Prediction of Host-Derived miRNAs with the Potential to Target PVY in Potato Plants.
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.
Centre of Excellence in Molecular Biology, University of the Punjab Lahore, Pakistan.
Muhammad S
MS
Iqbal
Centre of Excellence in Molecular Biology, University of the Punjab Lahore, Pakistan.
Muhammad N
MN
Hafeez
Faculty of Life Sciences, University of Central Punjab Lahore, Pakistan.
Javed I
JI
Wattoo
Centre of Excellence in Molecular Biology, University of the PunjabLahore, Pakistan; Institute of Molecular Biology and Biotechnology, The University of LahoreLahore, Pakistan.
Arfan
A
Ali
Centre of Excellence in Molecular Biology, University of the Punjab Lahore, Pakistan.
Muhammad N
MN
Sharif
Centre of Excellence in Molecular Biology, University of the Punjab Lahore, Pakistan.
Bushra
B
Rashid
Centre of Excellence in Molecular Biology, University of the Punjab Lahore, Pakistan.
Bushra
B
Tabassum
Centre of Excellence in Molecular Biology, University of the Punjab Lahore, Pakistan.
Idrees A
IA
Nasir
RNA hybrid; RNA-22; Solanum tuberosum; miRanda; microRNA; potato; potato virus Y; target prediction
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