Small RNA-Omics for Plant Virus Identification, Virome Reconstruction, and Antiviral Defense Characterization.

Mikhail M Pooggin

doi:10.3389/fmicb.2018.02779

Abstract

RNA interference (RNAi)-based antiviral defense generates small interfering RNAs that represent the entire genome sequences of both RNA and DNA viruses as well as viroids and viral satellites. Therefore, deep sequencing and bioinformatics analysis of small RNA population (small RNA-ome) allows not only for universal virus detection and genome reconstruction but also for complete virome reconstruction in mixed infections. Viral infections (like other stress factors) can also perturb the RNAi and gene silencing pathways regulating endogenous gene expression and repressing transposons and host genome-integrated endogenous viral elements which can potentially be released from the genome and contribute to disease. This review describes the application of small RNA-omics for virus detection, virome reconstruction and antiviral defense characterization in cultivated and non-cultivated plants. Reviewing available evidence from a large and ever growing number of studies of naturally or experimentally infected hosts revealed that all families of land plant viruses, their satellites and viroids spawn characteristic small RNAs which can be assembled into contigs of sufficient length for virus, satellite or viroid identification and for exhaustive reconstruction of complex viromes. Moreover, the small RNA size, polarity and hotspot profiles reflect virome interactions with the plant RNAi machinery and allow to distinguish between silent endogenous viral elements and their replicating episomal counterparts. Models for the biogenesis and functions of small interfering RNAs derived from all types of RNA and DNA viruses, satellites and viroids as well as endogenous viral elements are presented and discussed.

Highlights

Viral small RNAs have been discovered in Nicotiana benthamiana plants inoculated with potato virus X using RNA blot hybridization, and their abundance was found to gradually increase in the time course of viral infection (Hamilton and Baulcombe, 1999)
Small RNA-Omics in Plant Virology deep sequencing can be used for virus detection and assembly of viral genomes from fungi (Vainio et al, 2015; Yaegashi et al, 2016; Donaire and Ayllón, 2017; Velasco et al, 2018) and from invertebrate animals (Wu et al, 2010; Aguiar et al, 2015; Fung et al, 2018), including insect vectors of the plant viruses transmitted in a propagative manner (Xu et al, 2012; Fletcher et al, 2016; de Haro et al, 2017)
This review illustrates the mechanisms of viral small interfering RNAs (siRNAs) biogenesis and action in the aforementioned angiosperm plant species infected with RNA and DNA viruses (Figures 2–4) and, based on analysis of the available small RNA-seq data (Supplementary Tables S1, S2 and Supplementary List S1), discusses possible conservation of these mechanisms in other angiosperm and nonangiosperm plants infected with all types of viruses, satellites, and viroids

Summary

Introduction

Viral small RNAs have been discovered in Nicotiana benthamiana plants inoculated with potato virus X (genus Potexvirus, family Alphaflexiviridae) using RNA blot hybridization, and their abundance was found to gradually increase in the time course of viral infection (Hamilton and Baulcombe, 1999). This review illustrates the mechanisms of viral siRNA biogenesis and action in the aforementioned angiosperm plant species infected with RNA and DNA viruses (Figures 2–4) and, based on analysis of the available small RNA-seq data (Supplementary Tables S1, S2 and Supplementary List S1), discusses possible conservation of these mechanisms in other angiosperm and nonangiosperm plants infected with all types of viruses, satellites, and viroids.

Results

Conclusion