we performed microRNA deep sequencing, analyzed the microRNAs and revealed the function of the corresponding target genes, as the first step to understanding the role of microRNAs in S. officinarum. 268 candidate miRNAs were screened from sequencing microRNA library with the total RNA from sugarcane leaves using the RNA-seq ESTs of all tissue of Saccharum officinarum from our group， public sugarcane ESTs from NCBI and the reference sorghum genome from Phytozome V9. After further analysis, 43 homologous miRNAs and 9 novel miRNAs were identified. Out of the 52 miRNAs, 6 were randomly chosen and verified by qRT-PCR and the putative miRNA targets’ function was analyzed. The identification of miRNAs and their targets not only will enable to understand the roles of miRNAs in sugarcane development and growth, but also enhances the understanding of miRNA-dependent mechanisms in highly polyploid species. Identification and Characterization of microRNAs from Saccharum officinarum L by deep s

In modern sugarcane cultivars, around 70-80% of the genetic information originates from Saccharum officinarum, which contributed important sugar content traits. Although several studies have identified microRNAs in Saccharum hybrids, they have not yet been studied in S. officinarum. In this study, by deep sequencing and in silico approaches, 268 miRNA candidates were predicted in S. officinarum, and 52 were found to likely be miRNAs be based on our analysis with stringent criteria. Among these 52 miRNAs, 43 miRNAs from 26 miRNA families were found to have homologous miRNAs in public miRBase Release 21, and 9 miRNAs were identified to be novel in S. officinarum. Out of the 52 miRNAs, 6 were randomly chosen and verified by qRT-PCR. The 52 miRNAs were predicted to have 237 and 76 targets in sugarcane and sorghum, respectively, including Auxin response factor, MADS-box transcription factor, Zinc finger-like protein. MicroRNAs that target critical sugarcane pathways, such as sucrose metabolism and cellulose metabolism were identified. In addition, the first microRNA (sof-novel1) derived from the Saccharum chloroplast genome was identified. These results provide the foundation for future studies to distinguish the microRNAs from S. spontaneum and S. officinarum in Saccharum hybrid, and valuable information to further study the microRNA functions in Saccharum species.