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Deep sequencing analysis of viruses infecting grapevines: Virome of a vineyard.
- B. Coetzee, M. Freeborough, H. J. Maree, J. Celton, D. Rees, J. Burger
- Biology, MedicineVirology
- 10 May 2010
It was found that Grapevine leafroll-associated virus 3 (GLRaV-3) is the most prevalent species, constituting 59% of the total reads, followed by Grapevine rupestris stem pitting- associated virus and Grapevine virus A.
Grapevine leafroll-associated virus 3
The characterization of sgRNAs produced during the infection cycle of GLRaV-3 has given some insight into the replication strategy and the putative functionality of the ORFs, and the application of next-generation sequencing is proving to be a valuable tool to study the complexity of viral infection as well as plant pathogen interaction.
Three genetic grapevine leafroll-associated virus 3 variants identified from South African vineyards show high variability in their 5′UTR
- A. Jooste, H. J. Maree, D. Bellstedt, D. Goszczynski, G. Pietersen, J. Burger
- Biology, MedicineArchives of Virology
- 10 September 2010
Three genetic variants of grapevine leafroll-associated virus 3 (GLRaV-3) were identified in vineyards of the Western Cape, South Africa and the presence of two or three additional variant groups elsewhere in the world was supported.
Complete nucleotide sequence of a South African isolate of grapevine leafroll-associated virus 3 reveals a 5′UTR of 737 nucleotides
The sequence of GLRaV-3, isolate GP18, has a 50UTR of 737 nt and the 30-terminus of GP18 was found to be similar to that of the NY-1 isolate, and the efficacy of RLM-RACE to determine the 50-termini of multiple ssRNA viruses from total RNA in a single reaction was investigated.
Grapevine leafroll disease and associated viruses: a unique pathosystem.
A systems biology approach using contemporary technologies in molecular biology, -omics, and cell biology aids in exploring the comparative molecular biology of GLRaVs and deciphering the complex network of host-virus-vector interactions to bridge the gap between genomics and phenomics of leafroll disease.
Complete nucleotide sequence of a new strain of grapevine leafroll-associated virus 3 in South Africa
Phylogenetic analysis indicates that GH11 and GH30 cluster in a subgroup (group VI) that is separate from the previously described GLRaV-3 isolates and should be regarded as a different strain of GLRav-3.
Next-generation sequencing for virus detection: covering all the bases
The results suggest the use of ribo-depleted RNA in a de novo assembly-based approach for the detection of single-stranded RNA viruses and suggest that sequencing one million reads will provide sufficient genome coverage specifically for closterovirus detection.
Complete Genome of a Novel Endornavirus Assembled from Next-Generation Sequence Data
The complete genome of a novel endornavirus is reported, assembled from next-generation sequence data generated from Vitis vinifera-extracted dsRNA, suggesting that horizontal transmission of the virus is possible.
Identification and distribution of multiple virus infections in Grapevine leafroll diseased vineyards
- A. Jooste, N. Molenaar, +4 authors J. Burger
- BiologyEuropean Journal of Plant Pathology
- 20 February 2015
The complexity of virus populations detected in this study, highlights the need for detection methods able to identify all viruses and their variants in vineyards.
Targeted virus detection in next-generation sequencing data using an automated e-probe based approach.
The user-friendly software, named Truffle, is available for the design and screening of e-probes tailored for user-specific virus species and data, along with preloaded probe-sets for grapevine virus detection.