IN SILICO IDENTIFICATION AND TARGET PREDICTION OF microRNAs AND THEIR EXPRESSION PROFILING IN Sesamum indicum L. 2524
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Date
2018-04
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JAU,JUNAGADH
Abstract
Sesame (SesamumindicumL., 2n = 26), a member of the Pedaliaceae family, is one of the oldest oilseed crops. For its high oil content, it is known as the “queen of oilseeds”.Sesame seeds are important source of oil, protein, and carbohydrates.Sesame oil is used as an active ingredient in antiseptics, bactericides, viricides, disinfectants, moth repellants, and antitubercular agents because they contain natural antioxidants such as sesamin and sesamolin.
MicroRNAs (miRNAs) represent a class of endogenous non-coding small RNAs that playimportant roles in multiple biological processes by degrading targeted mRNAs or repressingmRNA translation. Thousands of miRNAs have been identified in many plant species,whereas there is no report of miRNAs in S.indicumtill date. In present study, previously known plant miRNAs were BLASTedagainst the Expressed Sequence Tag (EST),Genomic Survey Sequence (GSS) and Whole Genome Sequencing (WGS) database of sesame genes.The aligned miRNA hits were further aligned to protein database and BLASTX was carried out to remove protein coding primary miRNAs. The non-coding precursor miRNAs were subjected to online Mfold server in order to predict their secondary structures. Numbers of filtering criteria like proper hairpin-loop structure, Minimum Folding Free Energy (MFE), %A+U content etc. were applied. A total of 124 potential miRNAs belonging to 28miRNAs familieswere detected after applying the range of filtering.
The targets were predicted online by psRNATarget web server.320 uniquemiRNA:target pairs were subsequentlypredicted, most of which encode transcription factors or enzymes that participate in the regulationof development, growth, metabolism, and other physiological processes and stress response.
In order to analyze expression level of the predicted miRNAs, qRT-PCR was applied to detect the stress related expression levels of 20 putativemiRNAs in four samples viz., control, Seedlings treated for drought stress, Seedlings treated for salinity stress and Seedlings treated withFusariumoxysporumf. sp. sesami pathogen.The relative expression specified which miRNAs were up/down regulated during stress. The targets for respective miRNAs were compared with the findings of in silicoanalysis and similarities were found. It could be suggestive of the validity of the computational methods.
This study providessome important information about sesame pre-miRNAs, mature miRNAs, and miRNA targetgenes and these findings can be applied to future research of miRNA functions.
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BIOTECHNOLOGY