Identification of novel stress-induced microRNAs and their targets in Camelina sativa using computational approach

MicroRNAs (miRNAs) are a class of small noncoding, single-stranded RNA sequences that regulate gene expression at the post-transcriptional level and also reported to function in stress responses, but their role has not been studied in Camelina (Camelina sativa L.), an emerging oil crop. In this study, we predicted conserved as well as putative novel miRNAs from a Camelina drought stress cDNA library using comprehensive genomic approaches. Based on the sequence homology, we predicted 145 miRNAs, of which 61 were conserved, and 84 putative novel miRNAs were found to belong to 26 and 72 different miRNA families, respectively. In silico expression analysis indicated that 20 miRNAs were really expressed in Camelina genome, and several of them have tissue-specific expression character. We found that the 60 putative novel miRNA families target 117 genes. Most of the miRNA targets were predicted to genes including that regulate stress response, transcription factors, and fatty acid and lipid metabolism-related genes. Expression patterns of 6 randomly selected miRNAs under drought stress were validated by real-time quantitative polymerase chain reaction analysis. Coordinated expression changes between 6 randomly selected miRNAs and their target genes, suggested that the predicted miRNAs could be drought-responsive and that they would likely be directly involved in stress regulatory networks of Camelina. These results indicate that, in C. sativa, under drought stress, a large number of new miRNAs could be discovered, and the predicted stress-responsive miRNAs and their target transcripts will serve as valuable resources for future studies.