Shanghai Ocean University

The red swamp crayfish, Procambarus clarkii, is a commercially significant crustacean species for aquaculture globally. Growth traits are of great importance for economic efficiency in the aquaculture of the species. However, the molecular mechanisms of regulating growth rate in P. clarkii remain poorly understood. Here, to identify the hub genes and key pathways related to growth rate, transcriptome sequencing and Weighted Gene Co-expression Network Analysis (WGCNA) were conducted on the gill, heart, hepatopancreas, intestine, and muscle from P. clarkii with different growth rate in three full-sib families. A total of 906 differentially expressed genes (DEGs) in the gill (95 up-regulated and 811 down-regulated), 1042 DEGs in the heart (45 up-regulated and 997 down-regulated), 257 DEGs in the hepatopancreas (80 up-regulated and 177 down-regulated), 691 DEGs in the intestine (174 up-regulated and 517 down-regulated), and 158 DEGs in the muscle (30 up-regulated and 128 down-regulated) were identified, respectively. The DEGs were annotated into 101 GO terms, which mainly involved in chitin binding, structural components of the stratum corneum, extracellular region and extracellular space. Nine key pathways including the Wnt signaling pathway, autophagy-animal, phagosome, amino sugar and nucleotide sugar metabolism, TGF-β signaling pathway, drug metabolism-other enzymes, mTOR signaling pathway, lysine degradation, and lysosome pathway were identified based on the KEGG enrichment analysis. A hub module was identified by WGCNA analysis. The hub genes related to structural composition, such as cuticle protein 7-like and pro-resilin, as well as genes involved in various cellular processes, like ataxin-2 homolog were identified based on the PPI network analysis. Overall, the results would provide valuable insights into understanding the molecular regulatory mechanisms of growth rate of P. clarkii.

Low-temperature stress poses a critical challenge to the overwintering survival of black porgy (Acanthopagrus schlegelii), a commercially important marine fish distributed across the coastal waters of West Pacific region, including the continental shelves of China, Japan, and the Korean Peninsula. To unravel the molecular mechanisms underlying cold adaptation, this study employed quantitative proteomics was employed to analyze hepatic protein profiles of black porgy between three groups: control group (CG, 15 °C), cold-sensitive group (CS, 3.8 °C), and cold-tolerant group (CT, 2.8 °C). A total of 4437 proteins were identified, with 1616 differentially expressed protein (DEPs) detected among the groups. Bioinformatics analyses, including Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment, Gene Set Enrichment Analysis (GSEA), and trend analysis, revealed distinct adaptive strategies between CT and CS groups. The CT group exhibited a coordinated "energy conservation - metabolic remodeling - antioxidation" strategy: (1) significant downregulation of ribosomal subunits and protein export pathways to reduce Adenosine Triphosphate (ATP) consumption from protein synthesis (called "ribosomal hibernation"); (2) upregulation of Peroxisome Proliferator-Activated Receptor (PPAR) signaling pathway and peroxisomal functions to enhance fatty acid β-oxidation and ketone body production, facilitating efficient energy supply; (3) activation of antioxidant systems to mitigate damage induced by reactive oxygen species (ROS). In contrast, the CS group showed dysregulated energy metabolism, characterized by enhanced but inefficient glycolysis, impaired endoplasmic reticulum function, and excessive inflammatory responses, which may contribute to protential proteotoxic stress and metabolic dysfunction. Key DEPs and pathways, such as ribosomal proteins, PPAR family proteins, and peroxisomal enzymes, were identified as protential core regulators of cold tolerance in black porgy. This study provides the first comprehensive proteomic insights into the molecular mechanisms of cold tolerance in black porgy, highlighting the evolutionary significance of energy allocation and metabolic plasticity in teleosts. These findings offer potential molecular markers for breeding cold-tolerant strains, addressing critical challenges in aquaculture sustainability.

The Chinese mitten crab (Eriocheir sinensis) is a commercially important aquaculture species in China, with its survival highly vulnerable to abnormal water pH. This study subjected E. sinensis to chronic high-pH stress (control: pH = 8; experimental groups: pH = 9 and pH = 10) and integrated hepatopancreas transcriptomic/metabolomic analyses with intestinal microbiota 16S rRNA sequencing to explore its adaptive mechanisms. The results revealed distinct adaptive strategies across stress phases: under short-term (15 days) high-pH stress, E. sinensis maintained somatic homeostasis mainly via rapid regulation of carbohydrate, lipid, protein metabolism, and energy allocation. In contrast, long-term (30 days) stress drove a strategic shift toward accelerated lipid catabolism, enhanced energy metabolism, and activated immune-related pathways. Additionally, high-pH stress significantly altered the intestinal microbiota community structure, marked by increased abundances of Proteobacteria and Pseudomonas, indicating a potential risk of microbial dysbiosis. Collectively, these findings elucidate the physiological adaptation mechanisms of E. sinensis to high-pH environments and lay a theoretical foundation for improving the sustainability of its aquaculture under extreme pH conditions.