A ceRNA Network Mediates Salinity Adaptation Via miR-novel-3-LNC_015168-SLC17A9 Axis in Sea Cucumber

Sea cucumber aquaculture is a cornerstone of the mariculture industry in Liaoning Province, China, contributing significantly to both economic development and​​ coastal marine ecosystems balance. Recent frequent coastal water salinity fluctuations limited the survival, growth, and yield stability of sea cucumbers, and thus posing a challenge to the sustainable development of the sea cucumber aquaculture industry. To address this issue, this study aimed to identify the key molecular regulatory mechanisms underlying sea cucumber response to low-salt environments, thereby providing theoretical support for salt-tolerant sea cucumber breeding. Based on our previous transcriptomic sequencing data of sea cucumbers under low-salt stress, we identified a potential regulatory axis consisting of miR-novel-3 (a novel microRNA), LNC_015168 (a long non-coding RNA), and slc17a9 (a transmembrane transporter gene). Time-course qPCR demonstrated that miR-novel-3 and slc17a9 exhibited inverse expression patterns under salinity stress, peaking at 24 h. The 24 h inflection point in all three molecules highlights its critical role in low-salt acclimatization. Their reciprocal regulation over-expression of miR-novel-3 suppressed slc17a9, whereas LNC_015168 acted as a ​competitive endogenous RNA​​ (ceRNA) to sequester miR-novel-3, thereby enhancing slc17a9 expression. Bioinformatics analysis identified slc17a9 as a hydrophilic transmembrane protein with 76 phosphorylation sites, suggesting its role in ion transport. These findings highlight a ceRNA network as a pivotal mechanism for osmoregulatory plasticity in echinoderms, offering potential targets for breeding salt-tolerant sea cucumbers.