Identification of miRNAs involved in long-term simulated microgravity response in Solanum lycopersicum

To identify the miRNAs associated with the simulated microgravity response in plants and to ascertain the regulation network mediated by miRNAs under simulated microgravity conditions, we constructed a miRNA library by direct cloning method and analyzed the library. Seven miRNAs that are conserved in other plants were cloned for the first time in Solanum lycopersicum under simulated microgravity condition. The expressions of six of the seven miRNAs were up-regulated, especially by long-term simulated microgravity. Gene ontology analysis showed that most of the predicted targeted genes were involved in transcription regulation, signal transduction and stress response, implying a complicated relationship among the external signal, internal transduction and final phenotype. Six of the predicted targets were validated by 5' RACE and reverse transcription real-time quantitative PCR. The results showed that with increasing miRNA expression levels, the corresponding target genes were down-regulated. The target gene of one of miRNAs, miR159e*, was thought to be associated with an increasing of starch amount under microgravity condition. A multi-stresses response network mediated by miRNAs under simulated microgravity condition was proposed. Cis-elements located in the upstream sequences of each miRNA were identified and their roles in gene regulation were investigated. In addition to the seven miRNAs that had homologs in other plants, six conserved S. lycopersicum miRNAs were identified. In the study, miRNAs were identified in S. lycopersicum for the first time under long-term simulated microgravity condition, which will help reveal the regulation mechanism mediated by miRNAs under simulated microgravity condition and adaptation to Earth's gravity.