Abstract
The use of high-throughput sequencing (HTS) for virus diagnostics, as well as the importance of this technology as a valuable tool for discovery of novel viruses has been extensively investigated. In this review, we consider the application of HTS approaches to uncover novel plant viruses with a focus on the negative-sense, single-stranded RNA virosphere. Plant viruses with negative-sense and ambisense RNA (NSR) genomes belong to several taxonomic families, including Rhabdoviridae, Aspiviridae, Fimoviridae, Tospoviridae, and Phenuiviridae. They include both emergent pathogens that infect a wide range of plant species, and potential endophytes which appear not to induce any visible symptoms. As a consequence of biased sampling based on a narrow focus on crops with disease symptoms, the number of NSR plant viruses identified so far represents only a fraction of this type of viruses present in the virosphere. Detection and molecular characterization of NSR viruses has often been challenging, but the widespread implementation of HTS has facilitated not only the identification but also the characterization of the genomic sequences of at least 70 NSR plant viruses in the last 7 years. Moreover, continuing advances in HTS technologies and bioinformatic pipelines, concomitant with a significant cost reduction has led to its use as a routine method of choice, supporting the foundations of a diverse array of novel applications such as quarantine analysis of traded plant materials and genetic resources, virus detection in insect vectors, analysis of virus communities in individual plants, and assessment of virus evolution through ecogenomics, among others. The insights from these advancements are shedding new light on the extensive diversity of NSR plant viruses and their complex evolution, and provide an essential framework for improved taxonomic classification of plant NSR viruses as part of the realm Riboviria. Thus, HTS-based methods for virus discovery, our ‘new eyes,’ are unraveling in real time the richness and magnitude of the plant RNA virosphere.
Highlights
Viruses are the most numerous biological entities on Earth, but the number of reported and formally described virus species, the known virosphere, is exiguous
The number of negative-sense and ambisense RNA (NSR) plant viruses identified so far represents a negligible fraction of the potential number of NSR viruses present in the virosphere
The discovery and in-depth molecular characterization of these viruses has been challenging given their extensive divergence, their outstanding diversity in terms of genomic architecture, and mostly, the negligible share of plant species studied for virus discovery
Summary
Viruses are the most numerous biological entities on Earth, but the number of reported and formally described virus species, the known virosphere, is exiguous. The use of HTS technologies has allowed the identification and characterization of novel NSR viruses in several plant hosts (Table 1), but has enabled the completion of genome sequences of NSR viruses for which biological properties and only partial genome fragments were known (Table 2).
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