections and comparative diagnosis, chap 11. Elsevier/North-Holland Biomedical Press, pp 257–332Google Scholar
  19. 19.
    Kenyon L, Shoyinka SA, Hughes J d’A, Odu BO (2001) An overview of viruses infecting yams in Sub-Saharan Africa. In: 1st symposium of plant virology for sub-Saharan Africa (PVSSA), IITA, Ibadan.
  20. 20.
    Kunii M, Kanda M, Nagano H, Uyeda I, Kishima Y, Sano Y (2004) Reconstruction of putative DNA virus from endogenous rice tungro bacilliform virus-like sequences in the rice genome: implications for integration and evolution. BMC Genomics 5:80PubMedCrossRefGoogle Scholar
  21. 21.
    Lockhart B, Olszewski N (1993) Serological and genomic heterogeneity of banana streak badnavirus: Implications for virus detection in Musa germplasm. In: Ganry J (ed) Proceedings of international symposium on genetic improvement of bananas for resistance to diseases and pests. Breeding banana and plantain for resistance to diseases and pests, Montpellier, pp 105–113Google Scholar
  22. 22.
    Lockhart B, Olszewski N (1999) Badnaviruses. In: Granoff A, Webster RG (eds) Encyclopedia of virology. 2nd edn. Academic Press, San Diego, pp 1293–1299Google Scholar
  23. 23.
    Lodhi MA, Ye G-N, Weeden NF, Reisch BI (1994) A simple and efficient method for DNA extraction from grapevine cultivars and Vitis species. Plant Mol Biol Rep 12:6–13CrossRefGoogle Scholar
  24. 24.
    Mantell SH, Haque SQ (1979) Internal brown spot disease of yams. In: CARDI/ODM, St Augustine, Yam Virus Project Bulletin No. 3Google Scholar
  25. 25.
    Medberry SL, Lockhart BEL, Olszewski E (1990) Properties of Commelina yellow mottle virus’s complete DNA sequence, genomic discontinuities and transcript suggest that it is a pararetrovirus. Nucleic Acids Res 18:5505–5513PubMedCrossRefGoogle Scholar
  26. 26.
    Mohamed NA (1976) Virus-like particles and cytoplasmic inclusions associated with diseased Dioscorea spp. in the Eastern Caribbean. In: Tropical Agriculture, University of the West Indies, St Augustine, vol 53, pp 341–351Google Scholar
  27. 27.
    Muller E, Sackey S (2005) Molecular variability analysis of five new complete cacao swollen shoot virus genomic sequences. Arch Virol 150:53–66PubMedCrossRefGoogle Scholar
  28. 28.
    Mumford RA, Seal SE (1997) Rapid single-tube immunocapture RT-PCR for the detection of two yam Potyviruses. J Virol Methods 69:73–79PubMedCrossRefGoogle Scholar
  29. 29.
    Ndowora TC, Lockhart BEL (2000) Development of a serological assay for detecting serologically diverse Banana streak virus isolates. Acta Hortic 540:377–388Google Scholar
  30. 30.
    Ndowora TC, Lockhart BEL, Olszewski NE (1997) Relationship between integrated episomal badnavirus genomic sequences in Musa. Phytopathology 87:S69Google Scholar
  31. 31.
    Ndowora T, Dahal G, LaFleur D, Harper G, Hull R, Olszewski NE, Lockhart BEL (1999) Evidence that badnavirus infection in Musa can originate from integrated pararetroviral sequences. Virology 255:214–220PubMedCrossRefGoogle Scholar
  32. 32.
    Odu BO, Asiedu R, Shoyinka SA, Hughes J D’A (2006) Screening of water yam (Dioscorea alata L.) genotypes for reactions to viruses in Nigeria. J Phytopathol 154:716–724CrossRefGoogle Scholar
  33. 33.
    Orkwor GC (1998) The importance of yams. In: Orkwor GC, Asiedu R, Ekanayake IJ (eds) Food yams: advances in research. International Institute of Tropical Agriculture, pp 1–12Google Scholar
  34. 34.
    Phillips S, Briddon RW, Brunt AA, Hull R (1999) The partial characterization of badnavirus infecting the Greater asiatic or water yam (Dioscorea alata). J Phytopathol 147:265–269CrossRefGoogle Scholar
  35. 35.
    Qu R, Bhattacharyya M, Laco GS, De Kochko AS, Rao BL, Kaniewska MB, Elmer JS, Rochester DE, Smith CE, Beachy RN (1991) Characterization of the genome of rice tungro bacilliform virus: comparison with Commelina yellow mottle virus and caulimoviruses. Virology 185:354–364 (published erratum Virology 1992 Feb 186:798)PubMedCrossRefGoogle Scholar
  36. 36.
    Sambrook J, Fritsch EF, Maniatis T (1989) Small-scale preparation of plasmid DNA. In: Molecular cloning, a laboratory manual, 2nd edn, book 1: 1.25. Cold Spring Harbor Laboratory Press, Cold Spring HarborGoogle Scholar
  37. 37.
    Seal S, Muller E (2007) Molecular analysis of a full-length sequence of a new yam badnavirus from Dioscorea sansibarensis. Arch Virol. doi: 10.1007/s00705-006-0888-7, 1–7
  38. 38.
    Swofford DL (2002) PAUP*: phylogenetic analysis using parsimony (*and other methods), Version 4. Sinauer Associates, SunderlandGoogle Scholar
  39. 39.
    Thouvenel J-C, Dumont R (1990) Perte de rendement de l’igname infectée par le virus de la mosaïque en Côte-d’Ivoire. L’Agronomie Tropicale 45:125–129Google Scholar
  40. 40.
    Yang IC, Hafner GJ, Revill PA, Dale JL, Harding RM (2003) Sequence diversity of South Pacific isolates of Taro bacilliform virus and the development of a PCR-based diagnostic test. Arch Virol 148:1957–1968PubMedCrossRefGoogle Scholar

Copyright information

© Springer-Verlag 2008

Authors and Affiliations

  • Lawrence Kenyon
    • 1
    Email author
  • B. S. M. Lebas
    • 1
    • 2
  • S. E. Seal
    • 1
  1. 1.Natural Resources InstituteThe University of Greenwich at MedwayChatham MaritimeUK
  2. 2.Investigation and Diagnostic CentreMinistry of Agriculture and ForestryAucklandNew Zealand

Personalised recommendations