Genome-Wide Identification and Functional Analysis of Long Non-coding RNAs in Sesame Response to Salt Stress

Long non-coding RNAs (lncRNAs) play important roles in various biological regulatory processes in which complicated mechanisms are involved, as well as stress-responsive regulation. However, the number, characteristics, sequences and possible effects of lncRNAs in sesame response to salt stress are poorly understood. In this study, a total of 2482 lncRNAs were identified from two contrasting sesame genotypes under salt stress using high-throughput RNA sequencing, of which 599 were intergenic lncRNAs, 293 were antisense lncRNAs and 786 lncRNAs may encode proteins. Expression pattern analysis showed that most lncRNAs were expressed at a low level and a total of 700 differentially expressed lncRNAs were characterized as salt responsive in sesame. A large number of potential target genes of lncRNAs were predicted, and functional annotation analysis indicated that the differentially expressed lncRNAs in salt stress may regulate protein-coding genes involved in several important pathways related to glycolysis/gluconeogenesis, flavonoid biosynthesis, monoterpenoid biosynthesis, biotin metabolism, galactose metabolism, cyanoamino acid metabolism and carotenoid biosynthesis. Integrated analysis of lncRNAs and mRNAs revealed the regulatory role of lncRNAs associated with salt resistance in sesame, and provided convincing proof of the interplay of specific candidate target genes with lncRNAs. Our results indicated that a comprehensive set of lncRNAs with potential target genes were responsive to salt stress in sesame seedlings. These findings provided important information on salinity responses and adaptation of sesame to salt stress and may constitute useful resources for more comprehensive studies on gene regulation in sesame.