Pub Date : 2026-06-01Epub Date: 2026-02-08DOI: 10.1016/j.cbd.2026.101779
Huifan Chen , Zhaoyang Guo , Zhiyi Zhang , Songlin Cai , Jun Wang , Xiaowen Chen , Chenghui Wang
Ecological adaptation, the process by which organisms acquire beneficial traits through natural selection, enhances survival but its molecular mechanisms are often poorly understood. A prime example is the fish species Culter alburnus, which has evolved a dichotomous reproductive strategy: Producing adhesive eggs in still waters and semi-buoyant eggs in flowing rivers. To elucidate the molecular basis of this adaptation, a comparative study of the two egg types was conducted. Our findings revealed that adhesive and semi-buoyant eggs employ distinct developmental strategies. Semi-buoyant eggs prioritize energy mobilization and protein synthesis to fuel rapid development. In contrast, adhesive eggs upregulate genes involved in immune regulation and cell adhesion. Further analysis revealed that semi-buoyant eggs enhance hydration through protein degradation and undergo extensive cytoskeletal remodeling via tubulin folding and collagen production. Adhesive eggs, however, utilize integrin-mediated interactions with proteins like TMEM132 and FN to regulate adhesion, a process coupled with egg envelope hardening. Our results demonstrate that the aquatic environment profoundly shapes physiological and transcriptional programs in fish eggs, offering significant insights into population-specific adaptations in teleosts.
{"title":"Comparison of transcriptomics and proteomics revealed distinct molecular mechanisms underlying egg development of Culter alburnus between northern and southern China","authors":"Huifan Chen , Zhaoyang Guo , Zhiyi Zhang , Songlin Cai , Jun Wang , Xiaowen Chen , Chenghui Wang","doi":"10.1016/j.cbd.2026.101779","DOIUrl":"10.1016/j.cbd.2026.101779","url":null,"abstract":"<div><div>Ecological adaptation, the process by which organisms acquire beneficial traits through natural selection, enhances survival but its molecular mechanisms are often poorly understood. A prime example is the fish species <em>Culter alburnus</em>, which has evolved a dichotomous reproductive strategy: Producing adhesive eggs in still waters and semi-buoyant eggs in flowing rivers. To elucidate the molecular basis of this adaptation, a comparative study of the two egg types was conducted. Our findings revealed that adhesive and semi-buoyant eggs employ distinct developmental strategies. Semi-buoyant eggs prioritize energy mobilization and protein synthesis to fuel rapid development. In contrast, adhesive eggs upregulate genes involved in immune regulation and cell adhesion. Further analysis revealed that semi-buoyant eggs enhance hydration through protein degradation and undergo extensive cytoskeletal remodeling via tubulin folding and collagen production. Adhesive eggs, however, utilize integrin-mediated interactions with proteins like TMEM132 and FN to regulate adhesion, a process coupled with egg envelope hardening. Our results demonstrate that the aquatic environment profoundly shapes physiological and transcriptional programs in fish eggs, offering significant insights into population-specific adaptations in teleosts.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"58 ","pages":"Article 101779"},"PeriodicalIF":2.2,"publicationDate":"2026-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146173234","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: 2026-01-10DOI: 10.1016/j.cbd.2026.101751
Guoliang Chang , Fanqian Kong , Songyue Gao , Huajie Cai , Long Wang , Huaiyu Ding , Yongxu Cheng , Jiayao Li
The carapace coloration is of great significance to Procambarus clarkii, and the molecular mechanism of temperature affecting carapace color has not yet been reported. In this study, comparative transcriptome was used to study molecular mechanism of temperature-induced changes in carapace coloration of P. clarkii. This study identified many genes (such as tyrosinase, APOD) and signaling pathways (such as tyrosine metabolism) related to pigment accumulation. As an important environmental factor, temperature can change metabolism and accumulation of pigment in P. clarkii by changing expression patterns of related genes and pathways. High temperature can damage transport of related proteins (such as ABC transporters), thus affecting the metabolism of carotenoids and melanin, and finally lead to the change of body color of P. clarkii. Oxidative stress caused by high temperature can destroy pigment metabolism and accumulation, resulting in changes in body color. The results of this study revealed molecular mechanism of temperature affecting body color of P. clarkii, provided basic data for subsequent selective breeding and practical production, and provided new insights for crustacean body color formation and change.
{"title":"Comparative transcriptome analysis reveals molecular mechanism of temperature effect on body color of red swamp crayfish (Procambarus clarkii)","authors":"Guoliang Chang , Fanqian Kong , Songyue Gao , Huajie Cai , Long Wang , Huaiyu Ding , Yongxu Cheng , Jiayao Li","doi":"10.1016/j.cbd.2026.101751","DOIUrl":"10.1016/j.cbd.2026.101751","url":null,"abstract":"<div><div>The carapace coloration is of great significance to <em>Procambarus clarkii</em>, and the molecular mechanism of temperature affecting carapace color has not yet been reported. In this study, comparative transcriptome was used to study molecular mechanism of temperature-induced changes in carapace coloration of <em>P. clarkii</em>. This study identified many genes (such as <em>tyrosinase</em>, <em>APOD</em>) and signaling pathways (such as tyrosine metabolism) related to pigment accumulation. As an important environmental factor, temperature can change metabolism and accumulation of pigment in <em>P. clarkii</em> by changing expression patterns of related genes and pathways. High temperature can damage transport of related proteins (such as ABC transporters), thus affecting the metabolism of carotenoids and melanin, and finally lead to the change of body color of <em>P. clarkii</em>. Oxidative stress caused by high temperature can destroy pigment metabolism and accumulation, resulting in changes in body color. The results of this study revealed molecular mechanism of temperature affecting body color of <em>P. clarkii</em>, provided basic data for subsequent selective breeding and practical production, and provided new insights for crustacean body color formation and change.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"58 ","pages":"Article 101751"},"PeriodicalIF":2.2,"publicationDate":"2026-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145977220","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: 2025-12-08DOI: 10.1016/j.cbd.2025.101701
Weiqing Huang , Fengfang Zhou , Zongqiang Lian , Zhideng Lin , Zipeng Zhang
Saline-alkaline stress poses a significant environmental challenge to fish in aquaculture, yet the molecular mechanisms underlying adaptation remain poorly understood. In this study, we integrated transcriptomic, metabolomic, physiological, and histological analyses to elucidate the adaptive mechanisms of Acanthopagrus latus gills under saline-alkaline water (SAW) exposure. After 40 days of treatment, SAW caused evident histological alterations in gill structures but did not significantly affect growth performance. Physiological assays showed that glutathione peroxidase (GSH-Px), acid phosphatase (ACP) and alkaline phosphatase (ALP) activities showed no significant change, while malondialdehyde (MDA) levels increased, indicating oxidative stress and metabolic disturbance.
Transcriptomic analysis identified 2539 differentially expressed genes (DEGs), mainly enriched in immune-related pathways such as T-cell receptor signaling, Th17 cell differentiation, and IL-17 signaling. Metabolomic profiling detected 892 differentially expressed metabolites (DEMs), primarily involved in energy metabolism pathways, including arachidonic acid, α-linolenic acid, and linoleic acid metabolism. Integrated multi-omics analysis further revealed a significant co-enrichment in platelet activation, phospholipase D signaling, and glutathione metabolism pathways. Notably, 29 DEGs and 4 key metabolites (ATP, prostaglandin H₂, cyclic AMP, and ADP) were significantly altered in the platelet activation pathway. Among them, upregulated genes such as p2ry12, LOC119021196, and LOC119027230 were linked to energy metabolism, while lyn, fynb, pik3r1, pik3cd, and akt1 were associated with apoptosis and immune regulation.
Overall, this study provides comprehensive molecular and physiological evidence of how A. latus adapts to saline-alkaline stress through coordinated immune regulation and energy metabolism. These findings enhance our understanding of fish adaptive mechanisms and offer theoretical support for the sustainable utilization of saline-alkaline water resources in aquaculture.
{"title":"Physiological effects of long-term saline-alkaline stress on the gills of Acanthopagrus latus: A combined analysis of transcriptomics and metabolomics","authors":"Weiqing Huang , Fengfang Zhou , Zongqiang Lian , Zhideng Lin , Zipeng Zhang","doi":"10.1016/j.cbd.2025.101701","DOIUrl":"10.1016/j.cbd.2025.101701","url":null,"abstract":"<div><div>Saline-alkaline stress poses a significant environmental challenge to fish in aquaculture, yet the molecular mechanisms underlying adaptation remain poorly understood. In this study, we integrated transcriptomic, metabolomic, physiological, and histological analyses to elucidate the adaptive mechanisms of <em>Acanthopagrus latus</em> gills under saline-alkaline water (SAW) exposure. After 40 days of treatment, SAW caused evident histological alterations in gill structures but did not significantly affect growth performance. Physiological assays showed that glutathione peroxidase (GSH-Px), acid phosphatase (ACP) and alkaline phosphatase (ALP) activities showed no significant change, while malondialdehyde (MDA) levels increased, indicating oxidative stress and metabolic disturbance.</div><div>Transcriptomic analysis identified 2539 differentially expressed genes (DEGs), mainly enriched in immune-related pathways such as T-cell receptor signaling, Th17 cell differentiation, and IL-17 signaling. Metabolomic profiling detected 892 differentially expressed metabolites (DEMs), primarily involved in energy metabolism pathways, including arachidonic acid, α-linolenic acid, and linoleic acid metabolism. Integrated multi-omics analysis further revealed a significant co-enrichment in platelet activation, phospholipase D signaling, and glutathione metabolism pathways. Notably, 29 DEGs and 4 key metabolites (ATP, prostaglandin H₂, cyclic AMP, and ADP) were significantly altered in the platelet activation pathway. Among them, upregulated genes such as <em>p2ry12</em>, <em>LOC119021196</em>, and <em>LOC119027230</em> were linked to energy metabolism, while <em>lyn</em>, <em>fynb</em>, <em>pik3r1</em>, <em>pik3cd</em>, and <em>akt1</em> were associated with apoptosis and immune regulation.</div><div>Overall, this study provides comprehensive molecular and physiological evidence of how <em>A. latus</em> adapts to saline-alkaline stress through coordinated immune regulation and energy metabolism. These findings enhance our understanding of fish adaptive mechanisms and offer theoretical support for the sustainable utilization of saline-alkaline water resources in aquaculture.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"58 ","pages":"Article 101701"},"PeriodicalIF":2.2,"publicationDate":"2026-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145776697","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: 2025-12-29DOI: 10.1016/j.cbd.2025.101737
Bowen Yan , Zhaoshou Ran , Qiang Zhou , Jiaxin Zhu , Fei Kong , Jilin Xu
Docosahexaenoic acid (DHA), an essential omega-3 long-chain polyunsaturated fatty acid, is crucial for the development of marine mollusks. Despite its importance, the molecular mechanisms of DHA action in these organisms are poorly understood, primarily due to the lack of reliable in vitro models. This study utilizes the razor clam Sinonovacula constricta as a model organism, establishing a primary adherent cell culture from various tissues, with mantle tissue identified as the optimal source for its rapid migration and low contamination risk. Cells incubated with varying concentrations of DHA (0–400 μM) for 6 h exhibited a concentration-dependent accumulation of lipid droplets (LDs), highlighting the model's suitability for investigating lipid metabolism. Transcriptomic analysis of cells treated with 50 μM DHA identified 848 differentially expressed genes (DEGs), with 747 upregulated and 101 downregulated, indicating the complex effects of DHA. The top 20 significantly upregulated and downregulated DEGs revealed significant involvement in cell signaling transduction, extracellular matrix organization, and substance transport and metabolism. Particularly, lipid metabolism genes, including perilipin 2 and abhydrolase domain containing 2, as well as pathways such as the PPAR signaling pathway and sphingolipid metabolism, were significantly altered, suggesting a reprograming of fatty acid metabolism contributing to LD accumulation. Additionally, pathways related to immune response were notably affected, potentially enhancing cellular health. Collectively, this study provides the first comprehensive insights into the molecular mechanisms underlying DHA-induced LD accumulation in a marine mollusk model at the cellular level, laying a foundation for developing precise nutritional strategies involving DHA in S. constricta aquaculture.
{"title":"Transcriptional responses to DHA-induced lipid droplet accumulation in primary adherent mantle cells of Sinonovacula constricta (Lamarck, 1818)","authors":"Bowen Yan , Zhaoshou Ran , Qiang Zhou , Jiaxin Zhu , Fei Kong , Jilin Xu","doi":"10.1016/j.cbd.2025.101737","DOIUrl":"10.1016/j.cbd.2025.101737","url":null,"abstract":"<div><div>Docosahexaenoic acid (DHA), an essential omega-3 long-chain polyunsaturated fatty acid, is crucial for the development of marine mollusks. Despite its importance, the molecular mechanisms of DHA action in these organisms are poorly understood, primarily due to the lack of reliable <em>in vitro</em> models. This study utilizes the razor clam <em>Sinonovacula constricta</em> as a model organism, establishing a primary adherent cell culture from various tissues, with mantle tissue identified as the optimal source for its rapid migration and low contamination risk. Cells incubated with varying concentrations of DHA (0–400 μM) for 6 h exhibited a concentration-dependent accumulation of lipid droplets (LDs), highlighting the model's suitability for investigating lipid metabolism. Transcriptomic analysis of cells treated with 50 μM DHA identified 848 differentially expressed genes (DEGs), with 747 upregulated and 101 downregulated, indicating the complex effects of DHA. The top 20 significantly upregulated and downregulated DEGs revealed significant involvement in cell signaling transduction, extracellular matrix organization, and substance transport and metabolism. Particularly, lipid metabolism genes, including perilipin 2 and abhydrolase domain containing 2, as well as pathways such as the PPAR signaling pathway and sphingolipid metabolism, were significantly altered, suggesting a reprograming of fatty acid metabolism contributing to LD accumulation. Additionally, pathways related to immune response were notably affected, potentially enhancing cellular health. Collectively, this study provides the first comprehensive insights into the molecular mechanisms underlying DHA-induced LD accumulation in a marine mollusk model at the cellular level, laying a foundation for developing precise nutritional strategies involving DHA in <em>S. constricta</em> aquaculture.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"58 ","pages":"Article 101737"},"PeriodicalIF":2.2,"publicationDate":"2026-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145879667","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: 2025-12-25DOI: 10.1016/j.cbd.2025.101735
Ruiming Ren , Xingxing Hu , Shouwen Jiang , Jiulin Chan , Yan Zhou , Wanying Zhai , Qianghua Xu
Hypoxia is a critical environmental stressor that differentially impacts aquatic species. To investigate interspecific variations in hypoxia tolerance, we compared zebrafish (Danio rerio) and tilapia (Oreochromis niloticus) exposed to progressively decreasing oxygen levels. Behavioral observations revealed that zebrafish exhibited aquatic surface respiration and rapid mortality at 0.7 mg/L dissolved oxygen (DO), whereas tilapia maintained bottom-oriented swimming and higher survival, indicating stronger hypoxia tolerance. Transcriptomic analyses of zebrafish identified heart- and liver-specific gene modules strongly associated with acute hypoxia, with functional enrichment pointing to impaired cell proliferation, heme biosynthesis, and energy metabolism. TUNEL assays further confirmed severe apoptosis in zebrafish liver, underscoring its vulnerability to hypoxic damage. Comparative transcriptomics revealed divergent regulation of ribosome-related pathways: tilapia suppressed ribosomal gene expression and enhanced translation initiation factor activity, while zebrafish maintained protein biosynthesis, potentially exacerbating energy deficits. Metabolic assays showed increased hepatic phosphofructokinase (PFK) activity in zebrafish, suggesting reliance on glycolysis, whereas tilapia exhibited consistently higher basal PFK activity and reduced oxygen consumption under hypoxia, indicating metabolic suppression as an adaptive strategy. Antioxidant analysis revealed a significant decline in superoxide dismutase (SOD) activity in zebrafish but not tilapia, further reflecting species-specific oxidative stress responses. Together, these findings demonstrate that zebrafish and tilapia employ distinct hypoxia-coping strategies, with tilapia favoring metabolic suppression and oxidative stability, while zebrafish rely on glycolysis but suffer greater oxidative and apoptotic damage under acute hypoxia. These findings also provide new insights into divergent hypoxia adaptation strategies among teleosts.
{"title":"Divergent mechanisms of hypoxia tolerance in zebrafish (Danio rerio) and Nile tilapia (Oreochromis niloticus)","authors":"Ruiming Ren , Xingxing Hu , Shouwen Jiang , Jiulin Chan , Yan Zhou , Wanying Zhai , Qianghua Xu","doi":"10.1016/j.cbd.2025.101735","DOIUrl":"10.1016/j.cbd.2025.101735","url":null,"abstract":"<div><div>Hypoxia is a critical environmental stressor that differentially impacts aquatic species. To investigate interspecific variations in hypoxia tolerance, we compared zebrafish (<em>Danio rerio</em>) and tilapia (<em>Oreochromis niloticus</em>) exposed to progressively decreasing oxygen levels. Behavioral observations revealed that zebrafish exhibited aquatic surface respiration and rapid mortality at 0.7 mg/L dissolved oxygen (DO), whereas tilapia maintained bottom-oriented swimming and higher survival, indicating stronger hypoxia tolerance. Transcriptomic analyses of zebrafish identified heart- and liver-specific gene modules strongly associated with acute hypoxia, with functional enrichment pointing to impaired cell proliferation, heme biosynthesis, and energy metabolism. TUNEL assays further confirmed severe apoptosis in zebrafish liver, underscoring its vulnerability to hypoxic damage. Comparative transcriptomics revealed divergent regulation of ribosome-related pathways: tilapia suppressed ribosomal gene expression and enhanced translation initiation factor activity, while zebrafish maintained protein biosynthesis, potentially exacerbating energy deficits. Metabolic assays showed increased hepatic phosphofructokinase (PFK) activity in zebrafish, suggesting reliance on glycolysis, whereas tilapia exhibited consistently higher basal PFK activity and reduced oxygen consumption under hypoxia, indicating metabolic suppression as an adaptive strategy. Antioxidant analysis revealed a significant decline in superoxide dismutase (SOD) activity in zebrafish but not tilapia, further reflecting species-specific oxidative stress responses. Together, these findings demonstrate that zebrafish and tilapia employ distinct hypoxia-coping strategies, with tilapia favoring metabolic suppression and oxidative stability, while zebrafish rely on glycolysis but suffer greater oxidative and apoptotic damage under acute hypoxia. These findings also provide new insights into divergent hypoxia adaptation strategies among teleosts.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"58 ","pages":"Article 101735"},"PeriodicalIF":2.2,"publicationDate":"2026-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145840945","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: 2026-01-09DOI: 10.1016/j.cbd.2026.101746
An Xu , Zhenming Lü , Jing Liu , Tianwei Liu , Jing Yu , Yijing Yang , Kun Huang , Li Gong , Fenghui Li , Denghui Zhu , Hongling Ping , Huilai Shi , Liqin Liu
Sepiella japonica is a cephalopod of significant commercial value, commonly found throughout China's coastal waters, ranging from southern Hong Kong to the Korean Peninsula and western regions of Japan. However, under captive conditions, S. japonica frequently exhibits precocious sexual maturation, which can result in reduced adult body size and severely limit aquaculture development. Therefore, elucidating the molecular mechanisms on ovarian development has become a critical priority. In this study, RNA sequencing was performing of the ovary tissue of female S. japonica collected across four key ovarian developmental stages: oogonium production (stage I), protoplasmic growth (stage II), interstitial growth (stage III), and trophoplasmic growth (stage IV). A total of 354,393,214 clean reads (Q20>98.58%) were obtained from 16 samples. Pairwise comparative analyses of I vs II, II vs III, and III vs IV identified 10050, 2564, 2278 differentially expressed genes (DEGs), respectively. Through differential expression analysis, we identified 13,319 differentially expressed genes (DEGs), among of which exhibited consistently high expression across four developmental stages, such as FOXL2, HSD17B2, and BMP1, suggesting their critical roles in regulating ovarian development in S. japonica. Gene Ontology (GO) enrichment analysis showed that these DEGs were significantly enriched in processes including protein targeting to the ER, response to estradiol, oxidative phosphorylation, and female pregnancy. KEGG pathway analysis revealed that DEGs were significantly enriched in key functional pathways, such as Ribosome, Prolactin signaling, FOXO signaling, and Lysosome. Furthermore, the “response to estradiol” pathway was consistently enriched across multiple developmental stage comparisons, suggesting that genes associated with steroid-related signaling may play conserved roles during ovarian development in S. japonica. This study clarified the regulation of transcript expression and molecular mechanisms in the ovary of S. japonica at different ovarian development stages, thereby offering theoretical guidance for enhancing reproductive efficiency in mollusk aquaculture.
{"title":"Comparative transcriptomic analysis across ovarian developmental stages in Sepiella japonica provides novel insights into its molecular regulatory mechanisms","authors":"An Xu , Zhenming Lü , Jing Liu , Tianwei Liu , Jing Yu , Yijing Yang , Kun Huang , Li Gong , Fenghui Li , Denghui Zhu , Hongling Ping , Huilai Shi , Liqin Liu","doi":"10.1016/j.cbd.2026.101746","DOIUrl":"10.1016/j.cbd.2026.101746","url":null,"abstract":"<div><div><em>Sepiella japonica</em> is a cephalopod of significant commercial value, commonly found throughout China's coastal waters, ranging from southern Hong Kong to the Korean Peninsula and western regions of Japan. However, under captive conditions, <em>S. japonica</em> frequently exhibits precocious sexual maturation, which can result in reduced adult body size and severely limit aquaculture development. Therefore, elucidating the molecular mechanisms on ovarian development has become a critical priority. In this study, RNA sequencing was performing of the ovary tissue of female <em>S. japonica</em> collected across four key ovarian developmental stages: oogonium production (stage I), protoplasmic growth (stage II), interstitial growth (stage III), and trophoplasmic growth (stage IV). A total of 354,393,214 clean reads (Q20>98.58%) were obtained from 16 samples. Pairwise comparative analyses of I vs II, II vs III, and III vs IV identified 10050, 2564, 2278 differentially expressed genes (DEGs), respectively. Through differential expression analysis, we identified 13,319 differentially expressed genes (DEGs), among of which exhibited consistently high expression across four developmental stages, such as <em>FOXL2</em>, <em>HSD17B2</em>, and <em>BMP1</em>, suggesting their critical roles in regulating ovarian development in <em>S. japonica</em>. Gene Ontology (GO) enrichment analysis showed that these DEGs were significantly enriched in processes including protein targeting to the ER, response to estradiol, oxidative phosphorylation, and female pregnancy. KEGG pathway analysis revealed that DEGs were significantly enriched in key functional pathways, such as Ribosome, Prolactin signaling, FOXO signaling, and Lysosome. Furthermore, the “response to estradiol” pathway was consistently enriched across multiple developmental stage comparisons, suggesting that genes associated with steroid-related signaling may play conserved roles during ovarian development in <em>S. japonica</em>. This study clarified the regulation of transcript expression and molecular mechanisms in the ovary of <em>S. japonica</em> at different ovarian development stages, thereby offering theoretical guidance for enhancing reproductive efficiency in mollusk aquaculture.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"58 ","pages":"Article 101746"},"PeriodicalIF":2.2,"publicationDate":"2026-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145977218","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 initial detection of host-derived chemical cues is a key physiological event that strongly influences infection success in parasitic copepods such as Caligus fugu. Although ionotropic receptors were previously identified in C. fugu as potential host-sensing molecules, their ligands and specific roles in host recognition remain unknown. Since the infective copepodid I stage preferentially attaches to the fins of the puffer host, genes expressed at higher levels in fins may contribute to host recognition by C. fugu. In this study, differentially expressed genes between the pectoral fins and skin of Takifugu rubripes were comprehensively identified through RNA-seq to expand the list of candidate host-recognition genes beyond those detected earlier. To refine this list, genes expressed at higher levels in pectoral fins that were annotated with the gene ontology term “extracellular region” (Gene Ontology:0005576) were examined for predicted protein features, with emphasis on secreted, soluble molecules that the parasite could encounter in the surrounding water. From an initial set of 126 genes, intracellular and membrane-associated proteins were removed, and those possessing signal peptides or globular domains were retained. The remaining 92 proteins were considered likely secreted, water-soluble host-derived ligands. Relative qPCR analysis highlighted col10a1a, stc2a, mmp9, fibinb, bmp5, c4b, bmp6, and lipg as potential secreted cues for C. fugu. Antimicrobial peptides such as hamp and db1 were also identified as candidates. Overall, this study expands the pool of molecules that may function as chemoattractants for C. fugu and provides targets for future experimental validation.
{"title":"Identification of genes expressed in the pectoral fins and skin of Takifugu rubripes to reveal candidate genes involved in host recognition by the crustacean ectoparasite Caligus fugu","authors":"K.M. Shakil Rana , Ryohei Matsunaga , Yoshiki Sato , Hiroaki Suetake , Kiyoshi Kikuchi , Susumu Ohtsuka , Tomonari Kotani , Satoshi Tasumi","doi":"10.1016/j.cbd.2025.101731","DOIUrl":"10.1016/j.cbd.2025.101731","url":null,"abstract":"<div><div>The initial detection of host-derived chemical cues is a key physiological event that strongly influences infection success in parasitic copepods such as <em>Caligus fugu</em>. Although ionotropic receptors were previously identified in <em>C. fugu</em> as potential host-sensing molecules, their ligands and specific roles in host recognition remain unknown. Since the infective copepodid I stage preferentially attaches to the fins of the puffer host, genes expressed at higher levels in fins may contribute to host recognition by <em>C. fugu</em>. In this study, differentially expressed genes between the pectoral fins and skin of <em>Takifugu rubripes</em> were comprehensively identified through RNA-seq to expand the list of candidate host-recognition genes beyond those detected earlier. To refine this list, genes expressed at higher levels in pectoral fins that were annotated with the gene ontology term “extracellular region” (Gene Ontology:0005576) were examined for predicted protein features, with emphasis on secreted, soluble molecules that the parasite could encounter in the surrounding water. From an initial set of 126 genes, intracellular and membrane-associated proteins were removed, and those possessing signal peptides or globular domains were retained. The remaining 92 proteins were considered likely secreted, water-soluble host-derived ligands. Relative qPCR analysis highlighted <em>col10a1a</em>, <em>stc2a</em>, <em>mmp9</em>, <em>fibinb</em>, <em>bmp5</em>, <em>c4b</em>, <em>bmp6</em>, and <em>lipg</em> as potential secreted cues for <em>C. fugu</em>. Antimicrobial peptides such as <em>hamp</em> and <em>db1</em> were also identified as candidates. Overall, this study expands the pool of molecules that may function as chemoattractants for <em>C. fugu</em> and provides targets for future experimental validation.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"58 ","pages":"Article 101731"},"PeriodicalIF":2.2,"publicationDate":"2026-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145822337","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.2026.101756
Yufei Liu , Zonglin Yang , Min Zhang , Xiaowu Chen , Xiaodong Jiang
The Chinese mitten crab (Eriocheir sinensis) is a commercially important aquaculture species in China, with its survival highly vulnerable to abnormal water pH. This study subjected E. sinensis to chronic high-pH stress (control: pH = 8; experimental groups: pH = 9 and pH = 10) and integrated hepatopancreas transcriptomic/metabolomic analyses with intestinal microbiota 16S rRNA sequencing to explore its adaptive mechanisms. The results revealed distinct adaptive strategies across stress phases: under short-term (15 days) high-pH stress, E. sinensis maintained somatic homeostasis mainly via rapid regulation of carbohydrate, lipid, protein metabolism, and energy allocation. In contrast, long-term (30 days) stress drove a strategic shift toward accelerated lipid catabolism, enhanced energy metabolism, and activated immune-related pathways. Additionally, high-pH stress significantly altered the intestinal microbiota community structure, marked by increased abundances of Proteobacteria and Pseudomonas, indicating a potential risk of microbial dysbiosis. Collectively, these findings elucidate the physiological adaptation mechanisms of E. sinensis to high-pH environments and lay a theoretical foundation for improving the sustainability of its aquaculture under extreme pH conditions.
{"title":"Response mechanisms of hepatopancreatic metabolism and gut microbiota in Chinese mitten crab (Eriocheir sinensis) under chronic high-pH stress","authors":"Yufei Liu , Zonglin Yang , Min Zhang , Xiaowu Chen , Xiaodong Jiang","doi":"10.1016/j.cbd.2026.101756","DOIUrl":"10.1016/j.cbd.2026.101756","url":null,"abstract":"<div><div>The Chinese mitten crab (<em>Eriocheir sinensis</em>) is a commercially important aquaculture species in China, with its survival highly vulnerable to abnormal water pH. This study subjected <em>E. sinensis</em> to chronic high-pH stress (control: pH = 8; experimental groups: pH = 9 and pH = 10) and integrated hepatopancreas transcriptomic/metabolomic analyses with intestinal microbiota 16S rRNA sequencing to explore its adaptive mechanisms. The results revealed distinct adaptive strategies across stress phases: under short-term (15 days) high-pH stress, <em>E. sinensis</em> maintained somatic homeostasis mainly via rapid regulation of carbohydrate, lipid, protein metabolism, and energy allocation. In contrast, long-term (30 days) stress drove a strategic shift toward accelerated lipid catabolism, enhanced energy metabolism, and activated immune-related pathways. Additionally, high-pH stress significantly altered the intestinal microbiota community structure, marked by increased abundances of Proteobacteria and Pseudomonas, indicating a potential risk of microbial dysbiosis. Collectively, these findings elucidate the physiological adaptation mechanisms of <em>E. sinensis</em> to high-pH environments and lay a theoretical foundation for improving the sustainability of its aquaculture under extreme pH conditions.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"58 ","pages":"Article 101756"},"PeriodicalIF":2.2,"publicationDate":"2026-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146022553","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: 2026-01-21DOI: 10.1016/j.cbd.2026.101759
Zhi Yang , Wei Zhang , Wenyuan Lai
Transient receptor potential (TRP) ion channels play crucial roles in mediating responses to environmental stimuli. In this study, we identified 64 TRP genes from 6 subfamilies in the Urechis unicinctus genome and characterized their genomic locations, gene structures, and basic physicochemical properties. We also analyzed their expression across various developmental stages, tissues, and environmental conditions. The results revealed that TRP gene expression varied throughout development and exhibited distinct tissue-specific patterns. Notably, we identified 20 TRP genes as putative transcriptional memory genes following sulfide stress and another 7 as temperature-sensitive. We also found that both short-term drought and ultraviolet radiation affected the expression of TRP genes in U. unicinctus. Our pharmacological experiments suggested that TRPC5 is positively involved in the immune response of U. unicinctus. Furthermore, TRPC5-mediated immunoenhancement correlated with increased weight gain and a higher visceral index. Collectively, our findings provide a valuable foundation for future research into the functional roles of TRP channels in U. unicinctus.
{"title":"Identification and expression of transient receptor potential (TRP) genes in Urechis unicinctus and the role of TRPC5 in immune response","authors":"Zhi Yang , Wei Zhang , Wenyuan Lai","doi":"10.1016/j.cbd.2026.101759","DOIUrl":"10.1016/j.cbd.2026.101759","url":null,"abstract":"<div><div>Transient receptor potential (TRP) ion channels play crucial roles in mediating responses to environmental stimuli. In this study, we identified 64 TRP genes from 6 subfamilies in the <em>Urechis unicinctus</em> genome and characterized their genomic locations, gene structures, and basic physicochemical properties. We also analyzed their expression across various developmental stages, tissues, and environmental conditions. The results revealed that TRP gene expression varied throughout development and exhibited distinct tissue-specific patterns. Notably, we identified 20 TRP genes as putative transcriptional memory genes following sulfide stress and another 7 as temperature-sensitive. We also found that both short-term drought and ultraviolet radiation affected the expression of TRP genes in <em>U. unicinctus</em>. Our pharmacological experiments suggested that TRPC5 is positively involved in the immune response of <em>U. unicinctus</em>. Furthermore, TRPC5-mediated immunoenhancement correlated with increased weight gain and a higher visceral index. Collectively, our findings provide a valuable foundation for future research into the functional roles of TRP channels in <em>U. unicinctus</em>.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"58 ","pages":"Article 101759"},"PeriodicalIF":2.2,"publicationDate":"2026-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146022426","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: 2025-12-20DOI: 10.1016/j.cbd.2025.101733
Peng Huang , Yu Yao , Jiancao Gao , Jinliang Du , Haojun Zhu , Dezhi Chen , Wenyong Chen , Gangchun Xu
This study systematically analyzed the molecular expression patterns across the zoeal stages (ZI to ZV) of the Chinese mitten crab (Eriocheir sinensis) using comparative transcriptomics. It focused on core biological processes, including metabolism, organelle structure, and signal transduction, to reveal the molecular mechanisms underlying the crab's early development. Based on trend analysis, the differentially expressed genes (DEGs) profile of the ZI stage was significantly distinct from that of the other four developmental stages. Genes enriched and highly expressed in ZI were primarily associated with transmembrane signaling and calcium signaling pathways, which support the transition of early larvae from embryonic development to a free-living life. Meanwhile, enzyme activity analysis indicated that ZI activated the body's antioxidant defense system and nonspecific immune capacity. In the ZII-ZIII stages, DEGs were mainly related to endoplasmic reticulum (ER) structural components and pathways (e.g., ER protein processing and proteasome), suggesting the activation of ER-associated degradation to maintain protein homeostasis during morphological and dietary transitions. In the ZIV-ZV stages, DEGs were predominantly enriched in metabolic pathways (e.g., organic acid metabolism, tyrosine metabolism) and peroxisome/lysosome pathways, which enhance energy supply, exoskeleton sclerotization, immunity, and cell remodeling to facilitate megalopa metamorphosis. Overall, this study sheds new light on the molecular mechanisms underlying zoeal development in E. sinensis and provides theoretical support for aquaculture practices.
{"title":"A comparative transcriptomics reveals stage-specific molecular mechanisms during early zoeal development in the Chinese mitten crab, Eriocheir sinensis","authors":"Peng Huang , Yu Yao , Jiancao Gao , Jinliang Du , Haojun Zhu , Dezhi Chen , Wenyong Chen , Gangchun Xu","doi":"10.1016/j.cbd.2025.101733","DOIUrl":"10.1016/j.cbd.2025.101733","url":null,"abstract":"<div><div>This study systematically analyzed the molecular expression patterns across the zoeal stages (ZI to ZV) of the Chinese mitten crab (<em>Eriocheir sinensis</em>) using comparative transcriptomics. It focused on core biological processes, including metabolism, organelle structure, and signal transduction, to reveal the molecular mechanisms underlying the crab's early development. Based on trend analysis, the differentially expressed genes (DEGs) profile of the ZI stage was significantly distinct from that of the other four developmental stages. Genes enriched and highly expressed in ZI were primarily associated with transmembrane signaling and calcium signaling pathways, which support the transition of early larvae from embryonic development to a free-living life. Meanwhile, enzyme activity analysis indicated that ZI activated the body's antioxidant defense system and nonspecific immune capacity. In the ZII-ZIII stages, DEGs were mainly related to endoplasmic reticulum (ER) structural components and pathways (e.g., ER protein processing and proteasome), suggesting the activation of ER-associated degradation to maintain protein homeostasis during morphological and dietary transitions. In the ZIV-ZV stages, DEGs were predominantly enriched in metabolic pathways (e.g., organic acid metabolism, tyrosine metabolism) and peroxisome/lysosome pathways, which enhance energy supply, exoskeleton sclerotization, immunity, and cell remodeling to facilitate megalopa metamorphosis. Overall, this study sheds new light on the molecular mechanisms underlying zoeal development in <em>E. sinensis</em> and provides theoretical support for aquaculture practices.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"58 ","pages":"Article 101733"},"PeriodicalIF":2.2,"publicationDate":"2026-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145884356","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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