Determination of grapevine viral complexity through deep sequencing


Project Number
GENUS 11-03

Project title
Determination of grapevine viral complexity through deep sequencing

Project leader
Burger, J T

Institution
University of Stellenbosch. Faculty of Health Sciences. Department of Genetics

Team members
Burger, J T
Stephan, D
Maree, H J
Rees, D J G

Project description
The high incidence of GLRaV-3 in South African vineyards masks the contributions of other viruses to grapevine leafroll disease (LRD) and influences the symptom expression in other diseases. In this project we propose to sequence typical viral diseased vines to determine the basal level of virus infection commonly associated with LRD. Concurrently, we will also sequence control vines that are asymptomatic (healthy) or have atypical symptoms to determine their viral profile.

This study will generate sequence data that will give an unbiased profile of the viruses and their variants found in grapevines affected by leafroll and other diseases. The data will be critical to develop accurate diagnostic tests based on virus sequence like RT-PCR and qRT-PCR, and may identify novel pathogenic, non-pathogenic viruses and possibly naturally occurring virus variants associated with mild stain cross-protection.

Presentation(s)
Maree, H J. 2012. A study of Shiraz and leafroll disease. Paper presented at the 12th Winetech Virus Workshop. 29 May, Stellenbosch, South Africa.

Maree, H J, Nel, Y, Visser, M, Coetzee, B, Manicom, B, Burger, J T and Rees, D J G. 2012. The study of plant virus disease etiology using next-generation sequencing technologies. Paper presented at the 22nd International Conference on Virus and Other Graft Transmissible Diseases of Fruit Crops. 3-8 June, Rome, Italy.

Espach, Y, Maree, H J and Burger, J T. 2012. The use of next-generation sequencing to identify novel mycoviruses in individual grapevine plants. Paper presented at the 17th Congress of the International Council for the
Study of Virus and Virus-like Diseases of the Grapevine (ICVG). 7-14 October 2012, Davis, California, United States.

Maree, H J, Espach, Y, Rees, D J G, Burger, J T. 2012. A study of shiraz disease etiology using next generation sequencing technology. Paper presented at the 17th Congress of the International Council for the study of Virus and Virus-like Diseases of the Grapevine (ICVG). 7 – 14 October 2012, Davis, California, United States.

Espach, Y, Maree, H J, Burger, J T. 2012. The use of next-generation sequencing to identify novel mycoviruses in individual grapevine plants. COST Action FA1103 Workshop: Endophytes in Biotechnology and Agriculture. 14-16 November 2012, Fondazione Edmund Mach, Italy.

Maree, H J. 2012. Progress report GENUS US 11-03. Paper presented at the 11th Winetech Virus Workshop. 29 May 2012. Stellenbosch, South Africa.

Molenaar, N, Maree, H J and Burger, J T. 2013. Determination of the viral diversity associated with grapevine leafroll disease making use of next generation sequencing. Paper presented at the 35th South African Society for Enology and Viticulture Conference. 14-16 November, Somerset West, South Africa.

Maree, H J. 2014. Progress report GENUS US 11-03. Paper presented at the 12th Winetech Virus Workshop. 3 October 2014. Stellenbosch, South Africa.

Molenaar, N, Maree, H J, and Burger, J T. 2014. Determination of the efficiency of next generation sequencing as a diagnostic tool for plant viral diseases. Paper presented at the Agricultural Biotechnology International Conference (ABIC). 5-8 October 2014, Saskatoon, Canada.

Maree, H J, Bester, R, Prie, M D, Pepler, P T, Oosthuizen, K and Burger, J T. 2015. GLRaV-3 diversity, detection and quantitation. Paper presented at the 18th Congress of the International Council for the study of Virus and Virus-like Diseases of the Grapevine (ICVG). 7-11 September 2015, Anakara, Turkey.

Article
Maree, H J, Almeida, R P P, Bester, R, Chooi, K M, Cohen, D, Dolja, V V, Fuchs, M F, Golino, D A, Jooste, A E C, Martelli, G P, Rayapati, N, Rohwani, A, Saldarelli, P, Burger, J T. 2013. Grapevine leafroll-associated virus 3, Frontiers in Microbiology: Virology, Mnth Apr v. 4 (82)
http://dx.doi.org/10.3389%2Ffmicb.2013.00082

Bester, R, Pepler, P T, Burger, J T. 2014. Relative quantitation goes viral: An RT-qPCR assay for a grapevine virus, Journal of Virological Methods, Mnth Dec v. 210 (p. 65-75)
http://doi.org/10.1016/j.jviromet.2014.09.022

Jooste, A E C, Molenaar, N, Maree, H J, Bester, R, Morey, L, De Koker, W C, Burger, J T. 2015. Identification and distribution of multiple virus infections in Grapevine leafroll diseased vineyards, European Journal of Plant Pathology, v. 142 (2) (p. 363-375)
http://doi.org/10.1007/s10658-015-0620-0

Maree, H J, Pirie, M D, Oosthuizen, K, Bester, R, Jasper, D, Rees, G, Burger, J T. 2015. Phylogenomic analysis reveals deep divergence and recombination in an economically important grapevine virus, PLoS ONE, Mnth May v. 10 (5) (p. e0126819)
http://dx.doi.org/10.1371/journal.pone.0126819

Molenaar, N, Burger, J T, Maree, H J. 2015. Detection of a divergent variant of grapevine virus F by next-generation sequencing. Archives of Virology, v. 160 (8) (p. 2125-2127)
http://doi.org/10.1007/s00705-015-2466-3

Naidu, R A, Maree, H J, Burger, J T. 2015. Grapevine Leafroll Disease and Associated Viruses: A Unique Pathosystem, Annual Review of Phytopathology, Mnth Aug v. 53 (p. 613-634)

Chapter
Burger, J T, Maree, H J. 2015. Metagenomic next-generation sequencing of viruses infecting grapevines. 2015. IN: Lacomme, C (ed). Plant Pathology – Techniques and Protocols. Methods in Molecular Biology. v. 1302 (p. 315-330)
http://doi.org/10.1007/978-1-4939-2620-6_23

Paper
Maree, H J, Nel, Y, Visser, M, Coetzee, B, Manicom, B, Burger, J T, Rees, D J G. 2012. The study of plant virus disease etiology using next-generation sequencing technologies, IN: Proceedings of the 22nd International Conference on Virus and Other Graft Transmissible Diseases of Fruit Crops. 3-8 June 2012, Rome, Italy. (p. 283)

FinalReport.pdf

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