Molecular characterisation of six badnavirus species associated with leaf streak disease of banana in East Africa

James, Anthony P.; Geijskes, Robert J.; Dale, James L.; Harding, Robert M.

doi:10.1111/j.1744-7348.2011.00466.x

Cited by 49 publications

(34 citation statements)

References 25 publications

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“…(). Sequences from Clade I are both episomal and endogenous, and include infectious endogenous BSVs, whereas sequences from Clade II are exclusively endogenous and sequences from Clade III are most probably episomal (Gayral and Iskra‐Caruana, ; Iskra‐Caruana et al ., ; James et al ., ; M. Chabannes et al ., CIRAD, Montpellier, unpublished data). Likewise, badnaviruses of sugarcane, which are exclusively episomal, are classified into Clade I and Clade III, and display an important molecular diversity (Muller et al ., ).…”

Section: Discussionmentioning

confidence: 99%

“…(). The situation in yam in this regard is similar to that of M. balbisiana , for which BSV indexing had to be optimized in order to avoid ‘false’ positives resulting from the presence of endogenous BSVs (James et al ., , b; Le Provost et al ., ). Similar to BSV, RCA could be used for the specific detection of episomal forms of yam badnaviruses.…”

Section: Discussionmentioning

confidence: 99%

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The genome of African yam (Dioscorea cayenensis‐rotundata complex) hosts endogenous sequences from four distinct badnavirus species

Umber

Muller

Laboureau

et al. 2014

Molecular Plant Pathology

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Several endogenous viral elements (EVEs) have been identified in plant genomes, including endogenous pararetroviruses (EPRVs). Here, we report the first characterization of EPRV sequences in the genome of African yam of the Dioscorea cayenensis-rotundata complex. We propose that these sequences should be termed 'endogenous Dioscorea bacilliform viruses' (eDBVs). Molecular characterization of eDBVs shows that they constitute sequences originating from various parts of badnavirus genomes, resulting in a mosaic structure that is typical of most EPRVs characterized to date. Using complementary molecular approaches, we show that eDBVs belong to at least four distinct Badnavirus species, indicating multiple, independent, endogenization events. Phylogenetic analyses of eDBVs support and enrich the current taxonomy of yam badnaviruses and lead to the characterization of a new Badnavirus species in yam. The impact of eDBVs on diagnosis, yam germplasm conservation and movement, and breeding is discussed.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

The genome of African yam (Dioscorea cayenensis‐rotundata complex) hosts endogenous sequences from four distinct badnavirus species

Umber

Muller

Laboureau

et al. 2014

Molecular Plant Pathology

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“…), ten full length SCBV genome (SCBIMV, SCBMOV, SCBGAV‐1, SCBGAV‐2, SCBGDV, SCBV‐BB, SCBV‐BO, SCBV‐BR, SCBV‐BT and SCBV‐Iscam), 12 Banana streak viruses (James et al. ) and nine other badnaviruses infecting diverse crop species (Fig. ).…”

Section: Methodsmentioning

confidence: 99%

“…Nevertheless, it has been considered unequivocally that the genetic structure of badnaviruses infecting sugarcane and banana is highly complex and variable (Geijskes et al ; James et al. ; Karuppaiah et al. ; Muller et al.…”

Section: Introductionmentioning

confidence: 99%

Genetically Diverse Variants of Sugarcane bacilliform virus Infecting Sugarcane in India and Evidence of a Novel Recombinant Badnavirus Variant

Rao

Sharma

Singh³

et al. 2014

Journal of Phytopathology

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Sugarcane bacilliform viruses (SCBV; genus Badnavirus) cause leaf fleck disease in sugarcane worldwide. SCBV was detected in 28 sugarcane cultivars originating from eight states of India. Eight representative SCBV isolates from five different states showed sequence variability up to 27% in the reverse transcriptase and RNase H (RT/RNase H) genetic region. Five isolates [SCBV‐AP (): , SCBV‐Assam (CoBIN94063): , SCBV‐Bihar (Bo141): , SCBV‐UP (Co1424): and SCBV‐UP (CoSe6460): ] showed sequence identity of 86–88% with Sugarcane bacilliform IM virus (SCBIMV), but the other three isolates [SCBV‐Kerala (Co7219): , SCBV‐TN (): and SCBV‐UP (CoSe92423): ] showed maximum sequence identity of 75–79% with Sugarcane bacilliform MO virus (SCBMOV). In phylogenetic analysis, the SCBV isolates segregated into two new subclades and were distinct from the known SCBV genotypes. The rates of non‐synonymous and synonymous (dN/dS) substitution indicated the signs of purifying selection with strong functional constraints for RT/RNase H region in SCBV population. A variant (SCBV‐UP, CoSe92423) was identified to be a recombinant isolate having two other Indian SCBV isolates as parents. Although RT/RNase H region is a recombination cold spot, a strong recombination might have played a key role in the evolution of this new variant of SCBV. Our study provides an insight into the diverse genetic structure of SCBV population and presence of a novel recombinant SCBV species/variant infecting sugarcane cultivars in India. Our results will be helpful in devising a robust detection procedure for quarantine and field testing of sugarcane germplasm.

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“…However, this may not be the case given evidence from Uganda where diversity of BSV species has been found to be the highest so far (James et al, 2011b;Harper et al, 2004;2005). Therefore, there is a likelihood that when such field trials were being conducted, more than one BSV species could have been transmitted in a single infection.…”

Section: Screening Of Banana Genotypes For Bsv Resistancementioning

confidence: 78%

Assessment of Banana Streak MY virus-based infectious clone vectors in Musa ssp.

Onsarigo¹

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Banana streak disease, caused by a complex of different banana streak viruses (BSVs), occurs in all banana-producing countries. BSVs are genetically very diverse and can exist both as episomal forms or integrated into the host genome and both can be infectious to banana.Several field studies have assessed the infectivity of one or more BSV species on different banana genotypes with significant differences reported in virus incidence and symptom expression between and within genotypes. These studies used a severity index, based on symptom expression, to determine the resistance/susceptibility levels of the genotypes.Because of the great genetic variability amongst BSV species, symptoms of banana streak disease may vary widely and may be influenced by the cultivar and/or environmental conditions. Also this system of screening does not reflect the level of viral DNA accumulation In the current study, symptom variability was considerable with different Musa genotypes expressing distinct symptoms. Quantification of the levels of virus DNA showed that virus accumulation differs between genotypes, but also within plants of the same accession, and that severity scores do not correlate well with the viral load as measured using qPCR.Modified vectors with either ORF1 or ORF2 deleted were not infectious and the addition of a GFP ORF into two sites in the genome did not result in expression of this heterologous sequence from the constructs used in this study. Interestingly, two constructs with small inserts, initially designed for the purpose of gene silencing, were found to retain infectivity and maintain a heterologous sequence up to 110 nt. These studies confirm that BSMYV is infective in a broad range of Musa genotypes and cultivars but that further work is required to develop suitable vectors for either gene expression or gene silencing studies in banana

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Molecular characterisation of six badnavirus species associated with leaf streak disease of banana in East Africa

Cited by 49 publications

References 25 publications

The genome of African yam (Dioscorea cayenensis‐rotundata complex) hosts endogenous sequences from four distinct badnavirus species

The genome of African yam (Dioscorea cayenensis‐rotundata complex) hosts endogenous sequences from four distinct badnavirus species

Genetically Diverse Variants of Sugarcane bacilliform virus Infecting Sugarcane in India and Evidence of a Novel Recombinant Badnavirus Variant

Assessment of Banana Streak MY virus-based infectious clone vectors in Musa ssp.

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