Identification of microRNAs response to high light and salinity that involved in beta-carotene accumulation in microalga Dunaliella salina

MicroRNAs (miRNAs) are a class of endogenous non-coding RNAs that play a crucial role in post-transcriptional gene regulation not only in animals and land plants, but also in microalgae . Among all the microalga, Dunaliella salina ( D. salina ) has the highest content of beta-carotene, and a draft genome of this species was recently published. Thus far, few D. salina miRNAs have been identified. In this study, deep sequencing was performed to identify miRNAs in wild-type D. salina (Control) and in a high light and high salinity treatment group (HLS). Three small RNA (sRNA) libraries were constructed for Control and HLS, and an average of 11,542,169 and 16,877,598 clean tags were obtained, respectively. The sRNA length distribution showed that 21 nt sRNAs were the most abundant class in both Control and HLS, which is consistent with the sRNA distribution of model organism Chlamydomonas reinhardtii . Eighty-four known miRNAs and 1054 novel miRNAs were found in Control. Among them, nine known miRNAs and 39 novel miRNAs had altered levels in response to HLS treatment. The expression differences of selected miRNAs and their target genes in Control and HLS were verified by qRT-PCR, which showed that novel-m0533-3p was up-regulated and its predicted target malate dehydrogenase encoded gene was clearly down-regulated in HLS at both transcription and the protein level. Moreover, some key carotenoid pathway genes, such as PSY , PDS and LCYB were all up-regulated in HLS. These findings are providing a new insights into a miRNA-mediated beta-carotene accumulation mechanism in D. salina .