Pub Date : 2026-06-01Epub Date: 2025-12-13DOI: 10.1016/j.cbd.2025.101729
Xiaoli Zhang , Renhui Liu , Hua Ge , Ting Chen , Xinyue Ren , Caixia Long , Jiasheng Huang , Wenjie Pan , Haipeng Qin , Lihong Yuan , Aifen Yan
Sea cucumbers are renowned for their regenerative capabilities, making them ideal models for studying tissue and organ regeneration. Holothuria leucospilota possesses a unique defensive structure, the Cuvierian organ (CO), which is ejected upon threat and regenerates within weeks. However, the molecular mechanisms underlying CO regeneration remain poorly understood. In this study, we induced CO expulsion in H. leucospilota by mechanical stimulation and examined the regeneration process over 31 days. Histological analysis revealed that regeneration initiated with mesothelium formation, followed by connective tissue and epithelium development. Transcriptomic analysis identified numerous differentially expressed genes during regeneration. Key extracellular matrix (ECM)-related genes were upregulated, while matrix protease genes were downregulated. Signaling pathways including Wnt and Hippo were suppressed, whereas apoptosis and cell cycle pathways were activated. Additionally, several structural outer-layer proteins showed altered expression. These results indicate that ECM reorganization and coordinated regulation of cell proliferation and apoptosis are central to CO regeneration. This study provides important insights into the molecular mechanisms of organ regeneration in echinoderms and offers valuable clues for regenerative studies in higher animals.
{"title":"Transcriptomic analysis of Cuvierian Organs regeneration in the sea cucumber Holothuria leucospilota","authors":"Xiaoli Zhang , Renhui Liu , Hua Ge , Ting Chen , Xinyue Ren , Caixia Long , Jiasheng Huang , Wenjie Pan , Haipeng Qin , Lihong Yuan , Aifen Yan","doi":"10.1016/j.cbd.2025.101729","DOIUrl":"10.1016/j.cbd.2025.101729","url":null,"abstract":"<div><div>Sea cucumbers are renowned for their regenerative capabilities, making them ideal models for studying tissue and organ regeneration. <em>Holothuria leucospilota</em> possesses a unique defensive structure, the Cuvierian organ (CO), which is ejected upon threat and regenerates within weeks. However, the molecular mechanisms underlying CO regeneration remain poorly understood. In this study, we induced CO expulsion in <em>H. leucospilota</em> by mechanical stimulation and examined the regeneration process over 31 days. Histological analysis revealed that regeneration initiated with mesothelium formation, followed by connective tissue and epithelium development. Transcriptomic analysis identified numerous differentially expressed genes during regeneration. Key extracellular matrix (ECM)-related genes were upregulated, while matrix protease genes were downregulated. Signaling pathways including Wnt and Hippo were suppressed, whereas apoptosis and cell cycle pathways were activated. Additionally, several structural outer-layer proteins showed altered expression. These results indicate that ECM reorganization and coordinated regulation of cell proliferation and apoptosis are central to CO regeneration. This study provides important insights into the molecular mechanisms of organ regeneration in echinoderms and offers valuable clues for regenerative studies in higher animals.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"58 ","pages":"Article 101729"},"PeriodicalIF":2.2,"publicationDate":"2026-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145776674","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 : 2026-06-01Epub Date: 2025-11-26DOI: 10.1016/j.cbd.2025.101699
Hongshan Diao , Jianzhi Shi , Song Jiang , Qibin Yang , Wenzhe Li , Yundong Li , Jianhua Huang , Lishi Yang , Yangyang Ding , Falin Zhou
Salinity is a critical environmental factor affecting the growth of crustaceans. As an economically important aquaculture species, the farming of Penaeus monodon is currently facing challenges from salinity fluctuations caused by climate change. However, studies utilizing multi-omics approaches to elucidate its molecular adaptation mechanisms to low salinity remain limited. This study systematically investigated the molecular regulatory mechanisms of P. monodon under low salinity stress (3 ‰) at different time points (6 h, 24 h, 96 h) using transcriptomic and proteomic technologies. A total of 927 DEGs and 928 DEPs were identified compared to the control group. This study revealed a dynamic adaptive strategy. At 6 h, P. monodon exhibited disruptions in energy metabolism and immune suppression, alongside the activation of immediate compensatory pathways. As the stress continued to 24 h, P. monodon showed a broad enhancement of metabolic activity, indicating a systemic effort to mitigate stress damage. After 96 h of exposure, P. monodon demonstrated a sustained upregulation of energy metabolism and the activation of detoxification systems, facilitating stable adaptive regulation. Furthermore, transcriptome-proteome integration analysis uncovered coordinated gene-protein regulatory patterns. This study provides the first multi-omics atlas of P. monodon's response to low salinity, which delineates a time-resolved molecular adaptation strategy. Our findings not only offer novel insights into osmoregulation but also deliver valuable molecular targets for breeding stress-resistant strains, presenting scientific basis for sustainable aquaculture facing environmental challenges.
{"title":"Integrated transcriptomic and proteomic insights into low-salinity stress adaptation in Penaeus monodon","authors":"Hongshan Diao , Jianzhi Shi , Song Jiang , Qibin Yang , Wenzhe Li , Yundong Li , Jianhua Huang , Lishi Yang , Yangyang Ding , Falin Zhou","doi":"10.1016/j.cbd.2025.101699","DOIUrl":"10.1016/j.cbd.2025.101699","url":null,"abstract":"<div><div>Salinity is a critical environmental factor affecting the growth of crustaceans. As an economically important aquaculture species, the farming of <em>Penaeus monodon</em> is currently facing challenges from salinity fluctuations caused by climate change. However, studies utilizing multi-omics approaches to elucidate its molecular adaptation mechanisms to low salinity remain limited. This study systematically investigated the molecular regulatory mechanisms of <em>P. monodon</em> under low salinity stress (3 ‰) at different time points (6 h, 24 h, 96 h) using transcriptomic and proteomic technologies. A total of 927 DEGs and 928 DEPs were identified compared to the control group. This study revealed a dynamic adaptive strategy. At 6 h, <em>P. monodon</em> exhibited disruptions in energy metabolism and immune suppression, alongside the activation of immediate compensatory pathways. As the stress continued to 24 h, <em>P. monodon</em> showed a broad enhancement of metabolic activity, indicating a systemic effort to mitigate stress damage. After 96 h of exposure, <em>P. monodon</em> demonstrated a sustained upregulation of energy metabolism and the activation of detoxification systems, facilitating stable adaptive regulation. Furthermore, transcriptome-proteome integration analysis uncovered coordinated gene-protein regulatory patterns. This study provides the first multi-omics atlas of <em>P. monodon</em>'s response to low salinity, which delineates a time-resolved molecular adaptation strategy. Our findings not only offer novel insights into osmoregulation but also deliver valuable molecular targets for breeding stress-resistant strains, presenting scientific basis for sustainable aquaculture facing environmental challenges.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"58 ","pages":"Article 101699"},"PeriodicalIF":2.2,"publicationDate":"2026-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145776755","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 : 2026-06-01Epub Date: 2026-01-28DOI: 10.1016/j.cbd.2026.101767
Xinghua Lin , Tianli Wu , Dongneng Jiang , Hongjuan Shi , Changxu Tian , Huapu Chen , Guangli Li , Siping Deng
The spotted scat (Scatophagus argus), an economically valuable aquaculture species in southern China, exhibits a pronounced sexual dimorphism in growth performance, with females growing significantly faster than males. Nevertheless, progress in sex-controlled breeding remains limited due to limited understanding of its sex determination and differentiation mechanisms. To investigate sex-biased gene expression in this species, a comprehensive transcriptomic analysis was performed. A total of 62 transcriptomic libraries were analyzed, comprising 18 newly sequenced libraries derived from female gill, muscle, stomach, heart, and adipose tissue, and male adipose tissue, integrated with 44 publicly available libraries covering the brain, pituitary gland, liver, kidney, gonads, and other tissues. The analysis identified 33,214 unigenes, including 8958 novel genes, with 1724 receiving functional annotation. Principal component analysis (PCA) and heatmap clustering revealed distinct expression profiles in gonadal (ovary and testis) and somatic tissues. Differential expression analysis identified 2951 ovary-highly expressed and 1660 testis-highly expressed genes. Functional annotation revealed genes essential for folliculogenesis, spermatogenesis, and meiosis, including figla, gdf9, mos, amhr2, spata22, and dmc1. Additionally, 23 ovary-specific and 75 testis-specific genes were identified. KEGG enrichment analysis revealed significantly enriched pathways in the gonads, including oocyte meiosis, cell cycle, and DNA replication. RT-PCR and qRT-PCR validations confirmed the RNA-seq results, demonstrating consistent tissue-specific expression patterns of these genes. These findings advance the understanding of the molecular mechanisms of sex differentiation and gametogenesis in spotted scat and provided a foundation for studies of reproductive regulation and gonadal development in this species.
{"title":"Comprehensive transcriptome analysis of somatic and gonadal tissues for identification of sex-biased genes in spotted scat (Scatophagus argus)","authors":"Xinghua Lin , Tianli Wu , Dongneng Jiang , Hongjuan Shi , Changxu Tian , Huapu Chen , Guangli Li , Siping Deng","doi":"10.1016/j.cbd.2026.101767","DOIUrl":"10.1016/j.cbd.2026.101767","url":null,"abstract":"<div><div>The spotted scat (<em>Scatophagus argus</em>), an economically valuable aquaculture species in southern China, exhibits a pronounced sexual dimorphism in growth performance, with females growing significantly faster than males. Nevertheless, progress in sex-controlled breeding remains limited due to limited understanding of its sex determination and differentiation mechanisms. To investigate sex-biased gene expression in this species, a comprehensive transcriptomic analysis was performed. A total of 62 transcriptomic libraries were analyzed, comprising 18 newly sequenced libraries derived from female gill, muscle, stomach, heart, and adipose tissue, and male adipose tissue, integrated with 44 publicly available libraries covering the brain, pituitary gland, liver, kidney, gonads, and other tissues. The analysis identified 33,214 unigenes, including 8958 novel genes, with 1724 receiving functional annotation. Principal component analysis (PCA) and heatmap clustering revealed distinct expression profiles in gonadal (ovary and testis) and somatic tissues. Differential expression analysis identified 2951 ovary-highly expressed and 1660 testis-highly expressed genes. Functional annotation revealed genes essential for folliculogenesis, spermatogenesis, and meiosis, including <em>figla</em>, <em>gdf9</em>, <em>mos</em>, <em>amhr2</em>, <em>spata22</em>, and <em>dmc1</em>. Additionally, 23 ovary-specific and 75 testis-specific genes were identified. KEGG enrichment analysis revealed significantly enriched pathways in the gonads, including oocyte meiosis, cell cycle, and DNA replication. RT-PCR and qRT-PCR validations confirmed the RNA-seq results, demonstrating consistent tissue-specific expression patterns of these genes. These findings advance the understanding of the molecular mechanisms of sex differentiation and gametogenesis in spotted scat and provided a foundation for studies of reproductive regulation and gonadal development in this species.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"58 ","pages":"Article 101767"},"PeriodicalIF":2.2,"publicationDate":"2026-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146121417","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}
Ostariophysi has a history of successful adaptation to freshwater environments due to the evolution of a unique morphological structure, i.e. Weberian apparatus (WA). This structure transfers sound waves from the swim bladder to the inner ear by forming a physical linkage that leads to enhanced hearing sensitivity. However, there are very few reports on genes specifically linked to this modified structure in fish. In this study, we compared Weberian ossicles, the modified vertebrae, and unmodified vertebrae transcriptomes of representative species from ostariophysi and non-ostariophysi by mRNA sequencing. A total of 21 and 25 million high-quality reads were generated from Labeo rohita and Oreochromis niloticus, respectively, and differential expression analysis identified 161 upregulated and 98 down-regulated transcripts (>2 fold change) between modified and unmodified vertebrae. Functional annotation revealed their significant involvement in biological functions such as energy metabolism, osteoblast proliferation, differentiation, and matrix mineralization related to bone development. A total of 41 miRNA target interactions were found to be associated with differentially expressed transcripts (p<0.05). Fourteen hub genes were identified and categorized into six major GO terms: endoplasmic reticulum, large ribosomal subunit, rRNA binding, translation and metabolic process. Ontogenic expression of selected genes linked to ossification showed elevated expression till 3 days post-hatch (dph). A novel gene, LrOSSP1 (Ossicle Secretory Signal Protein 1), reported for the first time, exclusively found in ostariophysi, demonstrated significant up-regulation in the earliest stages of larval development in this study. This is the first report of its kind in Labeo rohita and will be helpful in understanding the molecular underplay of modified vertebrae in ostariophysans.
{"title":"Identification of genes involved in the development of Weberian apparatus in rohu, Labeo rohita (Hamilton, 1822), as revealed by comparative transcriptome analyses","authors":"Nirjharini Priyadarshini , Priyanka Nandanpawar , Bismay Sahoo , Pravati Kumari Mahapatra , Lakshman Sahoo , Paramananda Das","doi":"10.1016/j.cbd.2026.101776","DOIUrl":"10.1016/j.cbd.2026.101776","url":null,"abstract":"<div><div>Ostariophysi has a history of successful adaptation to freshwater environments due to the evolution of a unique morphological structure, i.e. Weberian apparatus (WA). This structure transfers sound waves from the swim bladder to the inner ear by forming a physical linkage that leads to enhanced hearing sensitivity. However, there are very few reports on genes specifically linked to this modified structure in fish. In this study, we compared Weberian ossicles, the modified vertebrae, and unmodified vertebrae transcriptomes of representative species from ostariophysi and non-ostariophysi by mRNA sequencing. A total of 21 and 25 million high-quality reads were generated from <em>Labeo rohita</em> and <em>Oreochromis niloticus</em>, respectively, and differential expression analysis identified 161 upregulated and 98 down-regulated transcripts (>2 fold change) between modified and unmodified vertebrae. Functional annotation revealed their significant involvement in biological functions such as energy metabolism, osteoblast proliferation, differentiation, and matrix mineralization related to bone development. A total of 41 miRNA target interactions were found to be associated with differentially expressed transcripts (<em>p</em> <em><</em> <em>0.05</em>). Fourteen hub genes were identified and categorized into six major GO terms: endoplasmic reticulum, large ribosomal subunit, rRNA binding, translation and metabolic process. Ontogenic expression of selected genes linked to ossification showed elevated expression till 3 days post-hatch (dph). A novel gene, LrOSSP1 (Ossicle Secretory Signal Protein 1), reported for the first time, exclusively found in ostariophysi, demonstrated significant up-regulation in the earliest stages of larval development in this study. This is the first report of its kind in <em>Labeo rohita</em> and will be helpful in understanding the molecular underplay of modified vertebrae in ostariophysans.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"58 ","pages":"Article 101776"},"PeriodicalIF":2.2,"publicationDate":"2026-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146168553","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 : 2026-06-01Epub Date: 2026-01-16DOI: 10.1016/j.cbd.2026.101754
Janki A. Bhalodi , Joachim M. Surm , Adam M. Reitzel
Heat shock proteins (HSPs) are molecular chaperones that function in protecting cells from proteotoxicity. Eukaryotes have multiple HSPs that localize in the cytoplasm, endoplasmic reticulum (ER), and mitochondria. In cnidarian species, where HSPs are often used as biomarkers of environmental stress, little is known about how particular HSPs vary in copy number, expression, inducibility, and regulation within a species. Here, we characterized the full repertoire of HSP70 and HSP90 genes in an emerging model cnidarian, Nematostella vectensis. We identified five HSP70 and three HSP90 genes, with at least one homolog from each family belonging to the three primary clades based on subcellular localization. Although transcriptional induction remained insignificant by a 10 °C temperature change, two cytosolic HSP70s and one cytosolic HSP90 were significantly upregulated with a 20 °C temperature increase. Most HSPs exhibited similar developmental expression patterns, with elevated expression during the early larval stage followed by reduced expression in the juvenile stage. HSPs showed evidence for differential expression across cell types, with multiple cytosolic and ER HSPs being highly expressed in neuronal and cnidocyte populations. Moreover, the putative promoters of N. vectensis HSPs differed in both the abundance and sequences of regulatory heat shock element motifs, providing a potential mechanism of functional diversification in response to temperature and development. By characterizing expression of all HSP70 and HSP90 genes in this cnidarian, we reveal distinct roles of these core chaperones in the proteostasis response, providing a foundation for future functional studies on contributions of HSPs to cnidarian life cycle and stress resilience.
{"title":"Transcription dynamics and regulation of heat shock protein genes during stress and development in the estuarine cnidarian Nematostella vectensis","authors":"Janki A. Bhalodi , Joachim M. Surm , Adam M. Reitzel","doi":"10.1016/j.cbd.2026.101754","DOIUrl":"10.1016/j.cbd.2026.101754","url":null,"abstract":"<div><div>Heat shock proteins (HSPs) are molecular chaperones that function in protecting cells from proteotoxicity. Eukaryotes have multiple HSPs that localize in the cytoplasm, endoplasmic reticulum (ER), and mitochondria. In cnidarian species, where HSPs are often used as biomarkers of environmental stress, little is known about how particular HSPs vary in copy number, expression, inducibility, and regulation within a species. Here, we characterized the full repertoire of HSP70 and HSP90 genes in an emerging model cnidarian, <em>Nematostella vectensis</em>. We identified five HSP70 and three HSP90 genes, with at least one homolog from each family belonging to the three primary clades based on subcellular localization. Although transcriptional induction remained insignificant by a 10 °C temperature change, two cytosolic HSP70s and one cytosolic HSP90 were significantly upregulated with a 20 °C temperature increase. Most HSPs exhibited similar developmental expression patterns, with elevated expression during the early larval stage followed by reduced expression in the juvenile stage. HSPs showed evidence for differential expression across cell types, with multiple cytosolic and ER HSPs being highly expressed in neuronal and cnidocyte populations. Moreover, the putative promoters of <em>N. vectensis</em> HSPs differed in both the abundance and sequences of regulatory heat shock element motifs, providing a potential mechanism of functional diversification in response to temperature and development. By characterizing expression of all HSP70 and HSP90 genes in this cnidarian, we reveal distinct roles of these core chaperones in the proteostasis response, providing a foundation for future functional studies on contributions of HSPs to cnidarian life cycle and stress resilience.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"58 ","pages":"Article 101754"},"PeriodicalIF":2.2,"publicationDate":"2026-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146020932","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 : 2026-06-01Epub Date: 2026-01-20DOI: 10.1016/j.cbd.2026.101755
Qiang Wang , Siyi Li , Yu Yang , Rubiao Xie , Lingbin Wang , Weijun Wang , Jianmin Yang , Guohua Sun
Heat temperature caused by changes in the global environment have significant impacts on marine organisms. Apostichopus japonicus (A. japonicus) is an economically important benthic species in China's shallow-sea aquaculture. However, its growth and survival are easily affected by rising seawater temperatures. Therefore, it is necessary to explore its response to environmental high temperature. Endoplasmic reticulum (ER)stressserves as an important regulatory strategy for organisms to respond to environmental changes. It acts as the core hub connecting stress and immunity. In this study, we analyzed the histology, ultrastructure, and transcriptome of the digestive tract of A. japonicus at three temperatures: normal (18 °C), aestivation (25 °C), and lethal (32 °C) temperatures, to explore the role of ER stress in response to high temperature. Histological and ultrastructural results indicate that high temperature caused morphological changes in the digestive tract and that the structure and morphology of the ER exhibit alterations and even varying degrees of damage. A total of 603 and 4615 differentially expressed genes (DEGs) were identified by transcriptome sequencing in the T25-vs-T18 and the T32-vs-T25 group comparisons, respectively. The GO results showed that DEGs were significantly enriched in GO terms related to protein folding, such as chaperone-mediated protein folding in both comparison groups. Additionally, KEGG enrichment analysis showed that both groups activated the pathway of protein processing in the ER and induced the ER stress response. The ER molecular chaperones, including BiP, GRP94, and HSP70, were all upregulated in expression. In addition to the aforementioned ER molecular chaperones, downstream factors in the unfolded protein response, such as S1P, TRAF2, and XBP, were also significantly upregulated in T32-vs-T25 group comparisons, indicating that UPR signaling pathways had enhanced expression. Our findings have characterized the internal molecular regulatory process of A. japonicus under high temperature from the perspective of ER stress and provides clues regarding immune response and homeostatic regulation in invertebrates under environment stress. These findings can provide a reference for the formulation of management measures to mitigate the impact of climate change on aquaculture.
{"title":"Different degrees of environmental high temperature induce varying endoplasmic reticulum stress responses in Apostichopus japonicus","authors":"Qiang Wang , Siyi Li , Yu Yang , Rubiao Xie , Lingbin Wang , Weijun Wang , Jianmin Yang , Guohua Sun","doi":"10.1016/j.cbd.2026.101755","DOIUrl":"10.1016/j.cbd.2026.101755","url":null,"abstract":"<div><div>Heat temperature caused by changes in the global environment have significant impacts on marine organisms. <em>Apostichopus japonicus (A. japonicus)</em> is an economically important benthic species in China's shallow-sea aquaculture. However, its growth and survival are easily affected by rising seawater temperatures. Therefore, it is necessary to explore its response to environmental high temperature. <em>Endoplasmic reticulum (</em>ER<em>)</em> <strong>stress</strong> <em>serves as an important regulatory strategy for organisms to respond to environmental changes. It acts as the core hub connecting stress and immunity</em>. In this study, we analyzed the histology, ultrastructure, and transcriptome of the digestive tract of <em>A. japonicus</em> at three temperatures: normal (18 °C), aestivation (25 °C), and lethal (32 °C) temperatures, to explore the role of ER stress in response to high temperature. Histological and ultrastructural results indicate that high temperature caused morphological changes in the digestive tract and that the structure and morphology of the ER exhibit alterations and even varying degrees of damage. A total of 603 and 4615 differentially expressed genes (DEGs) were identified by transcriptome sequencing in the T25-vs-T18 and the T32-vs-T25 group comparisons, respectively. The GO results showed that DEGs were significantly enriched in GO terms related to protein folding, such as chaperone-mediated protein folding in both comparison groups. Additionally, KEGG enrichment analysis showed that both groups activated the pathway of protein processing in the ER and induced the ER stress response. The ER molecular chaperones, including <em>BiP</em>, <em>GRP94</em>, and <em>HSP70</em>, were all upregulated in expression. In addition to the aforementioned ER molecular chaperones, downstream factors in the unfolded protein response, such as <em>S1P</em>, <em>TRAF2</em>, and <em>XBP</em>, were also significantly upregulated in T32-vs-T25 group comparisons, indicating that UPR signaling pathways had enhanced expression. Our findings have characterized the internal molecular regulatory process of <em>A. japonicus</em> under high temperature from the perspective of ER stress and provides clues regarding immune response and homeostatic regulation in invertebrates under environment stress. These findings can provide a reference for the formulation of management measures to mitigate the impact of climate change on aquaculture.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"58 ","pages":"Article 101755"},"PeriodicalIF":2.2,"publicationDate":"2026-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146069474","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 : 2026-06-01Epub Date: 2026-01-15DOI: 10.1016/j.cbd.2026.101748
Jingyang Li , Ruijian Sun , Tongxuan Zhao , Xiaojian Tang , Bo Gao , Guangping Xu , Yue Wang , Han Yu , Qian Meng , Zhiwei Zhang
Low-temperature stress poses a critical challenge to the overwintering survival of black porgy (Acanthopagrus schlegelii), a commercially important marine fish distributed across the coastal waters of West Pacific region, including the continental shelves of China, Japan, and the Korean Peninsula. To unravel the molecular mechanisms underlying cold adaptation, this study employed quantitative proteomics was employed to analyze hepatic protein profiles of black porgy between three groups: control group (CG, 15 °C), cold-sensitive group (CS, 3.8 °C), and cold-tolerant group (CT, 2.8 °C). A total of 4437 proteins were identified, with 1616 differentially expressed protein (DEPs) detected among the groups. Bioinformatics analyses, including Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment, Gene Set Enrichment Analysis (GSEA), and trend analysis, revealed distinct adaptive strategies between CT and CS groups. The CT group exhibited a coordinated “energy conservation - metabolic remodeling - antioxidation” strategy: (1) significant downregulation of ribosomal subunits and protein export pathways to reduce Adenosine Triphosphate (ATP) consumption from protein synthesis (called “ribosomal hibernation”); (2) upregulation of Peroxisome Proliferator-Activated Receptor (PPAR) signaling pathway and peroxisomal functions to enhance fatty acid β-oxidation and ketone body production, facilitating efficient energy supply; (3) activation of antioxidant systems to mitigate damage induced by reactive oxygen species (ROS). In contrast, the CS group showed dysregulated energy metabolism, characterized by enhanced but inefficient glycolysis, impaired endoplasmic reticulum function, and excessive inflammatory responses, which may contribute to protential proteotoxic stress and metabolic dysfunction. Key DEPs and pathways, such as ribosomal proteins, PPAR family proteins, and peroxisomal enzymes, were identified as protential core regulators of cold tolerance in black porgy. This study provides the first comprehensive proteomic insights into the molecular mechanisms of cold tolerance in black porgy, highlighting the evolutionary significance of energy allocation and metabolic plasticity in teleosts. These findings offer potential molecular markers for breeding cold-tolerant strains, addressing critical challenges in aquaculture sustainability.
{"title":"Proteomic analysis reveals the mechanism of cold tolerance in black porgy (Acanthopagrus schlegelii) via ribosome hibernation, metabolic remodeling, and antioxidant coordination","authors":"Jingyang Li , Ruijian Sun , Tongxuan Zhao , Xiaojian Tang , Bo Gao , Guangping Xu , Yue Wang , Han Yu , Qian Meng , Zhiwei Zhang","doi":"10.1016/j.cbd.2026.101748","DOIUrl":"10.1016/j.cbd.2026.101748","url":null,"abstract":"<div><div>Low-temperature stress poses a critical challenge to the overwintering survival of black porgy (<em>Acanthopagrus schlegelii</em>), a commercially important marine fish distributed across the coastal waters of West Pacific region, including the continental shelves of China, Japan, and the Korean Peninsula. To unravel the molecular mechanisms underlying cold adaptation, this study employed quantitative proteomics was employed to analyze hepatic protein profiles of black porgy between three groups: control group (CG, 15 °C), cold-sensitive group (CS, 3.8 °C), and cold-tolerant group (CT, 2.8 °C). A total of 4437 proteins were identified, with 1616 differentially expressed protein (DEPs) detected among the groups. Bioinformatics analyses, including Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment, Gene Set Enrichment Analysis (GSEA), and trend analysis, revealed distinct adaptive strategies between CT and CS groups. The CT group exhibited a coordinated “energy conservation - metabolic remodeling - antioxidation” strategy: (1) significant downregulation of ribosomal subunits and protein export pathways to reduce Adenosine Triphosphate (ATP) consumption from protein synthesis (called “ribosomal hibernation”); (2) upregulation of Peroxisome Proliferator-Activated Receptor (PPAR) signaling pathway and peroxisomal functions to enhance fatty acid β-oxidation and ketone body production, facilitating efficient energy supply; (3) activation of antioxidant systems to mitigate damage induced by reactive oxygen species (ROS). In contrast, the CS group showed dysregulated energy metabolism, characterized by enhanced but inefficient glycolysis, impaired endoplasmic reticulum function, and excessive inflammatory responses, which may contribute to protential proteotoxic stress and metabolic dysfunction. Key DEPs and pathways, such as ribosomal proteins, PPAR family proteins, and peroxisomal enzymes, were identified as protential core regulators of cold tolerance in black porgy. This study provides the first comprehensive proteomic insights into the molecular mechanisms of cold tolerance in black porgy, highlighting the evolutionary significance of energy allocation and metabolic plasticity in teleosts. These findings offer potential molecular markers for breeding cold-tolerant strains, addressing critical challenges in aquaculture sustainability.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"58 ","pages":"Article 101748"},"PeriodicalIF":2.2,"publicationDate":"2026-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145977219","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 : 2026-06-01Epub Date: 2026-01-23DOI: 10.1016/j.cbd.2026.101762
Xiufeng Fang , Yuexuan Wang , Renjie Yu , Dekun Tang , Zihan Li , Qiwei Qin , Shina Wei
In the context of increasing freshwater scarcity and the effects of climate change on aquatic environments, developing salt-tolerant fish strains has become a critical strategy for sustainable aquaculture. The limited availability of suitable species for saline-water aquaculture poses a significant challenge, severely impacting the development of the fishery economy. This study investigated the effects of 24 h exposure to freshwater, and seawater at salinities of 4, 9 ppt and 12 ppt, on juvenile grass carp (Ctenopharyngodon idella). Following these exposures, liver tissues were collected to assess physiological and biochemical indicators, as well as transcriptional and metabolic responses. Histological examination revealed that liver structure was compromised after 24 h of exposure to 9 ppt and 12 ppt salt stress. Concurrently, we observed a decrease in the levels of Superoxide Dismutase (SOD), whereas the levels of Malondialdehyde (MDA) exhibited an increase. Salinity exposure significantly altered the levels of 120 metabolic products (67% of which were lipid and lipophilic molecules) and the transcriptional expression of 1005 genes. Metabolomic analysis indicated that most of the significantly different metabolites were associated with the metabolism of lipids and amino acids. Transcriptome analysis revealed significant enrichment of 20 metabolic pathways, including glutathione metabolism, lipid digestion and absorption, bile secretion, glycerolipid metabolism, and the tricarboxylic acid cycle. Comprehensive multi-omics analysis revealed significant alterations in key metabolic pathways, including glycerophospholipid metabolism, α-linolenic acid metabolism, histidine metabolism, and β-alanine metabolism, along with several vital genes such as HO-1, NQO1, GCLM, and GSS, under salt stress. These changes closely correlate with variations in cellular membrane lipid composition and antioxidant activity. Further analysis demonstrated that acute salt stress induces oxidative damage in the liver, leading to lipid imbalance and oxidative stress. This is evidenced by impaired antioxidant function and disruptions in amino acid and fatty acid metabolism. Moreover, carnosine synthesis in liver tissue occurs via the activation of histidine and β-alanine metabolic pathways, leading to the upregulation of CNDP2. This process plays a crucial role in regulating lipid metabolism and redox homeostasis, effectively mitigating the damage caused by acute salinity stress. In summary, these findings provide a deeper understanding of the molecular mechanisms underlying salt stress responses in grass carp and offer valuable insights for the breeding of salt-tolerant strains of grass carp.
{"title":"A multi-omics investigation reveals the hepatic response to salinity stress in grass carp (Ctenopharyngodon idella)","authors":"Xiufeng Fang , Yuexuan Wang , Renjie Yu , Dekun Tang , Zihan Li , Qiwei Qin , Shina Wei","doi":"10.1016/j.cbd.2026.101762","DOIUrl":"10.1016/j.cbd.2026.101762","url":null,"abstract":"<div><div>In the context of increasing freshwater scarcity and the effects of climate change on aquatic environments, developing salt-tolerant fish strains has become a critical strategy for sustainable aquaculture. The limited availability of suitable species for saline-water aquaculture poses a significant challenge, severely impacting the development of the fishery economy. This study investigated the effects of 24 h exposure to freshwater, and seawater at salinities of 4, 9 ppt and 12 ppt, on juvenile grass carp (<em>Ctenopharyngodon idella</em>). Following these exposures, liver tissues were collected to assess physiological and biochemical indicators, as well as transcriptional and metabolic responses. Histological examination revealed that liver structure was compromised after 24 h of exposure to 9 ppt and 12 ppt salt stress. Concurrently, we observed a decrease in the levels of Superoxide Dismutase (SOD), whereas the levels of Malondialdehyde (MDA) exhibited an increase. Salinity exposure significantly altered the levels of 120 metabolic products (67% of which were lipid and lipophilic molecules) and the transcriptional expression of 1005 genes. Metabolomic analysis indicated that most of the significantly different metabolites were associated with the metabolism of lipids and amino acids. Transcriptome analysis revealed significant enrichment of 20 metabolic pathways, including glutathione metabolism, lipid digestion and absorption, bile secretion, glycerolipid metabolism, and the tricarboxylic acid cycle. Comprehensive multi-omics analysis revealed significant alterations in key metabolic pathways, including glycerophospholipid metabolism, α-linolenic acid metabolism, histidine metabolism, and β-alanine metabolism, along with several vital genes such as <em>HO-1, NQO1, GCLM,</em> and <em>GSS,</em> under salt stress. These changes closely correlate with variations in cellular membrane lipid composition and antioxidant activity. Further analysis demonstrated that acute salt stress induces oxidative damage in the liver, leading to lipid imbalance and oxidative stress. This is evidenced by impaired antioxidant function and disruptions in amino acid and fatty acid metabolism. Moreover, carnosine synthesis in liver tissue occurs via the activation of histidine and β-alanine metabolic pathways, leading to the upregulation of CNDP2. This process plays a crucial role in regulating lipid metabolism and redox homeostasis, effectively mitigating the damage caused by acute salinity stress. In summary, these findings provide a deeper understanding of the molecular mechanisms underlying salt stress responses in grass carp and offer valuable insights for the breeding of salt-tolerant strains of grass carp.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"58 ","pages":"Article 101762"},"PeriodicalIF":2.2,"publicationDate":"2026-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146077499","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 : 2026-06-01Epub Date: 2026-01-08DOI: 10.1016/j.cbd.2026.101747
Qingqing Li , Yao Huang , Xi Xie , Shaowen Liang , Li Lin
Nile tilapia (Oreochromis niloticus) is a widely farmed freshwater fish. Feeding with faba bean (Vicia faba L.) for 90–120 days can improve the muscle quality of tilapia. However, the underlying mechanism remain unclear. In the present study, tilapia were fed a faba bean–based diet for 120 days to induce muscle crisped, and ordinary tilapia fed a conventional diet were used as controls. Muscle histological characteristics were evaluated using hematoxylin and eosin staining, and transcriptome sequencing was conducted to explore molecular changes associated with the crisped muscle phenotype. The results showed that, as compared to ordinary tilapia, the fiber diameter and area were significantly reduced in crisped tilapia (p < 0.05), while the muscle fiber density was significantly increased (p < 0.05). In total, 576 differentially expressed genes (DEGs) were identified (FDR < 0.05), of which 211 were significantly up-regulated and 365 significantly down-regulated. Further analysis showed that DEGs associated with myofibroblast proliferation were up-regulated in crisped tilapia, while the glycolytic pathway was inhibited. The expression levels of muscle-related genes (i.e., actc1, myo7a, cib2, abcf2, and pfkfb2) were significantly higher in crisped tilapia than ordinary tilapia (p < 0.05), whereas the expression levels of gapdh, pgam2, eno3, and g6pi were significantly decreased (p < 0.05). Several DEGs and signaling pathways were identified. These findings provide transcriptomic evidence linking dietary faba bean feeding to muscle fiber remodeling and metabolic modulation in tilapia, offering a molecular basis for improving fillet quality through nutritional strategies.
{"title":"Transcriptome analysis revealed the effects of dietary faba bean (Vicia faba L.) on muscle quality of Nile tilapia (Oreochromis niloticus)","authors":"Qingqing Li , Yao Huang , Xi Xie , Shaowen Liang , Li Lin","doi":"10.1016/j.cbd.2026.101747","DOIUrl":"10.1016/j.cbd.2026.101747","url":null,"abstract":"<div><div>Nile tilapia (<em>Oreochromis niloticus</em>) is a widely farmed freshwater fish. Feeding with faba bean (<em>Vicia faba</em> L.) for 90–120 days can improve the muscle quality of tilapia. However, the underlying mechanism remain unclear. In the present study, tilapia were fed a faba bean–based diet for 120 days to induce muscle crisped, and ordinary tilapia fed a conventional diet were used as controls. Muscle histological characteristics were evaluated using hematoxylin and eosin staining, and transcriptome sequencing was conducted to explore molecular changes associated with the crisped muscle phenotype. The results showed that, as compared to ordinary tilapia, the fiber diameter and area were significantly reduced in crisped tilapia (<em>p</em> < 0.05), while the muscle fiber density was significantly increased (<em>p</em> < 0.05). In total, 576 differentially expressed genes (DEGs) were identified (FDR < 0.05), of which 211 were significantly up-regulated and 365 significantly down-regulated. Further analysis showed that DEGs associated with myofibroblast proliferation were up-regulated in crisped tilapia, while the glycolytic pathway was inhibited. The expression levels of muscle-related genes (i.e., actc1, myo7a, cib2, abcf2, and pfkfb2) were significantly higher in crisped tilapia than ordinary tilapia (<em>p</em> < 0.05), whereas the expression levels of gapdh, pgam2, eno3, and g6pi were significantly decreased (<em>p</em> < 0.05). Several DEGs and signaling pathways were identified. These findings provide transcriptomic evidence linking dietary faba bean feeding to muscle fiber remodeling and metabolic modulation in tilapia, offering a molecular basis for improving fillet quality through nutritional strategies.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"58 ","pages":"Article 101747"},"PeriodicalIF":2.2,"publicationDate":"2026-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145925915","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}
The Spotted Babylon (Babylonia areolata) is an economically marine species in Thailand and other Asian countries. Due to the high demand for its meat, improving aquaculture practices for this species is essential. Regarding the lack of neuroendocrine control of reproduction in this species, we performed transcriptome analysis of the central nervous system and ovaries, and we searched against the reported genome of this animal species to find out the neurohormones. Here, we reported the identification of corazonin (ba-Crz)-like and gonadotropin-releasing hormone (ba-GnRH)-like mRNAs in B. areolata. The ba-Crz-like mRNA encoded mature ba-Crz-like peptide as QNYHYSNGWHP. Two ba-GnRH-like mRNAs encoded ba-GnRH-I-, and ba-GnRH-II-like peptides containing active peptides as QIHFSPTWGT and QIHFSHSWGT. Two introns were found in the ba-Crz-like gene while one intron was present in each ba-GnRH-like gene. These three peptides were phylogenetically placed in the molluscan Crz and GnRH clades. RT-PCR of these three mRNAs revealed their ubiquitous expressions across various organs, with all three predominantly expressed in ganglia, which was further confirmed by in situ hybridization of the cerebral ganglia. Immunohistochemistry showed positive signals for the Crz-like peptide in both the CNS and ovaries. To examine expression across ovarian cycle, the ba-Crz-like, and ba-GnRH-I-like mRNAs were consistently expressed in the CNS and ovaries of both immature and mature female snails, while the ba-GnRH-II-like mRNA significantly reduced its expression in the CNS of mature snails. Conclusively, this study was preliminary to report on the existence of GnRH/AKH/Crz peptides in the B. areolata, Further characterization of their receptors and biological functions is ongoing to ensure the GnRH, AKH, and Crz identification in this species.
{"title":"Genome and transcriptome mining of the corazonin (Crz)-like peptide and gonadotropin-releasing hormone (GnRH)-like peptides in the spotted Babylon, Babylonia areolata","authors":"Uraipan Saetan , Napamanee Kornthong , Supawadee Duangprom , Supita Tanasawet , Wanida Sukketsiri , Montakan Tamtin , Phetcharat Phanthong , Amornrat Sanprick , Narainrit Chinfak , Jirawat Saetan","doi":"10.1016/j.cbd.2025.101738","DOIUrl":"10.1016/j.cbd.2025.101738","url":null,"abstract":"<div><div>The Spotted Babylon (<em>Babylonia areolata</em>) is an economically marine species in Thailand and other Asian countries. Due to the high demand for its meat, improving aquaculture practices for this species is essential. Regarding the lack of neuroendocrine control of reproduction in this species, we performed transcriptome analysis of the central nervous system and ovaries, and we searched against the reported genome of this animal species to find out the neurohormones. Here, we reported the identification of corazonin (ba-Crz)-like and gonadotropin-releasing hormone (ba-GnRH)-like mRNAs in <em>B. areolata</em>. The ba-Crz-like mRNA encoded mature ba-Crz-like peptide as QNYHYSNGWHP. Two ba-GnRH-like mRNAs encoded ba-GnRH-I-, and ba-GnRH-II-like peptides containing active peptides as QIHFSPTWGT and QIHFSHSWGT. Two introns were found in the <em>ba-Crz</em>-like gene while one intron was present in each <em>ba-GnRH</em>-like gene. These three peptides were phylogenetically placed in the molluscan Crz and GnRH clades. RT-PCR of these three mRNAs revealed their ubiquitous expressions across various organs, with all three predominantly expressed in ganglia, which was further confirmed by in situ hybridization of the cerebral ganglia. Immunohistochemistry showed positive signals for the Crz-like peptide in both the CNS and ovaries. To examine expression across ovarian cycle, the ba-Crz-like, and ba-GnRH-I-like mRNAs were consistently expressed in the CNS and ovaries of both immature and mature female snails, while the ba-GnRH-II-like mRNA significantly reduced its expression in the CNS of mature snails. Conclusively, this study was preliminary to report on the existence of GnRH/AKH/Crz peptides in the <em>B. areolata</em>, Further characterization of their receptors and biological functions is ongoing to ensure the GnRH, AKH, and Crz identification in this species.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"58 ","pages":"Article 101738"},"PeriodicalIF":2.2,"publicationDate":"2026-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145968043","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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