Correlation of Long Non-Coding RNAs and Gene Expression in Response to Reverse Development of Turritopsis dohrnii

Long non-coding RNAs (lncRNAs) are increasingly acknowledged as key players in various biological processes. However, the role of these lncRNAs in the response of cnidarians to the reverse development process remains unexplored. We conducted a genome-wide analysis of lncRNAs in immortal jellyfish (Turritopsis dohrnii) to examine their response to reverse development process across a substantial dataset of 82 RNA-seq samples. We identified 8,805 high-confidence lncRNA candidates, which are characterized by a shorter average length of 640 nucleotides and fewer exons (on average 1.41), compared to mRNAs. Remarkably, 79.73% of these lncRNAs were found to be species-specific among the thirteen jellyfish species. Within 836 lncRNAs and 1,395 mRNAs that are highly correlated with the reverse development, the key genes involving DNA repair, cell cycling, differentiation, and apoptosis (e.g., Tspan4, Aifm2, Wwox, eIF3C and those of the p53 signaling pathway and the cAMP signaling pathway) exhibited progressively increasing expression levels throughout the reverse stages. Among 64 lncRNA-mRNA pairs with putative trans- and cis-regulatory effects, the lncRNA (MSTRG.37048.1) exhibited strong correlation with Tspan4, Wwox and PIGA genes during the reverse stages. Our study provides a candidate lncRNA resource and prioritizes lncRNA-associated gene pairs potentially related to life-cycle reversal in T. dohrnii.