Pub Date : 2026-03-01Epub Date: 2025-11-19DOI: 10.1016/j.cbd.2025.101695
Mingmei Liu , Keyu Zhou , Zhuoling Liu , Sen Wei , Laia Ribas , Quanquan Cao
Globally, eel aquaculture holds significant economic and ecological importance, but it faces severe challenges from various diseases that hinder its sustainable development. This review aims to systematically explore how genomics can be utilized to enhance the disease resistance of eels, thereby promoting sustainable aquaculture practices. To achieve this goal, we first review the current status of eel aquaculture and the main disease threats, and then focus on the application of genomic technologies in understanding eel disease resistance. We elaborate on the progress in genome sequencing of multiple eel species, which provides a fundamental resource for identifying disease-resistant traits. We discuss the role of functional genomics tools such as CRISPR-Cas9 in accelerating the screening of favorable disease-resistant traits. We also detail how immune system genomics (e.g., genes like Tollip, interferon, and MHC), genome-wide association studies, and the interaction between epigenetics and the environment contribute to the identification of disease-resistant traits. In addition, this review analyzes the applications of marker-assisted selection and genomic selection in eel breeding programs, as well as biotechnological intervention methods such as gene editing, probiotics, and vaccine development as novel strategies to improve disease resistance. Finally, we present future prospects for eel disease-resistant breeding efforts.
{"title":"Harnessing genomics for identifying disease-resistant eels: Advances, applications, and sustainable aquaculture","authors":"Mingmei Liu , Keyu Zhou , Zhuoling Liu , Sen Wei , Laia Ribas , Quanquan Cao","doi":"10.1016/j.cbd.2025.101695","DOIUrl":"10.1016/j.cbd.2025.101695","url":null,"abstract":"<div><div>Globally, eel aquaculture holds significant economic and ecological importance, but it faces severe challenges from various diseases that hinder its sustainable development. This review aims to systematically explore how genomics can be utilized to enhance the disease resistance of eels, thereby promoting sustainable aquaculture practices. To achieve this goal, we first review the current status of eel aquaculture and the main disease threats, and then focus on the application of genomic technologies in understanding eel disease resistance. We elaborate on the progress in genome sequencing of multiple eel species, which provides a fundamental resource for identifying disease-resistant traits. We discuss the role of functional genomics tools such as CRISPR-Cas9 in accelerating the screening of favorable disease-resistant traits. We also detail how immune system genomics (e.g., genes like Tollip, interferon, and MHC), genome-wide association studies, and the interaction between epigenetics and the environment contribute to the identification of disease-resistant traits. In addition, this review analyzes the applications of marker-assisted selection and genomic selection in eel breeding programs, as well as biotechnological intervention methods such as gene editing, probiotics, and vaccine development as novel strategies to improve disease resistance. Finally, we present future prospects for eel disease-resistant breeding efforts.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"57 ","pages":"Article 101695"},"PeriodicalIF":2.2,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145623601","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}
Pub Date : 2026-03-01Epub Date: 2025-11-19DOI: 10.1016/j.cbd.2025.101688
Haochen Yang , Chenghao Li , Jing Huang , Haotong Jia , Yu Du , Yumei Chang
Leuciscus waleckii, a cyprinid fish of significant commercial value, exhibits remarkable adaptability to a range of environmental conditions, including extreme alkaline and saline environments. This adaptability positions it an important model for investigating the mechanisms underlying saline-alkali adaptation and osmoregulation. In light of the global challenge of land salinization and the increasing trend of aquaculture in saline-alkali environments, understanding the adaptation mechanisms of fish species such as L. waleckii is crucial for the success of aquaculture in these areas. In this study, gill tissue samples were collected from fish at 1, 5, and 10 days during alkali stress (AW1, AW5, AW10) and after transfer to freshwater (FW1, FW5, FW10), with AW10 serving as the control group. RNA sequencing identified a total of 444 and 856 differentially expressed genes (DEGs) during the stress and recovery phases, respectively. KEGG enrichment analysis highlighted key pathways: alkali stress activated ECM-receptor interaction, focal adhesion, and steroid hormone biosynthesis, while recovery involved cytokine-cytokine receptor interaction and Toll-like/FoxO signaling. Small RNA sequencing, combined with differential expression analysis, identified links between miRNAs and primary bile acid biosynthesis as well as immune regulation. Integrated miRNA-mRNA network analysis implicated specific genes and miRNAs in regulating ECM integrity, steroid metabolism, and immune response. These results demonstrate that L. waleckii employs ECM remodeling, steroid hormone dynamics, and miRNA-mediated immune modulation to survive extreme alkalinity, providing valuable insights for breeding saline-alkali tolerant aquaculture species. These findings not only enhance our understanding of the adaptive physiology of fish but also provide insights into strategies for improving stress resistance in commercially valuable species, thereby enhancing aquaculture productivity in saline-alkali ecosystems.
{"title":"Integrated miRNA and mRNA analysis in gills of Amur ide (Leuciscus waleckii) reveals novel insights into the molecular regulatory mechanism of alkaline acclimation","authors":"Haochen Yang , Chenghao Li , Jing Huang , Haotong Jia , Yu Du , Yumei Chang","doi":"10.1016/j.cbd.2025.101688","DOIUrl":"10.1016/j.cbd.2025.101688","url":null,"abstract":"<div><div><em>Leuciscus waleckii</em>, a cyprinid fish of significant commercial value, exhibits remarkable adaptability to a range of environmental conditions, including extreme alkaline and saline environments. This adaptability positions it an important model for investigating the mechanisms underlying saline-alkali adaptation and osmoregulation. In light of the global challenge of land salinization and the increasing trend of aquaculture in saline-alkali environments, understanding the adaptation mechanisms of fish species such as L. <em>waleckii</em> is crucial for the success of aquaculture in these areas. In this study, gill tissue samples were collected from fish at 1, 5, and 10 days during alkali stress (AW1, AW5, AW10) and after transfer to freshwater (FW1, FW5, FW10), with AW10 serving as the control group. RNA sequencing identified a total of 444 and 856 differentially expressed genes (DEGs) during the stress and recovery phases, respectively. KEGG enrichment analysis highlighted key pathways: alkali stress activated ECM-receptor interaction, focal adhesion, and steroid hormone biosynthesis, while recovery involved cytokine-cytokine receptor interaction and Toll-like/FoxO signaling. Small RNA sequencing, combined with differential expression analysis, identified links between miRNAs and primary bile acid biosynthesis as well as immune regulation. Integrated miRNA-mRNA network analysis implicated specific genes and miRNAs in regulating ECM integrity, steroid metabolism, and immune response. These results demonstrate that L. <em>waleckii</em> employs ECM remodeling, steroid hormone dynamics, and miRNA-mediated immune modulation to survive extreme alkalinity, providing valuable insights for breeding saline-alkali tolerant aquaculture species. These findings not only enhance our understanding of the adaptive physiology of fish but also provide insights into strategies for improving stress resistance in commercially valuable species, thereby enhancing aquaculture productivity in saline-alkali ecosystems.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"57 ","pages":"Article 101688"},"PeriodicalIF":2.2,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145623603","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}
Decapoda crabs inhabit diverse environments, which are mainly aquatic, while some intertidal crabs are semi-terrestrial. However, current research on the molecular basis of terrestrial adaptation in crabs remains insufficiently characterized. Orisarma neglectum (Sesarmidae), which inhabits low-salinity semi-terrestrial environments such as the Yangtze River Estuary and its surrounding wetland areas, is an ideal model for studying terrestrial adaptation mechanisms. Thus, the transcriptomic and histological methods were used to explore the terrestrial adaptation mechanism of O. neglectum in this study. Three experimental groups (aquatic, semi-terrestrial, terrestrial) under controlled habitat simulations were set up. Histological analyses revealed marked branchial lamellar hypertrophy with concomitant cytoplasmic exudation in terrestrial-acclimated O. neglectum compared to aquatic/semi-terrestrial groups under xeric conditions. Furthermore, the transcriptomics results of gills revealed that the desiccation stress imposed on O. neglectum mainly manifests in energy metabolism, RNA synthesis and Ribosome pathways, and immune-related genes. The results of histology and transcriptomics suggested that gills were more sensitive to habitat changes than hepatopancreas. Given all this, a completely terrestrial habitat may be detrimental to the survival of O. neglectum, and intertidal crabs cannot live completely without water. Investigating the adaptive mechanisms of O. neglectum to diverse habitats through histology and transcriptomics can provide critical insights into understanding the terrestrial adaptation of semi-terrestrial crab species, and references for solving the problems of oxygen supply and air exposure during crab breeding and transportation.
{"title":"Analysis of the histology and transcriptomics of Orisarma neglectum provides new insights into the terrestrial adaptation mechanisms of intertidal crabs","authors":"Zhengfei Wang , Zhilin Guo , Chenchen Shen , Lijie Cui , Jing Zhu , Sijia Hao , Yayun Guan , Yanhan Peng","doi":"10.1016/j.cbd.2025.101658","DOIUrl":"10.1016/j.cbd.2025.101658","url":null,"abstract":"<div><div>Decapoda crabs inhabit diverse environments, which are mainly aquatic, while some intertidal crabs are semi-terrestrial. However, current research on the molecular basis of terrestrial adaptation in crabs remains insufficiently characterized. <em>Orisarma neglectum</em> (Sesarmidae), which inhabits low-salinity semi-terrestrial environments such as the Yangtze River Estuary and its surrounding wetland areas, is an ideal model for studying terrestrial adaptation mechanisms. Thus, the transcriptomic and histological methods were used to explore the terrestrial adaptation mechanism of <em>O. neglectum</em> in this study. Three experimental groups (aquatic, semi-terrestrial, terrestrial) under controlled habitat simulations were set up. Histological analyses revealed marked branchial lamellar hypertrophy with concomitant cytoplasmic exudation in terrestrial-acclimated <em>O. neglectum</em> compared to aquatic/semi-terrestrial groups under xeric conditions. Furthermore, the transcriptomics results of gills revealed that the desiccation stress imposed on <em>O. neglectum</em> mainly manifests in energy metabolism, RNA synthesis and Ribosome pathways, and immune-related genes. The results of histology and transcriptomics suggested that gills were more sensitive to habitat changes than hepatopancreas. Given all this, a completely terrestrial habitat may be detrimental to the survival of <em>O. neglectum</em>, and intertidal crabs cannot live completely without water. Investigating the adaptive mechanisms of <em>O. neglectum</em> to diverse habitats through histology and transcriptomics can provide critical insights into understanding the terrestrial adaptation of semi-terrestrial crab species, and references for solving the problems of oxygen supply and air exposure during crab breeding and transportation.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"57 ","pages":"Article 101658"},"PeriodicalIF":2.2,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145369817","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}
Pub Date : 2026-03-01Epub Date: 2025-10-22DOI: 10.1016/j.cbd.2025.101660
Suhan Peng , Jie Lai , Shengyue Lin , Sixun Li , Binhua Deng , Weijian Chen , Weibin Li , Chong Han , Qiang Li
The demand for synthetic progesterone has surged due to its widespread use in contraceptives and veterinary drugs. However, these compounds are not fully removed by wastewater treatment plants, leading to their release into aquatic environments and potential disruption of fish reproduction and development. Etonogestrel (ETO), a third-generation synthetic progestogen, is widely used in oral contraceptives. In this study, adult female mosquitofish were exposed to ETO at measured concentrations of 0 ng/L, 3.88 ng/L, 39.5 ng/L, and 385.18 ng/L for 36 days. Morphology, ovarian histology, and transcriptomic analyses were conducted to assess the effects of ETO. Results showed that ETO exposure reduced the body weight-to-total length ratio and promoted gonopodia and skeletal modifications. Particularly notable was the finding of decreased ovarian weight and the induction of testicular structures in the 385.18 ng/L ETO group, indicating a significant masculinization effect. Transcriptomic analysis revealed that genes related to sexual differentiation (cyp17a1, hsd17b3 and sox9), which were enriched in the GnRH signaling pathway and steroid hormone biosynthesis, may drive masculinization by promoting androgen production and inhibiting estrogen synthesis. Additionally, ETO may promote morphological masculinization by altering lipid metabolism patterns. These findings indicate that ETO could induce masculinization and negatively impact reproductive health in mosquitofish, an effect potentially exacerbated by changes in lipid metabolism.
{"title":"Induction of masculinization in mosquitofish (Gambusia affinis) by the synthetic progestin etonogestrel exposure: Insights from morphology, ovarian histology, and transcriptomic analyses","authors":"Suhan Peng , Jie Lai , Shengyue Lin , Sixun Li , Binhua Deng , Weijian Chen , Weibin Li , Chong Han , Qiang Li","doi":"10.1016/j.cbd.2025.101660","DOIUrl":"10.1016/j.cbd.2025.101660","url":null,"abstract":"<div><div>The demand for synthetic progesterone has surged due to its widespread use in contraceptives and veterinary drugs. However, these compounds are not fully removed by wastewater treatment plants, leading to their release into aquatic environments and potential disruption of fish reproduction and development. Etonogestrel (ETO), a third-generation synthetic progestogen, is widely used in oral contraceptives. In this study, adult female mosquitofish were exposed to ETO at measured concentrations of 0 ng/L, 3.88 ng/L, 39.5 ng/L, and 385.18 ng/L for 36 days. Morphology, ovarian histology, and transcriptomic analyses were conducted to assess the effects of ETO. Results showed that ETO exposure reduced the body weight-to-total length ratio and promoted gonopodia and skeletal modifications. Particularly notable was the finding of decreased ovarian weight and the induction of testicular structures in the 385.18 ng/L ETO group, indicating a significant masculinization effect. Transcriptomic analysis revealed that genes related to sexual differentiation (<em>cyp17a1</em>, <em>hsd17b3</em> and <em>sox9</em>), which were enriched in the GnRH signaling pathway and steroid hormone biosynthesis, may drive masculinization by promoting androgen production and inhibiting estrogen synthesis. Additionally, ETO may promote morphological masculinization by altering lipid metabolism patterns. These findings indicate that ETO could induce masculinization and negatively impact reproductive health in mosquitofish, an effect potentially exacerbated by changes in lipid metabolism.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"57 ","pages":"Article 101660"},"PeriodicalIF":2.2,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145402882","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}
Pub Date : 2026-03-01Epub Date: 2025-11-26DOI: 10.1016/j.cbd.2025.101696
Yang Yanan , Shao Shucheng , Bao Chenchang , Cui Zhaoxia
The cerebral ganglion and eyestalk are pivotal regulators of reproduction in decapod crustaceans. To understand how mating drives ovarian development, we performed a comprehensive transcriptomic analysis of these neural tissues in the mud crab, Scylla paramamosain. Our findings reveal that mating induces significant molecular reprogramming, coordinating post-mating neuroendocrine functions. Functional specialization was also evident: the cerebral ganglion showed enrichment in pathways for tight junctions and cytoskeletal reorganization, while the eyestalk primarily activated second messenger signaling crucial for neurohormone release. Among the differentially expressed genes (DEGs), Follistatin-like and TDRD1 were implicated in neuroendocrine mechanisms that promote vitellogenesis. Other DEGs related to synaptic transmission (e.g., SERCA-like, 5-HT receptor) and neuroplasticity further highlighted the profound neural impact of mating. Furthermore, a weighted gene co-expression network analysis (WGCNA) identified hub genes involved in cytoskeletal dynamics, protein folding, and vesicular transport that regulate ovarian development. Collectively, these findings propose a model in which mating activates a conserved neuroendocrine interface. This process reshapes neural physiology by modulating calcium signaling, neurotransmission, and neurodevelopment, ultimately driving ovarian development and adaptive reproductive behaviors in S. paramamosain.
{"title":"Transcriptomic analysis of post-mating neural reprogramming and its coordinated control of ovarian development in the mud crab Scylla paramamosain","authors":"Yang Yanan , Shao Shucheng , Bao Chenchang , Cui Zhaoxia","doi":"10.1016/j.cbd.2025.101696","DOIUrl":"10.1016/j.cbd.2025.101696","url":null,"abstract":"<div><div>The cerebral ganglion and eyestalk are pivotal regulators of reproduction in decapod crustaceans. To understand how mating drives ovarian development, we performed a comprehensive transcriptomic analysis of these neural tissues in the mud crab, <em>Scylla paramamosain</em>. Our findings reveal that mating induces significant molecular reprogramming, coordinating post-mating neuroendocrine functions. Functional specialization was also evident: the cerebral ganglion showed enrichment in pathways for tight junctions and cytoskeletal reorganization, while the eyestalk primarily activated second messenger signaling crucial for neurohormone release. Among the differentially expressed genes (DEGs), <em>Follistatin-like</em> and <em>TDRD1</em> were implicated in neuroendocrine mechanisms that promote vitellogenesis. Other DEGs related to synaptic transmission (e.g., <em>SERCA-like</em>, <em>5-HT receptor</em>) and neuroplasticity further highlighted the profound neural impact of mating. Furthermore, a weighted gene co-expression network analysis (WGCNA) identified hub genes involved in cytoskeletal dynamics, protein folding, and vesicular transport that regulate ovarian development. Collectively, these findings propose a model in which mating activates a conserved neuroendocrine interface. This process reshapes neural physiology by modulating calcium signaling, neurotransmission, and neurodevelopment, ultimately driving ovarian development and adaptive reproductive behaviors in <em>S. paramamosain</em>.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"57 ","pages":"Article 101696"},"PeriodicalIF":2.2,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145662981","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}
Pub Date : 2026-03-01Epub Date: 2025-11-13DOI: 10.1016/j.cbd.2025.101689
Changlin Chen, Lei Wang, Chaoyue Deng, Wenyan Lin, Huapeng Chen, Xinxin Wang, Haoran Yu, Junlong Sun, Jian Luo, Feibiao Song
Previous research has demonstrated that the addition of exogenous glutamine in feed can enhance the growth and development of Trachinotus blochii. Nonetheless, there is limited knowledge about the specific regulatory pathways and essential regulatory genes implicated in glutamine's influence on the growth and development of T. blochii. This research utilized RNA interference technology to achieve sustained suppression of the gs and gls genes in live T. blochii. After 52 days of interference, we analyzed the growth and development of T. blochii, intestinal morphology, digestive and antioxidant enzyme activity, and intestinal transcriptome. The development of T. blochii was markedly inhibited by interference, with the intestinal diameter, villus length, width, and muscle layer in the interference group being greatly reduced compared to the control group. Measurements of intestinal enzyme activity showed a significant decrease in LPS content in T. blochii following interference, and antioxidant-related enzyme activities (T-AOC and GSH) were lowered, and MDA content was significantly raised. Transcriptome analysis indicated that following the knockdown of the gs and gls genes, there was a significant enrichment of growth-related serine metabolism pathways and lipid metabolism pathways, as well as immune inflammation-related pathways, including the complement and coagulation cascade and PPAR signaling pathway. Co-expression mRNA network analysis revealed a significant enrichment of genes associated with purine de novo synthesis and the coenzyme Q oxidoreductase family. In summary, knockdown of the gs and gls genes diminishes amino acid metabolism and fat utilization in the intestines of T. blochii, thus impacting intestinal structure and hindering growth. These findings offer significant insights for the control of intestinal health and agricultural practices of T. blochii.
{"title":"The effects of interfering with gs and gls genes on intestinal genes expression and metabolic pathways in Trachinotus blochii","authors":"Changlin Chen, Lei Wang, Chaoyue Deng, Wenyan Lin, Huapeng Chen, Xinxin Wang, Haoran Yu, Junlong Sun, Jian Luo, Feibiao Song","doi":"10.1016/j.cbd.2025.101689","DOIUrl":"10.1016/j.cbd.2025.101689","url":null,"abstract":"<div><div>Previous research has demonstrated that the addition of exogenous glutamine in feed can enhance the growth and development of <em>Trachinotus blochii</em>. Nonetheless, there is limited knowledge about the specific regulatory pathways and essential regulatory genes implicated in glutamine's influence on the growth and development of <em>T. blochii</em>. This research utilized RNA interference technology to achieve sustained suppression of the <em>gs</em> and <em>gls</em> genes in live <em>T. blochii</em>. After 52 days of interference, we analyzed the growth and development of <em>T. blochii</em>, intestinal morphology, digestive and antioxidant enzyme activity, and intestinal transcriptome. The development of <em>T. blochii</em> was markedly inhibited by interference, with the intestinal diameter, villus length, width, and muscle layer in the interference group being greatly reduced compared to the control group. Measurements of intestinal enzyme activity showed a significant decrease in LPS content in <em>T. blochii</em> following interference, and antioxidant-related enzyme activities (T-AOC and GSH) were lowered, and MDA content was significantly raised. Transcriptome analysis indicated that following the knockdown of the <em>gs</em> and <em>gls</em> genes, there was a significant enrichment of growth-related serine metabolism pathways and lipid metabolism pathways, as well as immune inflammation-related pathways, including the complement and coagulation cascade and PPAR signaling pathway. Co-expression mRNA network analysis revealed a significant enrichment of genes associated with purine de novo synthesis and the coenzyme Q oxidoreductase family. In summary, knockdown of the <em>gs</em> and <em>gls</em> genes diminishes amino acid metabolism and fat utilization in the intestines of <em>T. blochii</em>, thus impacting intestinal structure and hindering growth. These findings offer significant insights for the control of intestinal health and agricultural practices of <em>T. blochii</em>.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"57 ","pages":"Article 101689"},"PeriodicalIF":2.2,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145566583","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}
Hypoxic stress poses a significant challenge to aquaculture productivity. As a hypoxia-intolerant species, rainbow trout (Oncorhynchus mykiss) requires further investigation regarding their molecular and physiological adaptations to prolonged hypoxia. In this study, we investigated the temporal dynamics of the hypoxic response in rainbow trout gill cells through an integrated analysis of transcriptomics, histopathology, and biochemical analysis. Primary gill cells exposed to hypoxic conditions (3 % O2) for 0, 24, and 48 h exhibited a progressive increase in reactive oxygen species (ROS) levels. A total of 6744 differentially expressed genes (DEGs) were identified through RNA sequencing, with the Glycolysis/Gluconeogenesis and Biosynthesis of amino acids pathways significantly upregulated at both 24 and 48 h, indicating a metabolic shift toward anaerobic energy production and antioxidant defense. In contrast, steroid biosynthesis was enriched at 48 h, potentially supporting membrane repair and cortisol-mediated stress adaptation, whereas apoptosis transitioned from inhibition at 24 h to activation at 48 h, correlating with irreversible cellular damage. Weighted Gene Co-expression Network Analysis (WGCNA) identified the module most associated with 48-h hypoxia, which was also enriched in these four pathways. Histopathological and physiological indicators also proved time-dependent changes in tissues upon hypoxic stress. These findings indicated that during early hypoxia (24 h), metabolic adaptation, including Glycolysis/Gluconeogenesis and Biosynthesis of amino acids, was prioritized in rainbow trout. However, after 48 h of hypoxia, a transition from metabolic adaptation to apoptosis-mediated cell clearance was induced, accompanied by the upregulation of steroid biosynthesis to mitigate sustained oxidative damage.
{"title":"Transcriptomic and physiological responses of rainbow trout (Oncorhynchus mykiss) gill tissues to hypoxic stress","authors":"Ziyi Zhao, Mengqun Liu, Qiusheng Wang, Haishen Wen, Xin Qi","doi":"10.1016/j.cbd.2025.101672","DOIUrl":"10.1016/j.cbd.2025.101672","url":null,"abstract":"<div><div>Hypoxic stress poses a significant challenge to aquaculture productivity. As a hypoxia-intolerant species, rainbow trout (<em>Oncorhynchus mykiss</em>) requires further investigation regarding their molecular and physiological adaptations to prolonged hypoxia. In this study, we investigated the temporal dynamics of the hypoxic response in rainbow trout gill cells through an integrated analysis of transcriptomics, histopathology, and biochemical analysis. Primary gill cells exposed to hypoxic conditions (3 % O<sub>2</sub>) for 0, 24, and 48 h exhibited a progressive increase in reactive oxygen species (ROS) levels. A total of 6744 differentially expressed genes (DEGs) were identified through RNA sequencing, with the Glycolysis/Gluconeogenesis and Biosynthesis of amino acids pathways significantly upregulated at both 24 and 48 h, indicating a metabolic shift toward anaerobic energy production and antioxidant defense. In contrast, steroid biosynthesis was enriched at 48 h, potentially supporting membrane repair and cortisol-mediated stress adaptation, whereas apoptosis transitioned from inhibition at 24 h to activation at 48 h, correlating with irreversible cellular damage. Weighted Gene Co-expression Network Analysis (WGCNA) identified the module most associated with 48-h hypoxia, which was also enriched in these four pathways. Histopathological and physiological indicators also proved time-dependent changes in tissues upon hypoxic stress. These findings indicated that during early hypoxia (24 h), metabolic adaptation, including Glycolysis/Gluconeogenesis and Biosynthesis of amino acids, was prioritized in rainbow trout. However, after 48 h of hypoxia, a transition from metabolic adaptation to apoptosis-mediated cell clearance was induced, accompanied by the upregulation of steroid biosynthesis to mitigate sustained oxidative damage.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"57 ","pages":"Article 101672"},"PeriodicalIF":2.2,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145446733","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}
Pub Date : 2026-03-01Epub Date: 2025-11-22DOI: 10.1016/j.cbd.2025.101693
Jing Xie , Congping Ying , Zhen Tang , Yanping Yang , Kai Liu
The Chinese mitten crab (Eriocheir sinensis) is a crustacean widely distributed in coastal and estuarine waters across China. Due to its high nutritional value, it has become a significant commercial aquaculture species in China, generating substantial economic value. Polyascus sp., which is called crab slave, can parasitize on crabs, altering the host's morphological appearance and disrupting its endocrine regulation, thereby inhibiting growth and development. To further elucidate the molecular mechanisms underlying the host crab's response to crab slave parasitism and to elucidate the role of lncRNAs in this process, we performed comparative transcriptome sequencing analysis on the eyestalk tissues of parasitized and non-parasitized crabs. This study identified 2746 novel lncRNAs, including 735 differentially expressed lncRNAs in the male comparison groups and 394 differentially expressed lncRNAs in the female comparison groups. Concurrently, GSEA analysis of target mRNAs for differentially expressed lncRNAs revealed that Polyascus sp. parasitism influences lncRNA regulation of GO:0042302 (structural components of the cuticle), GO:0006040 (amino acid metabolism processes), and GO:0006030 (chitin metabolic process) were enriched in the male comparison (T1 vs. CK1), while GO:0044282 (small molecule catabolic process) and GO:0016627 (oxidoreductase activity, acting on the CH-CH group of donors), etc., were enriched in the female comparison (T2 vs. CK2). Furthermore, a molecular regulatory network of key lncRNA-mRNA interactions was constructed based on transcriptomic profiles. These findings provide new insights into lncRNA-mediated physiological regulation in crustaceans and highlight the pivotal role of lncRNAs in modulating expression patterns.
中华绒螯蟹（Eriocheir sinensis）是一种广泛分布于中国沿海和河口水域的甲壳类动物。由于其高营养价值，已成为中国重要的商业养殖品种，产生了可观的经济价值。Polyascus sp.被称为蟹奴，它可以寄生在螃蟹身上，改变寄主的形态外观，扰乱寄主的内分泌调节，从而抑制其生长发育。为了进一步阐明寄主蟹对从寄生反应的分子机制以及lncrna在这一过程中的作用，我们对被寄生和未被寄生的寄主蟹眼柄组织进行了转录组测序比较分析。本研究鉴定出2746个新的lncrna，其中男性对照组差异表达的lncrna为735个，女性对照组差异表达的lncrna为394个。同时，对lncRNAs差异表达的靶mrna进行GSEA分析发现，雄性对照（T1 vs CK1）中，Polyascus寄生影响GO:0042302（表皮结构成分）、GO:0006040（氨基酸代谢过程）和GO:0006030（几丁质代谢过程）的lncRNA调控富集，而GO:0044282（小分子分解代谢过程）和GO:0016627（氧化还原酶活性，作用于CH-CH供体组）等lncRNA调控富集。在女性对照中（T2 vs. CK2）表达丰富。此外，基于转录组谱构建了lncRNA-mRNA关键相互作用的分子调控网络。这些发现为研究lncrna介导的甲壳类动物生理调控提供了新的见解，并突出了lncrna在调节表达模式中的关键作用。
{"title":"Key lncRNA-mRNA networks regulated by Polyascus sp. infection: A comparative transcriptomic analysis of the eyestalk in the Eriocheir sinensis","authors":"Jing Xie , Congping Ying , Zhen Tang , Yanping Yang , Kai Liu","doi":"10.1016/j.cbd.2025.101693","DOIUrl":"10.1016/j.cbd.2025.101693","url":null,"abstract":"<div><div>The Chinese mitten crab (<em>Eriocheir sinensis</em>) is a crustacean widely distributed in coastal and estuarine waters across China. Due to its high nutritional value, it has become a significant commercial aquaculture species in China, generating substantial economic value. <em>Polyascus</em> sp., which is called crab slave, can parasitize on crabs, altering the host's morphological appearance and disrupting its endocrine regulation, thereby inhibiting growth and development. To further elucidate the molecular mechanisms underlying the host crab's response to crab slave parasitism and to elucidate the role of lncRNAs in this process, we performed comparative transcriptome sequencing analysis on the eyestalk tissues of parasitized and non-parasitized crabs. This study identified 2746 novel lncRNAs, including 735 differentially expressed lncRNAs in the male comparison groups and 394 differentially expressed lncRNAs in the female comparison groups. Concurrently, GSEA analysis of target mRNAs for differentially expressed lncRNAs revealed that <em>Polyascus</em> sp. parasitism influences lncRNA regulation of GO:0042302 (structural components of the cuticle), GO:0006040 (amino acid metabolism processes), and GO:0006030 (chitin metabolic process) were enriched in the male comparison (T1 vs. CK1), while GO:0044282 (small molecule catabolic process) and GO:0016627 (oxidoreductase activity, acting on the CH-CH group of donors), etc., were enriched in the female comparison (T2 vs. CK2). Furthermore, a molecular regulatory network of key lncRNA-mRNA interactions was constructed based on transcriptomic profiles. These findings provide new insights into lncRNA-mediated physiological regulation in crustaceans and highlight the pivotal role of lncRNAs in modulating expression patterns.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"57 ","pages":"Article 101693"},"PeriodicalIF":2.2,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145623604","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}
Pub Date : 2026-03-01Epub Date: 2025-11-08DOI: 10.1016/j.cbd.2025.101686
Xiaofeng Luo , Junru Pan , Haiyan Li , Wenrui Ye , Shehr Bano Mustafa , Siraj Ahmed , Khuram Shahzad , Yonggang Sun , Wangsheng Zhao
The yak, a ruminant species native to high-altitude plateaus, serves as a vulnerable model for studying adaptation to extreme environments. Exposed to hypoxia, low temperatures, and strong ultraviolet radiation, yaks have evolved unique physiological mechanisms to thrive under such conditions. Among its organs, the intestine is a crucial metabolic organ and plays a key role in environmental adaptation. Therefore, this study systematically compared the transcriptional regulatory mechanisms of the small and large intestine between yaks and cattle, thereby revealing the metabolic mechanisms underlying the high-altitude adaptation of yaks. The results showed that the expression of several key metabolic genes, including IDO1, KYNU (tryptophan metabolism), ACSL1 (lipid metabolism), and ABCG2 (vitamin transport), was significantly upregulated in the yak small intestine. This indicates that the yak small intestine has stronger physiological potential in nutrient metabolism and barrier function. In the large intestine, the expression of key genes in pathways such as lipid metabolism (PLA2), detoxification (UGT), cAMP signaling (ADCY, CREB3L), and bile secretion (ABCC) was significantly upregulated, indicating that the yak possesses unique physiological advantages in energy regulation and maintaining intestinal homeostasis. This study systematically elucidates the metabolic mechanisms of the yak intestine under the extreme conditions of the plateau, providing a basis for in-depth analysis of ruminant intestinal function and molecular breeding.
{"title":"Transcriptome analysis reveals intestinal gene expression and metabolic pathways in yaks","authors":"Xiaofeng Luo , Junru Pan , Haiyan Li , Wenrui Ye , Shehr Bano Mustafa , Siraj Ahmed , Khuram Shahzad , Yonggang Sun , Wangsheng Zhao","doi":"10.1016/j.cbd.2025.101686","DOIUrl":"10.1016/j.cbd.2025.101686","url":null,"abstract":"<div><div>The yak, a ruminant species native to high-altitude plateaus, serves as a vulnerable model for studying adaptation to extreme environments. Exposed to hypoxia, low temperatures, and strong ultraviolet radiation, yaks have evolved unique physiological mechanisms to thrive under such conditions. Among its organs, the intestine is a crucial metabolic organ and plays a key role in environmental adaptation. Therefore, this study systematically compared the transcriptional regulatory mechanisms of the small and large intestine between yaks and cattle, thereby revealing the metabolic mechanisms underlying the high-altitude adaptation of yaks. The results showed that the expression of several key metabolic genes, including <em>IDO1</em>, <em>KYNU</em> (tryptophan metabolism), <em>ACSL1</em> (lipid metabolism), and <em>ABCG2</em> (vitamin transport), was significantly upregulated in the yak small intestine. This indicates that the yak small intestine has stronger physiological potential in nutrient metabolism and barrier function. In the large intestine, the expression of key genes in pathways such as lipid metabolism (<em>PLA2</em>), detoxification (<em>UGT</em>), cAMP signaling (<em>ADCY</em>, <em>CREB3L</em>), and bile secretion (<em>ABCC</em>) was significantly upregulated, indicating that the yak possesses unique physiological advantages in energy regulation and maintaining intestinal homeostasis. This study systematically elucidates the metabolic mechanisms of the yak intestine under the extreme conditions of the plateau, providing a basis for in-depth analysis of ruminant intestinal function and molecular breeding.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"57 ","pages":"Article 101686"},"PeriodicalIF":2.2,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145497837","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}
Pub Date : 2026-03-01Epub Date: 2025-11-25DOI: 10.1016/j.cbd.2025.101697
William S. Bugg , Matt J. Thorstensen , Alyssa M. Weinrauch , Catherine Brandt , Ken M. Jeffries , W. Gary Anderson
In fishes, environmental change during early development may impact performance later in life. Exposure to elevated temperatures during these periods may result in a variety of changes to organismal physiology including both short-term and persistent impacts to growth. However, the underlying mechanisms which promote these physiological changes are unclear. In this study, we used mRNA-seq of white muscle tissue to investigate mechanisms underlying short-term (3 vs. 6 months post-hatch) and persistent (3 vs. 13 months post-hatch) impacts of temperature (16 °C, 18 °C, and 20 °C) during early development, which underlie enhanced growth performance in young of year lake sturgeon. Functional analysis of differentially expressed transcripts revealed that in the short-term, elevated temperatures of 20 °C had impacts on transcriptional regulation of epigenetic mechanisms, neuron development, muscle structure and function, and energy supply. Further, persistent effects led to the establishment of increased growth, altered muscle phenotypes, and transcriptional changes to alternative splicing, neuron signaling, as well as muscle type and function. Taken together, these results suggest that at 20 °C, epigenetic modifications may lead to a molecular switch inducing neuromuscular junction proliferation, which in turn alters developmental trajectories by increasing lake sturgeon muscle development and growth. These findings are pertinent to hatchery management processes and the impacts of increasing temperatures in natural environments such as from heat waves during early development, which both may have persistent impacts on the developmental trajectory of fishes.
{"title":"Short-term and persistent changes to the muscle transcriptome of Lake sturgeon (Acipenser fulvescens) following early-life exposures to elevated temperatures","authors":"William S. Bugg , Matt J. Thorstensen , Alyssa M. Weinrauch , Catherine Brandt , Ken M. Jeffries , W. Gary Anderson","doi":"10.1016/j.cbd.2025.101697","DOIUrl":"10.1016/j.cbd.2025.101697","url":null,"abstract":"<div><div>In fishes, environmental change during early development may impact performance later in life. Exposure to elevated temperatures during these periods may result in a variety of changes to organismal physiology including both short-term and persistent impacts to growth. However, the underlying mechanisms which promote these physiological changes are unclear. In this study, we used mRNA-seq of white muscle tissue to investigate mechanisms underlying short-term (3 vs. 6 months post-hatch) and persistent (3 vs. 13 months post-hatch) impacts of temperature (16 °C, 18 °C, and 20 °C) during early development, which underlie enhanced growth performance in young of year lake sturgeon. Functional analysis of differentially expressed transcripts revealed that in the short-term, elevated temperatures of 20 °C had impacts on transcriptional regulation of epigenetic mechanisms, neuron development, muscle structure and function, and energy supply. Further, persistent effects led to the establishment of increased growth, altered muscle phenotypes, and transcriptional changes to alternative splicing, neuron signaling, as well as muscle type and function. Taken together, these results suggest that at 20 °C, epigenetic modifications may lead to a molecular switch inducing neuromuscular junction proliferation, which in turn alters developmental trajectories by increasing lake sturgeon muscle development and growth. These findings are pertinent to hatchery management processes and the impacts of increasing temperatures in natural environments such as from heat waves during early development, which both may have persistent impacts on the developmental trajectory of fishes.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"57 ","pages":"Article 101697"},"PeriodicalIF":2.2,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145623605","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}
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