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    A sequence-independent strategy for amplification and characterisation of episomal badnavirus sequences reveals three previously uncharacterised yam badnaviruses

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    Date
    2016-07-07
    Author
    Bömer, M.
    Turaki, A.A.
    Silva, G.
    Kumar, P.L.
    Seal, S.E.
    Type
    Journal Article
    Target Audience
    Scientists
    Metadata
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    Abstract/Description
    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.
    https://dx.doi.org/10.3390/v8070188
    Multi standard citation
    Permanent link to this item
    https://hdl.handle.net/20.500.12478/1251
    Digital Object Identifier (DOI)
    https://dx.doi.org/10.3390/v8070188
    IITA Subjects
    Plant Diseases; Yam
    Agrovoc Terms
    Yams; Dioscorea Alata; Dioscorea Rotundata
    Regions
    Africa; West Africa
    Countries
    Nigeria
    Journals
    Viruses
    Collections
    • Journal and Journal Articles4501
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