Harnessing plant viruses in the metagenomics era: from the development of infectious clones to applications

Recent metagenomic studies which focused on virus characterization in the entire plant environment have revealed a remarkable viral diversity in plants. The exponential discovery of viruses also requires the concomitant implementation of high-throughput methods to perform their functional characterization. Despite several limitations, the development of viral infectious clones remains a method of choice to understand virus biology, their role in the phytobiome, and plant resilience. Here, we review the latest approaches for efficient characterization of plant viruses and technical advances built on high-throughput sequencing and synthetic biology to streamline assembly of viral infectious clones. We then discuss the applications of plant viral vectors in fundamental and applied plant research as well as their technical and regulatory limitations, and we propose strategies for their safer field applications.

Automated summary

Recent metagenomic studies have revealed a diverse range of viruses in plants, and high-throughput methods are needed to study their functions. The development of viral infectious clones is a preferred method to understand virus biology and their role in plant ecosystems. This review discusses efficient approaches for characterizing plant viruses, technological advances in high-throughput sequencing and synthetic biology to assemble viral infectious clones, applications of plant viral vectors in research, and proposals for safer field applications.