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A Sequence-Independent Strategy for Amplification and Characterisation of Episomal Badnavirus Sequences Reveals Three Previously Uncharacterised Yam Badnaviruses

1
Natural Resources Institute, University of Greenwich, Central Avenue, Chatham, Kent ME4 4TB, UK
2
International Institute of Tropical Agriculture (IITA), Oyo Road, PMB 5320, Ibadan, Nigeria
*
Author to whom correspondence should be addressed.
These authors contributed equally to the article.
Academic Editor: Thomas Hohn
Received: 14 April 2016 / Revised: 24 June 2016 / Accepted: 30 June 2016 / Published: 7 July 2016
(This article belongs to the Section Viruses of Plants, Fungi and Protozoa)
Yam (Dioscorea spp.) plants are potentially hosts to a diverse range of badnavirus species (genus Badnavirus, family Caulimoviridae), but their detection is complicated by the existence of integrated badnavirus sequences in some yam genomes. To date, only two badnavirus genomes have been characterised, namely, Dioscorea bacilliform AL virus (DBALV) and Dioscorea bacilliform SN virus (DBSNV). A further 10 tentative species in yam have been described based on their partial reverse transcriptase (RT)-ribonuclease H (RNaseH) sequences, generically referred to here as Dioscorea bacilliform viruses (DBVs). Further characterisation of DBV species is necessary to determine which represent episomal viruses and which are only present as integrated badnavirus sequences in some yam genomes. In this study, a sequence-independent multiply-primed rolling circle amplification (RCA) method was evaluated for selective amplification of episomal DBV genomes. This resulted in the identification and characterisation of nine complete genomic sequences (7.4–7.7 kbp) of existing and previously undescribed DBV phylogenetic groups from Dioscorea alata and Dioscorea rotundata accessions. These new yam badnavirus genomes expand our understanding of the diversity and genomic organisation of DBVs, and assist the development of improved diagnostic tools. Our findings also suggest that mixed badnavirus infections occur relatively often in West African yam germplasm. View Full-Text
Keywords: yam; Dioscorea spp.; badnavirus; endogenous pararetrovirus; episomal badnavirus; diagnostics; rolling circle amplification; Sub-Saharan Africa yam; Dioscorea spp.; badnavirus; endogenous pararetrovirus; episomal badnavirus; diagnostics; rolling circle amplification; Sub-Saharan Africa
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MDPI and ACS Style

Bömer, M.; Turaki, A.A.; Silva, G.; Kumar, P.L.; Seal, S.E. A Sequence-Independent Strategy for Amplification and Characterisation of Episomal Badnavirus Sequences Reveals Three Previously Uncharacterised Yam Badnaviruses. Viruses 2016, 8, 188. https://0-doi-org.brum.beds.ac.uk/10.3390/v8070188

AMA Style

Bömer M, Turaki AA, Silva G, Kumar PL, Seal SE. A Sequence-Independent Strategy for Amplification and Characterisation of Episomal Badnavirus Sequences Reveals Three Previously Uncharacterised Yam Badnaviruses. Viruses. 2016; 8(7):188. https://0-doi-org.brum.beds.ac.uk/10.3390/v8070188

Chicago/Turabian Style

Bömer, Moritz, Aliyu A. Turaki, Gonçalo Silva, P. L. Kumar, and Susan E. Seal 2016. "A Sequence-Independent Strategy for Amplification and Characterisation of Episomal Badnavirus Sequences Reveals Three Previously Uncharacterised Yam Badnaviruses" Viruses 8, no. 7: 188. https://0-doi-org.brum.beds.ac.uk/10.3390/v8070188

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