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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

Abstract

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.

Keywords

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.

Notes

Acknowledgments

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.

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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

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