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Plant viruses cause many important diseases and are responsible for reducing crop yield and quality throughout the world. Fast and accurate identification of viruses in a sample is desirable for inspection, quarantine services and disease management. Recently, Next-generation sequencing (NGS) techniques have been developed that represent a flexible approach to plant pathogen detection. Since 2009, NGS techniques have begun to apply in some areas of plant virology consisting of virus/viroid genome sequencing, detection, and discovery, ecology, and epidemiology. The NGS techniques are rapid, highly efficient, and low cost, and allow the sequencing of many data gigabases in a few hours. It’s a generic approach to virus/viroid identification that requires no prior knowledge of the host or virus. Only by sequencing of total small RNAs in an NGS run, identification of DNA/RNA containing viruses and viroids are possible. This article reviews the rapid and recent achievement in the applying of NGS techniques for the diagnosis of viruses and viroids in their hosts.

Keywords: next generation sequencing, identification, virus, viroid, platform, plant pathology

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