Bioinformatic tools for microRNA dissection and identify thier target genes in sugarcane

Recently, microRNAs (miRNAs) have emerged as important elements of gene regulatory networks. MiRNAsare endogenous single-stranded non-coding RNAs (∼۲۲-nt long) that regulate gene expression at the posttranscriptionallevel. Through pairing with mRNA, miRNAs can down-regulate gene expression by inhibitingtranslation or stimulating mRNA degradation. In some cases they can also up-regulate the expression of atarget gene. Sugarcane is an important industrial crop accounting for nearly ۸۵% of sugar producedworldwide and it is fast becoming an energy crop for the production of bio-fuel ethanol. Waterlogging is oneof the serious environmental constraints for optimum growth and yield of sugarcane. Current research hasshown that microRNAs (miRNAs) play vital roles in plant response to stresses caused abiotic stress such aswaterlogging.The expression of six candidate miRNAs and their targets were validated using quantitative real-time PCR(qRT-PCR) technology. To identify the mechanisms involved in miRNA-mediated tolerance, it wasnecessary to first identify the miRNA-modulated genes by bioinformatics mthodes. The mature miRNAsequences were obtained from the miRbase database, and miRNA-modulated genes were predicted usingpsRNATarget software. Target annotation (biological process, molecular function, and subcellularlocalization) was performed using Gene Ontology and Uniprot online tools. Co-expression networks wereconstructed using the GeneMANIA prediction server software, with default analysis parameters. Arabidopsisthaliana and sorghum bicolor were used as the reference genome for all analyses.Our results showed that miRNAs and their respective target genes were differentially expressed insugarcane seedling leaves exposed to waterlogging stress. Relative expression data revealed significantdifferences between miR۱۶۰, miR۱۶۶, miR۱۷۱, miR۳۹۳, miR۳۹۶ and miR۳۹۸ expression levels in sugarcaneleaves under waterlogging stress. The predicted target genes regulated by the evaluated miRNAs also showsignificant difference in relative expression.

Keywords:

Bioinformatic , Gene ontology , miRNA , Target genes