The Plant Negative-Sense RNA Virosphere: Virus Discovery Through New Eyes

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.

Next-Generation Sequencing Reveals a Novel Emaravirus in Diseased Maple Trees From a German Urban Forest

“…During the last decade a significant number of novel DNA and RNA viruses ( Villamor et al, 2019 ) and viroids ( Hadidi, 2019 ) have been uncovered in herbaceous as well as in woody hosts by applying a wide range of NGS methods for virus detection and discovery ( Hadidi et al, 2016 ; Olmos et al, 2018 ; Villamor et al, 2019 ). In comparison to other viruses, emaraviruses were until recently overlooked, not only when applying conventional methods, but also by metagenomic studies ( Bejerman et al, 2020 ). The application of NGS resulted in the discovery of 13 emaraviruses during the last 5 years ( Bejerman et al, 2020 ).…”

“…In comparison to other viruses, emaraviruses were until recently overlooked, not only when applying conventional methods, but also by metagenomic studies ( Bejerman et al, 2020 ). The application of NGS resulted in the discovery of 13 emaraviruses during the last 5 years ( Bejerman et al, 2020 ). By employing NGS methodologies a significant presence of emaraviruses in forests has been revealed.…”

A novel emaravirus identified in maple with leaf mottle symptoms by deep sequencing

“…Until recently, only a low number of viral agents in forest trees had been characterized, due to two main reasons; (a) biased sampling based on a narrow focus on agricultural crops and fruit trees viruses (Büttner et al, 2013) and (b) a general bias against the identification of the most divergent genomes (Zhang et al, 2018). Emaraviruses are negative-sense single-stranded viruses that were until recently overlooked, not only when applying conventional methods, but also by metagenomic studies (Bejerman et al, 2020). The application of HTS resulted in the discovery of 13 emaraviruses during the last five years (Bejerman et al, 2020).…”

“…Emaraviruses are negative-sense single-stranded viruses that were until recently overlooked, not only when applying conventional methods, but also by metagenomic studies (Bejerman et al, 2020). The application of HTS resulted in the discovery of 13 emaraviruses during the last five years (Bejerman et al, 2020). Employing deep sequencing methodologies significant presence of emaraviruses in forests has been revealed.…”

Table_1.DOC

“…During the last decade a significant number of novel DNA and RNA viruses (Villamor et al, 2019) and viroids (Hadidi, 2019) have been uncovered in herbaceous as well as in woody hosts by applying a wide range of NGS methods for virus detection and discovery (Hadidi et al, 2016;Olmos et al, 2018;Villamor et al, 2019). In comparison to other viruses, emaraviruses were until recently overlooked, not only when applying conventional methods, but also by metagenomic studies (Bejerman et al, 2020). The application of NGS resulted in the discovery of 13 emaraviruses during the last 5 years (Bejerman et al, 2020).…”