Next Article in Journal
Properties of African Cassava Mosaic Virus Capsid Protein Expressed in Fission Yeast
Previous Article in Journal
A Truncated Nef Peptide from SIVcpz Inhibits the Production of HIV-1 Infectious Progeny
Article Menu

Export Article

Open AccessArticle
Viruses 2016, 8(7), 188; doi:10.3390/v8070188

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
These authors contributed equally to the article.
*
Author to whom correspondence should be addressed.
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)
View Full-Text   |   Download PDF [2709 KB, uploaded 9 July 2016]   |  

Abstract

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
Figures

This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. (CC BY 4.0).

Supplementary material

Scifeed alert for new publications

Never miss any articles matching your research from any publisher
  • Get alerts for new papers matching your research
  • Find out the new papers from selected authors
  • Updated daily for 49'000+ journals and 6000+ publishers
  • Define your Scifeed now

SciFeed Share & Cite This Article

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.

Show more citation formats Show less citations formats

Note that from the first issue of 2016, MDPI journals use article numbers instead of page numbers. See further details here.

Related Articles

Article Metrics

Article Access Statistics

1

Comments

[Return to top]
Viruses EISSN 1999-4915 Published by MDPI AG, Basel, Switzerland RSS E-Mail Table of Contents Alert
Back to Top