Cold exposure triggers distinct RNA editing, alternative splicing, and gene expression patterns in cold domestication...

Low temperature impacts physiological adaptability of fish, especially those with weaker cold tolerance, potentially affecting growth, immunity and survival. After five generations of artificial domestication, a cold-tolerant strain of Takifugu obscurus with an extreme low temperature of 5 °C has been successfully developed. It provides a valuable resource for exploring the mechanisms of cold tolerance in teleosts. Histological and transcriptomic analyses were integrated to investigate the gill responses in cold-tolerant (CT) and wild-type (WT) pufferfish under cold stress. CT gill tissue showed fewer lesions and remained more intact than WT. Based on the weighted gene co-expression network (WGCNA) revealed that fatty acid and glucose metabolism, which provide energy and antioxidant defense via insulin, peroxisome proliferator-activated receptor (PPAR), and mechanistic target of rapamycin (mTOR) signaling, play a critical role in CT pufferfish under cold stress. In contrast, WT pufferfish exhibited weaker energy metabolism and stronger inflammation and apoptosis pathways, including the NOD-like receptor, the RIG-I-like receptor, and the apoptosis signaling pathway. Notably, both CT and WT pufferfish exhibited enrichment of the base excision repair and spliceosome pathways under cold stress. The number of RNA alternative splicing (AS) and RNA editing genes increased with decreasing temperature, and these genes were found to be enriched in canonical cold response pathways such as mitogen-activated protein kinase (MAPK), PPAR, and mRNA surveillance. Integrating the interactome network of the genes with the results of WGCNA, AS and RNA editing, cold-acclimation genes such as ache, arsd, nectin4, polr3g, and prr5 were identified, which are known to be involved in redox, immunity, and energy regulation. These studies contribute to our understanding of the transcriptional regulation of cold stress and to the genetic breeding of cold tolerance in T. obscurus.