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In Silico Plum Pox Virus Silencing Via Host-retrieved miRNAs in Peach Plant


Affiliations
1 Department of Botany, Division of Science and Technology, University of Education, Lahore, Pakistan
2 Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
3 Science and Research College of Nursing, Ummal Qura University, Makkah, Saudi Arabia
4 Department of Botany, Lahore College for Woman University, Lahore, Pakistan
 

Peach (Prunus persica) is a deciduous, edible, stone fruit producing plant, belonging to the family Rosaceae. The plant is prone to various pathogens and one of them is the plum pox virus (PPV). This is a lethal virus of peach plant causing pox disease of plum. Its attack results in 83%–100% yield loss in highly susceptible varieties of peach plant. The complete genome of PPV is 9791 base pairs with positive-sense single strand. The full-length genome of PPV encodes a large polyprotein initially, which cleaves proteolytically into ten mature proteins – coat protein, helper component proteinase, P1, P3, viral genome-linked protein, 6K1, 6K2, cylindrical inclusion protein, cylindrical inclusion protein b and NIa-pro-proteins. The objective of this study is to identify such sites in the PPV genome which can be targeted by PPV-derived miRNAs through target prediction computational tools/algorithms. A total of 214 mature miRNAs were chosen from the miRNA data­base to check their complementarity with the PPV genome. Minimum free energy, folding energy, seed pairing, target-site accessibility, pattern recognition and multiple target sites were the parameters considered for target prediction algorithms. Two out of 214 miRNAs were predicted as potential against plum pox virus by three of four tools used for target prediction. Thus, the results encourage generating transgenic, PPV-resi­stant peach plants by expression of predicted miRNAs.

Keywords

miRNAs, Peach Plant, Plum Pox Virus, Yield Loss, Target Prediction Algorithms.
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  • In Silico Plum Pox Virus Silencing Via Host-retrieved miRNAs in Peach Plant

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Authors

Muhammad Naveed Shahid
Department of Botany, Division of Science and Technology, University of Education, Lahore, Pakistan
Syeda Shehnaz
Department of Botany, Division of Science and Technology, University of Education, Lahore, Pakistan
Muhammad Shehzad Iqbal
Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
Aneela Shabbeer
Department of Botany, Division of Science and Technology, University of Education, Lahore, Pakistan
Adil Jamal
Science and Research College of Nursing, Ummal Qura University, Makkah, Saudi Arabia
Sana Khalid
Department of Botany, Lahore College for Woman University, Lahore, Pakistan

Abstract


Peach (Prunus persica) is a deciduous, edible, stone fruit producing plant, belonging to the family Rosaceae. The plant is prone to various pathogens and one of them is the plum pox virus (PPV). This is a lethal virus of peach plant causing pox disease of plum. Its attack results in 83%–100% yield loss in highly susceptible varieties of peach plant. The complete genome of PPV is 9791 base pairs with positive-sense single strand. The full-length genome of PPV encodes a large polyprotein initially, which cleaves proteolytically into ten mature proteins – coat protein, helper component proteinase, P1, P3, viral genome-linked protein, 6K1, 6K2, cylindrical inclusion protein, cylindrical inclusion protein b and NIa-pro-proteins. The objective of this study is to identify such sites in the PPV genome which can be targeted by PPV-derived miRNAs through target prediction computational tools/algorithms. A total of 214 mature miRNAs were chosen from the miRNA data­base to check their complementarity with the PPV genome. Minimum free energy, folding energy, seed pairing, target-site accessibility, pattern recognition and multiple target sites were the parameters considered for target prediction algorithms. Two out of 214 miRNAs were predicted as potential against plum pox virus by three of four tools used for target prediction. Thus, the results encourage generating transgenic, PPV-resi­stant peach plants by expression of predicted miRNAs.

Keywords


miRNAs, Peach Plant, Plum Pox Virus, Yield Loss, Target Prediction Algorithms.

References





DOI: https://doi.org/10.18520/cs%2Fv121%2Fi10%2F1316-1322