Sugar in Small Bits: Epigenetic Regulation in the Saccharum Complex

Modern sugarcane cultivars are hybrids of Saccharum officinarum and Saccharum spontaneum species. Hybrids have complex polyploidy genomes that difficult the studies of structure and organization of the genome. To understand role of the small RNA regulation in species of the Saccharum complex, small RNA and degradome libraries were prepared from RNA obtained from leaves of S. officinarum, S. spontaneum, S. sinensis and S. robustum, as well as from two commercial hybrids, RB867515 and SP701143. Deep sequencing identified a large set of conserved miRNA and novel miRNA candidates. Annotation of the confirmed degraded mRNAs identified most of the canonical sequences found in plants. In addition, novel targets, not previously described in plants, were also identified. We used the miTRATA pipeline with a subset of 11 conserved microRNAs to evaluate microRNA turn over in the six genotypes. The results indicate that the rate of turnover is dependent of both microRNA sequence and genotype. Together, our data provides insights on the overall composition of sRNAs in wild Saccharum species and hybrids, and also improve the understanding of sRNA-triggered regulation in the context of hybridization in sugarcane.