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Plant miRNAome and antiviral resistance: a retrospective view and prospective challenges

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Abstract

MicroRNAs (miRNAs) are small regulatory RNAs that play a defining role in post-transcriptional gene silencing of eukaryotes by either mRNA cleavage or translational inhibition. Plant miRNAs have been implicated in innumerable growth and developmental processes that extend beyond their ability to respond to biotic and abiotic stresses. Active in an organism’s immune defence response, host miRNAs display a propensity to target viral genomes. During viral invasion, these virus-targeting miRNAs can be identified by their altered expression. All the while, pathogenic viruses, as a result of their long-term interaction with plants, have been evolving viral suppressors of RNA silencing (VSRs), as well as viral-encoded miRNAs as a counter-defence strategy. However, the gene silencing attribute of miRNAs has been ingeniously manipulated to down-regulate the expression of any gene of interest, including VSRs, in artificial miRNA (amiRNA)-based transgenics. Since we currently have a better understanding of the intricacies of miRNA-mediated gene regulation in plant–virus interactions, the majority of miRNAs manipulated to confer antiviral resistance to date are in plants. This review will share the insights gained from the studies of plant-virus combat and from the endeavour to manipulate miRNAs, including prospective challenges in the context of the evolutionary dynamics of the viral genome. Next generation sequencing technologies and bioinformatics analysis will further delineate the molecular details of host–virus interactions. The need for appropriate environmental risk assessment principles specific to amiRNA-based virus resistance is also discussed.

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Abbreviations

amiRNA:

Artificial miRNA

DCL1:

Dicer-like 1

ERA:

Environmental risk assessment

EST:

Expressed sequence tag

hpRNA:

Hairpin RNA

ihpRNA:

Intron-spliced hairpin RNA

miRNA:

MicroRNA

NBS–LRR:

Nucleotide binding site–leucine-rich repeat

NGS:

Next generation sequencing

ncRNAs:

Non-coding RNAs

Pre-miRNA:

Precursor miRNA

Pri-miRNA:

Primary miRNA

RISC:

RNA-induced silencing complex

PTGS:

Post-transcriptional gene silencing

RNAi:

RNA interference

siRNA:

Small interfering RNA

SMRT:

Single molecule real time

tasiRNA:

Transacting siRNA

VSRs:

Viral suppressors of RNA silencing

VRTP:

Virus resistant transgenic plants

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Acknowledgments

The authors express their gratitude to Dr. S.K. Srivastava, Director, Directorate of Soybean Research, Indore, for providing amenities during the study. The work is an integral part of the Directorate’s Institute Research Council (IRC) approved project (Project ID: DSR 1.24/12).

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  1. Directorate of Soybean Research, Indian Council of Agricultural Research (ICAR), Khandwa Road, Indore, 452001, Madhya Pradesh, India

    Shunmugiah Veluchamy Ramesh, Milind B. Ratnaparkhe, Giriraj Kumawat, Girish Kumar Gupta & Syed Masroor Husain

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  1. Shunmugiah Veluchamy Ramesh
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Ramesh, S.V., Ratnaparkhe, M.B., Kumawat, G. et al. Plant miRNAome and antiviral resistance: a retrospective view and prospective challenges. Virus Genes 48, 1–14 (2014). https://doi.org/10.1007/s11262-014-1038-z

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