Genome-wide profiling of the potential regulatory network of lncRNA and mRNA in Melilotus albus under salt stress

• 9437 lncRNAs were identified from Melilotus albus genome, most of which (7238, 76.7 %) were lincRNAs. • LncRNA exhibited higher tissue-specificity in response to salt stress than mRNA. • LncRNA plays a regulatory role in response to salt stress in M. albus . • MSTRG.50852.2 might regulate WD40 domain protein expression by competitively binding mtr-miR7696a-3p under salt stress. Salt stress is a major abiotic stress limiting crop productivity. Long noncoding RNAs (lncRNAs) are transcripts with more than 200 nucleotides but lacking protein-encoding potential and generally plays a regulatory role in plant response to abiotic stresses. However, no information is known about lncRNAs in Melilotus albus , a wonderful leguminous forage with excellent salt tolerance. In this study, 9437 lncRNAs were identified based on high-throughput sequencing from M. albus shoots and roots, most of which (7238, 76.7 %) were lincRNAs. Totally, 550 lncRNAs and 8273 mRNAs were differentially expressed in M. albus under salt stress, and lncRNA exhibited higher tissue-specificity in response to salt stress than mRNA. Five hundred and fifteen differentially expressed transcription factors were identified, many of which (AP2/ERF, MYB, bHLH, NAC) were related to abiotic stress. We predicted that 545 (99.1 %) differentially expressed lncRNAs (DELs) regulated 6616 (80.0 %) differentially expressed mRNA (DEGs) in cis, trans and miR-mediated manner. Numerous target genes of DELs were relevant to oxidation-reduction process, cellular protein metabolic process, cell communication, ribosome, carbon metabolism and biosynthesis of amino acid pathway. The competitive endogenous RNA (ceRNA) network contained 99 miRNA, 67 lncRNA, and 128 mRNA, among which qRT-PCR and tobacco dual-luciferase (LUC) assays further demonstrated that MSTRG.50852.2 might regulate the expression of EVM0029402 encoding WD40 domain protein by competitively binding mtr-miR7696a-3p under salt stress. Our results firstly characterize salt stress-responsive lncRNAs from M. ablus genome, which help to further research on the molecular mechanism of M. ablus adapting to salt stress and to provide useful information for resistance genetic improvement of other crops.