Identification and Characterization of microRNAs from Saccharum officinarum L by Deep Sequencing

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 real miRNAs 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 stem-loop RT-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 were found to be involved in critical sugarcane pathways, such as sucrose metabolism and cellulose metabolism. In addition, the first miRNA (sof-novel1) derived from the Saccharum chloroplast genome was identified. These results provide the foundation for future studies to distinguish the miRNAs from S. spontaneum and S. officinarum in Saccharum hybrid, and valuable information to further study the miRNA functions in Saccharum species.