Non-coding RNA regulatory networks underlying intestinal degradation in Apostichopus japonicus under starvation...

Starvation stress is one of the most common environmental challenges faced by aquatic animals, often leading to compensatory growth, a widespread phenomenon in the animal kingdom, especially among aquatic species. The sea cucumber (Apostichopus japonicus), a key marine economic species in China, has been shown to utilize long non-coding RNAs (lncRNAs) in responding to environmental changes, pathogen infections, and tissue regeneration. In this study, strand-specific high-throughput sequencing was employed to analyze transcriptomic data from degenerated intestines of A. japonicus under starvation conditions. High-quality lncRNAs were identified and classified, and key differentially expressed mRNAs and lncRNAs associated with intestinal degradation were screened. A gene interaction network model based on the competing endogenous RNA (ceRNA) theory was then constructed. The analysis revealed that the "AjSOX9/Aja-miR-2012-5p/MSTRG.2956.1 and MSTRG.5699.1" axes, as well as the "AjWNT9B/Aja-miR-200-3p/MSTRG.19757.1 and MSTRG.21788.1" axes, play significant roles in degraded intestines and may promote intestinal regeneration during compensatory growth. Additionally, the "AjFABP2/Aja-miR-9-5p/MSTRG.9667.1" axis appears to regulate energy metabolism under starvation stress. These findings provide valuable insights into the non-coding gene regulatory networks in invertebrates under starvation stress and offer a scientific foundation for developing stress-resistant sea cucumber strains, contributing to the sustainable development of the sea cucumber aquaculture industry.