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.

高通量测序（HTS）用于病毒诊断的方法以及该技术作为发现新型病毒的有价值工具的重要性已得到广泛研究。在这篇综述中，我们考虑将HTS方法应用于发现新型植物病毒，重点是负义单链RNA病毒层。具有负义和歧义RNA（NSR）基因组的植物病毒属于几个分类学家族，包括横纹病毒科，斜纹病毒科，菲莫病毒科，弓形病毒科和 hen病毒科。它们既包括感染广泛植物物种的紧急病原体，又包括似乎不会引起任何可见症状的潜在内生菌。由于偏向于对具有疾病症状的农作物的偏狭取样而导致的结果是，到目前为止，鉴定出的NSR植物病毒数量仅代表病毒层中这种病毒的一小部分。NSR病毒的检测和分子表征通常具有挑战性，但是在过去7年中，HTS的广泛实施不仅促进了至少70种NSR植物病毒的鉴定，而且还促进了基因组序列的表征。此外，HTS技术和生物信息学管道的不断进步，伴随着成本的大幅降低，使其成为常规的选择方法，支持各种新颖应用程序的基础，例如对贸易植物材料和遗传资源的隔离分析，昆虫载体中的病毒检测，单个植物中的病毒群落分析以及通过生态基因组学评估病毒进化等。这些进步的见解为NSR植物病毒的广泛多样性及其复杂进化提供了新的思路，并为改进植物NSR病毒作为该领域的分类标准提供了必要的框架。核病毒。因此，基于HTS的病毒发现方法（我们的“新眼睛”）实时揭示了植物RNA病毒层的丰富程度和大小。