Target prediction of candidate miRNAs from Oryza sativa for silencing the RYMV genome

Basit Jabbar; Muhammad Shahzad Iqbal; Anicet A Batcho; Idrees A Nasir; Bushra Rashid; Tayyab Husnain; Robert J Henry

doi:10.1016/j.compbiolchem.2019.107127

Target prediction of candidate miRNAs from Oryza sativa for silencing the RYMV genome

Comput Biol Chem. 2019 Dec:83:107127. doi: 10.1016/j.compbiolchem.2019.107127. Epub 2019 Sep 13.

Authors

Basit Jabbar¹, Muhammad Shahzad Iqbal², Anicet A Batcho³, Idrees A Nasir⁴, Bushra Rashid⁵, Tayyab Husnain⁶, Robert J Henry⁷

Affiliations

¹ Center of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan. Electronic address: basit.ibb.pu@gmail.com.
² Center of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan; Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, Australia. Electronic address: shahzad.iqbal@cemb.edu.pk.
³ Center of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan. Electronic address: batcho.anicet@cemb.edu.pk.
⁴ Center of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan. Electronic address: idreesnasir.cemb@pu.edu.pk.
⁵ Center of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan. Electronic address: bushra.cemb@pu.edu.pk.
⁶ Center of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan. Electronic address: tayyabhusnain@yahoo.com.
⁷ Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, Australia. Electronic address: robert.henry@uq.edu.au.

PMID: 31542706
DOI: 10.1016/j.compbiolchem.2019.107127

Abstract

In order to maintain a consistent supply of rice globally, control of pathogens affecting crop production is a matter of due concern. Rice yellow mottle virus(RYMV) is known to cause a variety of symptoms which can result in reduced yield. Four ORFs can be identified in the genome of RYMV encoding for P1 (ORF1), Polyprotein (processed to produce VPg, protease, helicase, RdRp4) (ORF2), putative RdRp (ORF3) and capsid/coat protein (ORF4). This research was aimed at identifying genome encoded miRNAs of O. sativa that are targeted to the genome of Rice Yellow Mottle Virus (RYMV). A consensus of four miRNA target prediction algorithms (RNA22, miRanda, TargetFinder and psRNATarget) was computed, followed by calculation of free energies of miRNA-mRNA duplex formation. A phylogenetic tree was constructed to portray the evolutionary relationships between RYMV strains isolated to date. From the consensus of algorithms used, a total of seven O. sativa miRNAs were predicted and conservation of target site was finally evaluated. Predicted miRNAs can be further evaluated by experiments involving the testing of the success of in vitro gene silencing of RYMV genome; this can pave the way for development of RYMV resistant rice varieties in the future.

Keywords: Gene silencing; Oryza sativa; Rice yellow mottle virus; Target prediction; miRNAs.

MeSH terms

Gene Silencing*
Genome, Viral / genetics*
MicroRNAs / genetics*
Oryza / genetics*
Oryza / virology*
Plant Viruses / genetics*

Substances

MicroRNAs

Supplementary concepts

Rice yellow mottle virus