Identification of miRNA in Lycium chinense by deep sequencing

In order to reveal small RNAs and to discover miRNAs and their potential target genes in fruit and shoot tissues, high-throughput RNA sequencing technology (Illumina-Solexa) was applied in Lycium chinense (wolfberry), an important traditional Chinese medicinal plant. The bioinformatics analyses have identified 60 conserved miRNAs belonging to 31 families, and 30 putative novel miRNAs. A total of 62 significantly differentially expressed known and novel miRNAs were identified where 15 (14 known and 1 novel) were shoot specific and 12 (7 known and 5 novel) were fruit specific. Additionally, 28 differentially expressed miRNAs were recorded as up-regulating in fruit development significantly. The predicted potential targets were involved in a wide range of metabolic and regulatory pathways. Especially, five miRNAs were found to be related to fruit maturation, lycopene biosynthesis and signaling pathways and might be important for further fruit molecular biology study.This study is the first time to report the identification of miRNA and the prediction of miRNA target genes in wolfberry. The data and findings presented here might be not only a good source for functional genomic study of medicinal plants but also helpful to understand the links among diversified biological pathways.