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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...

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Autores principales: Iqbal, Muhammad S., Hafeez, Muhammad N., Wattoo, Javed I., Ali, Arfan, Sharif, Muhammad N., Rashid, Bushra, Tabassum, Bushra, Nasir, Idrees A.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2016
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5022016/
https://www.ncbi.nlm.nih.gov/pubmed/27683585
http://dx.doi.org/10.3389/fgene.2016.00159
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author Iqbal, Muhammad S.
Hafeez, Muhammad N.
Wattoo, Javed I.
Ali, Arfan
Sharif, Muhammad N.
Rashid, Bushra
Tabassum, Bushra
Nasir, Idrees A.
author_facet Iqbal, Muhammad S.
Hafeez, Muhammad N.
Wattoo, Javed I.
Ali, Arfan
Sharif, Muhammad N.
Rashid, Bushra
Tabassum, Bushra
Nasir, Idrees A.
author_sort Iqbal, Muhammad S.
collection PubMed
description 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.
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spelling pubmed-50220162016-09-28 Prediction of Host-Derived miRNAs with the Potential to Target PVY in Potato Plants Iqbal, Muhammad S. Hafeez, Muhammad N. Wattoo, Javed I. Ali, Arfan Sharif, Muhammad N. Rashid, Bushra Tabassum, Bushra Nasir, Idrees A. Front Genet Genetics 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. Frontiers Media S.A. 2016-09-14 /pmc/articles/PMC5022016/ /pubmed/27683585 http://dx.doi.org/10.3389/fgene.2016.00159 Text en Copyright © 2016 Iqbal, Hafeez, Wattoo, Ali, Sharif, Rashid, Tabassum and Nasir. http://creativecommons.org/licenses/by/4.0/ 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) or licensor 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.
spellingShingle Genetics
Iqbal, Muhammad S.
Hafeez, Muhammad N.
Wattoo, Javed I.
Ali, Arfan
Sharif, Muhammad N.
Rashid, Bushra
Tabassum, Bushra
Nasir, Idrees A.
Prediction of Host-Derived miRNAs with the Potential to Target PVY in Potato Plants
title Prediction of Host-Derived miRNAs with the Potential to Target PVY in Potato Plants
title_full Prediction of Host-Derived miRNAs with the Potential to Target PVY in Potato Plants
title_fullStr Prediction of Host-Derived miRNAs with the Potential to Target PVY in Potato Plants
title_full_unstemmed Prediction of Host-Derived miRNAs with the Potential to Target PVY in Potato Plants
title_short Prediction of Host-Derived miRNAs with the Potential to Target PVY in Potato Plants
title_sort prediction of host-derived mirnas with the potential to target pvy in potato plants
topic Genetics
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5022016/
https://www.ncbi.nlm.nih.gov/pubmed/27683585
http://dx.doi.org/10.3389/fgene.2016.00159
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