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PCR-DGGE analysis: Unravelling complex mixtures of badnavirus sequences present in yam germplasm

PCR-DGGE analysis: Unravelling complex mixtures of badnavirus sequences present in yam germplasm

Turaki, Aliyu A., Bömer, Moritz ORCID: 0000-0003-1003-9622, Silva, Gonçalo ORCID: 0000-0001-5544-2947, Kumar, P. Lava and Seal, Susan E. ORCID: 0000-0002-3952-1562 (2017) PCR-DGGE analysis: Unravelling complex mixtures of badnavirus sequences present in yam germplasm. Viruses, 9 (7). p. 181. ISSN 1999-4915 (Print), 1999-4915 (Online) (doi:https://doi.org/10.3390/v9070181)

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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.

Item Type: Article
Additional Information: © 2017 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).
Uncontrolled Keywords: Badnavirus; Denaturing gradient gel electrophoresis (DGGE); Sequence diversity; Yam; Dioscorea spp.; Endogenous pararetrovirus (EPRV); Episomal badnavirus; Integration; Detection
Subjects: S Agriculture > S Agriculture (General)
Faculty / Department / Research Group: Faculty of Engineering & Science
Faculty of Engineering & Science > Natural Resources Institute
Faculty of Engineering & Science > Natural Resources Institute > Agriculture, Health & Environment Department
Faculty of Engineering & Science > Natural Resources Institute > Molecular Virology and Entomology Research Group
Last Modified: 25 Apr 2019 09:17
Selected for GREAT 2016: None
Selected for GREAT 2017: GREAT a
Selected for GREAT 2018: GREAT a
Selected for GREAT 2019: GREAT 3
URI: http://gala.gre.ac.uk/id/eprint/17490

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