Differential microRNA expression between shoots and rhizomes in Oryza longistaminata using high-throughput RNA sequencing

Plant microRNAs (miRNAs) play important roles in biological processes such as development and stress responses. Although the diverse functions of miRNAs in model organisms have been well studied, their function in wild rice is poorly understood. In this study, high-throughput small RNA sequencing was performed to characterize tissue-specific transcriptomes in Oryza longistaminata. A total of 603 miRNAs, 380 known rice miRNAs, 72 conserved plant miRNAs, and 151 predicted novel miRNAs were identified as being expressed in aerial shoots and rhizomes. Additionally, 99 and 79 miRNAs were expressed exclusively or differentially, respectively, in the two tissues, and 144 potential targets were predicted for the differentially expressed miRNAs in the rhizomes. Functional annotation of these targets suggested that transcription factors, including squamosa promoter binding proteins and auxin response factors, function in rhizome growth and development. The expression levels of several miRNAs and target genes in the rhizomes were quantified by RT-PCR, and the results indicated the existence of complex regulatory mechanisms between the miRNAs and their targets. Eight target cleavage sites were verified by RNA ligase-mediated rapid 5′ end amplification. These results provide valuable information on the composition, expression and function of miRNAs in O. longistaminata, and will aid in understanding the molecular mechanisms of rhizome development.