In Silico Identification of Novel microRNAs and Targets Using EST Analysis in Allium cepa L

microRNAs (miRNAs) are a newly discovered class of non-coding small RNAs roughly 22 nucleotides long. Increasing evidence has shown that miRNAs play multiple roles in biological processes, including development, cell proliferation, apoptosis and stress responses. The identification of miRNAs and their targets is an important need to understand their roles in the development and physiology of sweet onion (Allium cepa). In this research, several computational approaches were combined to make concise prediction of the potential miRNAs and their targets. We used previously known miRNAs from other plant species against Expressed Sequence Tags (EST) database to search for the potential miRNAs. As a result, nine potential miRNAs were identified in eight ESTs of A. cepa, belonging to eight families. We could further BLAST the mRNA database and found total 154 number of the potential targets in A. cepa based on these potential miRNAs. According to the mRNA target information provided by NCBI, most of the target mRNAs appeared to be involved in plant growth, signal transduction, development, and stress responses. Gene ontology (GO) analysis implicated these targets in 32 biological processes such as protein ubiquitination, plant hormone signalling pathways and heme biosynthesis.