Pearl gentian grouper (Epinephelus fuscoguttatus ♀ × Epinephelus lanceolatus ♂) is a fish of high commercial value in the aquaculture industry in Asia. However, this hybrid fish is not cold-tolerant, and its molecular regulation mechanism underlying cold stress remains largely elusive. This study thus investigated the liver transcriptomic responses of pearl gentian grouper by comparing the gene expression of cold stress groups (20, 15, 12, and 12 °C for 6 h) with that of control group (25 °C) using PacBio SMRT-Seq and Illumina RNA-Seq technologies. In SMRT-Seq analysis, a total of 11,033 full-length transcripts were generated and used as reference sequences for further RNA-Seq analysis. In RNA-Seq analysis, 3271 differentially expressed genes (DEGs), two low-temperature specific modules (tan and blue modules), and two significantly expressed gene sets (profiles 0 and 19) were screened by differential expression analysis, weighted gene co-expression networks analysis (WGCNA), and short time-series expression miner (STEM), respectively. The intersection of the above analyses further revealed some key genes, such as PCK, ALDOB, FBP, G6pC, CPT1A, PPARα, SOCS3, PPP1CC, CYP2J, HMGCR, CDKN1B, and GADD45Bc. These genes were significantly enriched in carbohydrate metabolism, lipid metabolism, signal transduction, and endocrine system pathways. All these pathways were linked to biological functions relevant to cold adaptation, such as energy metabolism, stress-induced cell membrane changes, and transduction of stress signals. Taken together, our study explores an overall and complex regulation network of the functional genes in the liver of pearl gentian grouper, which could benefit the species in preventing damage caused by cold stress.

Trachinotus ovatus is an economically important mariculture fish, and hypoxia has become a critical threat to this hypoxia-sensitive species. However, the molecular adaptation mechanism of T. ovatus liver to hypoxia remains unclear. In this study, we investigated the effects of acute hypoxic stress (1.5 ± 0.1 mg·L⁻¹ for 6 h) and re-oxygenation (5.8 ± 0.3 mg·L⁻¹ for 12 h) in T. ovatus liver at both the transcriptomic and metabolic levels to elucidate hypoxia adaptation mechanism. Integrated transcriptomics and metabolomics analyses identified 36 genes and seven metabolites as key molecules that were highly related to signal transduction, cell growth and death, carbohydrate metabolism, amino acid metabolism, and lipid metabolism, and all played key roles in hypoxia adaptation. Of these, the hub genes FOS and JUN were pivotal hypoxia adaptation biomarkers for regulating cell growth and death. During hypoxia, up-regulation of GADD45B and CDKN1A genes induced cell cycle arrest. Enhancing intrinsic and extrinsic pathways in combination with glutathione metabolism triggered apoptosis; meanwhile, anti-apoptosis mechanism was activated after hypoxia. Expression of genes related to glycolysis, gluconeogenesis, amino acid metabolism, fat mobilization, and fatty acid biosynthesis were up-regulated after acute hypoxic stress, promoting energy supply. After re-oxygenation for 12 h, continuous apoptosis favored cellular function and tissue repair. Shifting from anaerobic metabolism (glycolysis) during hypoxia to aerobic metabolism (fatty acid β-oxidation and TCA cycle) after re-oxygenation was an important energy metabolism adaptation mechanism. Hypoxia 6 h was a critical period for metabolism alteration and cellular homeostasis, and re-oxygenation intervention should be implemented in a timely way. This study thoroughly examined the molecular response mechanism of T. ovatus under acute hypoxic stress, which contributes to the molecular breeding of hypoxia-tolerant cultivars.

Trachinotus ovatus is a major economically important cultured marine fish in the South China Sea. However, extreme weather and increased culture density result in uncontrollable problems, such as increases in water temperature and a decline in dissolved oxygen (DO), hindering the high-quality development of aquaculture. In this study, liver transcriptional profiles of T. ovatus were investigated under acute high-temperature stress (31 °C and 34 °C) and normal water temperature (27 °C) using RNA sequencing (RNA-Seq) technology. Differential expression analysis and STEM analysis showed that 1347 differentially expressed genes (DEGs) and four significant profiles (profiles 0, 3, 4, and 7) were screened, respectively. Of these DEGs, some genes involved in heat shock protein (HSPs), hypoxic adaptation, and glycolysis were up-regulated, while some genes involved in the ubiquitin-proteasome system (UPS) and fatty acid metabolism were down-regulated. Our results suggest that protein dynamic balance and function, hypoxia adaptation, and energy metabolism transformation are crucial in response to acute high-temperature stress. Our findings contribute to understanding the molecular response mechanism of T. ovatus under acute heat stress, which may provide some reference for studying the molecular mechanisms of other fish in response to heat stress.

The Late Pleistocene-Holocene climate fluctuations have greatly influenced the phylogeographic structure and historical dynamics of many marine organisms in the western Pacific marginal seas. Here, we investigated the impact of Pleistocene glacial-interglacial cycles on the phylogeographic structure and demographic dynamics of Decapterus maruadsi, an economically important fish along the coast of the East China Sea (ECS) and northern South China Sea (NSCS). We obtained 430 concatenated sequences (Cyt b + control region, 1548–1554 bp) of D. maruadsi, including 246 newly sampled from the ECS and 184 previously determined from the NSCS. Genetic structure and phylogenetic analysis demonstrated a lack of significant population structure among 16 populations. Moreover, there was no significant differentiation among populations from Chinese coastal waters and northern Vietnam. Neutrality tests, unimodal mismatch distributions, Bayesian skyline plots, and the star-like haplotype networks all indicated a recent demographic expansion for D. maruadsi population during the Late Pleistocene-Holocene, explaining the low genetic diversity in D. maruadsi along the southeast coast of China. Notably, phylogenetic analyses and net genetic distances based on Cyt b jointly confirmed that 57 Cyt b haplotypes identified as D. maruadsi from the previously defined Sundaland-Rosario-Ranong clade actually represented D. russelli. These results not only reveal the complex effects of Pleistocene-Holocene climate fluctuations on the phylogeographic structure and demographic history of D. maruadsi but also provide useful genetic information for the management of genetic resources.

Oxygen level is an important environmental factor affecting the circadian rhythm. However, little is known about the molecular mechanism by which clock genes regulate the circadian rhythm in fish under hypoxia. To explore changes in the transcription and expression of clock genes and related molecular regulatory mechanisms in pearl gentian grouper under hypoxia, liver transcriptome data were analyzed after exposure to acute hypoxic stress (dissolved oxygen 0.5 mg/L) for 1, 3, 6, and 9 h. miR-210 and m0044-5p inhibited the expression of period3 (per3) and casein kinase 1 delta b (csnk1db) in the core loop of the circadian clock, respectively. The nuclear receptor subfamily 1 group d member 1 (nr1d1) and RAR-related orphan receptor b (rorb) genes in the auxiliary loop were jointly up-regulated by three miRNAs (miR-144-3p/5p, miR-361-5p, and miR-133) and the transcription factor nuclear receptor subfamily 1 group d member 2 (Nr1d2). The pearl gentian grouper maintains the stability of circadian clock systems and normal physiological metabolism under hypoxic stress by regulating the transcriptional expression of these genes via miRNAs and transcription factors to improve hypoxic tolerance. These findings provide important basic data for future research on hypoxic tolerance in pearl gentian grouper and provide new insights into the interaction between hypoxia and the circadian rhythm in fish.