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.

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Virus symptoms on the leaves of indigenous ornamental plants (Ornithogalum, Lachenalia and Eucomis)
sampled for virus discovery through Next generation sequencing (NGS).

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Full genome coverage was obtained for some viruses, e.g. Nerine latent virus (NeLV) in an Ornithogalum sample.
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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).

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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 reads).



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

Reference

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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