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.
Highlights
Badnaviruses are plant pararetroviruses infecting a broad range of economically important crop plants and have emerged as serious pathogens especially affecting the cultivation of tropical crops, such as banana, black pepper, cacao, citrus, sugarcane, taro and yam [1]
Four species of the genus Badnavirus described in banana genomes of Musa balbisiana species, namely Banana streak OL virus (BSOLV), Banana streak IM virus (BSIMV), Banana streak MY virus (BSMYV), and Banana streak GF virus (BSGFV) [21,24,25,26], as well as the petuvirus Petunia vein clearing virus (PVCV) in petunia [22], and the solendovirus Tobacco vein-clearing virus (TVCV) in tobacco [16,23] are the only activatable endogenous pararetroviruses (EPRVs) discovered to date
Activation is considered in banana to be triggered by tissue culture, hybridization, or temperature differences in newly created banana interspecific hybrids [27,28,29], and a homologous recombination-based model is proposed to explain the release of the BSOLV genome from its endogenous counterpart [30]
Summary
Badnaviruses are plant pararetroviruses (family Caulimoviridae, genus Badnavirus) infecting a broad range of economically important crop plants and have emerged as serious pathogens especially affecting the cultivation of tropical crops, such as banana, black pepper, cacao, citrus, sugarcane, taro and yam [1]. Termed endogenous pararetroviruses (EPRVs) [11,12,13], integration events have been most studied in banana [14], petunia [15], tobacco [16], rice [17], potato [18] and tomato [19], and the majority of these integrated sequences described so far are fragmented and rearranged [7,20,21,22] Few of these EPRVs can be activated to give rise to infective episomal forms initiating systemic badnavirus infections de novo [20,22,23]. Activation is considered in banana to be triggered by tissue culture, hybridization, or temperature differences in newly created banana interspecific hybrids [27,28,29], and a homologous recombination-based model is proposed to explain the release of the BSOLV genome from its endogenous counterpart [30]
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