MicroRNAs and their targets by high-throughput sequencing and differentially expressed analysis in five Miscanthus species

MicroRNAs (miRNAs) are noncoding small endogenous RNAs with approximate 22 nucleotides and have been identified as the key regulators in the translational level regulation of gene expression by either directly binding or cleaving target mRNAs. In plant, miRNAs have been shown to control numerous genes involved in a wide variety of metabolic and biological processes. Increasing extensive studies have been performed on model species and important agricultural crops including Arabidopsis thaliana L., Oryza sativa L. and Zea mays L., but miRNAs have not yet been complete identified in Miscanthus, a promising potential bioenergy candidate. In this study, miRNAs in Miscanthus lutarioriparius L., Miscanthus sacchariflorus N.，Miscanthus floridulus W., Miscanthus sinensis A., and Miscanthus x giganteous were constructed by Solexa high throughput sequencing and subsequently performed the bioinformatics analysis. Totally, 93 conserved miRNA families as well as 485 novel miRNA families were discovered in the five Miscanthus species libraries. Gene ontology (GO) analysis revealed these novel miRNAs' targets involved in 94 biological processes in M. lutarioriparius, which 25 of these processes participated in the metabolism of carbon, glucose, starch, fatty acid, and lignin formation. In the pathway enrichment analysis of Kyoto Encyclopedia of Genes and Genomes (KEGG), 10 metabolism networks were found, including starch and sucrose metabolism, fatty acid metabolism, phenylpropanoid biosynthesis, oxidative phosphorylation, and the processing of other metabolites. This study provides a large scale identification of miRNAs and their potential targets in Miscanthus species. These miRNAs add the growing database of new miRNAs and lay the foundation for further understanding of miRNA evolution, diversification and regulation in Miscanthus.