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Phytopathology. 2019 May;109(5):716-725. doi: 10.1094/PHYTO-07-18-0257-RVW. Epub 2019 Apr 1.

High Throughput Sequencing For Plant Virus Detection and Discovery.

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1 Department of Plant Pathology, Division of Agriculture, University of Arkansas System, Fayetteville, AR 72701.
2 Department of Plant Pathology, University of California, Davis 95616; and.
3 Horticulture Crops Research Unit, U.S. Department of Agriculture-Agricultural Research Service, Corvallis, OR 97330.


Over the last decade, virologists have discovered an unprecedented number of viruses using high throughput sequencing (HTS), which led to the advancement of our knowledge on the diversity of viruses in nature, particularly unraveling the virome of many agricultural crops. However, these new virus discoveries have often widened the gaps in our understanding of virus biology; the forefront of which is the actual role of a new virus in disease, if any. Yet, when used critically in etiological studies, HTS is a powerful tool to establish disease causality between the virus and its host. Conversely, with globalization, movement of plant material is increasingly more common and often a point of dispute between countries. HTS could potentially resolve these issues given its capacity to detect and discover. Although many pipelines are available for plant virus discovery, all share a common backbone. A description of the process of plant virus detection and discovery from HTS data are presented, providing a summary of the different pipelines available for scientists' utility in their research.


certification; clean plant; disease control and pest management; etiology; high throughput sequencing; techniques; virology; virus detection pipelines; virus discovery

[Indexed for MEDLINE]

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