MicroRNAs (miRNAs) are a class of small endogenous non-coding RNAs that modulate gene expression in both plants and animals and are involved in several biological processes, ranging from organ differentiation to biotic and abiotic stress responses. The comparative analysis of the target genes for miRNAs families may augment our understanding of conserved regulatory mechanisms in the plant kingdom. Here, we used a high throughput sequencing and computational approach to identify new miRNAs in S. lycopersicum. Using this approach 18 miRNAs were identified in S.lycopersicum leaf samples. We found a closely related mature sequence for Sly-miR319 that derived from distinct precursor sequences and genomic loci. Furthermore, a qRT-PCR-based assay was performed to validate the prediction of five identified miRNAs. Identification of miRNA targets showed that most of the identified miRNAs such as Sly-miR156a, Sly-miR164, Sly-miR166a, Sly-miR172a, Sly-miR319a and Sly-miR482c, modulate the expression of transcription factors that regulate plant development, signaling and metabolism. In brief, our reliable computational analysis of miRNAs and their targets suggests that many important miRNA-targets circuits are also conserved in S.lycopersicum and fulfill critical roles in growth and development. These findings provide valuable information for functional characterization of miRNAs in S.lycopersicum

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