MicroRNAs (miRNAs) are a new class of non-protein coding small RNAs that regulate gene expression at the post-transcriptional level in plants and animals. Although thousands of miRNAs were identified in many plant species, only 3 miRNAs have been reported in Lotus Japonicus, a model legume plant. In this study, 80 potential miRNA candidates were identified in 28 ESTs and 52 GSSs of L. japonicus using a homology-based computational analysis. A total of 735 miRNA targets were predicted and some of them encoded transcription factors as well as genes that function in stress response, signal transduction, methylation and others. Quantitative real-time PCR (qRT-PCR) analysis indicated that miR156a, miR160a and miR399a participated in seed germination of L. japonicus. GO and KEGG analysis suggested that the predicted miRNAs might target genes involved in lipid, nitrogen, starch sucrose metabolism and signal transduction.
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