Abstract
MicroRNAs (miRNAs) are small, noncoding RNAs that can play important roles in eukaryotes. To investigate whether miRNAs regulate gene expression in tree species, we analyzed small RNAs expressed at flowering stage of Eucalyptus. Twenty-two bases of the small RNAs were sequenced by MPSS method, and about 130,000 unique sequences were determined. After removing rRNA, tRNA, sn/snoRNA, 30,000 genome sequences including the small RNAs were extracted. A total of 370 candidate miRNAs belonging to 236 miRNA families were identified by prediction of secondary structures of the sequences. Most of the candidate miRNAs are novel and Eucalyptus specific. A total of 404 target genes with not more than 3 mismatches in the miRNA duplexes were predicted for the 65 miRNA families using genome sequence information. The cleavage sites of some target genes were validated by 5'-RACE analysis. These results suggest that miRNAs in Eucalyptus control gene expression in various processes.
