Computational prediction and experimental validation of a novel miRNA in Suaeda maritima, a halophyte

The lack of available transcriptome data for plants of no economic or agronomic importance limits the identification of miRNAs in many species. Considering the possible similarity of the transcriptome between related species, the present study used expressed sequence tags (ESTs) of Suaeda salsa and Suaeda glauca to identify conserved miRNAs, which were validated in a halophyte, Suaeda maritima, with the aim of identifying salt-responsive miRNAs from naturally salt-tolerant plants, information on which is limited. In this study, computational analysis predicted three miRNA sequences by mapping non-redundant miRNA sequences from miRBase 16.0 on 1534 ESTs of S. salsa and S. glauca. The expression of one could be validated in S. maritima, and was named sma-miR1867. This miRNA was downregulated in response to NaCl treatment. It was predicted to target ferredoxin-thioredoxin reductase (FTR), cell division control protein 6 (CDC6), and ubiquitin-protein ligase (UPL) in S. salsa and/or S. glauca. However, only UPL could be amplified in S. maritima, and RT-qPCR showed that it was upregulated in response to NaCl treatment. These results indicate that, in halophytes, FTR and CDC6 may promote carbon metabolism and cell division, respectively, in the presence of salt, while UPL may regulate the abundance of proteins that are important for salt tolerance in halophytes. Thus, sma-miR1867 could be an essential component of salt resistance in halophytes.