Target prediction of candidate miRNAs from Oryza sativa for silencing the RYMV genome |
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| Affiliation: | 1. Center of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan;2. Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, Australia;1. Department of Cardiology, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang Province, 150001, China;2. Department of Cardiology, Daqing No. 5 Hospital, Daqing, Heilongjiang Province, 163714, China;3. Department of General Surgery, Heilongjiang Provincial Hospital, Harbin, Heilongjiang Province, 150036, China;4. Department of Endocrinology, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang Province, 150001, China;5. Department of Cardiothoracic Surgery, Da Qing Long Nan Hospital, No. 35 Patriotic Road, Ranghulu District, Daqing, Heilongjiang Province, 163453, China;1. Department of Microbiology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada;2. Life Sciences Division, National Research Council of Canada, Ottawa, Ontario, Canada;3. Immunology and Infectious Diseases, Faculty of Medicine, Memorial University of Newfoundland, St. John''s, Newfoundland, Canada;4. Department of Medical Microbiology and Edmonton, Alberta, Canada;5. Li Ka Shing Institute of Virology, Katz Centre for Pharmacy and Health Research, Edmonton, Alberta, Canada;6. Department of Chemistry, Faculty of Science, University of Ottawa, Ottawa, Ontario, Canada;1. Department of Chemistry, Indian Institute of Technology Ropar, Punjab, 140001, India;2. School of Basic Sciences, Indian Institute of Technology Mandi, Himachal Pradesh, 175005, India;3. Department of Chemistry, Punjab University, Chandigarh, 160014, India;1. Department of Chemical, Biological and Macromolecular Sciences, S.N. Bose National Centre for Basic Sciences, Block JD, Sector 3, Salt Lake, Kolkata 700106, India;2. Research and Development Division, Dey’s Medical Stores (Mfg.) Ltd., 62, Bondel Road, Ballygunge, Kolkata 700019, India;3. Department of Zoology, Uluberia College, University of Calcutta, Uluberia, Howrah 711315, India |
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| 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. |
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| Keywords: | miRNAs Rice yellow mottle virus Target prediction Gene silencing |
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