Comparative Biochemistry and Physiology D-Genomics & Proteomics最新文献

{"title":"Identification and characterization of hsp70 gene family in Acrossocheilus fasciatus based on genome and full-length transcripts","authors":"Yongyao Guo ,&nbsp;Shun Wang ,&nbsp;Fidele Niyompano ,&nbsp;Tong Li ,&nbsp;Junhao Chen ,&nbsp;Ziwei Luo ,&nbsp;Xinqin Jiang ,&nbsp;Ye Chen ,&nbsp;Bo Zhao","doi":"10.1016/j.cbd.2025.101480","DOIUrl":"10.1016/j.cbd.2025.101480","url":null,"abstract":"<div><div>Global warming and temperature extremes are increasingly recognized as critical environmental stressors for aquatic species, particularly stream fish, which are becoming more vulnerable due to fluctuating water temperatures and a scarcity of thermal refuges. The <em>hsp70</em> gene family plays a crucial role in maintaining cellular homeostasis and mediating stress responses, especially under thermal stress. However, the evolutionary dynamics and functional diversity of this gene family remain relatively unexplored in stream fish. In this study, we investigated the <em>hsp70</em> gene family in <em>Acrossocheilus fasciatus</em>, an economically important stream fish, by integrating full-length transcriptome data with genomic. Through the use of genomic and full-length transcriptome sequencing, we refined the genome annotation of <em>A. fasciatus</em> and identified 18 <em>hsp70</em> family members, including six novel genes previously unannotated in the genome. Phylogenetic, domain, and motif analyses revealed significant structural variation among these genes. Chromosomal localization demonstrated their distribution across multiple chromosomes, while synteny analysis confirmed evolutionary conservation with <em>A. fasciatus, Danio rerio</em> and <em>Onychostoma macrolepis</em>. RNA-seq and qRT-PCR analyses revealed that <em>hsp70</em> genes showed minimal differential expression in brain tissue under acute thermal stress and in muscle tissue under chronic thermal stress. qRT-PCR analysis revealed significant differential expression of <em>hsp70</em> genes in muscle tissue under acute thermal stress, with <em>hspa8b</em>, <em>hspa13</em>, and <em>hyou1</em> exhibited marked upregulation, whereas <em>hspa14</em> was significantly downregulated. These genes could serve as potential biomarkers. The integration of full-length transcriptome data with genomic information improved the precision of gene identification and genome annotation. These findings carry significant and far-reaching implications for advancing our comprehension of thermal stress in aquatic organisms, potentially informing and enhancing conservation and breeding initiatives.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"55 ","pages":"Article 101480"},"PeriodicalIF":2.2,"publicationDate":"2025-03-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143654670","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Diet-driven transcriptional changes in weaning red abalone (Haliotis rufescens) and its hybrid (H. rufescens [♀] x H. fulgens [♂])","authors":"Miguel A. Tripp-Valdez ,&nbsp;Clara E. Galindo-Sánchez ,&nbsp;Claudia Ventura-López ,&nbsp;Francesco Cicala ,&nbsp;Vincent Montes-Orozco ,&nbsp;Fabiola Lafarga-De la Cruz","doi":"10.1016/j.cbd.2025.101484","DOIUrl":"10.1016/j.cbd.2025.101484","url":null,"abstract":"<div><div>The abalone (<em>Haliotis</em> sp) aquaculture industry is on the rise fueled by its high commercial demand. The use of abalone interspecific hybrids is gaining attention due to their improved growth and tolerance to environmental challenges. However, hybrids may respond differently to dietary inputs compared to their parental species, which could be optimized to achieve maximum growth potential. Accordingly, we previously reported that the postlarvae of a hybrid cross obtained by mating red and green abalone (<em>H. rufescens</em> [♀] x <em>H. fulgens</em> [♂]) presented higher growth and survival rates than red abalone postlarvae when fed with <em>Macrocystis pyrifera</em> (M) and a mixture of <em>Ulva onhoi</em> and <em>Navicula incerta</em> (UN). Here, to gain a deeper insight into the physiological and metabolic responses of both crosses, we report the results of a transcriptome sequencing analysis to unveil the diet-driven physiological changes within each cross. Our findings indicate that the diet induces modulation in the transcriptional machinery related to macromolecules breakdown, especially, the mixed diet UN induced higher expression of lysosomal enzymes, especially in enzymes involved in glycosaminoglycan catabolism, such as arylsulfatases, glucosidases, and alpha-fucosidases, which might indicate a higher ability to break down complex carbohydrates from algae. These transcriptional responses might explain the growth difference between pure and hybrid as well as for abalone fed with M and UN.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"55 ","pages":"Article 101484"},"PeriodicalIF":2.2,"publicationDate":"2025-03-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143654705","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Transcriptome research conducted on the liver and spleen of Jinhu grouper (Epinephelus fuscoguttatus♀ × Epinephelus tukula♂) reveals the mechanism in response to Vibrio anguillarum infection","authors":"Huimin Duan ,&nbsp;Yongsheng Tian ,&nbsp;Zhentong Li","doi":"10.1016/j.cbd.2025.101482","DOIUrl":"10.1016/j.cbd.2025.101482","url":null,"abstract":"<div><div><em>Vibrio anguillarum</em> serves as a pathogenic organism in aquaculture, leading to a lethal hemolytic septicemia in aquatic species. Whereas little study has evaluated the molecular mechanism of the infection caused by <em>V. anguillarum</em> in Jinhu grouper. In this study, analysis of the transcriptome was conducted on the liver and spleen tissues from Jinhu groupers infected with <em>V. anguillarum</em> infection. We identified 2978 DEGs in the liver group and 2506 DEGs in spleen group, including 1689 and 1502 up-regulated genes and 1289 and 1004 down-regulated genes, respectively. Gene set enrichment analysis revealed a significant reduction in genes associated with metabolism such as carbon metabolism and glycolysis/gluconeogenesis in the liver, while upregulation of genes linked to the above pathways as well as in the citrate cycle in the spleen. In addition, the upregulated genes in the liver and spleen are both enriched in the cell cycle. Subsequent investigation into the principal DEGs implicated in the TLR pathways showed that <em>V. anguillarum</em> infection may activate the TLR pathway by overexpression of the <em>tlr</em>5 and promote the synthesis of proinflammatory cytokines <em>il1β</em> and <em>il-8</em>. Among these, 11 genes related to metabolism, cell cycle and immunity were selected and characterized. Overall, our research indicates that <em>V. anguillarum</em> can affect the metabolism and cell cycle while also triggering immune defense reactions in Jinhu grouper.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"55 ","pages":"Article 101482"},"PeriodicalIF":2.2,"publicationDate":"2025-03-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143697916","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Gene co-expression network analysis reveals key regulatory and responsive genes regulating the intensity of carotenoid coloration in scallop muscle","authors":"Yihan Zhang ,&nbsp;Shiqi Liu ,&nbsp;Xue Li ,&nbsp;Tingting Li ,&nbsp;Huizhen Wang ,&nbsp;Zhenmin Bao ,&nbsp;Xiaoli Hu","doi":"10.1016/j.cbd.2025.101483","DOIUrl":"10.1016/j.cbd.2025.101483","url":null,"abstract":"<div><div>Carotenoids are biologically active pigments widely distributed in nature, playing crucial roles in the growth, development, immunity, and coloration of animals. As important nutrients, carotenoids are also considered important parameters for evaluating the economic value of farmed animals, including aquatic organisms. However, for marine animals that accumulate a large amount of specific carotenoids, the molecular mechanism underlying the bioavailability of carotenoids remains insufficiently explored, particularly with regard to the regulation of carotenoid pigmentation intensity. This study investigated the carotenoid coloration mechanism in the adductor muscle of “Haida golden scallop”, a variety of Yesso scallop (<em>Patinopecten yessoensis</em>), with high carotenoid content and varying coloration intensity in adductor muscle. Through transcriptomic analysis and weighted gene co-expression network analysis (WGCNA), three carotenoid accumulation-associated modules (MEgreenyellow module, MEgreen, and MEsalmon) were identified. Two <em>PARP9/14/15</em> genes, previously identified as crucial regulators of carotenoid accumulation at the genomic level, were identified as the hub genes of MEgreenyellow module, which exhibited a significant positive correlation with the concentrations of both pectenolone and pectenoxanthin. Specifically, <em>PARP9/14/15–1</em> showed strong connectivity with genes involved in carotenoid absorption and transport, such as <em>LRP1</em>, <em>SRB-like 1</em>, <em>ABCA3</em>, and <em>StARD</em>; while <em>PARP9/14/15–2</em> was associated with <em>NPC1L1</em>, a gene critical for carotenoid absorption. It is proposed that <em>PARP9/14/15</em>s may modulate the accumulation of pectenolone and pectenoxanthin in the adductor muscle of “Haida golden scallop” by regulating the expression of these carotenoid-related genes. Furthermore, genes within the other two carotenoid accumulation-associated modules were significantly enriched in pathways related to immune response (MEgreen) and DNA damage repair (MEsalmon), suggesting that these pathways may be in response to carotenoid accumulation levels. This study provides valuable insights into the molecular mechanisms underlying carotenoid accumulation and pigmentation intensity in bivalves, offering theoretical guidance for the breeding of carotenoid-rich aquaculture strains.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"55 ","pages":"Article 101483"},"PeriodicalIF":2.2,"publicationDate":"2025-03-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143636857","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Transcriptomic analysis reveals the survival strategies of Mytilus coruscus under short-term rising seawater temperatures","authors":"Bingqi Wei ,&nbsp;Hao Wang ,&nbsp;Zhenyu Dong ,&nbsp;Zhenqi Xin ,&nbsp;Wanliang Zhang ,&nbsp;Huajian Lin ,&nbsp;Weifeng Wang ,&nbsp;Mingshan Song ,&nbsp;Baoying Guo","doi":"10.1016/j.cbd.2025.101481","DOIUrl":"10.1016/j.cbd.2025.101481","url":null,"abstract":"<div><div><em>Mytilus coruscus</em> is an ecologically and economically important species in China. However, in recent years, ocean warming has seriously threatened the survival of <em>M. coruscus</em> and the development of its aquaculture industry. In this study, we analyzed the transcriptomes of <em>M. coruscus</em> pediveliger larvae and adults reared under rising seawater temperatures to explore heat adaptation mechanisms. <em>M. coruscus</em> pediveliger larvae were exposed to artificial seawater at 18 °C, 21 °C and 23 °C for 24 h, while adults were exposed to 18 °C, 26 °C and 33 °C for 24 h to simulate high-temperature conditions during low tide. Results showed that the genes associated with antioxidant activity, oxidative phosphorylation, and glycosaminoglycan biosynthesis were gradually up-regulated in response to high temperature in pediveliger larvae, indicating that the regulation of oxidative stress and energy regulation was a primary response to heat stress. HSPs, apoptosis, NF-κB signaling pathway and TNF signaling pathway were significantly up-regulated in <em>M. coruscus</em> adults. Additionally, KEGG analysis revealed significant enrichment in protein processing in endoplasmic reticulum, PI3K-Akt signaling pathway, HIF-1 signaling pathway and NF-<span><math><mi>κ</mi></math></span>B signaling pathway. Hence, adult <em>M. coruscus</em> coped with heat stress through the regulation of signal transduction and immune responses. Our findings suggest that <em>M. coruscus</em> pediveliger larvae and adults employed different strategies to cope with high-temperature stress, providing preliminary insights into the heat adaptation mechanisms of mussels. This study represents the first step toward a deeper understanding of the complexity of heat adaptation mechanisms in marine bivalves and is instrumental in elucidating the adaptive strategies of marine organisms amid climate change. Furthermore, our findings also lay a foundation for breeding stress-resistant <em>M. coruscus.</em></div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"55 ","pages":"Article 101481"},"PeriodicalIF":2.2,"publicationDate":"2025-03-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143654671","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Clam age constrains thermal tolerance: Insights from burrowing behavior and transcriptomics","authors":"Zhiyang Cui ,&nbsp;Biao Wu ,&nbsp;Liqing Zhou ,&nbsp;Zhihong Liu ,&nbsp;Peizhen Ma ,&nbsp;Zhuanzhuan Li ,&nbsp;Xiujun Sun","doi":"10.1016/j.cbd.2025.101479","DOIUrl":"10.1016/j.cbd.2025.101479","url":null,"abstract":"<div><div>Thermal stress in marine environments is likely to become more widespread in marine environments. Understanding age-related physiological adaptations to thermal stress is critically important for predicting the impacts of global climate change on marine biodiversity. The typical burrowing bivalve, Manila clam <em>Ruditapes philippinarum</em>, was selected to explore molecular and physiological responses to thermal stress and how the effects varied with ages (juvenile VS. adults). When the temperature increased to 30.6 °C, the significantly higher rates of burrowing behavior was found in juvenile clams than that of adult clams (60 % VS. 26.7 %). As the thermal stress increased to 44.6 °C, the survival rate was found to be 49.7 % in juvenile clams, compared to 100 % mortality in adult clams. According to the comparative transcriptomics, the significant up-regulation of genes related to neuropeptide and extracellular matrix (ECM) were potentially involved in active muscle contractility and wound healing ability in juveniles. This may be responsible for their high rates of burrowing behavior in response to the thermal stress. In contrast to juveniles, multiple down-regulated genes involved in antioxidant and energy metabolism were detected in adults, which may be associated with disruption of their energy homeostasis, cell damage and dysfunction, resulting in less capability of adult clams to resist the thermal conditions. The present study will provide new evidences on age differences of clams in response to thermal stress, suggesting clam age or body size constrains their thermal tolerance. These findings will not only shed lights on the molecular mechanism of clams with different ages or sizes in response to thermal stress, but also provide insights into the prediction of future biodiversity and sustainable aquaculture production in a warming world.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"55 ","pages":"Article 101479"},"PeriodicalIF":2.2,"publicationDate":"2025-03-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143620509","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Analysis of circRNA expression profile of Litopenaeus vannamei under pH and alkalinity interactive stress and verification of novel_circ_021024 and novel_circ_004981 regulating stress compounds metabolism","authors":"Baoyi Fan,&nbsp;Ruiqi Zhang,&nbsp;Yujun Kang,&nbsp;Xue Mao,&nbsp;Xiang Shi,&nbsp;Jintao Guo,&nbsp;Ziguo Wang","doi":"10.1016/j.cbd.2025.101469","DOIUrl":"10.1016/j.cbd.2025.101469","url":null,"abstract":"<div><div>The global issue of salinization has made the use of saline-alkaline water in aquaculture increasingly vital. CircRNAs are a new type of endogenous non-coding RNA. Under high saline-alkaline stress, how circRNAs regulate the stress response of <em>Litopenaeus vannamei</em>, especially the mechanism of its immune and metabolic functions, is still unclear. This study aimed to analyze the expression profile of circRNAs and explore their response mechanisms in <em>L. vannamei</em> under the combined influence of high alkalinity and high pH. The results indicated that 127, 157, and 146 differentially expressed circRNAs (DECs) and 1401, 1547, and 1540 differentially expressed mRNAs (DEGs) were identified in the high-pH, alkalinity, and interaction groups, respectively. KEGG enrichment analysis revealed that DECs were mainly enriched in pathways such as sulfur metabolism, glycerophospholipids, and oxidative phosphorylation. The activities of antioxidant-related enzymes, such as superoxide dismutase (SOD) and glutathione peroxidase (GSH - PX), increased, while the activities of energy - metabolism-related enzymes, like hexokinase (HK) and pyruvate kinase (PK), decreased. By combining weighted gene-related network analysis (WGCNA) with circRNA - mRNA data, it was found that the expression levels of essential genes related to metabolisms, such as novel_circ_007011, novel_circ_004981, and novel_circ_021024, declined. Gene-silencing experiments demonstrated that novel_circ_004981 and novel_circ_021024 could regulate the expression of glutathione peroxidase (<em>GPx</em>) and carbonic anhydrase - 3 (<em>cah - 3</em>) and further regulate the metabolic pathway and antioxidant system of <em>L. vannamei</em>. This study provides theoretical support for further understanding the stress-response mechanisms of circRNAs in <em>L. vannamei</em> under high-pH and alkalinity stress and offers a scientific basis for the development of saline-alkali aquaculture.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"55 ","pages":"Article 101469"},"PeriodicalIF":2.2,"publicationDate":"2025-03-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143601355","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Responses of gut microbiota to altitude in a small mammal on Qinghai-Tibetan Plateau","authors":"Yan Zhang ,&nbsp;Yihong Wang ,&nbsp;Baohui Yao ,&nbsp;Zhaoxian Tan ,&nbsp;Xinyang Chen ,&nbsp;Rong Wang ,&nbsp;Weihong Ji ,&nbsp;Jiapeng Qu","doi":"10.1016/j.cbd.2025.101467","DOIUrl":"10.1016/j.cbd.2025.101467","url":null,"abstract":"<div><div>Altitude of the plateau may affect the composition and functional diversity of animal gut microbiota. However, the specific effects of altitude on the composition, community structure, and function of the host's gut microbiota, as well as how these effects, through interactions between microbial metabolic products (e.g., SCFAs) and microbial diversity, support host adaptation to high-altitude environments, remain unclear. This study investigates the variations of gut microbial community structure and function in plateau pikas (<em>Ochotona curzoniae</em>) along altitude on Qinghai-Tibetan Plateau. Cecum contents were analyzed using 16S rRNA sequencing and short-chain fatty acid (SCFA) content analyses to explore the structure, function and metabolic characteristics gut microbiota across different altitudes. As altitude increases, pikas' gut microbiota diversity significantly decreased, SCFA levels did not significantly change, while both diversity and complexity of the microbiota co-occurrence networks significantly decreased. The microbial community shifted toward better suited to high-altitude environments, as significantly increased in Bacteroidetes abundance but decreased in Firmicutes abundance. The microbial community assembly process became more deterministic, and KEGG analysis revealed the upregulation of metabolic, genetic information processing, and organismal system pathways. These results indicated that the gut microbiota diversity and complexity decreased in plateau pikas with increasing altitude, along with the upregulation of key metabolic pathways, as well as the stability of SCFA levels which reflecting balanced supply-demand relationships, contribute to adaptation of high-altitude environments. These findings reveal the substantial impact of altitude on the gut microbiota of a small mammal inhabiting the plateau, providing new insights into its adaptation mechanisms to high-altitude environments.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"55 ","pages":"Article 101467"},"PeriodicalIF":2.2,"publicationDate":"2025-03-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143578411","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Whole transcriptomic analysis reveals the lncRNA-miRNA-mRNA regulatory mechanism underlying the heat-hardening formation in Mytilus coruscus","authors":"Hao Wang ,&nbsp;Bingqi Wei ,&nbsp;Zhenyu Dong ,&nbsp;Zhenqi Xin ,&nbsp;Huajian Lin ,&nbsp;Wanliang Zhang ,&nbsp;Yingying Ye ,&nbsp;Zhi Liao ,&nbsp;Weifeng Wang ,&nbsp;Xiaojun Yan ,&nbsp;Mingshan Song ,&nbsp;Baoying Guo","doi":"10.1016/j.cbd.2025.101468","DOIUrl":"10.1016/j.cbd.2025.101468","url":null,"abstract":"<div><div>Heat-hardening is a critical adaptation mechanism that enables the mussel <em>Mytilus coruscus</em> to endure high-temperature events caused by low tides and adverse weather condition. However, the molecular regulatory mechanism underlying heat-hardening remains unclear. Herein, we analyzed the whole transcriptome of heat-hardening <em>M. coruscus</em> to explore formation mechanism of heat-hardening. <em>M. coruscus</em> were treated with 27 °C for 5 days, 3 h per day, to promote heat-hardening formation, and sampled at 6, 8, 10, 12, 14, and 16 days. We identified 203 differentially expressed lncRNAs (DE-lncRNAs), 11 differentially expressed miRNAs (DE-miRNAs) and 207 differentially expressed mRNAs (DE-mRNAs). GO and KEGG enrichment analysis revealed that the DE-mRNAs were mainly enriched in arachidonic acid metabolism pathway, apoptosis pathway, NOD-like receptor signaling pathway and the platelet-activated pathway, WGCNA results suggested that arachidonic acid metabolism and cytochrome P450 were significantly correlated with heat-hardening during formation. <em>PLA2</em> was identified as an essential gene in heat-hardening, with high node degrees, enriched in the arachidonic acid metabolism pathway and regulated by a lncRNA (MSTRG.113849.1) and a miRNA (novel_miR_425). MSTRG.113849.1-novel_miR_425-<em>PLA2</em> relationship pairs were identified for heat-hardening in <em>M. coruscus.</em> Our finding suggests that miRNAs and lncRNAs play pivotal roles in heat-hardening by targeting <em>PLA2</em>, providing a mechanism for <em>M. coruscus</em> to adapt to heat stress, which also offers a mechanism to adapt to stressors arising from a rapidly changing oceanic environment.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"55 ","pages":"Article 101468"},"PeriodicalIF":2.2,"publicationDate":"2025-03-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143697904","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"α-Ketoglutarate modulates the mechanisms of toxicity in crucian carp kidneys chronically exposed to NaHCO3: Metabolomics insights","authors":"Wenzhi Liu ,&nbsp;Lin Han ,&nbsp;Fangying Yuan ,&nbsp;Qianwen Liu ,&nbsp;Hongyu Cheng ,&nbsp;Xiaofeng Jin ,&nbsp;Yanchun Sun","doi":"10.1016/j.cbd.2025.101466","DOIUrl":"10.1016/j.cbd.2025.101466","url":null,"abstract":"<div><div>Due to the unique physicochemical properties of saline-alkaline water, aquatic organisms find it challenging to survive under such conditions. This study established a freshwater control group (C), a 20 mmol/L NaHCO₃ exposure group (T), a 40 mmol/L NaHCO₃ exposure group (F), a 20 mmol/L NaHCO₃ exposure with α-ketoglutarate (AKG)-supplemented feed group (TA), and a 40 mmol/L NaHCO₃ exposure with AKG-supplemented feed group (FA). Histopathological analysis, biochemical assays, and UPLC-QTOF/MS metabolomics were employed to explore the potential mechanisms by which AKG alleviates oxidative damage in freshwater teleosts induced by saline-alkaline stress. Histopathological results showed that as the concentration of carbonate alkali exposure increased, the severity of kidney lesions in crucian carp (<em>Carassius auratus</em>) worsened. However, in the TA and FA groups, the damage showed varying degrees of repair, with the kidney tissue morphology in the TA group almost restored to the state of the C group. Under carbonate alkali exposure, compared to the C group, the activity of antioxidant enzymes Catalase and Superoxide dismutase in crucian carp kidneys decreased in a dose-dependent manner, but increased upon AKG supplementation. Conversely, the levels of Malondialdehyde, blood ammonia, Urea nitrogen, and Uric acid showed the opposite trend. Metabolomics analysis revealed that carbonate-alkali stress caused a series of metabolic disruptions in fish, including amino acid metabolism, lipid metabolism, and energy metabolism. AKG positively regulated metabolic pathways such as the pentose phosphate pathway, arachidonic acid metabolism, and amino acid metabolism, thereby enhancing the antioxidant, anti-inflammatory, and immune capabilities of fish under saline-alkaline stress, alleviating oxidative damage induced by the stress. Overall, our research indicates that saline-alkaline stress significantly alters kidney function and metabolic characteristics, disrupts the antioxidant system and energy homeostasis, inhibits protein catabolism, and induces kidney damage in crucian carp. Exogenous AKG supplementation effectively mitigates oxidative damage and metabolic disorders in crucian carp kidneys under carbonate-alkaline stress. This study elucidates the physiological mechanisms by which AKG alleviates kidney tissue damage under saline-alkaline stress at the metabolic level, providing scientific evidence for the development of aquaculture in saline-alkaline water.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"55 ","pages":"Article 101466"},"PeriodicalIF":2.2,"publicationDate":"2025-03-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143562129","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}