Next-generation sequencing (NGS) provides an efficient unbiased method to determine the entire virus population (virome) of symptomatic plants. This strategy enabled the discovery of new viruses and identified new genetic variants of existing viruses occurring in indigenous South African ornamental plants.
Virus symptoms on the leaves of indigenous ornamental plants (Ornithogalum, Lachenalia and
sampled for virus discovery through Next generation sequencing (NGS).
This is a representation of a full virus genome (polyprotein open
reading frame (ORF) represented by the yellow arrow) and how it is covered
(coverage graph in pink) by sequence reads obtained with NGS (blue lines
represent paired reads).
Paired sequence reads are indicated in blue, while single reads or a
broken pair is indicated in green (for forward reads) and red (for reverse
Viral genome sequence information will allow crop protection specialists to develop rapid and sensitive sequence-specific molecular diagnostic tools. Accurate virus diagnoses is essential to develop and recommend integrated disease management (IDM) strategies to producers, to improve their productivity of export quality products.
Contact: Dr Inge Gazendam
Gazendam I., Cloete M., Maree H.J., Visser M., Burger J.T. and Oelofse D. 2017. Identification of viruses infecting indigenous ornamental bulbous plants in South Africa using Next Generation Sequencing. 50th Anniversary congress of the Southern African Society for Plant Pathology (SASPP), Champagne Sports Resort, Drakensberg, South Africa, 15-17 January 2017.
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