Rolling-circle amplification of viral DNA genomes using phi29 polymerase

Johne, Reimar; Müller, Hermann; Rector, Annabel; Ranst, Marc Van; Stevens, Hans

doi:10.1016/j.tim.2009.02.004

Cited by 183 publications

(135 citation statements)

References 58 publications

Supporting

Mentioning

131

Contrasting

Order By: Relevance

“…The purified plasmids were amplified with phi29 DNA polymerase (Fig. S1C), previously used for viral DNA amplification (33,34). This process was carried out in parallel with an Escherichia coli plasmid (8 kb) as a positive control.…”

Section: Resultsmentioning

confidence: 99%

Insights into the bovine rumen plasmidome

Kav

Sasson

Jami

et al. 2012

Proc. Natl. Acad. Sci. U.S.A.

136

115

View full text Add to dashboard Cite

Plasmids are self-replicating genetic elements capable of mobilization between different hosts. Plasmids often serve as mediators of lateral gene transfer, a process considered to be a strong and sculpting evolutionary force in microbial environments. Our aim was to characterize the overall plasmid population in the environment of the bovine rumen, which houses a complex and dense microbiota that holds enormous significance for humans. We developed a procedure for the isolation of total rumen plasmid DNA, termed rumen plasmidome, and subjected it to deep sequencing using the Illumina paired-end protocol and analysis using public and custom-made bioinformatics tools. A large number of plasmidome contigs aligned with plasmids of rumen bacteria isolated from different locations and at various time points, suggesting that not only the bacterial taxa, but also their plasmids, are defined by the ecological niche. The bacterial phylum distribution of the plasmidome was different from that of the rumen bacterial taxa. Nevertheless, both shared a dominance of the phyla Firmicutes, Bacteroidetes, and Proteobacteria. Evidently, the rumen plasmidome is of a highly mosaic nature that can cross phyla. Interestingly, when we compared the functional profile of the rumen plasmidome to two plasmid databases and two recently published rumen metagenomes, it became apparent that the rumen plasmidome codes for functions, which are enriched in the rumen ecological niche and could confer advantages to their hosts, suggesting that the functional profiles of mobile genetic elements are associated with their environment, as has been previously implied for viruses.

show abstract

Section: Resultsmentioning

confidence: 99%

Insights into the bovine rumen plasmidome

Kav

Sasson

Jami

et al. 2012

Proc. Natl. Acad. Sci. U.S.A.

136

115

View full text Add to dashboard Cite

show abstract

“…Khan and Ahmad (2005) also used begomovirus specific primer to detect the presence of cotton leaf curl virus in the infected samples of cottonleaves. However, now a days, Rolling circle amplification (RCA) technique is successfully used to increase the virus concentration which helps in avoiding any false negatives and the increased amount of circular viral DNA gives better results in restriction analysis (Johne et al, 2009;Zaffalon et al, 2012).…”

Section: Detection Of Begomovirusesmentioning

confidence: 99%

Occurrence of begomoviruses in cotton-vegetable agro ecosystem in India

Kaur¹,

Kang²,

Sharma³

2015

Afr. J. Microbiol. Res.

View full text Add to dashboard Cite

Begomoviruses are the important pathogens of variety of crop plants and are responsible for causing huge economic losses. It is assumed that cotton vegetable agro eco system plays a vital role in the complex etiology of the diseases caused by begomoviruses. Therefore, the present work was planned to study the relationship among begomoviruses infecting cotton, chilli, radish, tomato and papaya. For this purpose, the symptomatic leaves of these plants were collected and were processed for DNA isolation. The amplified coat protein gene of begomoviruses was cloned and sequenced. The phylogenetic analysis showed that begomoviruses infecting cotton are totally different from the begomoviruses infecting other crops. Based on the coat protein gene sequences, the viruses infecting cotton were identified as cotton leaf curl virus, chilli leaf curl virus in chilli, radish leaf curl virus in radish, tomato leaf curl virus in tomato and papaya leaf curl virus in papaya.

show abstract

“…Another efficient amplification strategy is the use of random primers in combination with a displacement polymerase (Johne et al 2009). Phi29 is a high fidelity displacement polymerase with high processivity that can incorporate over 70,000 bases prior to detaching from its template (Blanco et al 1989;Esteban et al 1993), and only a few nanograms of starting material can produce several micrograms of DNA in one reaction.…”

Section: Displacement Amplificationmentioning

confidence: 99%

Viral metagenomics as an emerging and powerful tool in veterinary medicine

Blomström

2011

Veterinary Quarterly

View full text Add to dashboard Cite

New diseases continue to emerge in both human and animal populations, and the importance of animals, as reservoirs for viruses that can cause zoonoses are evident. Thus, an increased knowledge of the viral flora in animals, both in healthy and diseased individuals, is important both for animal and human health. Viral metagenomics is a culture-independent approach that is used to investigate the complete viral genetic populations of a sample. This review describes and discusses the different possible steps of a viral metagenomic study utilizing sequence-independent amplification, high-throughput sequencing, and bioinformatics to identify viruses. With this technology, multiple viruses can be detected simultaneously and novel and highly divergent viruses can be discovered and genetically characterized for the first time. This review also briefly discusses the applications of viral metagenomics in veterinary science and lists some of the viruses discovered within this field.

show abstract

Rolling-circle amplification of viral DNA genomes using phi29 polymerase

Cited by 183 publications

References 58 publications

Insights into the bovine rumen plasmidome

Insights into the bovine rumen plasmidome

Occurrence of begomoviruses in cotton-vegetable agro ecosystem in India

Viral metagenomics as an emerging and powerful tool in veterinary medicine

Contact Info

Product

Resources

About