Prediction of Host-Derived miRNAs with the Potential to Target PVY in Potato Plants

Abstract

Potato virus Y has emerged as a threatening problem in all potato growing areas around the globe. PVY reduces the yield and quality of potato cultivars. During the last 30 years, significant genetic changes in PVY strains have been observed with an increased incidence associated with crop damage. In the current study, computational approaches were applied to predict Potato derived miRNA targets in the PVY genome. The PVY genome is approximately 9 thousand nucleotides, which transcribes the following 6 genes:CI, NIa, NIb-Pro, HC-Pro, CP, and VPg. A total of 343 mature miRNAs were retrieved from the miRBase database and were examined for their target sequences in PVY genes using the minimum free energy (mfe), minimum folding energy, sequence complementarity and mRNA-miRNA hybridization approaches. The identified potato miRNAs against viral mRNA targets have antiviral activities, leading to translational inhibition by mRNA cleavage and/or mRNA blockage. We found 86 miRNAs targeting the PVY genome at 151 different sites. Moreover, only 36 miRNAs potentially targeted the PVY genome at 101 loci. The CI gene of the PVY genome was targeted by 32 miRNAs followed by the complementarity of 26, 19, 18, 16, and 13 miRNAs. Most importantly, we found 5 miRNAs (miR160a-5p, miR7997b, miR166c-3p, miR399h, and miR5303d) that could target the CI, NIa, NIb-Pro, HC-Pro, CP, and VPg genes of PVY. The predicted miRNAs can be used for the development of PVY-resistant potato crops in the future.

Integrated mRNA and microRNA transcriptome analysis reveals miRNA regulation in response to PVA in potato

“…Overexpression of stu-miR482e down-regulated the target gene NBS-LRR protein, and enhanced sensitivity to Verticillium dahliae infection in potato 16 . Using a computational approach, 36 miRNAs were found to potentially target the PVY genome at 101 loci 17 . The co-infection of Nicotiana benthamiana with PVX or PVY altered the accumulation of miR156, miR171, miR168 and miR398 and their target transcripts 18 .…”

An Algorithmic framework for genome-wide identification of Sugarcane (Saccharum officinarumL.)-encoded microRNA targets against SCBV

“…Previous studies have also reported the silencing of plant viruses using host-derived miRNAs applying a set of computational algorithms. Identification and evaluation of best-fit candidate miRNA targets of different crops plants was concluded successfully in PVY [54], maize chlorotic mottle virus (MCMV) [55], CLCuKoV-Bu [56], RYMV [57] and SCBGAV to find miRNA-target interaction [58]. We have designed the same novel bioinformatics approach for target prediction in the SCBV genome to control the emerging badnavirus in sugarcane cultivars.…”

In silico MCMV Silencing Concludes Potential Host-Derived miRNAs in Maize

“…miRanda algorithm (John et al, 2004) has been used for plant miRNA target prediction (Archak and Nagaraju, 2007; Iqbal et al, 2016). It considers the properties of sequence complementarity, free energy of RNA-RNA duplex and cross-species conservation of the target site to produce the output which is a weighted sum of match and mismatch scores for base pairs and gap penalties.…”

“…RNA silencing, through miRNAs present in host plant species, thus imparts natural immunity and resistance to the host against foreign genetic elements including plant viruses (Qu et al, 2007; Iqbal et al, 2016). In maize genome, 321 mature miRNAs have been found (Griffiths-Jones et al, 2008; Kozomara and Griffiths-Jones, 2014); a subset of these mature miRNAs in Zea mays should have targets in MCMV genome and these miRNAs, once identified, can be expressed through cloning to enhance the resistance against infection from MCMV (Ali et al, 2014, 2016).…”