Yams (Dioscorea spp.) host a diverse range of badnaviruses (genus Badnavirus, family Caulimoviridae). The first complete genome sequence of Dioscorea bacilliform RT virus 3 (DBRTV3), which belongs to the monophyletic species group K5, is described. This virus is most closely related to Dioscorea bacilliform SN virus (DBSNV, group K4) based on a comparison of genome sequences. Recombination analysis identified a unique recombination event in DBRTV3, with DBSNV likely to be the major parent and Dioscorea bacilliform AL virus (DBALV) the minor parent, providing the first evidence for recombination in yam badnaviruses. This has important implications for yam breeding programmes globally.
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http://dx.doi.org/10.1007/s00705-017-3605-9 | DOI Listing |
Front Plant Sci
May 2022
Natural Resources Institute, University of Greenwich, Chatham Maritime, United Kingdom.
Viruses of the genus (family ) are double-stranded DNA-reverse transcribing (dsDNA-RT) plant viruses and have emerged as serious pathogens of tropical and temperate crops globally. Endogenous badnaviral sequences are found integrated in the genomes of several economically important plant species. Infection due to activation of replication-competent integrated copies of the genera , and has been described.
View Article and Find Full Text PDFPhysiol Mol Plant Pathol
January 2019
Natural Resources Institute, University of Greenwich, Central Avenue, Chatham Maritime, Kent, ME4 4TB, UK.
culture offers many advantages for yam germplasm conservation, propagation and international distribution. However, low virus titres in the generated tissues pose a challenge for reliable virus detection, which makes it difficult to ensure that planting material is virus-free. In this study, we evaluated next-generation sequencing (NGS) for virus detection following yam propagation using a robust tissue culture methodology.
View Article and Find Full Text PDFVirology
March 2019
Centre for Tropical Crops and Biocommodities (CTCB), Faculty of Science and Engineering (SEF), Queensland University of Technology (QUT), Brisbane 4001, Australia.
The genus Badnavirus is characterized by members that are genetically and serologically heterogeneous which presents challenges for their detection and characterization. The presence of integrated badnavirus-like sequences in some host species further complicates detection using PCR-based protocols. To address these challenges, we have assessed and optimized various RCA protocols including random-primed RCA (RP-RCA), primer-spiked random-primed RCA (primer-spiked RP-RCA), directed RCA (D-RCA) and specific-primed RCA (SP-RCA).
View Article and Find Full Text PDFSci Rep
December 2018
CIRAD, BGPI, Montpellier, France.
We here assessed the capability of the MinION sequencing approach to detect and characterize viruses infecting a water yam plant. This sequencing platform consistently revealed the presence of several plant virus species, including Dioscorea bacilliform virus, Yam mild mosaic virus and Yam chlorotic necrosis virus. A potentially novel ampelovirus was also detected by a complimentary Illumina sequencing approach.
View Article and Find Full Text PDFBio Protoc
January 2018
Natural Resources Institute, University of Greenwich, London, UK.
Since the first discovery of badnaviruses (family , genus ) in yam ( spp.) germplasm in the 1970s (Harrison and Roberts, 1973), several hundred partial badnavirus reverse transcriptase (RT)-ribonuclease H (RNaseH) sequences have been characterised ( Kenyon , 2008 ; Bousalem , 2009 ), but only a few complete bacilliform virus (DBV) genome sequences have been reported ( Phillips , 1999 ; Seal and Muller, 2007; Bömer , 2016 and 2017; Sukal , 2017 ; Umber , 2017 ). We have optimised a workflow involving total nucleic acid extractions and rolling circle amplification (RCA) combined with restriction enzyme analysis for the detection and amplification of DBVs present in yam germplasm.
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