Annotation of miRNAs from Developing Seeds in Avena sativa

miRNAs are small RNAs that regulate gene expression in plants and animals.  In plants, miRNAs are ~21 nucleotides long and suppress translation of mRNA through complement-directed cleavage of the message.  Although many miRNAs have been identified in other plant species, few have been identified or characterized in Avena sativa (oat).  In oat, miRNAs could be responsible for the decaying endosperm mRNA levels in late seed development ((Johnson, Chaverra, Cranston, Pleban, and Dyer. Plant Mol Bio, 1999, 39(4):823-833)).   Small RNA libraries from three time points in early seed development were chosen for analysis along with several varieties of oat with varying seed metabolite compositions profiles. Sequences were generated using the Illumina sequencing platform. When a genome sequence is available, after data preprocessing (trimming adapters, N filter, length filter, Rfam filter), miRNAs are mapped to the genome to find candidate miRNA precursors and for target prediction.  However, with limited availability of genomic sequence for Avena sativa, 454 sequencing runs and RNA-seq data for the same three time points, and ESTs are used for precursor and target prediction.  Despite these challenges,  we have identified miRNAs that are involved in seed development in oat and are characterizing our results.  Comparatively, we find miRNAs conserved among all plants, among the grass family Poaceae, and miRNAs novel in Avena sativa.