Journal of Biotechnology & Biomaterials
Open Access

Abstract

The advancement in sequencing techniques has made it possible to study small RNAs like miRNA, siRNA, etc., comprehensively and efficiently. The microRNAs are short (~20-24 nucleotides) non-coding RNAs that negatively regulate the gene expression post-transcriptionally in animals and plants. This negative regulation can be either by degradation of messenger RNA (mRNA) or by inhibition of protein translation. The existence of miRNAs in plants and animals is well studied in plants but in fungi, it is limited. Here, we report the prediction of miRNAs in fungus Puccinia striiformis tritici (Pst) using EST data available in NCBI. In silico approach has been used to predict the miRNAs and their hairpin precursors in this fungal pathogen. A total of 7550 ESTs were available in NCBI for Pst which were pre-processed using a perl program named �ESTtrimmer� and then assembled using CAP3 assembly program and resulted into 6106 assembled ESTs. Of 6106 ESTs, 1215 precursor miRNAs were predicted that resulted into 120 miRNAs of which 71 were unique sequences. We identified targets of 120 predicted miRNAs. For target identification, 6106 initial EST sequences of Pst were used. Of these, 3167 ESTs were scanned for sequence complementary sites on hit sequences from BLAST (allowed 4 mismatches). These complementary targets were allowed to fold and their secondary structures were analyzed for efficient folding that result into stable complex with lower MFE (minimal free energy). Of these, 232 potential targets were annotated successfully. The targets identified were mostly from fatty acid metabolism and its biosynthesis, signaling pathways, amino acid metabolism, purine metabolism, basal transcription factors, etc. It is well known that PAMP-triggered immunity (PTI) plays a vital role in the resistance of plants to numerous potential pathogens. Our further study will include experimental validation of these predicted miRNAs to evaluate the effectiveness of our method. Our findings will improve the understanding towards the role of these small RNAs in fungal kingdom and pathogenicity of Pst.

Biography

Email: teenaiari1@gmail.com