GSE62521
High-throughput deep sequencing reveals that microRNAs play important roles in salt adaptation of euhalophyte Salicornia europaea
Backgroud: microRNA (miRNA) is implicated in plant development processes, playing pivotal roles in plant adaptation to environmental stresses. Salicornia europaea, a salt mash euhalophyte, is a good model plant to study salt adaptation mechanisms. It is also attractive in being vegetables, forage and oilseed that can be used for saline land reclamation and biofuel precursor production on marginal lands. However, none of the miRNAs from S. europaea have been identified so far. Results: Deep sequencing was performed to investigate small RNA transcriptome of S. europaea. Two hundred and twelve conserved miRNAs comprising 51 families and 31 novel miRNAs (including 7 miRNA star sequences) belonging to 30 families were identified. Interestingly, about half (13 out of 31) of the novel miRNAs were only detected in salt-treated samples. The expression of 43 conserved and 13 novel miRNAs changed significantly in response to salinity. In addition, 53 conserved miRNAs and 13 novel miRNAs were differentially expressed between shoots and roots. Furthermore, a total of 306 and 195 S. europaea unigenes were predicted to be targets of 41 conserved and 29 novel miRNA families, respectively. These targets encode a wide range of proteins, and genes involved in transcription regulation constitute the largest category. Four of them, which encode laccase, F-box family protein, SAC3/GANP family protein, and nadph-cytochrome P450 oxydoreductase, were validated using 5''-RACE. Conclusions: Our results indicate specific miRNAs are tightly regulated by salinity in shoots and/or roots of S. europaea, which play important roles in salt adaptation of this euhalophyte. The S. europaea salt-responsive miRNAs and miRNAs that target transcription factors, nucleotide binding site-leucine-rich repeat proteins and enzymes involved in lignin biosynthesis as well as carbon and nitrogen metabolism may be applied in genetic engineering of crops with higher stress tolerance, and genetic modification of biofuel crops with higher biomass and regulatable lignin biosynthesis. Overall design: The aim of this study is to investigate the miRNAs transcriptome in S. europaeaand identify salt-responsive miRNAs in this euhalophyte. Six sRNA libraries were constructed from the shoots and roots of S. europaea seedlings treated with 200 mM NaCl for 0, 12 hours and 7 days and were sequenced using Illumina HiSeq 2000.