Discovery of novel miRNAs and their variant analysis usingbioinformatics approaches: Citrus model organism

Objective: The aim of this study is discovering of the novel micro RNAs (miRNAs) accurately through the analysis of existing NGS data with the bioinformatics methods, obtaining the conserved miRNAs with their variant analysis and identifying the impact of the miRNAs on their target genes and their roles in the metabolic pathways. Method: Since all the required data for this study such as the whole genome and sRNA sequencing were exist for Citrus species, we used it as the model organism in this work. The preprocessed and filtered data were inputed into The UEA sRNA Workbench software for miRNA identification. The identified miRNAs were controlled by tRNAscan-SE and NOVOMIR tools to detect the false positive miRNA results. The conserved miRNAs across 34 Citrus species were determined using their whole genome and single nucleotide variant (SNV) data. The conserved miRNAs were searched in the literature and databases to obtain the list of novel Citrus miRNAs which were discovered for the first time in our study. psRNAtarget web tool was used for the target gene analysis of the conserved miRNAs. To find the metabolic pathways that are regulated by the conserved miRNAs, we mapped the target genes into the metabolic pathways of two Citrus species that were available in CitrusCyc database. Results: In our study, we identified 1504 miRNAs. 270 miRNAs were found common across 34 Citrus species. Sequence of 111 out of 270 miRNAs were conserved and 36 of these conserved miRNAs were novel for Citrus. The isomirs which have been found by another research group were discarded from our study by the filtering steps applied. We found that the conserved miRNAs had different target genes in different Citrus species and these miRNAs were regulating different metabolic pathways through their target genes. Conclusion: In this bioinformatics based study, we integrated the different types of data from varied sources using the bioinformatics algorithms. By using the genomics data in our study, we add a distinctive frame to miRNA research studies. Keywords: micro RNA, next generation sequencing, bioinformatics.