Identification and Characterization of Long Non-Coding RNAs Involved in Sex-Related Gene Regulation in Kelp Saccharina japonica

Long non-coding RNAs (lncRNAs) regulate a variety of biological processes, including sexual reproduction and differentiation. Saccharina japonica , a commercially important brown alga in China, shows remarkable sexual dimorphism in haploid gametophytes. The sex of Saccharina japonica gametophytes is determined by UV sexual system. However, no results have been reported on the lncRNAs involved in the sex-related gene regulation of S. japonica . This study identified a number of lncRNAs and assessed their expression levels in male and female gametophytes. Among them, a total of 405 lncRNAs and 211 mRNAs showed differential expressions. Furthermore, the functions of target genes of differentially expressed lncRNAs (DELs) differed from those of differentially expressed genes (DEGs), suggesting that lncRNA may interact with other functional proteins, in addition to DEGs, to involve sex regulation in S. japonica . There were 32 and 90 potential cis-regulatory and trans-regulatory interactions between DELs-DEGs, respectively. Five of these lncRNAs (LNC_002974, LNC_021059, LNC_038466, LNC_051584, and LNC_027400) interacted with putative male sex determination region (SDR) genes, suggesting that they act as regulators in gametophytes’ sex regulation potentially. Findings from this study contribute to our understanding of the roles of lncRNAs in sex differentiation and lay the foundation for functional studies of candidate lncRNAs in the future.