Pub Date : 2025-12-04DOI: 10.1016/j.cbd.2025.101711
Jing Zhang , Xiao-qin Fu , Run-xin Lin , Yang Zhang , Pei-ming Zheng , Huo Li
MicroRNAs are defined as a class of short noncoding RNAs, which play important function in cell differentiation, developmental process and gender determination. The sea cucumber Holothuria leucospilota is a member of the Echinodermata, known for its excellent nutritional and economic value. Breeding efficiency of sea cucumbers is low due to the difficulty in distinguishing between male and female individuals. Discovering molecular markers that distinguish between genders will provide a robust strategy for elucidating the genetic mechanisms governing gender determination and differentiation. In this investigation, high-throughput sequencing was utilized to compare miRNA expression patterns in the gonadal tissues of male and female specimens of H. leucospilota. A total of 584 known miRNAs and 404 novel miRNAs were identified, of which 97 miRNAs were identified as significantly differentially expressed miRNAs (DEMs) between male and female sea cucumbers. These findings enabled the construction of a miRNA-mRNA regulatory network. Pathway analysis of target genes highlighted the potential roles of neuroactive ligand-receptor interactions, calcium signaling, Salmonella infection, endocytosis, and MAPK signaling in governing gender differentiation processes. The expression results of high-throughput sequencing were validated in sc-miR121, sc-miR41, sc-miR67, sc-miR90, sc-miR104 and sc-miR189 by quantitative real-time quantity polymerase chain reaction (RT-qPCR). In summary, our results will provide a foundation for future studies of miRNA regulation in gender differentiation of sea cucumber H. leucospilota.
{"title":"Differential expression miRNAs in the gonad of sea cucumber Holothuria leucospilota","authors":"Jing Zhang , Xiao-qin Fu , Run-xin Lin , Yang Zhang , Pei-ming Zheng , Huo Li","doi":"10.1016/j.cbd.2025.101711","DOIUrl":"10.1016/j.cbd.2025.101711","url":null,"abstract":"<div><div>MicroRNAs are defined as a class of short noncoding RNAs, which play important function in cell differentiation, developmental process and gender determination. The sea cucumber <em>Holothuria leucospilota</em> is a member of the Echinodermata, known for its excellent nutritional and economic value. Breeding efficiency of sea cucumbers is low due to the difficulty in distinguishing between male and female individuals. Discovering molecular markers that distinguish between genders will provide a robust strategy for elucidating the genetic mechanisms governing gender determination and differentiation. In this investigation, high-throughput sequencing was utilized to compare miRNA expression patterns in the gonadal tissues of male and female specimens of <em>H. leucospilota</em>. A total of 584 known miRNAs and 404 novel miRNAs were identified, of which 97 miRNAs were identified as significantly differentially expressed miRNAs (DEMs) between male and female sea cucumbers. These findings enabled the construction of a miRNA-mRNA regulatory network. Pathway analysis of target genes highlighted the potential roles of neuroactive ligand-receptor interactions, calcium signaling, Salmonella infection, endocytosis, and MAPK signaling in governing gender differentiation processes. The expression results of high-throughput sequencing were validated in sc-miR121, sc-miR41, sc-miR67, sc-miR90, sc-miR104 and sc-miR189 by quantitative real-time quantity polymerase chain reaction (RT-qPCR). In summary, our results will provide a foundation for future studies of miRNA regulation in gender differentiation of sea cucumber <em>H. leucospilota</em>.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"58 ","pages":"Article 101711"},"PeriodicalIF":2.2,"publicationDate":"2025-12-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145738489","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 : 2025-12-04DOI: 10.1016/j.cbd.2025.101710
Xuechun Zang , Yuxi Liu , Zijiao Wang , Yanqing Wu , Bo Qin , Shaowu Yin , Tao Wang
Thamnaconus septentrionalis, a high-value commercial fish, exhibits significant sensitivity to low temperatures. Understanding its cold response mechanism is vital for the aquaculture industry development. This study analyzed the hepatic response of T. septentrionalis to 24-h exposure at four temperature (10 °C, 15 °C, 20 °C, and 25 °C) using histology, biochemical parameters, and proteomics. Results showed that decreased temperature exacerbated hepatic damage, increased ROS accumulation, and induced oxidative stress. The cold-induced ROS accumulation was further validated by primary T. septentrionalis hepatocyte. Low-temperature groups (10 °C, 15 °C) exhibited elevated oxidative stress enzyme activities (SOD, CAT, GSH-Px), and the MDA level and decreased hepatic triglycerides compared to the control group (25 °C). Proteomic result revealed significant enrichment in energy metabolism pathways. It is hypothesized that cold stress tended to inhibited aerobic respiration and oxidative phosphorylation but enhanced fatty acid catabolism and potentially ketone body utilization as alternative fuels. The proteomic data also suggesting that liver also maintains cellular function by modulating lipid metabolism, activating autophagy, and suppressing apoptosis. This study reveals the physiological and proteomic response of T. septentrionalis to temperature variation, providing insights into its cold tolerance.
{"title":"Astral-based DIA proteomics explored the cold response mechanism in the liver of juvenile greenfin horse-faced filefish (Thamnaconus septentrionalis)","authors":"Xuechun Zang , Yuxi Liu , Zijiao Wang , Yanqing Wu , Bo Qin , Shaowu Yin , Tao Wang","doi":"10.1016/j.cbd.2025.101710","DOIUrl":"10.1016/j.cbd.2025.101710","url":null,"abstract":"<div><div><em>Thamnaconus septentrionalis</em>, a high-value commercial fish, exhibits significant sensitivity to low temperatures. Understanding its cold response mechanism is vital for the aquaculture industry development. This study analyzed the hepatic response of <em>T. septentrionalis</em> to 24-h exposure at four temperature (10 °C, 15 °C, 20 °C, and 25 °C) using histology, biochemical parameters, and proteomics. Results showed that decreased temperature exacerbated hepatic damage, increased ROS accumulation, and induced oxidative stress. The cold-induced ROS accumulation was further validated by primary <em>T. septentrionalis</em> hepatocyte. Low-temperature groups (10 °C, 15 °C) exhibited elevated oxidative stress enzyme activities (SOD, CAT, GSH-Px), and the MDA level and decreased hepatic triglycerides compared to the control group (25 °C). Proteomic result revealed significant enrichment in energy metabolism pathways. It is hypothesized that cold stress tended to inhibited aerobic respiration and oxidative phosphorylation but enhanced fatty acid catabolism and potentially ketone body utilization as alternative fuels. The proteomic data also suggesting that liver also maintains cellular function by modulating lipid metabolism, activating autophagy, and suppressing apoptosis. This study reveals the physiological and proteomic response of <em>T. septentrionalis</em> to temperature variation, providing insights into its cold tolerance.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"58 ","pages":"Article 101710"},"PeriodicalIF":2.2,"publicationDate":"2025-12-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145717140","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 : 2025-12-02DOI: 10.1016/j.cbd.2025.101704
Weiren Zhang , Jun Luo , Yijia Shih , Yaodong Zhang , Siyi Zhou , Qionghui Qin , Kewei Huang , Qi Wang , Xiaopeng Wang , Haihui Ye
Scylla paramamosain is an economically important marine crab species in Asia, yet the genetic architecture of its growth traits remains poorly characterized. This study employed an integrated approach combining genome-wide association studies (GWAS) and genomic prediction to dissect the genetic basis of four body size traits (carapace width, carapace length, posterior width of carapace, and body height) in 346 individuals genotyped at 3.9 million high-confidence SNPs. GWAS identified five pleiotropic loci and six candidate genes (including Exportin-5 and FANCI) shared among traits, with KEGG enrichment analysis underscoring the importance of metabolic pathways, particularly the citrate cycle. We further evaluated the genomic prediction performance of the GFBLUP model using two types of prior biological knowledge: functionally annotated SNPs derived from the top-enriched KEGG pathways, and trait-associated SNPs selected under varying GWAS significance thresholds. GFBLUP using trait-associated SNPs significantly outperformed standard GBLUP, with prediction accuracy gains of 0.528–0.888. Prediction accuracy increased with SNP panel size, exceeding 0.819 for all traits with the top 1000 SNPs and stabilizing beyond 5000 SNPs (0.837–0.865). An FDR threshold of 0.05 offered an optimal balance, achieving high accuracy (0.840–0.862) with a practical number of SNPs (7980–9302). In contrast, functionally informed GFBLUP provided only modest improvements (0.020–0.197), likely due to the inclusion of non-causal variants. These results demonstrate that low-density SNP panels informed by GWAS prior knowledge substantially enhance genomic prediction for body size traits in S. paramamosain, providing a practical breeding strategy and valuable insights into the genetic mechanisms of growth in non-model crustaceans.
{"title":"Incorporating GWAS-derived prior information enhances genomic prediction for body size traits in the mud crab (Scylla paramamosain)","authors":"Weiren Zhang , Jun Luo , Yijia Shih , Yaodong Zhang , Siyi Zhou , Qionghui Qin , Kewei Huang , Qi Wang , Xiaopeng Wang , Haihui Ye","doi":"10.1016/j.cbd.2025.101704","DOIUrl":"10.1016/j.cbd.2025.101704","url":null,"abstract":"<div><div><em>Scylla paramamosain</em> is an economically important marine crab species in Asia, yet the genetic architecture of its growth traits remains poorly characterized. This study employed an integrated approach combining genome-wide association studies (GWAS) and genomic prediction to dissect the genetic basis of four body size traits (carapace width, carapace length, posterior width of carapace, and body height) in 346 individuals genotyped at 3.9 million high-confidence SNPs. GWAS identified five pleiotropic loci and six candidate genes (including <em>Exportin-5</em> and <em>FANCI</em>) shared among traits, with KEGG enrichment analysis underscoring the importance of metabolic pathways, particularly the citrate cycle. We further evaluated the genomic prediction performance of the GFBLUP model using two types of prior biological knowledge: functionally annotated SNPs derived from the top-enriched KEGG pathways, and trait-associated SNPs selected under varying GWAS significance thresholds. GFBLUP using trait-associated SNPs significantly outperformed standard GBLUP, with prediction accuracy gains of 0.528–0.888. Prediction accuracy increased with SNP panel size, exceeding 0.819 for all traits with the top 1000 SNPs and stabilizing beyond 5000 SNPs (0.837–0.865). An FDR threshold of 0.05 offered an optimal balance, achieving high accuracy (0.840–0.862) with a practical number of SNPs (7980–9302). In contrast, functionally informed GFBLUP provided only modest improvements (0.020–0.197), likely due to the inclusion of non-causal variants. These results demonstrate that low-density SNP panels informed by GWAS prior knowledge substantially enhance genomic prediction for body size traits in <em>S. paramamosain</em>, providing a practical breeding strategy and valuable insights into the genetic mechanisms of growth in non-model crustaceans.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"58 ","pages":"Article 101704"},"PeriodicalIF":2.2,"publicationDate":"2025-12-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145727731","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 : 2025-12-02DOI: 10.1016/j.cbd.2025.101706
Xiaohua He , Siyi Li , Shuhai Wang , Qiang Wang , Xiaohui Xu , Yanwei Feng , Weijun Wang , Zan Li , Jianmin Yang , Qihao Luo , Guohua Sun
Sea cucumber Apostichopus japonicus is an important aquaculture species along the North Pacific coast. Its farming efficiency faces a growing threat from the impacts of global climate change, which characterized by either extreme low-temperature events or extended periods of cold stress. This study employed integrated physiological, transcriptomic, and metabolomic analyses to investigate A. japonicus responses to low temperatures (7.5 °C and 2.5 °C). When the temperature decreased to 7.5 °C and 2.5 °C, both significantly increased the activities of antioxidant enzymes (superoxide dismutase, SOD; catalase, CAT; glutathione peroxidase, GPX), thereby alleviating oxidative damage. Transcriptomic data showed that at 7.5 °C, genes related to antioxidant defense (e.g., ALDH7A1) were significantly upregulated, as were genes associated with lipid metabolism, such as SCP2. At 2.5 °C, the number of differentially expressed genes increased significantly, including the upregulation of lipid metabolism-related gene acox1, antioxidant defense-related genes (gclm, pdxk), and the downregulation of lipid metabolism-related gene hmgcr. Metabolomic profiling revealed enrichment of unsaturated fatty acids (e.g., linoleic acid) and primary bile acid biosynthesis at 7.5 °C, enhancing membrane fluidity and lipid utilization. Key metabolites at 2.5 °C (e.g., glutathione, L-aspartic acid) were involved in amino acid metabolism pathways. Integrated analyses highlighted co-enrichment of genes and metabolites linked to bile acid synthesis and fatty acid metabolism at 7.5 °C, supporting membrane stability and energy balance, while 2.5 °C induced pathways related to vitamin B6 metabolism, the TCA cycle, oxidative phosphorylation, and fatty acid degradation. These results indicate that A. japonicus primarily counters cold stress through antioxidant defense and energy homeostasis regulation. The findings provide a theoretical basis for understanding temperature adaptation in echinoderms and establish a foundation for developing precise cultivation strategies and breeding novel stress-resistant strains of A. japonicus to mitigate the impacts of global climate change.
{"title":"Unveiling the roles of oxidative stress defense and energy metabolism adjustment in low-temperature stress responses of Apostichopus japonicus: An integrated physiological, transcriptomic and metabolomic analysis","authors":"Xiaohua He , Siyi Li , Shuhai Wang , Qiang Wang , Xiaohui Xu , Yanwei Feng , Weijun Wang , Zan Li , Jianmin Yang , Qihao Luo , Guohua Sun","doi":"10.1016/j.cbd.2025.101706","DOIUrl":"10.1016/j.cbd.2025.101706","url":null,"abstract":"<div><div>Sea cucumber <em>Apostichopus japonicus</em> is an important aquaculture species along the North Pacific coast. Its farming efficiency faces a growing threat from the impacts of global climate change, which characterized by either extreme low-temperature events or extended periods of cold stress. This study employed integrated physiological, transcriptomic, and metabolomic analyses to investigate <em>A. japonicus</em> responses to low temperatures (7.5 °C and 2.5 °C). When the temperature decreased to 7.5 °C and 2.5 °C, both significantly increased the activities of antioxidant enzymes (superoxide dismutase, SOD; catalase, CAT; glutathione peroxidase, GPX), thereby alleviating oxidative damage. Transcriptomic data showed that at 7.5 °C, genes related to antioxidant defense (e.g., <em>ALDH7A1</em>) were significantly upregulated, as were genes associated with lipid metabolism, such as <em>SCP2</em>. At 2.5 °C, the number of differentially expressed genes increased significantly, including the upregulation of lipid metabolism-related gene acox1, antioxidant defense-related genes (<em>gclm</em>, <em>pdx</em>k), and the downregulation of lipid metabolism-related gene <em>hmgcr</em>. Metabolomic profiling revealed enrichment of unsaturated fatty acids (e.g., linoleic acid) and primary bile acid biosynthesis at 7.5 °C, enhancing membrane fluidity and lipid utilization. Key metabolites at 2.5 °C (e.g., glutathione, L-aspartic acid) were involved in amino acid metabolism pathways. Integrated analyses highlighted co-enrichment of genes and metabolites linked to bile acid synthesis and fatty acid metabolism at 7.5 °C, supporting membrane stability and energy balance, while 2.5 °C induced pathways related to vitamin B6 metabolism, the TCA cycle, oxidative phosphorylation, and fatty acid degradation. These results indicate that <em>A. japonicus</em> primarily counters cold stress through antioxidant defense and energy homeostasis regulation. The findings provide a theoretical basis for understanding temperature adaptation in echinoderms and establish a foundation for developing precise cultivation strategies and breeding novel stress-resistant strains of <em>A. japonicus</em> to mitigate the impacts of global climate change.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"58 ","pages":"Article 101706"},"PeriodicalIF":2.2,"publicationDate":"2025-12-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145685744","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 : 2025-12-02DOI: 10.1016/j.cbd.2025.101705
Kaichun Chen , Weibin Li , Weijian Chen , Shengyue Lin , Ziyan Deng , Guojun Cai , Qiang Li , Chong Han
Estrone (E1) is one of the primary natural estrogens found in aquatic environments and has the potential to impact the reproductive and endocrine systems of fish. To evaluate the impact of E1 on Siniperca chuatsi, in this study, male S. chuatsi were exposed to E1 at concentrations of 0.0, 0.01, 0.1, and 1.0 μg/L for 60 consecutive days. Subsequently, we analyzed the gonadal histology, hepatic histology, antioxidant enzyme activities, and transcriptomic analysis of the fish. Histological examination of the gonads revealed that high concentrations of E1 can induce the transformation of testes into ovaries in male S.chuatsi, with an induction rate of 80 %. Moreover, significant changes in the levels of the androgen 11-ketotestosterone and the estrogen were observed at high concentrations. Hepatic histology revealed that E1 exposure led to vacuolization of hepatocytes, pyknosis, and inflammation in the liver. Additionally, exposure to 1.0 μg/L E1 significantly increased the activities of SOD (superoxide dismutase) and T-AOC (total antioxidant capacity) in the liver. Transcriptomic analysis of the liver identified several genes significantly associated with sex differentiation, including vtg1, cyp19a, hsd17β3, and esr1, among others. GO and KEGG enrichment analyses suggested that E1 exposure significantly altered the level of lipid metabolism in the liver of male S. chuatsi. In summary, these results indicate that E1 exposure not only causes oxidative damage to the liver but also induces alterations in hepatic steroid hormone synthesis and lipid metabolism pathways, which are indicative of feminizing endocrine effects, thereby leading to the feminization of male S.chuatsi.
{"title":"Estrone exposure-induced feminization in male Siniperca chuatsi: A multidimensional study on sex reversal, liver damage, and changes in gene expression","authors":"Kaichun Chen , Weibin Li , Weijian Chen , Shengyue Lin , Ziyan Deng , Guojun Cai , Qiang Li , Chong Han","doi":"10.1016/j.cbd.2025.101705","DOIUrl":"10.1016/j.cbd.2025.101705","url":null,"abstract":"<div><div>Estrone (E1) is one of the primary natural estrogens found in aquatic environments and has the potential to impact the reproductive and endocrine systems of fish. To evaluate the impact of E1 on <em>Siniperca chuatsi</em>, in this study, male <em>S. chuatsi</em> were exposed to E1 at concentrations of 0.0, 0.01, 0.1, and 1.0 μg/L for 60 consecutive days. Subsequently, we analyzed the gonadal histology, hepatic histology, antioxidant enzyme activities, and transcriptomic analysis of the fish. Histological examination of the gonads revealed that high concentrations of E1 can induce the transformation of testes into ovaries in male <em>S.chuatsi</em>, with an induction rate of 80 %. Moreover, significant changes in the levels of the androgen 11-ketotestosterone and the estrogen were observed at high concentrations. Hepatic histology revealed that E1 exposure led to vacuolization of hepatocytes, pyknosis, and inflammation in the liver. Additionally, exposure to 1.0 μg/L E1 significantly increased the activities of SOD (superoxide dismutase) and T-AOC (total antioxidant capacity) in the liver. Transcriptomic analysis of the liver identified several genes significantly associated with sex differentiation, including <em>vtg1</em>, <em>cyp19a</em>, <em>hsd17β3</em>, and <em>esr1</em>, among others. GO and KEGG enrichment analyses suggested that E1 exposure significantly altered the level of lipid metabolism in the liver of male <em>S. chuatsi</em>. In summary, these results indicate that E1 exposure not only causes oxidative damage to the liver but also induces alterations in hepatic steroid hormone synthesis and lipid metabolism pathways, which are indicative of feminizing endocrine effects, thereby leading to the feminization of male <em>S.chuatsi</em>.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"58 ","pages":"Article 101705"},"PeriodicalIF":2.2,"publicationDate":"2025-12-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145658889","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 : 2025-12-02DOI: 10.1016/j.cbd.2025.101707
Anicet Philippe Mane Sany , Songlin Chen , Qianqian Qin , Jinjin Luo , Han Wang , Loic Kemmadzong Foning , Addise Kerebih , Guodong Zheng , Shuming Zou
Blunt snout bream (Megalobrama amblycephala) is an important commercial freshwater fish species in China's aquaculture system. It is unknown how the interaction of bacterial infections and dissolved oxygen concentration affects the gene expression and physiological function of the gill tissues in this fish species. Therefore, fish were exposed to hypoxic conditions and challenged with Aeromonas hydrophila. Then, fish were classified into resistant (H-RMA) and sensitive (H-SMA) groups based on their survival outcomes. Gill tissues were collected for RNA-Seq and functional analysis. A total of 36,774 expressed genes, encompassing 33,852 known genes and 2922 novel genes were identified and around 93 % of these genes were correctly mapped to the reference genome. A comparative expression analysis between H-RMA and H-SMA fish revealed 5482 differentially expressed genes (DEGs) encompassing 2557 up-regulated and 2925 down-regulated genes. The examination of KEGG pathways revealed significant enrichment in DNA replication, proteasome, cell cycle, mismatch repair, oxidative phosphorylation and cellular senescence. Obviously structural alterations were observed in the gill tissues, resulting from the compounded impact of hypoxic stress and bacterial infection. Moreover, antioxidant enzymes (SOD, CAT) and immune enzyme activity modulation (ACP and AKP) were significantly (p < 0.05) changed between H-RMA and H-SMA groups. Our findings suggest a strong connection between cell cycle arrest and cellular senescence, indicating that resistance to these environmental stresses may depend on the capacity of the cellular senescence pathway to coordinate an immune response localized in the gills.
{"title":"Transcriptomic analysis of gill tissues in blunt snout bream (Megalobrama amblycephala) under hypoxia and bacterial infection","authors":"Anicet Philippe Mane Sany , Songlin Chen , Qianqian Qin , Jinjin Luo , Han Wang , Loic Kemmadzong Foning , Addise Kerebih , Guodong Zheng , Shuming Zou","doi":"10.1016/j.cbd.2025.101707","DOIUrl":"10.1016/j.cbd.2025.101707","url":null,"abstract":"<div><div>Blunt snout bream (<em>Megalobrama amblycephala</em>) is an important commercial freshwater fish species in China's aquaculture system. It is unknown how the interaction of bacterial infections and dissolved oxygen concentration affects the gene expression and physiological function of the gill tissues in this fish species. Therefore, fish were exposed to hypoxic conditions and challenged with <em>Aeromonas hydrophila</em>. Then, fish were classified into resistant (H-RMA) and sensitive (H-SMA) groups based on their survival outcomes. Gill tissues were collected for RNA-Seq and functional analysis. A total of 36,774 expressed genes, encompassing 33,852 known genes and 2922 novel genes were identified and around 93 % of these genes were correctly mapped to the reference genome. A comparative expression analysis between H-RMA and H-SMA fish revealed 5482 differentially expressed genes (DEGs) encompassing 2557 up-regulated and 2925 down-regulated genes. The examination of KEGG pathways revealed significant enrichment in DNA replication, proteasome, cell cycle, mismatch repair, oxidative phosphorylation and cellular senescence. Obviously structural alterations were observed in the gill tissues, resulting from the compounded impact of hypoxic stress and bacterial infection. Moreover, antioxidant enzymes (SOD, CAT) and immune enzyme activity modulation (ACP and AKP) were significantly (<em>p</em> < 0.05) changed between H-RMA and H-SMA groups. Our findings suggest a strong connection between cell cycle arrest and cellular senescence, indicating that resistance to these environmental stresses may depend on the capacity of the cellular senescence pathway to coordinate an immune response localized in the gills.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"58 ","pages":"Article 101707"},"PeriodicalIF":2.2,"publicationDate":"2025-12-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145685743","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 : 2025-12-02DOI: 10.1016/j.cbd.2025.101708
Feng Qin , Fan Liu , Qi Cao , Zhen Wei , Hujun Gao , Wei Zheng , Zhenlin Ke , Yinlin Xiong , Hui Luo , Ronghua Wu , Zhongwei Wang , Hua Ye
The Chinese longsnout catfish (Leiocassis longirostris) is a commercially valuable freshwater species in China. We elucidated molecular mechanisms underlying testicular development of L. longirostris across five stages (stages I to V) through integrated transcriptomic and proteomic analyses, which is crucial for enhancing its sperm quality and efficient reproduction. Enrichment analyses identified several key pathways as essential for testicular development, including TGF-β signaling, Wnt signaling, ECM-receptor interaction, ferroptosis, cell cycle regulation, and ubiquitin-mediated proteolysis. Gene Ontology (GO) enrichment highlighted core biological processes such as germ cell proliferation, differentiation, meiotic progression, and spermatogenesis regulation involved in development. Notably, qPCR validation showed peak expression levels of wnt7a, pax6, and kiss1r at distinct spermatogenic phases (p < 0.01), suggesting their potential as temporal biomarkers for identification of development stages. Furthermore, protein-protein interaction (PPI) analyses revealed C-type lysozyme (LysC) as a potential regulatory factor, with peak expression at stages I and III, possibly linking testicular immunity and reproductive processes. These findings elucidate the molecular mechanisms of testicular development and provide insights for developing efficient artificial breeding strategies for L. longirostris.
{"title":"A multi-omics atlas of testicular development in Leiocassis longirostris: dynamic regulation of spermatogenesis","authors":"Feng Qin , Fan Liu , Qi Cao , Zhen Wei , Hujun Gao , Wei Zheng , Zhenlin Ke , Yinlin Xiong , Hui Luo , Ronghua Wu , Zhongwei Wang , Hua Ye","doi":"10.1016/j.cbd.2025.101708","DOIUrl":"10.1016/j.cbd.2025.101708","url":null,"abstract":"<div><div>The Chinese longsnout catfish (<em>Leiocassis longirostris</em>) is a commercially valuable freshwater species in China. We elucidated molecular mechanisms underlying testicular development of <em>L. longirostris</em> across five stages (stages I to V) through integrated transcriptomic and proteomic analyses, which is crucial for enhancing its sperm quality and efficient reproduction. Enrichment analyses identified several key pathways as essential for testicular development, including TGF-β signaling, Wnt signaling, ECM-receptor interaction, ferroptosis, cell cycle regulation, and ubiquitin-mediated proteolysis. Gene Ontology (GO) enrichment highlighted core biological processes such as germ cell proliferation, differentiation, meiotic progression, and spermatogenesis regulation involved in development. Notably, qPCR validation showed peak expression levels of <em>wnt7a</em>, <em>pax6,</em> and <em>kiss1r</em> at distinct spermatogenic phases (<em>p</em> < 0.01), suggesting their potential as temporal biomarkers for identification of development stages. Furthermore, protein-protein interaction (PPI) analyses revealed C-type lysozyme (LysC) as a potential regulatory factor, with peak expression at stages I and III, possibly linking testicular immunity and reproductive processes. These findings elucidate the molecular mechanisms of testicular development and provide insights for developing efficient artificial breeding strategies for <em>L. longirostris</em>.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"58 ","pages":"Article 101708"},"PeriodicalIF":2.2,"publicationDate":"2025-12-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145685749","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 : 2025-12-01DOI: 10.1016/j.cbd.2025.101703
Weifeng Zhang , Tiancheng Chen , Yazhuo Hu , Xizhi Shi , Yongbo Bao
In recent decades, various globin groups have been identified and characterized in vertebrates, while studies on invertebrates remain limited. Therefore, we conducted this study to explore the repertoire, evolution, and functions of globin genes in the blood clam Anadara granosa, an economically significant bivalve known for its hemoglobin. A total of 31 globin genes were identified, driven by tandem gene duplications that played a pivotal role in their expansion. Phylogenetic analysis identifies two previously unreported basal clades, provisionally named cluster A and B, alongside the well-known ancient globin groups neuroglobin, androglobin, globin X, and globin X-like. This suggests that invertebrates may have retained a more complete ancestral globin gene repertoire compared to vertebrates, and that the globin gene repertoire in the last common ancestor of vertebrates and invertebrates was more diverse than previously hypothesized. Protein structural analyses indicate that evolutionary changes in hemoglobin's oxygen-transport function may be driven by structural alterations in the CD region and EF helices or substitutions at select residues therein. Furthermore, the ancient globin groups exhibit widespread N-myristoylation and 3C-palmitoylation modifications, indicating their potential membrane-associated ancestral functions. Transcriptome analysis and hypoxia stress experiments indicate that globins are involved in the development and hypoxia tolerance of A. granosa. The pentacoordinate heme in animal globins likely switched from a hexacoordinate form, possibly associated with the evolution of oxygen-carrying functionality. This study expands our understanding of the globin superfamily's structure, function, and evolution, particularly in mollusks.
{"title":"Evolution of the animal globin superfamily: Insights from the blood clam Anadara granosa","authors":"Weifeng Zhang , Tiancheng Chen , Yazhuo Hu , Xizhi Shi , Yongbo Bao","doi":"10.1016/j.cbd.2025.101703","DOIUrl":"10.1016/j.cbd.2025.101703","url":null,"abstract":"<div><div>In recent decades, various globin groups have been identified and characterized in vertebrates, while studies on invertebrates remain limited. Therefore, we conducted this study to explore the repertoire, evolution, and functions of globin genes in the blood clam <em>Anadara granosa</em>, an economically significant bivalve known for its hemoglobin. A total of 31 globin genes were identified, driven by tandem gene duplications that played a pivotal role in their expansion. Phylogenetic analysis identifies two previously unreported basal clades, provisionally named cluster A and B, alongside the well-known ancient globin groups neuroglobin, androglobin, globin X, and globin X-like. This suggests that invertebrates may have retained a more complete ancestral globin gene repertoire compared to vertebrates, and that the globin gene repertoire in the last common ancestor of vertebrates and invertebrates was more diverse than previously hypothesized. Protein structural analyses indicate that evolutionary changes in hemoglobin's oxygen-transport function may be driven by structural alterations in the CD region and EF helices or substitutions at select residues therein. Furthermore, the ancient globin groups exhibit widespread N-myristoylation and 3C-palmitoylation modifications, indicating their potential membrane-associated ancestral functions. Transcriptome analysis and hypoxia stress experiments indicate that globins are involved in the development and hypoxia tolerance of <em>A. granosa</em>. The pentacoordinate heme in animal globins likely switched from a hexacoordinate form, possibly associated with the evolution of oxygen-carrying functionality. This study expands our understanding of the globin superfamily's structure, function, and evolution, particularly in mollusks.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"57 ","pages":"Article 101703"},"PeriodicalIF":2.2,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145673128","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 : 2025-11-30DOI: 10.1016/j.cbd.2025.101700
Lijie Cui , Sijia Hao , Yayun Guan , Zhuofan Chen , Yan Wang , Zhengfei Wang
Helice tientsinensis is a typical species in the intertidal ecosystem, which is easily affected by fluctuations in salinity. This study systematically investigated the physiological and molecular responses of H. tientsinensis under freshwater (0 ‰), low-salinity (15 ‰, control group), and high salinity (30 ‰) stress conditions at 24 and 48 h, using histological observation, enzyme activity detection, and transcriptome sequencing. The results showed that there were relatively few differentially expressed genes between different salinity groups, indicating that H. tientsinensis has a certain degree of adaptability to salinity fluctuations, which is consistent with its intertidal lifestyle. The gill tissue shows structural damage in the freshwater environment, and immune-related genes were downregulated, indicating that freshwater stress damages the gill tissue and suppresses the immune response. At the same time, H. tientsinensis responds to salinity stress through strategies related to energy metabolism, such as enhancing glycolysis, lipid metabolism, and purine synthesis. The study further reveals that H. tientsinensis adopts a tissue-specific osmoregulation strategy: osmoregulation-related genes (e.g., SLC34A, nptA) are significantly upregulated in gill tissue to enhance ion transport efficiency; in contrast, ion transport-related osmoregulation genes (e.g., ABCA1, ABCC2, ABCC3) are downregulated in the hepatopancreas to reduce metabolic load by saving energy consumption. The gene expression patterns of the two tissues act synergistically to maintain the overall osmotic balance homeostasis of the organism. The purpose of this study was to systematically elucidate the physiological and molecular mechanisms underlying the adaptation of H. tientsinensis to different salinity stresses, thereby filling the gap in current research on its molecular response to salinity changes and providing molecular evidence for the environmental adaptation of intertidal crustaceans.
{"title":"Transcriptomic profiling of Helice tientsinensis reveals its adaptation mechanisms to different salinity levels","authors":"Lijie Cui , Sijia Hao , Yayun Guan , Zhuofan Chen , Yan Wang , Zhengfei Wang","doi":"10.1016/j.cbd.2025.101700","DOIUrl":"10.1016/j.cbd.2025.101700","url":null,"abstract":"<div><div><em>Helice tientsinensis</em> is a typical species in the intertidal ecosystem, which is easily affected by fluctuations in salinity. This study systematically investigated the physiological and molecular responses of <em>H. tientsinensis</em> under freshwater (0 ‰), low-salinity (15 ‰, control group), and high salinity (30 ‰) stress conditions at 24 and 48 h, using histological observation, enzyme activity detection, and transcriptome sequencing. The results showed that there were relatively few differentially expressed genes between different salinity groups, indicating that <em>H. tientsinensis</em> has a certain degree of adaptability to salinity fluctuations, which is consistent with its intertidal lifestyle. The gill tissue shows structural damage in the freshwater environment, and immune-related genes were downregulated, indicating that freshwater stress damages the gill tissue and suppresses the immune response. At the same time, <em>H. tientsinensis</em> responds to salinity stress through strategies related to energy metabolism, such as enhancing glycolysis, lipid metabolism, and purine synthesis. The study further reveals that <em>H. tientsinensis</em> adopts a tissue-specific osmoregulation strategy: osmoregulation-related genes (e.g., <em>SLC34A</em>, <em>nptA</em>) are significantly upregulated in gill tissue to enhance ion transport efficiency; in contrast, ion transport-related osmoregulation genes (e.g., <em>ABCA1</em>, <em>ABCC2</em>, <em>ABCC3</em>) are downregulated in the hepatopancreas to reduce metabolic load by saving energy consumption. The gene expression patterns of the two tissues act synergistically to maintain the overall osmotic balance homeostasis of the organism. The purpose of this study was to systematically elucidate the physiological and molecular mechanisms underlying the adaptation of <em>H. tientsinensis</em> to different salinity stresses, thereby filling the gap in current research on its molecular response to salinity changes and providing molecular evidence for the environmental adaptation of intertidal crustaceans.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"58 ","pages":"Article 101700"},"PeriodicalIF":2.2,"publicationDate":"2025-11-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145738492","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 : 2025-11-28DOI: 10.1016/j.cbd.2025.101702
Ying Liu , Le Chang , Lingran Wang , Chang Liu , Di Feng , Lei Wang
To elucidate the genetic mechanism underlying body color variation within a single breeding family of captive Yellow River carp (Cyprinus carpio haematopterus), individuals exhibiting normal and aberrant pigmentation from the same concrete pond were selected for analysis. Using bulked segregant analysis combined with whole-genome resequencing, DNA pools were constructed from progeny with extreme phenotypes for sequencing. SNP variation detection followed by linkage analysis identified a candidate region on chromosome 25, spanning approximately 10.1 Mb (from 15,881,284 bp to 26,645,798 bp). Gene Ontology (GO) enrichment analysis revealed four candidate genes potentially associated with aberrant pigmentation: dkk1, kndc1, lyst, and opn3. Based on the candidate genes' mutation sites, certain primers were created, and the PCR products were then sequenced. Notably, a mutation was detected at the 8th bp of the opn3 cDNA corresponding to transcript HHLG25g0668 in the aberrant-color offspring. At this position, 81.25 % of wild-type individuals carried the cytosine (C) allele, whereas all mutant individuals carried an adenine (A) substitution, resulting in an amino acid change from serine to tyrosine at position 3 of the protein. This suggests that opn3 may play a key role in the development of abnormal pigmentation in Yellow River carp. These findings provide a theoretical foundation for further functional studies of pigmentation-related genes and the genetic improvement of novel germplasm in Yellow River carp.
{"title":"Aberrant body coloration in captive Yellow River carp (Cyprinus carpio haematopterus): A genomic perspective from whole-genome resequencing and bulk segregant analysis","authors":"Ying Liu , Le Chang , Lingran Wang , Chang Liu , Di Feng , Lei Wang","doi":"10.1016/j.cbd.2025.101702","DOIUrl":"10.1016/j.cbd.2025.101702","url":null,"abstract":"<div><div>To elucidate the genetic mechanism underlying body color variation within a single breeding family of captive Yellow River carp (<em>Cyprinus carpio haematopterus</em>), individuals exhibiting normal and aberrant pigmentation from the same concrete pond were selected for analysis. Using bulked segregant analysis combined with whole-genome resequencing, DNA pools were constructed from progeny with extreme phenotypes for sequencing. SNP variation detection followed by linkage analysis identified a candidate region on chromosome 25, spanning approximately 10.1 Mb (from 15,881,284 bp to 26,645,798 bp). Gene Ontology (GO) enrichment analysis revealed four candidate genes potentially associated with aberrant pigmentation: <em>dkk1</em>, <em>kndc1, lyst</em>, and <em>opn3</em>. Based on the candidate genes' mutation sites, certain primers were created, and the PCR products were then sequenced. Notably, a mutation was detected at the 8th bp of the <em>opn3</em> cDNA corresponding to transcript HHLG25g0668 in the aberrant-color offspring. At this position, 81.25 % of wild-type individuals carried the cytosine (C) allele, whereas all mutant individuals carried an adenine (A) substitution, resulting in an amino acid change from serine to tyrosine at position 3 of the protein. This suggests that <em>opn3</em> may play a key role in the development of abnormal pigmentation in Yellow River carp. These findings provide a theoretical foundation for further functional studies of pigmentation-related genes and the genetic improvement of novel germplasm in Yellow River carp.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"58 ","pages":"Article 101702"},"PeriodicalIF":2.2,"publicationDate":"2025-11-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145685745","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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