The Chilean oyster (Ostrea chilensis) is a flat oyster native to Chile and New Zealand. Over-exploitation has led to local extinctions in some areas. Two phenotypes, distinguished by dark or white mantle edge pigmentation, have been identified, with the dark-edged mantle oysters being more commercially valuable due to perceived quality. In this study, transcriptomic data were obtained from the mantles of both phenotypes. Total RNA was extracted of adult Chilean Oyster mantle, and samples were sequenced using HiSeq X Illumina technology. A total of 935,620,583 paired-end reads were de novo assembled, 50,908 transcripts produced, and a reference transcriptome created with 37.92% GC content and an N50 of 1929 bp. Functional annotation showed a total of 51,315 GO terms, with 21,322 annotations on Biological Process, 14,578 annotations on Molecular Functions, and 15,415 annotations on Cellular Component. The RNA-seq analysis revealed 746 differentially expressed transcripts, 573 up-regulated and 173 transcripts down-regulated, between dark- and white-mantle edge Chilean Oyster. KEGG enrichment analysis revealed notable differences in the expression profiles allowing the detection of differential expressed transcripts associated with specific pathways such as Ribosome, Citrate cycle, and Protein processing in endoplasmic reticulum. Other interesting differentially represented pathways include Tyrosine metabolism, Tryptophan metabolism, cAMP signaling pathway, ABC transporters, Notch signaling pathway, Endocytosis, and Calcium signaling pathway. This dataset provides a valuable molecular resource for O. chilensis and the understanding of the molecular mechanisms involved in mantle edge pigmentation.

The red sea urchin Loxechinus albus is a species of high commercial importance in Chilean aquaculture, whose performance is strongly influenced by environmental conditions such as temperature. The gut microbiota plays a central role in host physiology; however, its interaction with stress-induced molecular responses remains poorly understood. This study evaluated the effects of thermal stress on food consumption, gut microbial composition, oxidative status, and immune- and stress-related gene expressions in L. albus gut. Sea urchins were exposed to control (16 °C) and elevated temperature (22 °C) conditions for 7 and 14 days. Gut microbiota was characterized using 16S rRNA sequencing, while oxidative damage to DNA and proteins was quantified. Gene expression analyses targeted markers of apoptosis (casp3, casp10, bak1), cellular growth (mtor, raptor), stress response (hsp70), and immune regulation (nfκb, foxo). Thermal stress induced a marked reduction in microbial alpha diversity and promoted a shift toward opportunistic taxa. Heat-stressed individuals exhibited significantly increased oxidative DNA damage, whereas protein oxidation remained unchanged. Gene expression analyses revealed early upregulation of casp3, casp10, nfκb, foxo, and hsp70, suggesting activation of apoptotic, immune, and stress-response pathways. In contrast, bak1, mtor, and raptor showed limited or no significant modulation. These findings demonstrate that thermal stress disrupts host–microbiota homeostasis and induces oxidative and molecular responses in L. albus. This integrative response provides insight into mechanisms underlying physiological performance under thermal stress, with important implications for aquaculture sustainability.

Smoltification is stressful for salmonids, and cortisol is one of the central endocrine regulators for seawater adaptation. It has been established that cortisol plays both mineralocorticoid and glucocorticoid functions by MR and GR, respectively, since the aldosterone hormone is absent. Recently, investigations have proposed that the 11-deoxycorticosterone (DOC) mineralocorticoid precursor might support cortisol effects, but this mechanism remains unclear. Hence, we assessed the early effects of DOC on rainbow trout pre-smolts, the key smoltification stage, via metabolic and transcriptomic approaches. Thirty-six juveniles (~120 g) were treated for 3 h with DOC (1 mg/kg) and/or mineralocorticoid (eplerenone) or glucocorticoid (mifepristone) receptor antagonists (n = 6 for each group). DOC decreased plasma glucose and pyruvate and increased phosphate and liver glycogen. DOC also downregulated carbohydrate metabolism-related genes in the liver. Finally, gill RNA-seq analysis presented 1660 differentially expressed transcripts in DOC versus vehicle, 1022 for eplerenone + DOC versus DOC and 3324 for mifepristone + DOC versus DOC. The enrichment analysis mainly revealed the upregulation of ion transmembrane transport and carbohydrate metabolism and the downregulation of stress and innate immune responses. This suggests a significant role of DOC in liver carbohydrate metabolism and gill osmoregulation of pre-smolts through both receptors. Hence, this could contribute to improving animal welfare monitoring during smoltification by featuring novel and potential biomarkers.

Cortisol, the principal glucocorticoid in teleosts, coordinates the physiological response to stress by regulating metabolism, protein turnover, and growth. Although the molecular effects of acute cortisol exposure have been extensively characterized, the epigenomic mechanisms underlying skeletal muscle remodeling during prolonged cortisol elevation remain poorly understood. Here, we investigated how chronic cortisol reshapes chromatin accessibility and gene expression in rainbow trout (Oncorhynchus mykiss) skeletal muscle using an integrative ATAC-seq and RNA-seq approach. Fish received a single intraperitoneal injection of cortisol (50 μg g⁻¹ body weight) formulated in coconut oil for sustained hormone release and were sampled after 14 days. Cortisol treatment significantly increased plasma cortisol levels, reduced specific growth rate, and increased skeletal muscle protein carbonylation, indicating impaired growth and oxidative protein damage. ATAC-seq revealed extensive chromatin remodeling, including 126,780 cortisol-specific accessible regions and 3393 genes associated with increased accessibility. These genes were enriched in pathways related to FoxO signaling, autophagy, and apoptosis, whereas regions with reduced accessibility were associated with TGF-β signaling, extracellular matrix interactions, and muscle structural maintenance. RNA-seq identified 2170 differentially expressed genes (844 upregulated and 1326 downregulated), revealing a parallel transcriptional shift toward protein turnover, autophagy, and metabolic adaptation, together with repression of extracellular matrix organization, focal adhesion, integrin signaling, and cytoskeletal organization. Integrative analysis identified 113 genes with coordinated increases and 46 genes with coordinated decreases in chromatin accessibility and transcript abundance, highlighting ubiquitin-mediated proteolysis, mitophagy, FoxO signaling, and metabolic pathways as core components of the chronic cortisol response. Collectively, these findings demonstrate that sustained cortisol elevation drives coordinated epigenomic and transcriptomic remodeling of skeletal muscle, promoting a catabolic phenotype characterized by enhanced protein turnover, oxidative protein damage, and impaired structural maintenance, ultimately contributing to reduced growth and potentially compromising fish welfare under aquaculture conditions.