A metagenomic sequencing approach to elucidate Shiraz disease etiology


Project Number
GENUS 10-01

Project title
A metagenomic sequencing approach to elucidate Shiraz disease etiology

Project leader
Burger, J T

Institution
University of Stellenbosch. Faculty of AgriSciences. Department of Genetics

Team members
Burger, J T
Stephan, D
Maree, H J
Spreeth, N
Oosthuizen, T

Project description
Virus diseases detrimentally affect both the quality and quantity of grapevine fruit production, and the longevity of infected vineyards. The major viral disease in South African vineyards is leafroll, however, new diseases, such as Shiraz disease (SD) and Shiraz decline are becoming more prevalent. The etiological agents of these diseases are unclear at present. The aim of this project is to elucidate the complex viral disease etiology associated with Shiraz disease with a metagenomic sequencing approach using the latest technology in next generation sequencing.

Objectives of the project:
1. identify the viruses (incl. variants) associated with Shiraz disease through deep sequencing of diseased and healthy plants.
2. design accurate diagnostic assays for Shiraz disease and confirm association of viruses (incl. variants) in larger survey.
3. determine the biological contributions of individual viruses to the etiology of Shiraz disease.
4. plan effective disease control strategies.

Poster(s)
Maree, H J, Coetzee, B, Nel, Y, Burger, J T and Rees, D J G. 2011. Unravelling the complexity of grapevine viral diseases using next generation sequencing. Poster presented at the Africa Virology Conference. 29 November – 2 December, Cape Town, South Africa.

Maree, H J, Coetzee, B, Nel, Y, Burger, J T and Rees, D J G. 2011. Unravelling the complexity of grapevine viral diseases using next-generation sequencing. Poster presented at the Agricultural Biotechnology International Conference. 6-9 September, Johannesburg, South Africa.

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

Presentation(s)
Maree, H J. 2010. A metagenomic sequencing approach to elucidate Shiraz disease aetiology. Presentation at the 10th Winetech Virus Workshop. Stellenbosch, South Africa.

Maree, H J. 2012. Study of grapevine viral diseases using next-generation sequencing technology: A study of Shiraz and leafroll disease. Paper presented at the 12th Winetech Virus Workshop. 29 May, Stellenbosch, South Africa.

Coetzee, B, Maree, H J, Nel, Y, Rees, D J G and Burger, J T. 2011. The use of next-generation sequencing in metagenomic studies of plant viruses. Paper presented at the Virology Africa Conference. 29 November – 2 December 2011, Cape Town, South Africa.

Maree, H J, Coetzee, B, Nel, Y, Burger, J T and Rees, D J G. 2011. Unravelling the complexity of grapevine viral diseases using next-generation sequencing. Paper presented at the Virology Africa Conference. 29 November – 2 December 2011, Cape Town, 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 International Council for the Study of Virus and Virus-like Diseases of the Grapevine. 7-14 October, Davis, California, United States.

Espach, Y, Maree, H J and Burger, J T. 2012. The use of next-generation sequencing to identify novel mycoviruses in single grapevine plants. Paper presented at the 34th National Congress of the South African Society for Enology and Viticulture. 14-16 November, Stellenbosch, South Africa.

Maree, H J, Espach, Y, Smyth, N, Rees, D J G and Burger, J T. 2012. A study of Shiraz disease etiology using next-generation sequencing technology. Paper presented at the 34th National Congress of the South African Society for Enology and Viticulture. 14-16 November, Somerset West, South Africa.

Article
Espach, Y, Maree, H J, Burger, J T. 2012. The complete genome of a novel endornavirus assembled from next-generation sequence data, Journal of Virology, Mnth Dec v. 86 (23) (p. 13142)
http://dx.doi.org/10.1128/JVI.02538-12 http://jvi.asm.org/content/86/23/13142.full

Paper
Maree, H J, Espach, Y, Rees, D J G, Burger, J T. Furgeson, B (ed). 2012. Study of Shiraz disease etiology using next-generation sequencing technology, IN: Ferguson, B (ed). 2012. Proceedings of the 17th Congress of the International Council for the Study of Virus and Virus-like Diseases of the Grapevine. 7-14 October 2012, Davis, California, United States. (p. 100-101) Foundation Plant Services, University of California, Davis, California.
http://ucanr.edu/sites/ICVG/files/156711.pdf

FinalReport.pdf

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