Identification of conserved microRNAs and their targets in Chinese cabbage (Brassica rapa subsp. pekinensis)

The microRNAs (miRNAs) are a new class of small nonprotein-coding RNAs that have been identified to regulate gene expression at the post-transcriptional level by targeting mRNAs for degradation or by inhibiting protein translation. Until now, thousands of miRNAs have been identified in many plants species. However, only 23 miRNAs have been reported from the microRNA database in Chinese cabbage (Brassica rapa subsp. pekinensis), one of the most widely cultivated vegetables in China and East Asia. In the present study, 168 potential miRNAs, derived from 22 EST and 119 GSS sequences in Chinese cabbage were identified and classified into 38 miRNA families by well-defined computational analysis, in which most belonged to the miRNA1533, miRNA156, and miRNA2911 families. Totally, there are 129 identified miRNAs potentially targeting 1386 Chinese cabbage EST genes, which play roles in multiple biological and metabolic processes including metabolism, cell growth, signal transduction, stress response, and plant development. Gene ontology analysis, based on these target proteins, showed that 688, 532, and 287 genes were involved in molecular functions, biological processes, and cellular components, respectively. KEGG pathway analysis demonstrated that these miRNAs participated in 214 metabolism pathways, including, amongst others, plant-pathogen interaction, fatty acid metabolism, amino acid metabolism, nitrogen metabolism, plant hormone signal transduction.