1st International and 10th National Iranian Conference on Bioinformatics

Home Accepted Papers

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

Paper ID : 1081-ICB10

Authors:

Rahim Ghezzi¹, Leila Nejadsadeghi *², Khosro Mehdi Khanloo², Daryoosh Nabati ahmadi³

¹دانشجوی کارشناسی ارشد دانشگاه شهید چمران اهواز

²استادیار دانشگاه شهید چمران اهواز

³دانشیار دانشگاه شهید چمران اهواز

Abstract:

Recently, microRNAs (miRNAs) have emerged as important elements of gene regulatory networks. MiRNAs are endogenous single-stranded non-coding RNAs (∼22-nt long) that regulate gene expression at the post-transcriptional level [1]. Through pairing with mRNA, miRNAs can down-regulate gene expression by inhibiting translation or stimulating mRNA degradation. In some cases they can also up-regulate the expression of a target gene [2]. Sugarcane is an important industrial crop accounting for nearly 85% of sugar produced worldwide and it is fast becoming an energy crop for the production of bio-fuel ethanol. Waterlogging is one of the serious environmental constraints for optimum growth and yield of sugarcane [3]. Current research has shown that microRNAs (miRNAs) play vital roles in plant response to stresses caused abiotic stress such as waterlogging [4].
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 was necessary to first identify the miRNA-modulated genes by bioinformatics mthodes. The mature miRNA sequences were obtained from the miRbase database, and miRNA-modulated genes were predicted using psRNATarget software [5]. Target annotation (biological process, molecular function, and subcellular localization) was performed using Gene Ontology and Uniprot online tools. Co-expression networks were constructed using the GeneMANIA prediction server software, with default analysis parameters [6]. Arabidopsis thaliana 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 in sugarcane seedling leaves exposed to waterlogging stress. Relative expression data revealed significant differences between miR160, miR166, miR171, miR393, miR396 and miR398 expression levels in sugarcane leaves under waterlogging stress. The predicted target genes regulated by the evaluated miRNAs also show significant difference in relative expression.

Keywords:

Bioinformatic, Gene ontology, miRNA, Target genes

Status : Paper Accepted (Poster Presentation)