Mitochondrial plasmids of sugar beet amplified via rolling circle method detected during curtovirus screening

Homs, María; Kober, Sigrid; Kepp, Gabi; Jeske, Holger

doi:10.1016/j.virusres.2008.04.027

Cited by 22 publications

(11 citation statements)

References 41 publications

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“…Since RCA exponentially amplifies only circular DNA molecules, the absence of a product for G. arboreum , G. herbaceum and G. therburi is a good indication that these species were not infected with begomoviruses. However, the presence of a high molecular weight DNA product is not necessarily indicative of the presence of a circular DNA virus, since non-viral molecules, such as mitochondrial plasmids, can be amplified by RCA [31]. Following restriction digestion, a total of 34 molecules of ∼2800 nt, 87∼1400 nt and 4 smaller clones were obtained and sequenced in their entirety, in both orientations, with no ambiguities remaining.…”

Section: Resultsmentioning

confidence: 99%

A Melting Pot of Old World Begomoviruses and Their Satellites Infecting a Collection of Gossypium Species in Pakistan

2012

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CLCuD in southern Asia is caused by a complex of multiple begomoviruses (whitefly transmitted, single-stranded [ss]DNA viruses) in association with a specific ssDNA satellite; Cotton leaf curl Multan betasatellite (CLCuMuB). A further single ssDNA molecule, for which the collective name alphasatellites has been proposed, is also frequently associated with begomovirus-betasatellite complexes. Multan is in the center of the cotton growing area of Pakistan and has seen some of the worst problems caused by CLCuD. An exhaustive analysis of the diversity of begomoviruses and their satellites occurring in 15 Gossypium species (including G. hirsutum, the mainstay of Pakistan's cotton production) that are maintained in an orchard in the vicinity of Multan has been conducted using φ29 DNA polymerase-mediated rolling-circle amplification, cloning and sequence analysis. The non-cultivated Gossypium species, including non-symptomatic plants, were found to harbor a much greater diversity of begomoviruses and satellites than found in the cultivated G. hirsutum. Furthermore an African cassava mosaic virus (a virus previously only identified in Africa) DNA-A component and a Jatropha curcas mosaic virus (a virus occurring only in southern India) DNA-B component were identified. Consistent with earlier studies of cotton in southern Asia, only a single species of betasatellite, CLCuMuB, was identified. The diversity of alphasatellites was much greater, with many previously unknown species, in the non-cultivated cotton species than in G. hirsutum. Inoculation of newly identified components showed them to be competent for symptomatic infection of Nicotiana benthamiana plants. The significance of the findings with respect to our understanding of the role of host selection in virus diversity in crops and the geographical spread of viruses by human activity are discussed.

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Section: Resultsmentioning

confidence: 99%

A Melting Pot of Old World Begomoviruses and Their Satellites Infecting a Collection of Gossypium Species in Pakistan

2012

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“…To amplify circular molecules from DNA of petunia plants, rolling circle amplification (RCA) was performed following the manufacturer’s protocol (TempliPhiTM, GE Healthcare), as it is most reliable method to look into the diversity of begomoviruses in the infected samples [32]. Briefly, 20 ng of DNA was diluted in 13ul of Phi mixture (100 μM hexamer primers, 10 mM dNTPs and ɸ 29 DNA polymerase buffer) and denatured at 85 °C for 5 min.…”

Section: Methodsmentioning

confidence: 99%

Characterization, phylogeny and recombination analysis of Pedilanthus leaf curl virus-Petunia isolate and its associated betasatellite

Shakir

Nawaz-ul-Rehman

Mubin

et al. 2018

Virol J

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BackgroundGeminiviruses cause major losses to several economically important crops. Pedilanthus leaf curl virus (PeLCV) is a pathogenic geminivirus that appeared in the last decade and is continuously increasing its host range in Pakistan and India. This study reports the identification and characterization of PeLCV-Petunia from ornamental plants in Pakistan, as well as geographical, phylogenetic, and recombination analysis.MethodsViral genomes and associated satellites were amplified, cloned, and sequenced from Petunia atkinsiana plants showing typical geminivirus infection symptoms. Virus-satellite complex was analyzed for phylogenetic and recombination pattern. Infectious clones of isolated virus and satellite molecules were constructed using a partial dimer strategy. Infectivity analysis of PeLCV alone and in combination with Digera yellow vein betasatellite (DiYVB) was performed by Agrobacterium infiltration of Nicotiana benthamiana and Petunia atkinsiana plants with infectious clones.ResultsPeLCV, in association with DiYVB, was identified as the cause of leaf curl disease on P. atkinsiana plants. Sequence analysis showed that the isolated PeLCV is 96–98% identical to PeLCV from soybean, and DiYVB has 91% identity to a betasatellite identified from rose. Infectivity analysis of PeLCV alone and in combination with DiYVB, performed by Agrobacterium infiltration of infectious clones in N. benthamiana and P. atkinsiana plants, resulted in mild and severe disease symptoms 14 days after infiltration, respectively, demonstrating that these viruses are natural disease-causing agents. Southern blot hybridization indicated successful replication of the virus-betasatellite complex in the infected plants. Phylogenetic analysis suggests that PeLCV originated from Pakistan and later spread to India. Recombination analysis predicted that PeLCV is a donor parent for recombination and evolution of two important begomoviruses, Papaya leaf curl virus (PaLCuV) and Radish leaf curl virus (RaLCuV). The molecular phylogeny of genes encoding coat protein (CP) and replication associated protein (Rep) depict a complex evolutionary pattern of the viruses, with wide diversity in both of the genes.ConclusionsThis study presents PeLCV and DiYVB as a new natural combination resulting in leaf curl disease on P. atkinsiana plants. Phylogenetic analysis, in addition to recent agricultural reports, identify PeLCV as an emerging broad host range Begomovirus that is resident in Pakistan and, more recently, has also spread to India. Recombination analysis showed that PeLCV was involved in a natural recombinational event leading to the evolution of two recombinant begomoviruses, RaLCuV and PaLCuV.Electronic supplementary materialThe online version of this article (10.1186/s12985-018-1047-y) contains supplementary material, which is available to authorized users.

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“…RCA is a sequence-independent approach that is often used in the laboratory for the amplification of circular DNA virus genomes, thus overcoming the shortcoming of primer dependency in PCR for the amplification of viruses with a circular DNA genome [ 33 , 38 , 39 ]. The RCA technique has been used successfully for the study of several other circular DNA viruses such as sweet potato leaf curl virus [ 40 ] and beet curly top virus [ 41 ] of the family Geminiviridae , and BSV [ 39 , 42 ] and fig badnavirus 1 [ 34 ] of the family Caulimoviridae. It was proposed that RCA could be used for the specific detection of episomal forms of yam badnaviruses [ 30 ].…”

Section: Introductionmentioning

confidence: 99%

A Sequence-Independent Strategy for Amplification and Characterisation of Episomal Badnavirus Sequences Reveals Three Previously Uncharacterised Yam Badnaviruses

Bömer

Turaki

Silva

et al. 2016

Viruses

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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.

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Mitochondrial plasmids of sugar beet amplified via rolling circle method detected during curtovirus screening

Cited by 22 publications

References 41 publications

A Melting Pot of Old World Begomoviruses and Their Satellites Infecting a Collection of Gossypium Species in Pakistan

A Melting Pot of Old World Begomoviruses and Their Satellites Infecting a Collection of Gossypium Species in Pakistan

Characterization, phylogeny and recombination analysis of Pedilanthus leaf curl virus-Petunia isolate and its associated betasatellite

A Sequence-Independent Strategy for Amplification and Characterisation of Episomal Badnavirus Sequences Reveals Three Previously Uncharacterised Yam Badnaviruses

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