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Front. Microbiol. | doi: 10.3389/fmicb.2018.02779

Small RNA-omics for plant virus identification, virome reconstruction and antiviral defense characterization

  • 1Institut National de la Recherche Agronomique Centre Montpellier, France

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

Keywords: small RNA, RNA Interference, siRNA - small interfering RNA, Antiviral defense, Next generation sequencing (NGS), bioinformatics, Virus diagnostics, virome reconstruction

Received: 01 Oct 2018; Accepted: 30 Oct 2018.

Edited by:

Annette Niehl, Julius Kühn-Institut, Germany

Reviewed by:

Francesco Di Serio, Istituto per la Protezione Sostenibile delle Piante, Sede secondaria di Bari, Italy
CARMEN HERNANDEZ, Instituto de Biología Molecular y Celular de Plantas (IBMCP), Spain  

Copyright: © 2018 Pooggin. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

* Correspondence: Dr. Mikhail M. Pooggin, Institut National de la Recherche Agronomique Centre Montpellier, Montpellier, France, mikhail.pooggin@inra.fr