Transcriptome and co-expression network analyses reveal the regulatory pathways and key genes associated with temperature adaptability in the yellow drum (Nibea albiflora)

Long-term thermal stress reshapes the tolerance of head kidney of Hong Kong catfish (Clarias fuscus) to acute heat shock by regulating energy metabolism and immune response

Elevated water temperatures caused by climate warming can affect fish survival. However, fish can maintain normal physiological functions through physiological plasticity. When temperature fluctuations exceed their tolerance range, even stress-resistant species like Siluriformes are affected. It is known that fish have adaptive regulation mechanisms to reshape their tolerance to temperature stress, but the ability to respond to acute thermal shock and recover after adaptive remodeling remains unclear. This study investigated the effects of different culture temperatures on the ability of Hong Kong catfish (Clarias fuscus) to respond to acute heat stress and stress recovery. C. fuscus were cultured at normal temperature (NT, 26 °C) or high temperature (HT, 34 °C) for 90 days, and then their head kidney transcriptome was analyzed after acute heat stress (34 °C) and subsequent recovery (26 °C). The results revealed 8165 differentially expressed genes (DEGs) in the NT group and 8537 DEGs in the HT group during the entire temperature treatment process, with each group responding differently to various stages of temperature treatment. Enrichment analysis showed that both NT and HT groups had enriched pathways related to energy metabolism and immune response during acute heat stress. However, acute heat stress disrupted the energy supply and oxidative metabolism in the NT group, while enhancing the HT group's ability to respond to repeated heat stress. This experiment demonstrated that high-temperature culture reshaped the energy metabolism balance in the head kidney tissue, improving anti-stress and stress recovery abilities. These findings lay a foundation for further research on the plasticity of fish in coping with acute temperature changes.

Selection of heat-resistant strains in Bohai Red Scallops and their transcriptomic responses to heat stress

Temperature has consistently been a critical environmental factor in the cultivation of scallops, and with global warming, marine animals will likely experience even more exposure to heat stress. Thus, it is necessary to select heat-resistant strains in scallops. In this study, heat stress selection was performed on the unselected Bohai Red scallop (CG) using the measured upper median lethal temperature (LT50), yielding an elite group (EG), from which the heat-resistant F1 offspring (EGF1) were reproduced. Tolerance to heat stress was significantly increased in EGF1, as evidenced by the elevated LT50 and the activities of certain antioxidant enzymes. Transcriptomic analyses and GO and KEGG analyses demonstrated that both EG and CG animals may mitigate heat stress and maintain cellular homeostasis through pathways associated with protein folding, energy metabolism, and antioxidant mechanisms. Furthermore, the scallops in the EG group showed a strong immune profile, with immune-related DEGs enriched mainly in interleukin-1 receptor binding and Toll-like receptor pathways. Conduct GO and KEGG enrichment analyses on the MM.darkolivegreen module, which demonstrates the strongest positive correlation with heat stress in Weighted Gene Co-expression Network Analysis (WGCNA). These analyses revealed pathways consistent with those identified in differentially expressed genes (DEGs), thereby providing mutual validation of the results. These results enhance our understanding of the molecular mechanisms driving heat stress adaptation in Bohai Red scallops and establish a theoretical foundation for the inheritance and evolution of heat-resistant traits.

Transcriptomic profiling revealed the regulatory pathways and key genes associated with cold tolerance in two eel gobies

Closely related species of the eel goby family (Gobiidae) have evolved divergent resistance to low temperatures, but the molecular mechanisms remain poorly understood. This study used a comparative transcriptomic approach to identify key pathways and genes associated with cold tolerance in two eel goby species. Expression profiles of the cold-tolerant O. lacepedii and the cold-sensitive O. rebecca in control (23 °C) and cold stress groups (15 °C and 11 °C) were analyzed. Differentially expressed genes closely linked to interspecific cold tolerance divergence were identified through transcriptome profiling and Venn diagram analysis. GO and KEGG enrichment analyses revealed that processes related to cellular homeostasis, the PPAR signaling pathway, cellular respiration, and oxidative phosphorylation were activated during the cold tolerance response of eel gobies. WGCNA analysis indicated that the hub genes related to thermogenesis and microtubular stability, specifically PPARGC1A and α-tubulin, may contribute to the high cold tolerance in O. lacepedii. These findings provide key clues for dissection of the molecular mechanisms behind the formation of cold tolerance in eel gobies.

Analysis of Differential Alternative Splicing in Largemouth Bass After High Temperature Exposure

Temperature is one of the critical factors affecting the physiological functions of fish. With ongoing global warming, changes in water temperature have a profound impact on fish species. Alternative splicing, being a significant mechanism for gene expression regulation, facilitates fish to adapt and thrive in dynamic and varied aquatic environments. Our study used transcriptome sequencing to analyze alternative splicing in largemouth bass gills at 34 °C for 24 h. The findings indicated an increase in both alternative splicing events and alternative splicing genes after high temperature treatment. Specifically, the comparative analysis revealed a total of 674 differential alternative splicing events and 517 differential alternative splicing genes. Enrichment analysis of differential alternative splicing genes revealed significant associations with various gene ontology (GO) terms and KEGG pathways, particularly in immune-related pathways like necroptosis, apoptosis, and the C-type lectin receptor signaling pathway. These results emphasize that some RNA splicing-related genes are involved in the response of largemouth bass to high temperatures.

Long-term thermal acclimation enhances heat resistance of Hong Kong catfish (Clarias fuscus) by modulating gill tissue structure, antioxidant capacity and immune metabolic pathways

The rapid temperature changes caused by global warming significantly challenge fish survival by affecting various biological processes. Fish generally mitigate stress through physiological plasticity, but when temperature changes exceed their tolerance limits, even adaptable species like Siluriformes can experience internal disruptions. This study investigates the effects of extreme thermal climate on Hong Kong catfish (Clarias fuscus), native to tropical and subtropical regions. C. fuscus were exposed to normal temperature (NT, 26 ℃) or high temperature (HT, 34 ℃) condition for 90 days. Subsequently, histological, biochemical, and transcriptomic changes in gill tissue were observed after exposure to acute high temperatures (34 ℃) and subsequent temperature recovery (26 ℃). Histological analysis revealed that C. fuscus in the HT group exhibited less impact from sudden temperature shifts compared to the NT group, as they adapted by reducing the interlamellar cell mass (ILCM) and lamellae thickness (LT) of gill tissue, thereby mitigating the aftermath of acute heat shock. Biochemical analysis showed that catalase (CAT) activity in the high temperature group continued to increase, while malondialdehyde (MDA) levels decreased, suggesting establishment of a new oxidative balance and enhanced environmental adaptability. Transcriptome analysis identified 520 and 463 differentially expressed genes in the NT and HT groups, respectively, in response to acute temperature changes. Enrichment analysis highlighted that in response to acute temperature changes, the NT group inhibited apoptosis and ferroptosis by regulating the activity of alox12, gclc, and hmox1a, thereby attenuating the adverse effects of heat stress. Conversely, the HT group increased the activity of pfkma and pkma to provide sufficient energy for tissue repair. The higher degree of heat shock protein (Hsp) response in NT group also indicated more severe heat stress injury. These findings demonstrate alterations in gill tissue structure, regulation of oxidative balance, and the response of immune metabolic pathways to acute temperature fluctuations in C. fuscus following thermal exposure, suggesting potential avenues for further exploration into the thermal tolerance plasticity of fish adapting to global warming.

Tissue-specific transcriptional response of post-larval clownfish to ocean warming

Anthropogenically driven climate change is predicted to increase average sea surface temperatures, as well as the frequency and intensity of marine heatwaves in the future. This increasing temperature is predicted to have a range of negative physiological impacts on multiple life-stages of coral reef fish. Nevertheless, studies of early-life stages remain limited, and tissue-specific transcriptomic studies of post-larval coral reef fish are yet to be conducted. Here, in an aquaria-based study we investigate the tissue-specific (brain, liver, muscle, and digestive tract) transcriptomic response of post-larval (20 dph) Amphiprion ocellaris to temperatures associated with future climate change (+3 °C). Additionally, we utilized metatranscriptomic sequencing to investigate how the microbiome of the digestive tract changes at +3 °C. Our results show that the transcriptional response to elevated temperatures is highly tissue-specific, as the number of differentially expressed genes (DEGs) and gene functions varied amongst the brain (102), liver (1785), digestive tract (380), and muscle (447). All tissues displayed DEGs associated with thermal stress, as 23 heat-shock protein genes were upregulated in all tissues. Our results indicate that post-larval clownfish may experience liver fibrosis-like symptoms at +3 °C as genes associated with extracellular matrix structure, oxidative stress, inflammation, glucose transport, and metabolism were all upregulated. We also observe a shift in the digestive tract microbiome community structure, as Vibrio sp. replace Escherichia coli as the dominant bacteria. This shift is coupled with the dysregulation of various genes involved in immune response in the digestive tract. Overall, this study highlights post-larval clownfish will display tissue-specific transcriptomic responses to future increases in temperature, with many potentially harmful pathways activated at +3 °C.

Exploring the effect of Ulva prolifera decay on the immune tissue of Paralichthys olivaceus based on transcriptomics and histopathological analysis

For 17 consecutive years, the outbreak of Ulva prolifera in the South Yellow Sea area of China has caused significant negative impacts on coastal ecological environment. However, its specific influence on fish immunity is rare. In this study, the juvenile Paralichthys olivaceus was exposed to fresh U. prolifera algae (FU) and decomposing algal effluent (DU). After short-term stress for 14 days, the histopathological and transcriptome analysis were performed to study the effect of U. prolifera decay on P. olivaceus. Histopathological analysis found that the liver, spleen and head kidneys of P. olivaceus were damaged after the short-term stress. The transcriptome results showed that the steroid biosynthesis signaling pathway and the PI3K-Akt signaling pathway were significantly enriched. Some immune related genes, including c1qc-like, dusp1, dusp16, HSP90 and metabolic related genes serotransferrin, were differentially expressed. These results highlighted the harmfulness of U. prolifera on marine fish, setting a solid foundation for further analyses.

Transcriptional Modulation Reveals Physiological Responses to Temperature Adaptation in Acrossocheilus fasciatus

In order to explore the molecular regulatory mechanism of temperature acclimation under long-term temperature stress in Acrossocheilus fasciatus, this study used high-throughput sequencing technology to analyze 60 days of breeding under five temperature conditions (12 °C, 16 °C, 20 °C, 24 °C, 28 °C). Compared with 20 °C, 9202, 4959 differentially expressed genes (DEGs) were discovered in low-temperature groups (12 °C, 16 °C), whereas 133 and 878 DEGs were discovered in high-temperature groups (24 °C, 28 °C), respectively. The KEGG functional enrichment analysis revealed that DEGs were primarily enriched in tight junction, PI3 K-Akt signaling pathway and protein digestion and absorption in low-temperature groups, and mainly enriched in proximal tubule bicarbonate reclamation, protein digestion and absorption, and HIF-1 signaling pathway in high-temperature groups. The viability of transcriptome sequencing-based screening of DEGs for temperature adaptation in A. fasciatus was shown by the selection of eight DEGs for further validation by quantitative real-time PCR (qRT-PCR), the findings of which were consistent with the RNA-seq data. According to the findings, protein digestion and absorption were primarily regulated by temperature variations, physiological stress was a significant regulator in regulation under high-temperature stress, and the immune system was a significant regulator in regulation under low-temperature stress. The transcriptional patterns of A. fasciatus under temperature stress are revealed in this study. This knowledge is crucial for understanding how A. fasciatus adapts to temperature and can help us better comprehend the environmental difficulties that A. fasciatus adaptation faces.

High-quality Japanese flounder genome aids in identifying stress-related genes using gene coexpression network

The Japanese flounder is one of the most economically important marine flatfish. However, due to the increased frequency of extreme weather events and high-density industrial farming, an increasing number of environmental stresses have become severe threats to the healthy development of the Japanese flounder culture industry. Herein, we produced a high-quality chromosome-scale Japanese flounder genome using PacBio Circular Consensus Sequencing technologies. The assembled Japanese flounder genome spanned 588.22 Mb with a contig N50 size of 24.35 Mb. In total, 105.89 Mb of repetitive sequences and 22,565 protein-coding genes were identified by genome annotation. In addition, 67 candidate genes responding to distinct stresses were identified by gene coexpression network analysis based on 16 published stress-related RNA-seq datasets encompassing 198 samples. A high-quality chromosome-scale Japanese flounder genome and candidate stress-related gene set will not only serve as key resources for genomics studies and further research on the underlying stress responsive molecular mechanisms in Japanese flounder but will also advance the progress of genetic improvement and comprehensive stress-resistant molecular breeding of Japanese flounder.

Measurement(s)	genome assembly
Technology Type(s)	PacBio RS II

Identification of stress-related genes by co-expression network analysis based on the improved turbot genome

Turbot (Scophthalmus maximus), commercially important flatfish species, is widely cultivated in Europe and China. With the continuous expansion of the intensive breeding scale, turbot is exposed to various stresses, which greatly impedes the healthy development of turbot industry. Here, we present an improved high-quality chromosome-scale genome assembly of turbot using a combination of PacBio long-read and Illumina short-read sequencing technologies. The genome assembly spans 538.22 Mb comprising 27 contigs with a contig N50 size of 25.76 Mb. Annotation of the genome assembly identified 104.45 Mb repetitive sequences, 22,442 protein-coding genes and 3,345 ncRNAs. Moreover, a total of 345 stress responsive candidate genes were identified by gene co-expression network analysis based on 14 published stress-related RNA-seq datasets consisting of 165 samples. Significantly improved genome assembly and stress-related candidate gene pool will provide valuable resources for further research on turbot functional genome and stress response mechanism, as well as theoretical support for the development of molecular breeding technology for resistant turbot varieties.

Measurement(s)	whole genome sequencing
Technology Type(s)	PacBio long-read and Illumina short-read sequencing technologies

Scale Development-Related Genes Identified by Transcriptome Analysis

Scales, as key structures of fish skin, play an important role in physiological function. The study of fish scale development mechanisms provides a basis for exploring the molecular-level developmental differences between scaled and non-scaled fishes. In this study, alizarin red staining was used to divide the different stages of zebrafish (Danio rerio) scale development. Four developmental stages, namely stage I (~17 dpf, scales have not started to grow), stage II (~33 dpf, the point at which scales start to grow), stage III (~41 dpf, the period in which the scales almost cover the whole body), and stage IV (~3 mpf, scales cover the whole body), were determined and used for subsequent transcriptome analysis. WGCNA (weighted correlation network analysis) and DEG (differentially expressed gene) analysis were used for screening the key genes. Based on the comparison between stage II and stage I, 54 hub-genes were identified by WGCNA analysis. Key genes including the Scpp family (Scpp7, Scpp6, Scpp5, and Scpp8), the Fgf family (Fgfr1b and Fgfr3), Tcf7, Wnt10b, Runx2b, and Il2rb were identified by DEG analysis, which indicated that these genes played important roles in the key nodes of scale development signal pathways. Combined with this analysis, the TGF-β, Wnt/β-catenin, and FGF signaling pathways were suggested to be the most important signal pathways for scales starting to grow. This study laid a foundation for exploring the scale development mechanism of other fishes. The scale development candidate genes identified in the current study will facilitate functional gene identifications in the future.