Abstract: As an important representative of Gracilaria, Gracilaria changii has valuable industrial value. With deterioration of the global marine environment, Gracilaria resources are in urgent need for further development and utilization. As an important regulator of gene post-transcriptional expression, microRNA (miRNA) plays a key role in regulating plant tissues and organs, physiological status, stress response and so on. However, there have been no any reports about G. changii miRNA (gch-miRNA) in the world, which greatly hampers the further study on non-coding RNA and its function. Based on bioinformatics, six gch-miRNAs were predicted by sequences alignment analysis of gch-ESTs and miRNAs in miRBase databases in this study. The sequences and structural features showed that our prediction results were reliable. Moreover, the results of sequences alignment analysis showed that gch-miRNAs had both conservative and polymorphic features among other plants. Furthermore, gch-miRNAs validation showed our identifying results are high confidence by stem-loop qRT-PCR. The phylogenetic results of some miRNA families with NJ algorithm revealed the gch-miRNAs located in the outer group of the phylogenetic tree and the evolutionary rate of miRNAs is not synchronized with their corresponding host species. Eight potential gch-miRNA targets had been screened by TargetFinder software, and cleavage is the main inhibition type of miRNA(target in G. changii thorough psRNATarget analysis). This research firstly reported the miRNAs and their putative targets in G. changii, and comprehensively analyzed the phylogenetic relationship of some miRNAs across different plant species. The researching results lay a foundation for the non-coding RNA research on G. changii, as well as the molecular breeding of high-quality Gracilaria species and the development and utilization of them in future.

Key words: microRNA (miRNA), Gracilaria changii, target, phylogenetic evolution