Next Article in Journal
Chromosomally Integrated Human Herpesvirus 6: Models of Viral Genome Release from the Telomere and Impacts on Human Health
Previous Article in Journal
Variability of Emaravirus Species Associated with Sterility Mosaic Disease of Pigeonpea in India Provides Evidence of Segment Reassortment
Article Menu
Issue 7 (July) cover image

Export Article

Open AccessArticle
Viruses 2017, 9(7), 181; doi:10.3390/v9070181

PCR-DGGE Analysis: Unravelling Complex Mixtures of Badnavirus Sequences Present in Yam Germplasm

1
Natural Resources Institute, University of Greenwich, Central Avenue, Chatham Maritime, Kent ME4 4TB, UK
2
Kebbi State University of Science and Technology Aliero, Sokoto Road, PMB 1144 Birnin Kebbi, Nigeria
3
International Institute of Tropical Agriculture (IITA), Oyo Road, PMB 5320 Ibadan, Nigeria
These authors contributed equally to the work.
*
Author to whom correspondence should be addressed.
Academic Editor: K. Andrew White
Received: 28 April 2017 / Revised: 29 June 2017 / Accepted: 4 July 2017 / Published: 11 July 2017
(This article belongs to the Section Viruses of Plants, Fungi and Protozoa)
View Full-Text   |   Download PDF [3762 KB, uploaded 24 July 2017]   |  

Abstract

Badnaviruses (family Caulimoviridae, genus Badnavirus) have emerged as serious pathogens especially affecting the cultivation of tropical crops. Badnavirus sequences can be integrated in host genomes, complicating the detection of episomal infections and the assessment of viral genetic diversity in samples containing a complex mixture of sequences. Yam (Dioscorea spp.) plants are hosts to a diverse range of badnavirus species, and recent findings have suggested that mixed infections occur frequently in West African yam germplasm. Historically, the determination of the diversity of badnaviruses present in yam breeding lines has been achieved by cloning and sequencing of polymerase chain reaction (PCR) products. In this study, the molecular diversity of partial reverse transcriptase (RT)-ribonuclease H (RNaseH) sequences from yam badnaviruses was analysed using PCR-dependent denaturing gradient gel electrophoresis (PCR-DGGE). This resulted in the identification of complex ‘fingerprints’ composed of multiple sequences of Dioscorea bacilliform viruses (DBVs). Many of these sequences show high nucleotide identities to endogenous DBV (eDBV) sequences deposited in GenBank, and fall into six monophyletic species groups. Our findings highlight PCR-DGGE as a powerful tool in badnavirus diversity studies enabling a rapid indication of sequence diversity as well as potential candidate integrated sequences revealed by their conserved nature across germplasm. View Full-Text
Keywords: Badnavirus; denaturing gradient gel electrophoresis (DGGE); sequence diversity; yam; Dioscorea spp.; endogenous pararetrovirus (EPRV); episomal badnavirus; integration; detection Badnavirus; denaturing gradient gel electrophoresis (DGGE); sequence diversity; yam; Dioscorea spp.; endogenous pararetrovirus (EPRV); episomal badnavirus; integration; detection
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

Turaki, A.A.; Bömer, M.; Silva, G.; Kumar, P.L.; Seal, S.E. PCR-DGGE Analysis: Unravelling Complex Mixtures of Badnavirus Sequences Present in Yam Germplasm. Viruses 2017, 9, 181.

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