Comp. Biochem. Physiol. Part D Genomics Proteomics [JOURNAL]
Sun
200 papers
Integrated transcriptomic and co-expression analyses reveal hypoxia-responsive patterns in the gills of Mytilus coruscus.
Zhao R, Li J, Li H … +2 more , Ye Y, Li J
Comp Biochem Physiol Part D Genomics Proteomics · 2026 Sep · PMID 42114497 · Publisher ↗
Hypoxia is a significant environmental stressor that negatively affects the growth, survival, and overall health of marine bivalves. This study aimed to investigate the physiological and molecular responses of Mytilus co...
Hypoxia is a significant environmental stressor that negatively affects the growth, survival, and overall health of marine bivalves. This study aimed to investigate the physiological and molecular responses of Mytilus coruscus (thick-shell mussel) to hypoxic stress by integrating histological analysis, enzyme activity assays, whole-transcriptome sequencing, and Weighted Gene Co-expression Network Analysis (WGCNA) of gill tissues. The results revealed marked structural damage to gill filaments under prolonged hypoxia, including epithelial swelling, exfoliation, and lamellar fusion. Enzyme activities, including acid phosphatase (ACP), alkaline phosphatase (AKP), superoxide dismutase (SOD), catalase (CAT), and glutathione peroxidase (GSH-Px), exhibited distinct temporal fluctuations, with an initial decrease followed by partial recovery at later time points. WGCNA identified four gene co-expression modules associated with hypoxia exposure, and these modules were enriched in pathways related to metabolic regulation, stress response, and antioxidant defense. Transcriptome sequencing identified 56 differentially expressed miRNAs, 1393 mRNAs, 392 lncRNAs, and 21 circRNAs, and RT-qPCR validation confirmed the consistency of the expression trends of selected mRNAs. Functional enrichment analysis indicated that hypoxia-responsive coding and non-coding transcripts were associated with signaling pathways involved in stress response, energy metabolism, and antioxidant defense. Together, these findings support a transcriptome-based working model in which FOXO and HIF-1-related pathways may participate in hypoxia-associated metabolic and antioxidant adjustment in M. coruscus. These results provide candidate targets for future functional validation and may offer a basis for aquaculture management strategies aimed at improving stress resilience.
Role of Activin A in regulating ovarian development during vitellogenesis in Japanese eel (Anguilla japonica).
Zuo C, Zhang Y, Ci Y … +4 more , Zhang X, Jing X, Zhao Z, Qi X
Comp Biochem Physiol Part D Genomics Proteomics · 2026 Sep · PMID 42114496 · Publisher ↗
Activin A, a member of the TGF-β superfamily, plays pivotal roles in vertebrate reproductive regulation. This research investigated the biological functions and potential regulatory mechanisms of Activin A during vitello...
Activin A, a member of the TGF-β superfamily, plays pivotal roles in vertebrate reproductive regulation. This research investigated the biological functions and potential regulatory mechanisms of Activin A during vitellogenesis in Japanese eel. Analysis of the structural characteristics and evolutionary relationships confirmed that Japanese eel Activin A is highly conserved, providing a molecular basis for elucidating its role in ovarian development. Using a prokaryotic expression system, recombinant Japanese eel Activin A protein was successfully produced, and a series of in vitro functional assays were subsequently conducted. Results demonstrated that Activin A significantly promoted vitellogenin uptake by oocytes and enhanced the efficiency of gonadotropin-mediated downstream signaling by upregulating receptor expression during vitellogenesis. Transcriptomic analysis of ovarian cells revealed that Activin A is involved in multiple physiological processes closely associated with ovarian development, including substance transport, energy metabolism, steroid receptor activity, and key reproductive signaling pathways. These findings indicate that Activin A orchestrates ovarian development during vitellogenesis in Japanese eel.
Histological and transcriptomic analysis of the white hepatopancreas in Amphioctopus fangsiao.
Huang Z, Liu J, Chen M … +8 more , Li R, Wang W, Sun G, Xu X, Li Z, Li B, Feng Y, Yang J
Comp Biochem Physiol Part D Genomics Proteomics · 2026 Sep · PMID 42114495 · Publisher ↗
Ink production and release is one of the most important defense strategies in cephalopods. Previous studies have shown that ink production and release are closely associated with the hepatopancreas. In octopuses, the ink...
Ink production and release is one of the most important defense strategies in cephalopods. Previous studies have shown that ink production and release are closely associated with the hepatopancreas. In octopuses, the ink sac is embedded within the hepatopancreas, and the surrounding hepatopancreatic tissue appears white. To explore the differences between the white hepatopancreas and normal hepatopancreas, as well as the potential function of the white hepatopancreas, this study took Amphioctopus fangsiao as the research object and conducted histological and transcriptomic studies on white hepatopancreas and normal hepatopancreas tissues. Histological analysis revealed clear structural differences between the two tissues, with lipid droplets absent in the white hepatopancreas. Transcriptomic analysis identified 6530 differentially expressed genes (DEGs). Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and protein-protein interaction (PPI) analyses found that oxidative phosphorylation and the Apelin signaling pathways were significantly enriched in white hepatopancreas, suggesting an increase in ATP production and the alleviation of oxidative stress. Members of the ABHD gene family enriched may regulate lipid droplet metabolism. TAT, SLC6A6, Dop1R1 and Dop2R could potentially influence the levels of tyrosine, taurine and dopamine in the white hepatopancreas. Considering that these substances are involved in the main components of ink, we speculate that these genes may be related to the precursor supply for ink production. Our study demonstrates that the white hepatopancreas is structurally distinct from the normal hepatopancreas, and may be functionally related to the ink sac to some extent.
Transcriptome profiling to decipher molecular mechanisms of diapause in Chilo partellus (Swinhoe) (Lepidoptera: Crambidae).
Dhillon MK, Singh SK, Jaiswal S … +5 more , Tanwar AK, Ashok K, Ramaiah M, Asif Iquebal M, Kumar D
Comp Biochem Physiol Part D Genomics Proteomics · 2026 Sep · PMID 42114494 · Publisher ↗
Diapause is a critical adaptive strategy in insects to survive unfavourable environmental conditions. The present study investigated molecular mechanisms underlying diapause in Chilo partellus, using high-throughput RNA...
Diapause is a critical adaptive strategy in insects to survive unfavourable environmental conditions. The present study investigated molecular mechanisms underlying diapause in Chilo partellus, using high-throughput RNA sequencing and de novo transcriptome assembly. Six transcriptome libraries from diapause and non-diapause larvae yielded over 50 million reads per sample, with >98% mapping efficiency. The Evidential Gene-refined assembly produced 67,116 high-quality transcripts, and BUSCO analysis confirmed its completeness. DEG analysis identified 1204 DEGs, including 660 upregulated and 544 downregulated in diapause larvae. GO enrichment revealed significant activation of stress response pathways, including heat shock proteins, protein folding, and redox homeostasis. Hormone-related genes such as juvenile hormone epoxide hydrolase and juvenile hormone esterase-like transcripts that are associated primarily with hormone degradation or early steps of ecdysteroidogenesis rather than direct synthesis of active ecdysteroids, were upregulated, suggesting endocrine regulation of diapause. Conversely, downregulation of insulin-like peptides, mitochondrial respiratory genes, and ribosomal proteins reflected suppressed metabolic and translational activity, hallmarks of diapause. PCA and hierarchical clustering confirmed clear transcriptional separation between diapause and non-diapause stages. Ten representative DEGs were validated using qRT-PCR, demonstrating strong concordance with RNA-seq. Notably, upregulated genes included Hsp70-like proteins, cytochrome P450s, and cuticle proteins, while insulin signaling and oxidative phosphorylation were downregulated. This study provides a comprehensive molecular framework for diapause in C. partellus, highlighting stress tolerance, metabolic suppression, and hormonal control as key regulatory themes. The identified genes offer potential targets for disrupting diapause, contributing to improved pest management strategies against this economically important insect.
Stage-resolved transcriptomic analysis of GPCR expression during settlement and metamorphosis in the sea urchin Heliocidaris crassispina.
Jia J, Ge L, Ding K … +5 more , Yang J, Wang J, Weng J, Yang J, Wang T
Comp Biochem Physiol Part D Genomics Proteomics · 2026 Sep · PMID 42105464 · Publisher ↗
Larval settlement and metamorphosis are critical developmental transitions in sea urchins and represent a major bottleneck in aquaculture. Here, we used stage-resolved transcriptome sequencing to characterize genome-wide...
Larval settlement and metamorphosis are critical developmental transitions in sea urchins and represent a major bottleneck in aquaculture. Here, we used stage-resolved transcriptome sequencing to characterize genome-wide gene expression dynamics during settlement and metamorphosis in the purple sea urchin Heliocidaris crassispina, with a particular focus on G protein-coupled receptors (GPCRs). Based on a refined chromosome-level genome annotation, 763 GPCR candidate genes were identified and their expression patterns were systematically examined across six-arm larvae, eight-arm competent larvae, and early juveniles. Transcriptomic analyses revealed pronounced stage-dependent remodeling, with the competent larval stage showing a marked expansion of expressed GPCRs. Time-series clustering identified two major GPCR expression patterns: one associated with the competence stage and characterized by transient or peak-shaped upregulation, and another that became more prominent after settlement and remained highly expressed in early juveniles. PPI network analysis further suggested that these temporal patterns were associated with coordinated network organization rather than isolated receptor-level changes. Representative GPCR expression patterns were independently validated by qRT-PCR. These results provide a stage-resolved transcriptomic framework for understanding GPCR expression dynamics during sea urchin settlement and metamorphosis and offer a basis for future functional studies in echinoderms.
Exploring peptidases from the milkweed bug Spilostethus pandurus (Hemiptera: Lygaeidae) by proteomics, transcriptomics and gene expression analysis for the hydrolysis of food proteins.
Albuquerque W, Ghezellou P, Sharweda M … +7 more , Li B, Maheshwari G, Rühl M, Spengler B, Vilcinskas A, Zorn H, Gand M
Comp Biochem Physiol Part D Genomics Proteomics · 2026 Sep · PMID 42105463 · Publisher ↗
The evolutionary success of insects in terms of biodiversity is promoted by their ability to adapt to a wide variety of feeding habits. As a polyphagous pest, the milkweed bug Spilostethus pandurus (Hemiptera: Lygaeidae)...
The evolutionary success of insects in terms of biodiversity is promoted by their ability to adapt to a wide variety of feeding habits. As a polyphagous pest, the milkweed bug Spilostethus pandurus (Hemiptera: Lygaeidae) feeds on various seeds and plants, using a rich portfolio of peptidases for nutrition acquisition. However, there is only sparse knowledge about its proteolytic system. In the present study, peptidases from S. pandurus were purified using chromatographic techniques, putatively identified using mass spectrometry-based proteomics, comparative transcriptome analyses and gene amplification via polymerase chain reaction. Their complete sequences, catalytic functions, and physiological roles were further predicted based on bioinformatic tools and literature review, while their applicability for the hydrolysis of food proteins has been demonstrated. Understanding the proteolytic profile of S. pandurus could offer valuable insights into its interactions with the environment and host plants. Furthermore, these findings could contribute in the future to pest management strategies, plant protection efforts and the application of insect-derived enzymes as essential part of yellow biotechnology applications.
Genome-wide association study reveals molecular markers and genetic basis associated with hypoxia tolerance in darkbarbel catfish (Pelteobagrus vachelli).
Wu CS, Jin JL, Zhang J … +4 more , Yue HM, Ye H, Li CJ, Ruan R
Comp Biochem Physiol Part D Genomics Proteomics · 2026 Sep · PMID 42105462 · Publisher ↗
Hypoxia poses a major threat to the aquaculture industry of darkbarbel catfish, resulting in substantial economic losses for fish farmers. The utilization of molecular markers linked to target traits can improve the effi...
Hypoxia poses a major threat to the aquaculture industry of darkbarbel catfish, resulting in substantial economic losses for fish farmers. The utilization of molecular markers linked to target traits can improve the efficiency and accuracy of traditional fish breeding. In this study, a genome-wide association study (GWAS) was performed based on whole-genome resequencing data to identify potential single-nucleotide polymorphisms (SNPs) and candidate genes associated with hypoxia tolerance in darkbarbel catfish. A total of 36 SNPs associated with hypoxia tolerance were detected, 17 of which were mapped to linkage group (LG) 25. Combined with Fst scanning analysis, a significantly associated genomic region was identified on LG25, spanning approximately 3.48 Mb from 13,159,434 bp to 16,642,858 bp. Within this region, 37 candidate genes were further annotated, seven of which are involved in the regulation of glycolipid metabolic homeostasis, including scap, klf10, azin1a, srsf10, cthrc1, ptdss1a, and fabp10a. These findings provide novel insights into the genetic basis of hypoxia tolerance in fish and are expected to facilitate the genetic selection and breeding of hypoxia-tolerant in darkbarbel catfish.
Pathogen-specific immune modulation in Nile tilapia: A comparative transcriptomic study of infections by Nocardia asteroides and Providencia vermicola.
Rajme-Manzur D, Olivas-Bernal CA, de Jesús-Campos D … +7 more , Hernández-Oñate MÁ, Martínez-Porchas M, Garibay-Valdez E, Vargas-Albores F, Hernández-López J, Martínez-Córdova LR, Méndez-Martínez Y
Comp Biochem Physiol Part D Genomics Proteomics · 2026 Sep · PMID 42105461 · Publisher ↗
Bacterial diseases have a significant impact on the Nile tilapia (Oreochromis niloticus) industry in Mexico. Understanding the mechanisms of host-pathogen interactions enables the design of effective control and diagnost...
Bacterial diseases have a significant impact on the Nile tilapia (Oreochromis niloticus) industry in Mexico. Understanding the mechanisms of host-pathogen interactions enables the design of effective control and diagnostic strategies to reduce losses during cultivation. This work aimed to analyze the transcriptome of Nile tilapia infected with emerging bacterial pathogens. Three experimental groups were established: two infected with Nocardia asteroides or Providencia vermicola, and a healthy control (non-infected group). Results showed that both infections caused mortality and signs of disease, most notably the group infected with N. asteroides registering the highest mortality rate. The transcriptomic analysis revealed that both N. asteroides and P. vermicola modulated pathways related to amino acid metabolism, cell adhesion molecule expression, innate immune response, antigen processing and presentation, and neuropeptide signaling. Remarkably, N. asteroides infection significantly modulated immune pathways involved in cytokine signaling, phagocytosis, and complement activation. Comparative analysis revealed that N. asteroides downregulates cell-mediated adaptive immunity and upregulates cytokines associated with the anti-inflammatory response, as well as cell proliferation and differentiation. Meanwhile, P. vermicola induced hormonal and neurotransmitter signaling pathways, including genes related to antimicrobial peptides and tumor necrosis factor receptors, while energy production-related metabolic pathways were downregulated.
Dual-omics links host genomic variation to gut microbiome restructuring under Mycobacterium marinum challenge in Cynoglossus semilaevis.
Ma C, Chang M, Zang S … +2 more , Shi K, Sha Z
Comp Biochem Physiol Part D Genomics Proteomics · 2026 Sep · PMID 42105460 · Publisher ↗
Disease outbreaks caused by Mycobacterium marinum pose a major challenge to marine aquaculture and threaten the sustainable production of Cynoglossus semilaevis. Increasing evidence suggests that host genetic variation a...
Disease outbreaks caused by Mycobacterium marinum pose a major challenge to marine aquaculture and threaten the sustainable production of Cynoglossus semilaevis. Increasing evidence suggests that host genetic variation and gut microbial communities may jointly influence disease-related phenotypes, yet their interaction under mycobacterial challenge remains poorly understood. In this study, we combined host whole-genome resequencing and gut 16S rRNA sequencing to explore host-microbiome associations in C. semilaevis following M. marinum challenge. Gut microbiota analysis revealed significant differences in community structure and composition between the experimental and control groups, with marked shifts in dominant taxa and differential enrichment of several bacterial genera. Genome-wide association analysis identified nine significant SNPs (λ = 1.02) associated with infection status, distributed across chromosomes 5, 10, 13, 18, and 19. Functional annotation showed that most of these loci were located in non-coding or regulatory regions, including six intronic SNPs, one ncRNA_exonic SNP, one ncRNA_intronic SNP, and one intergenic SNP. Correlation network analysis further linked host genetic variants with changes in gut microbial taxa, suggesting a potential association between host genomic variation and microbiome restructuring under challenge conditions. Overall, these results provide preliminary evidence that host genomic variation may be associated with gut microbiome dynamics during M. marinum infection in C. semilaevis. Although limited by sample size, this dual-omics framework offers a useful basis for future validation of host-microbiome markers relevant to disease-resilience breeding in aquaculture. CONCLUSION: Host genomic variation in C. semilaevis may be associated with gut microbiome restructuring under M. marinum challenge, particularly involving Acinetobacter dynamics. Although limited by sample size, this dual-omics framework provides a preliminary basis for future disease-resilience breeding in aquaculture.
Flow velocity regulates gonadal development via actin cytoskeleton and lipid metabolic pathways: A transcriptomic study in juvenile Acrossocheilus fasciatus (Steindachner, 1892).
Guo Y, Huang H, Murielle I … +3 more , Lu T, Chu Z, Zhao B
Comp Biochem Physiol Part D Genomics Proteomics · 2026 Sep · PMID 42102772 · Publisher ↗
Flow regimes strongly influence fish reproduction, yet how water velocity shapes gonadal development at the molecular level remains unclear. We examined juvenile Acrossocheilus fasciatus, a stream cyprinid, under static...
Flow regimes strongly influence fish reproduction, yet how water velocity shapes gonadal development at the molecular level remains unclear. We examined juvenile Acrossocheilus fasciatus, a stream cyprinid, under static (0 BL s) and high-flow (4 BL s) conditions for 30 days in a recirculating system. Growth and gonadosomatic indices showed upward trends in flow but no significant differences, and histology revealed comparable gonadal stages. In contrast, transcriptome analysis revealed pronounced sex-specific responses. In ovaries, differentially expressed genes were enriched in cytoskeletal remodeling, adhesion, and lipid metabolism, with activation of PPAR signaling and regulators such as e2f8, notably upregulation of fabp10a and fads2 indicating reinforced fatty acid transport and synthesis, suggesting enhanced oocyte provisioning. In testes, gene shifts indicated actin remodeling, fatty acid elongation, steroidogenesis, and spermatogonial stem cell regulation, with upregulation of zbtb16a, etv5b, and steroid receptors pgr and esr1, reflecting a pro-spermatogenic state. These findings show that sustained flow does not alter gonadal morphology in the short term but drives molecular reprogramming that may prime reproductive readiness. This work provides new insight into hydrodynamic regulation of fish reproduction.
Dietary soybean or seaweed (Kappaphycus sp.) modulates taste-related gene (tas1r1 and tas1r2.2) expression in Nile tilapia (Oreochromis niloticus).
Dos Anjo Viagem L, Hakizimana JN, da Silva Cerozi B … +2 more , Rumisha C, Misinzo G
Comp Biochem Physiol Part D Genomics Proteomics · 2026 Sep · PMID 42092395 · Publisher ↗
Taste perception plays a central role in fish feeding behaviour by influencing feed recognition, intake, and nutrient sensing. As aquaculture increasingly adopts plant-based ingredients to replace fishmeal, understanding...
Taste perception plays a central role in fish feeding behaviour by influencing feed recognition, intake, and nutrient sensing. As aquaculture increasingly adopts plant-based ingredients to replace fishmeal, understanding how these diets affect gustatory mechanisms is critical. This study evaluated TAS-family taste receptor genes in Nile tilapia (Oreochromis niloticus) fed nutritionally formulated diets containing fishmeal (TFM), soybean meal (TSB), red seaweed (Kappaphycus sp., TSW), alongside a natural meal (TNM) reference. Fish were reared for 62 days under controlled conditions, after which growth performance was evaluated, and tongue transcriptomes were analysed using RNA sequencing to identify diet-associated gene expression changes. Candidate TAS1R and TAS2R receptors were identified through conserved domain screening and phylogenetic validation, and differential expression analysis was performed using DESeq2. Growth performance did not differ significantly among diets, although the soybean group showed the highest weight gain. Under the conditions of this study, most taste-related genes remained transcriptionally stable across formulated diets, indicating limited responsiveness of the gustatory system to ingredient substitution. Transcriptional differences were mainly observed in comparisons involving the TNM (TSB vs TNM and TSW vs TNM), where tas1r1 was upregulated, suggesting altered amino acid sensing relative to the non-formulated diet. Among formulated diets, tas1r2.2 was upregulated in the TSW vs TFM comparison, indicating potential modulation of carbohydrate-related taste pathways associated with seaweed inclusion. No reliable TAS2R transcripts were detected, likely due to low expression or tissue-specific distribution. Overall, taste receptor expression in Nile tilapia appears resilient to dietary variation, with selective modulation of TAS1R genes providing molecular insight into chemosensory adaptation to sustainable feed ingredients.
Papillae growth and molecular responses of juvenile sea cucumbers (Apostichopus japonicus) exposed to different light intensities.
Li W, Liu Z, Deng Y … +7 more , Liu J, Yu J, Xiao H, Tian F, Han L, Zhao C, Ding J
Comp Biochem Physiol Part D Genomics Proteomics · 2026 Sep · PMID 42085802 · Publisher ↗
The present study investigated the effects of different intensities of blue light on papillae number growth and associated molecular mechanisms in the sea cucumber Apostichopus japonicus. The sea cucumber were exposed fo...
The present study investigated the effects of different intensities of blue light on papillae number growth and associated molecular mechanisms in the sea cucumber Apostichopus japonicus. The sea cucumber were exposed for 60 days under three blue light intensities (1500 lx, 3000 lx, and 4500 lx). Papillae numbers and body weight were measured regularly. Transcriptomic sequencing was performed to analyze gene expression differences in spine tissues. The results showed that the number of papillae was significantly highest in the sea cucumbers exposed to 1500 lx. Body weight growth was not significantly affected by any light intensity treatment. Compared with the control group, the 1500 lx group showed differentially expressed genes (DEGs) significantly enriched in pathways including the ras signaling pathway, ascorbate and aldarate metabolism, and fatty acid elongation. Seven key genes potentially related to the growth of papillae number were identified: Survivin, PHB2, SoxB, traf6, TRPML3, TGF-β1, and Rps13. In contrast, compared with the 1500 lx group, both the 3000 lx group and the 4500 lx group showed differentially expressed genes (DEGs) mainly enriched in pathways including axon regeneration, regulation of actin cytoskeleton, fc gamma R-mediated phagocytosis, and chemokine signaling. Six genes potentially inhibiting the growth of papillae number were identified: CRK, Smad4, Rac1, Arf6, ASAP2, and Wnt7. In conclusion, the light intensity of 1500 lx effectively increased the papillae number in A. japonicus. This study provides molecular evidence for enhancing papillae number in cultured sea cucumbers through light intensity regulation.
Gradual warming reshapes respiratory metabolism and metabolic responses in the clam Mactra veneriformis.
Shao XJ, Cui YW, Jia JF … +7 more , Liu WK, Wang JH, Zhong M, Jiang WL, Wang S, Huo ZM, Wang H
Comp Biochem Physiol Part D Genomics Proteomics · 2026 Sep · PMID 42068774 · Publisher ↗
Increasing frequency and intensity of marine heatwaves pose growing challenges to intertidal bivalves. This study investigated the effects of gradual temperature elevation on respiratory metabolism and associated physiol...
Increasing frequency and intensity of marine heatwaves pose growing challenges to intertidal bivalves. This study investigated the effects of gradual temperature elevation on respiratory metabolism and associated physiological responses in the clam Mactra veneriformis. Oxygen consumption rate (OCR), ammonia excretion rate (AER), gill histology, Na/K-ATPase activity, and metabolomic profiles were examined at 17-28 °C. OCR increased significantly with temperature (p < 0.05), suggesting elevated aerobic metabolic demand. In contrast, AER showed a unimodal pattern, increasing to a peak at 26 °C and declining at higher temperatures, possibly reflecting physiological constraints under thermal stress. O:N ratios remained above 7, indicating a mixed utilization of metabolic substrates with a greater contribution of lipids and carbohydrates. Gill structure remained intact at lower temperatures but exhibited looser architecture at 26-28 °C, suggesting structural adjustment. Na/K-ATPase activity increased progressively with temperature, indicating higher ion-transport demand. Metabolomic analysis identified 2426 metabolites, with differential metabolites mainly enriched in lipid-related pathways. Overall, gradual warming induced coordinated physiological and metabolic responses in Mactra veneriformis, providing an integrated perspective on its response to thermal stress.
Electrical stimulation-induced mucus secretion and skin transcriptome responses in Amur catfish (Silurus asotus).
Lu X, Long Y, He X … +1 more , Cui Z
Comp Biochem Physiol Part D Genomics Proteomics · 2026 Sep · PMID 42068773 · Publisher ↗
Fish skin mucus is a key defensive barrier, yet its secretion and regulation remain poorly characterized in Amur catfish (Silurus asotus). Here, controlled electrical stimulation significantly enhanced mucus secretion un...
Fish skin mucus is a key defensive barrier, yet its secretion and regulation remain poorly characterized in Amur catfish (Silurus asotus). Here, controlled electrical stimulation significantly enhanced mucus secretion under optimized parameters of 10 V and 15 cycles, resulting in a 3.59-fold increase in mucus-associated protein output and clear electrophoretic protein profiles. Histological and ultrastructural analyses showed a more disordered distribution of mucous cells, greater morphological heterogeneity, reduced mean mucous-cell area, and fewer intracellular granular inclusions in stimulated fish than in unstimulated controls. Serum glucose increased significantly at 6 h after stimulation but returned by 24 h to a level not significantly different from that of the control group, indicating a transient acute physiological response. Comparative transcriptomic analysis between the 10 V_15 cycles stimulated group and the 0 V_15 cycles control group identified 650 differentially expressed genes (DEGs), enriched mainly in polysaccharide metabolism, glycogen biosynthesis, and protein ubiquitination. KEGG enrichment further implicated MAPK signaling and endoplasmic reticulum (ER) protein-processing pathways as potentially involved in mucin biosynthesis, folding, and exocytosis. RT-qPCR validation of selected DEGs involved in immunity, metabolism, and cellular regulatory processes showed a strong concordance with the RNA-seq results. Together, these findings provide a novel insight into electrically stimulated mucus secretion in Amur catfish and support controlled electrical stimulation as a practical approach for mucus collection.
Genome-wide identification and transcriptomic reprogramming of the hsd17b gene family during endocrine-induced sex reversal in mandarin fish (Siniperca chuatsi).
Li W, Lin S, Chen W … +8 more , Deng Z, Cai G, Xie Z, Zhang Y, Yang H, Deng B, Li Q, Han C
Comp Biochem Physiol Part D Genomics Proteomics · 2026 Sep · PMID 42068772 · Publisher ↗
The 17β-hydroxysteroid dehydrogenase (hsd17b) gene family plays a pivotal role in sex steroid metabolism and gonadal differentiation in teleosts; however, their evolutionary dynamics and regulatory mechanisms during sex...
The 17β-hydroxysteroid dehydrogenase (hsd17b) gene family plays a pivotal role in sex steroid metabolism and gonadal differentiation in teleosts; however, their evolutionary dynamics and regulatory mechanisms during sex reversal in the mandarin fish (Siniperca chuatsi) remain poorly understood. In this study, we identified ten hsd17b family members in the S. chuatsi genome. Structural and phylogenetic analyses revealed the conservation of the core SDR domain across all members, alongside significant structural divergence in hsd17b4, which uniquely fused with SCP2 and PLN domains, indicating a pleiotropic role in both steroidogenesis and peroxisomal lipid metabolism. Spatiotemporal expression profiling demonstrated pronounced subfunctionalization: hsd17b4 exhibited robust testis-biased expression during spermatogenesis, whereas hsd17b1 was transiently upregulated during critical windows of ovarian differentiation. Furthermore, exogenous hormone treatments (MT, ETO, and E1) successfully induced functional sex reversal, accompanied by profound transcriptional reprogramming. Notably, ETO- and MT-induced masculinization was driven by a synergistic metabolic shift within the gonads. This process involved the significant up-regulation of the core testis-associated gene (hsd17b4), coordinated with genes facilitating cholesterol biosynthesis (hsd17b7) and estrogen inactivation (hsd17b8), effectively suppressing the female steroidogenic network (hsd17b1, hsd17b12a). Conversely, E1-induced feminization repressed male-pathway genes and promoted hsd17b1 transcription. Taken together, our findings demonstrate that the transcriptional antagonism and synergistic metabolic coordination among hsd17b members constitute the core molecular underpinning of endocrine-induced sexual plasticity. This study provides crucial molecular insights and viable targets for sex control breeding in teleost aquaculture.
Integrated transcriptomic and metabolomic analysis reveals the molecular mechanisms of salinity stress adaptation in the intertidal gastropod (Chlorostoma rustica).
Lin J, Zhang F, Han Z
Comp Biochem Physiol Part D Genomics Proteomics · 2026 Sep · PMID 42068771 · Publisher ↗
Chlorostoma rustica is an economically important species that thrives in rocky intertidal zones and is frequently exposed to salinity fluctuations. In this study, RNA sequencing and metabolomic profiling were performed o...
Chlorostoma rustica is an economically important species that thrives in rocky intertidal zones and is frequently exposed to salinity fluctuations. In this study, RNA sequencing and metabolomic profiling were performed on foot muscle tissues from C. rustica exposed to four salinity levels (18, 23, 28 control, and 38 psu) for 6 and 24 h to profile transcriptional and metabolic responses, respectively. A total of 93.18 Gb of high-quality clean reads were generated, resulting in 130,291 unigenes with N50 = 1113 bp and a mean length of 890.64 bp. Compared with the control group, the high-salinity group demonstrated 3370 and 3468 differentially expressed genes (DEGs) at 6 and 24 h, respectively. In the low-salinity Group 1 (18 psu), 3522 and 3489 DEGs were identified at 6 and 24 h, respectively. In the low-salinity Group 2 (23 psu), 3103 and 4293 DEGs were detected at 6 and 24 h, respectively. KEGG analysis showed that DEGs in low- and high-salinity groups were significantly enriched in core immune response and apoptosis-related pathways. ABCA3, MAP3K7IP2, and CLEC4G were identified as key genes in terms of salinity adaptation. Six DEGs were randomly selected for quantitative RT-PCR validation, confirming the reliability of the transcriptomic data. Metabolomic profiling identified 488 differential metabolites (DMs) in low-salinity group 1 (18 psu), mainly enriched in lipid and amino acid metabolism pathways. In the high-salinity group (38 psu), 363 DMs were detected, primarily enriched in amino acid metabolism and nutrient absorption-related pathways. In low-salinity group 2 (23 psu), 308 DMs were identified; however, no metabolic pathways were significantly enriched. Integrative transcriptomic and metabolomic analyses revealed coordinated changes in pathways related to osmotic regulation, energy metabolism, membrane lipid metabolism, and oxidative stress responses. These findings indicate that salinity induces the stress response of C. rustica by regulating osmotic balance (e.g., L-proline, spermine), lipid metabolism (e.g., acylcarnitines, sphingolipids), and transport systems. Overall, this study provides valuable insights into the molecular mechanisms underlying salinity tolerance in intertidal gastropods.
Genome-wide analysis of carboxyl/cholinesterases (CCE) genes in Phenacoccus solenopsis.
Du QK, Ding XH, Guo WC … +1 more , Li GQ
Comp Biochem Physiol Part D Genomics Proteomics · 2026 Sep · PMID 42066691 · Publisher ↗
Carboxyl/cholinesterases (CCEs) are hydrolases converting carboxylic esters into acids and alcohols. Although CCE genes are systematically identified in 14 Hemipteran insects, the classification of CCEs is not performed...
Carboxyl/cholinesterases (CCEs) are hydrolases converting carboxylic esters into acids and alcohols. Although CCE genes are systematically identified in 14 Hemipteran insects, the classification of CCEs is not performed in any Coccoidea insects. Here 77 CCE genes were categorized in a polyphagous Coccoidea herbivore, Phenacoccus solenopsis. Most CCEs had catalytic triad Ser-Asp/Glu-His, where serine formed a conserved sequence of GXSXG (X, any amino acid residue). Phylogenetic analysis and multiple sequence alignment revealed that 77 CCE genes fell into dietary/xenobiotic detoxification, hormone/pheromone processing and neuro/developmental function classes, including 32 α-esterases (AEs), 22 β-esterases (BEs), 9 juvenile hormone esterases (JHEs), 2 acetylcholinesterases (ACEs), 2 glutactins, 8 neuroligins and 1 glioactin. Genomic distribution and collinearity analysis, along with phylogenetic analysis, showed that a total of 12 tandem duplication events within the CCE gene family occurred in whole genome. Intron-exon structure analysis discovered there was an intronless PsCCE gene. Long PsCCEs had more exon and intron numbers. Moreover, several tandemly duplicated PsCCEs possessed identical or similar exon numbers. All CCEs were actively transcribed throughout the development and 73 CCEs were expressed when the larvae feeding on three host plants estimated by RPKM values. PsAE7, PsAE9 and PsJHE9 were only expressed in males. Therefore, a framework of information on CCE genes was established in P. solenopsis. The results facilitate exploring the resistant modes to environmental toxins.
Integrated ceRNA network analysis reveals the lncRNA-miRNA-mRNA axis in hypoxic stress response of yellow catfish (Pelteobagrus fulvidraco).
Han B, Shi Y, Liu X … +4 more , Tao Y, Qiang J, Yin S, Ning X
Comp Biochem Physiol Part D Genomics Proteomics · 2026 Sep · PMID 42061356 · Publisher ↗
Hypoxia poses a serious threat to aquatic organisms, yet the regulatory roles of non-coding RNAs, particularly the competing endogenous RNA (ceRNA) network, in fish under hypoxic stress remain poorly understood. In this...
Hypoxia poses a serious threat to aquatic organisms, yet the regulatory roles of non-coding RNAs, particularly the competing endogenous RNA (ceRNA) network, in fish under hypoxic stress remain poorly understood. In this study, we conducted whole-transcriptome sequencing of yellow catfish (Pelteobagrus fulvidraco) liver tissue under hypoxic conditions to systematically identify hypoxia-responsive lncRNAs and miRNAs and construct a comprehensive ceRNA network. A total of 14 differentially expressed lncRNAs (DElncs) and 112 miRNAs (DEmiRs) were identified. Functional enrichment analysis revealed that the target genes of DElncs were significantly involved in mitochondrial membrane permeability, energy metabolism, and the HIF-1 and mTOR signaling pathways, while those of DEmiRs were enriched in MAPK, calcium, and ErbB signaling pathways. Furthermore, we identified 22 DEmiRs commonly regulated under both hypoxic and hypoxic-bacterial dual stresses, representing core regulators of environmental adaptation. By integrating expression correlation and target prediction, we constructed the first lncRNA-miRNA-mRNA ceRNA network in hypoxic yellow catfish, comprising 5 DElncs, 11 DEmiRs, and 17 ceDETGs. Within this network, lnc162 (significantly down-regulated) and lnc1375 (markedly up-regulated) may act to regulate key apoptotic and metabolic genes such as fosb, sgk1, pkm, and hopx by sponging specific miRNAs, as predicted by our ceRNA analysis. These results reveal that lncRNAs mediate hypoxic adaptation by coordinating apoptosis and metabolic reprogramming via ceRNA mechanisms. Our study provides novel insights into the molecular basis of hypoxia tolerance in teleosts and offers potential genetic targets for breeding hypoxia-resistant fish strains.
Stage-resolved multi-tissue transcriptomics reveals coordinated molecular responses during feeding in Babylonia areolata.
Hong X, Ren P, Huang Y … +6 more , Chen W, Zhang Y, Yu F, Yang Y, Wang A, Liu C
Comp Biochem Physiol Part D Genomics Proteomics · 2026 Sep · PMID 42048951 · Publisher ↗
Feeding is a fundamental physiological process in mollusks and requires coordinated sensory, neural, and metabolic responses across multiple tissues. However, the cross-tissue molecular mechanisms underlying feeding in g...
Feeding is a fundamental physiological process in mollusks and requires coordinated sensory, neural, and metabolic responses across multiple tissues. However, the cross-tissue molecular mechanisms underlying feeding in gastropods remain largely unexplored. In this study, we conducted a multi-tissue comparative transcriptomic analysis of Babylonia areolata across four key feeding stages, including pre-feeding, feeding initiation, satiation, and post-feeding, to characterize dynamic molecular responses in the osphradium, cephalic region, and hepatopancreas. Integrated analyses of differential expression, functional enrichment, and weighted gene co-expression network analysis (WGCNA) were used to reconstruct a cross-tissue regulatory framework. Feeding triggered distinct yet temporally coordinated transcriptional programs across tissues. The osphradium showed rapid activation of neuroactive ligand-receptor interaction, calcium signaling, and Wnt pathways, supporting its role as the primary chemosensory gateway that converts food-derived cues into neural signals. The cephalic region exhibited multi-phasic neuroactive and Wnt signaling responses, corresponding to phases of sensory readiness, neural activation, and post-feeding modulation. In contrast, the hepatopancreas displayed a stage-specific metabolic progression, transitioning from lysosomal digestive activation to enhanced amino acid and nucleotide biosynthesis, followed by lipid remodeling, antioxidant defense, and immune regulation during the post-feeding period. Together, these results reveal a hierarchical "sensing-integration-execution" cascade that links chemosensory perception to neural processing and metabolic execution during feeding. This study provides the first cross-tissue molecular atlas of feeding regulation in B. areolata, offering new insights into neuro-metabolic integration in gastropods and informing feed optimization and health-oriented aquaculture strategies.
Transcriptomic and metabolomic analyses of the livers of high- and low-egg-producing pigeons.
Chen H, Zhang B, Wang M … +8 more , Fu Y, Li J, Zhao K, Chen Y, Song Y, Li Y, Xu S, Dai D
Comp Biochem Physiol Part D Genomics Proteomics · 2026 Sep · PMID 42048950 · Publisher ↗
Egg production is an essential metric used to assess poultry reproductive efficiency. The liver, functioning as a vital metabolic organ, is integral to avian reproduction and the overall productivity of laying birds. In...
Egg production is an essential metric used to assess poultry reproductive efficiency. The liver, functioning as a vital metabolic organ, is integral to avian reproduction and the overall productivity of laying birds. In this research, we aimed to explore various aspects of the mechanisms behind egg production across different poultry species by conducting transcriptomic and metabolomic analyses, as well as integrated assessments, of liver tissues from high- and low-producing pigeons to investigate the biosynthesis processes and identify pivotal genes and metabolic pathways in the liver during egg production. There were 1380 differentially expressed genes (DEGs) identified between the low- and high-production groups. The low-production group had 670 upregulated and 710 downregulated genes. Five genes identified were linked to egg production in the transcriptome: PRLR, HMGCR, CDK6, PTGR1 and RBPJ. The pathways that were identified to be the most significant encompass cytokine-cytokine receptor interaction, PI3K-AKT and JAK-STAT signalling pathways. Of the 229 significantly differentially abundant metabolites (DAMs) identified, 71 were upregulated, and 158 were downregulated, of which forskolin, methionine, prostaglandin F2α and adenosine 5'-diphosphate emerged as key metabolites associated with reproduction. By integrating transcriptomic and metabolomic data, we uncovered correlations between specific DEGs and DAMs, revealing significant gene-metabolite pairs, namely, PRLR-prostaglandin F2α and PRLR-adenosine 5'-diphosphate, involved in egg production. The new knowledge substantially enhances our comprehension of the molecular distinctions in hepatic physiology of high- and low-producing pigeons and establishes a valuable theoretical framework for future investigations into the mechanistic basis of avian egg-laying performance.
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