High throughput sequencing for plant virus detection and discovery

Authors: VILLAMOR, D - University Of Arkansas; HO, T - University Of Arkansas; AL RWAHNIH, M - University Of California, Davis; Martin, Robert; TZANETAKIS, I - University Of Arkansas

Submitted to: Phytopathology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/20/2019
Publication Date: 5/9/2019
Citation: Villamor, D.E., Ho, T., Al Rwahnih, M., Martin, R.R., Tzanetakis, I.E. 2019. High throughput sequencing for plant virus detection and discovery. Phytopathology. 109(5):716-725. https://doi.org/10.1094/PHYTO-07-18-0257-RVW.
DOI: https://doi.org/10.1094/PHYTO-07-18-0257-RVW

Interpretive Summary: There have been great strides in sequencing and bioinformatic technologies over the past decade. Virologists have discovered an unprecedented number of viruses using high throughput sequencing (HTS), which has increased our understanding on virus diversity in natural and agricultural systems. However, these new virus discoveries have often identified gaps in our understanding of virus biology. In particular, many new viruses have been identified, without an understanding if they have any role as causal agents in a disease, though the information developed often leads to knew insights into the importance of virus complexes in causing disease. As international trade in agriculture increases, the 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 viruses. Concurrent with development of the sequencing technologies many pipelines have been developed to analyze the massive amounts of data generated. A description of the more common sequencing platforms in use today, along with the process of plant virus detection and discovery from HTS data is presented, providing a summary of the different pipelines available for scientists to use in their research.

Technical Abstract: 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 unravelling 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 is presented, providing a summary of the different pipelines available for scientists’ utility in their research.