Abstract

Understanding the molecular mechanisms underlying physiological adaptations in marine species is crucial for assessing their resilience to environmental stressors. The Southern king crab (Lithodes santolla), an ecologically and commercially important species in sub-Antarctic waters, inhabits dynamic fjord ecosystems characterized by fluctuating salinity, temperatures, and oxygen levels. However, the molecular basis of its adaptive responses remains largely unexplored. In this study, we assembled the first de novo transcriptome of L. santolla and compared gene expression between two localities in the Strait of Magellan (Ballena Sound and Choiseul Bay). Sequencing yielded 731,879,912 clean reads, which were assembled into 210,093 transcripts, of which 56,064 contigs were successfully annotated. Differential expression analysis identified 4474 differentially expressed genes (DEGs), with individuals from Ballena Sound exhibiting upregulation of heat shock proteins (HSPs) and Na+/K+-ATPase (NKA), consistent with proteostasis support and ion-transport demands. Conversely, individuals from Choiseul Bay showed higher expression of Na+/H+ exchanger (NHE), V-type proton ATPase (V-ATPase), and antioxidant enzymes, indicating enhanced pH/ion regulation and redox buffering. Gene Ontology and KEGG enrichment analyses further highlighted ion transport, oxidative stress mitigation, and energy metabolism. Weighted gene co-expression analysis (WGCNA) recovered modules associated with locality and allowed the identification of high-connectivity hub genes as candidate biomarkers, yielding a panel for environmental stress monitoring. Taken together, these results reveal the gill-level coregulation of ion/osmotic regulation, proteostasis, and redox control, enhancing our understanding of L. santolla's physiological plasticity. This transcriptomic resource and biomarker candidates provide a valuable molecular framework for hypothesis-driven experiments and for monitoring the resilience and conservation status of sub-Antarctic crustaceans under ongoing environmental change. © 2025 The Author(s). Ecology and Evolution published by British Ecological Society and John Wiley & Sons Ltd.