Comp. Biochem. Physiol. Part D Genomics Proteomics [JOURNAL]
Sun
200 papers
Identification, expression and functional prediction of odorant degrading enzymes in the antennal transcriptome of Anoplophora glabripennis.
Yang H, Li H, Hao E … +2 more , Lu P, Qiao H
Comp Biochem Physiol Part D Genomics Proteomics · 2026 Sep · PMID 41921261 · Publisher ↗
Anoplophora glabripennis, a major pest causing significant economic harm in China, affects a variety of hosts such as Salix, Ulmus, and Populus. Our research uncovered the mechanism of antennal odorant-degrading enzymes...
Anoplophora glabripennis, a major pest causing significant economic harm in China, affects a variety of hosts such as Salix, Ulmus, and Populus. Our research uncovered the mechanism of antennal odorant-degrading enzymes (ODEs) in this pest, identifying 97 ODEs, which include 9 GSTs, 20 CXEs, 66 P450s, and 2 UGTs. qPCR revealed sex-biased expression of specific ODEs, with some potentially involved in detoxification and pheromone degradation in males, and others in plant odor detection for oviposition in females. Highly expressed ODEs in both sexes may perceive food source odors. Molecular docking showed 3-Carene had the highest binding affinity to key ODEs, with AglaCYP345N1 binding most effectively and AglaGSTD4 the least. This research provides insights into the chemical ecology of A. glabripennis, potentially aiding in the development of monitoring and control strategies for this pest.
Genome-wide characterization, molecular evolution of twelve toll-like receptors in fat greenling (Hexagrammos otakii) and their response following Vibrio harveyi infection.
Zhang Y, Zhang Y, Xiang J … +6 more , Wei X, Zhang T, He T, Zhang Y, Li X, Wang W
Comp Biochem Physiol Part D Genomics Proteomics · 2026 Sep · PMID 41915955 · Publisher ↗
As critical constituents of the innate immune system, toll-like receptors (TLRs) primarily function to detect and recognize pathogens. In teleost fish, TLRs exhibit considerable complexity and diversity, playing a vital...
As critical constituents of the innate immune system, toll-like receptors (TLRs) primarily function to detect and recognize pathogens. In teleost fish, TLRs exhibit considerable complexity and diversity, playing a vital role in providing a robust and flexible first line of immunological defense. However, their genome structure, molecular evolution in Hexagrammos otakii remain poorly understood. In the present study, twelve TLR genes were characterized in H. otakii and assigned to five subfamilies (TLR1, TLR3, TLR5, TLR7, TLR11). These genes possess conserved protein architectures, containing typical extracellular leucine-rich repeat (LRR) domains, a transmembrane (TM) domain, and intracellular Toll/IL-1 receptor (TIR) domains, and they exhibit a clustered chromosomal distribution. Phylogenetic reconstruction demonstrated that HoTLRs share the closest evolutionary relationship with their orthologs from Anarrhichthys ocellatus, a fellow perciform fish. Tissue expression analysis revealed a broad yet distinct expression profile for all HoTLR genes across homeostasis. Furthermore, experimental challenge with the bacterial pathogen Vibrio harveyi induced significant, spatiotemporally specific upregulation of key genes, including TLR1 and TLR5m, highlighting their active involvement in orchestrating antibacterial innate immune defenses in H. otakii. This study provides new insights into the evolutionary patterns of the TLR family in teleosts, and lays a molecular theoretical foundation for disease prevention and control strategies in the aquaculture of H. otakii.
Integrated analysis of transcriptome and metabolome reveals the muscle cold adaptation strategy in silver pomfret (Pampus argenteus).
Zhu F, Song Y, Du S … +7 more , Xu D, Wang T, Ning X, Zhang G, Gao B, Zhao C, Yin S
Comp Biochem Physiol Part D Genomics Proteomics · 2026 Sep · PMID 41905289 · Publisher ↗
Low temperature represents a critical environmental stressor for teleost fish, disrupting metabolic homeostasis, enhancing oxidative damage, and ultimately compromising physiological performance. As a warm-water-adapted...
Low temperature represents a critical environmental stressor for teleost fish, disrupting metabolic homeostasis, enhancing oxidative damage, and ultimately compromising physiological performance. As a warm-water-adapted marine species, silver pomfret (Pampus argenteus) exhibits pronounced sensitivity to cold stress, which constrains its survival and aquaculture potential. In the present study, silver pomfret were subjected to a control temperature (25 °C) and two cold stress temperatures (18 °C and 13 °C) for 96 h. Muscle responses were assessed through histological examination, antioxidant enzyme activity assays, transcriptomic sequencing, and metabolomic profiling. Cold stress induced marked pathological alterations in muscle tissue, including myofibrillar disorganization, cytoplasmic degradation, and cellular vacuolization. Antioxidant defenses were rapidly activated during the early phase of cold stress and subsequently reached a relatively stable state with prolonged exposure. The omics data suggested that the enhanced polyunsaturated fatty acid synthesis and elongation appeared to support membrane fluidity, accompanied by the upregulation of fatty acid β-oxidation and lipid catabolic pathways to satisfy elevated energy demands at 18 °C. In contrast, exposure to 13 °C resulted in pronounced disruption of cytoskeletal integrity and functional impairment, together with the activation of apoptosis-related pathways in muscle cells. Collectively, these results elucidate temperature-dependent regulatory strategies underlying cold stress responses in silver pomfret muscle and provide a mechanistic basis for improving cold tolerance in aquaculture practices.
Genome-wide identification and expression profiling of Fox gene family reveals the potential functions of sex determination in Crassostrea gigas.
Chen S, Li Q, Hu B … +1 more , Du S
Comp Biochem Physiol Part D Genomics Proteomics · 2026 Sep · PMID 41905288 · Publisher ↗
Pacific oysters (Crassostrea gigas) are a major aquaculture species among molluscs worldwide, possessing significant ecological and economic value. The mechanism governing sex determination in oysters remains largely unk...
Pacific oysters (Crassostrea gigas) are a major aquaculture species among molluscs worldwide, possessing significant ecological and economic value. The mechanism governing sex determination in oysters remains largely unknown. Fox transcription factors are key regulators of vital biological processes, controlling important functions such as tissue development and reproduction. This study presents a genome-wide identification and characterization of the Fox gene family in C. gigas. Through systematic identification, 16 Fox genes were discovered and classified into 13 subfamilies based on phylogenetic analysis and conservation domain analysis. Transcriptomic profiling revealed that FoxK2 and FoxG1 were significantly upregulated during the resting stage, whereas FoxG1 expression was higher in females and males throughout the active gametogenesis stage (P < 0.05). FoxE1 and FoxL2 exhibited elevated expression profiles during female maturation, whereas FoxO, FoxN4, and FoxK2 showed higher expression profiles during male maturation (P < 0.05). At the spawning stage, FoxE1 and FoxK2 were significantly expressed in females, whereas FoxJ1B and FoxK2 exhibited elevated expression in males (P < 0.05). Our findings indicate sexually dimorphic expression patterns of FoxB1, FoxE1, FoxL2, FoxP1, and FoxC1 and their gonad-specific functions. Our research has significant ecological implications for comprehending the sex determination process and offers fresh insights into the Fox gene regulation mechanisms in bivalves.
Transcriptomic analysis of gene expression in the longissimus dorsi muscle and liver of Tibetan yaks under different rearing management models in the cold season.
Zhang Z, Cao Q, Chen Y … +6 more , Yu Y, Yang X, Zhang Z, Liu Y, Lv W, Dong Q
Comp Biochem Physiol Part D Genomics Proteomics · 2026 Sep · PMID 41895084 · Publisher ↗
The Longissimus dorsi muscle is a key skeletal muscle in yaks, significantly influencing their growth, motor function, and meat quality. Meanwhile, the liver of yaks also performs essential metabolic roles in their adapt...
The Longissimus dorsi muscle is a key skeletal muscle in yaks, significantly influencing their growth, motor function, and meat quality. Meanwhile, the liver of yaks also performs essential metabolic roles in their adaptation to high-altitude environments. Both tissues are influenced by multiple factors, including living conditions and management models. Different feeding and management strategies may impact the growth and health of yaks, and these effects are often mediated through the regulation of gene expression. In this study, thirty-two yaks were randomly divided into four groups during the cold season: one group was subjected to traditional outdoor grazing, while the other three groups were housed indoors and fed diets with different roughage-to-concentrate ratios (50:50, 70:30, and 90:10). At the end of the experiment, longissimus dorsi muscle and liver tissues were collected from all four groups for transcriptome sequencing to investigate the effects of different feeding management models on yak growth and gene expression. A total of 24 cDNA libraries were constructed, producing 166.56 Gb of high-quality clean data. Subsequently, we identified 3598 differentially expressed genes (DEGs) in the muscle and 4343 in the liver, indicating that different feeding management models modulated gene expression across various tissues in yaks. KEGG enrichment analyses revealed DEGs significantly enriched in the "MAPK signaling pathway" in muscle and "cancer-related pathways" in liver tissue, suggesting that different feeding strategies may influence metabolic processes and potentially influence yak health outcomes. This study establishes the foundation for optimizing yak management models, with broader implications for livestock systems in similar environments.
Metagenomic insights into sex-specific taxonomic and functional differentiation of epidermal mucus microbiota in the humphead wrasse (Cheilinus undulatus).
Huang J, Fu Z, Zhou S … +4 more , Hu J, Yu G, Qin C, Ma Z
Comp Biochem Physiol Part D Genomics Proteomics · 2026 Sep · PMID 41887041 · Publisher ↗
The humphead wrasse (Cheilinus undulatus) is a large coral reef fish of high ecological and economic importance, whose epidermal mucus microbiota plays a critical role in host defense, immune regulation, and environmenta...
The humphead wrasse (Cheilinus undulatus) is a large coral reef fish of high ecological and economic importance, whose epidermal mucus microbiota plays a critical role in host defense, immune regulation, and environmental adaptation. However, the influence of host sex on the structure and functional potential of epidermal mucus microbiota remains poorly understood. In this study, epidermal mucus samples were collected from sexually mature female and male humphead wrasse, and shotgun metagenomic sequencing was performed to systematically compare microbial community composition, diversity, and functional gene profiles between sexes. The results showed no significant differences in alpha diversity (ACE and Shannon indices) between female (FM) and male (M) groups. In contrast, beta diversity analyses and hierarchical clustering revealed clear sex-related separation of microbial community structures at both phylum and genus levels. Although both groups were dominated by Pseudomonadota, Bacillota, Bacteroidota, and Verrucomicrobiota, their relative abundances and sex-specific taxa differed markedly. Functional annotation based on KEGG indicated that female-specific taxa harbored a greater number and broader range of functional genes, mainly associated with carbohydrate, amino acid, energy, and cofactor metabolism, as well as disease-related pathways. Furthermore, Comprehensive Antibiotic Resistance Database (CARD) and the Virulence Factor Database (VFDB) analyses revealed that female-specific taxa exhibited higher diversity of antibiotic resistance genes and virulence factors, whereas male-specific taxa showed a more limited functional repertoire, primarily related to basic metabolism and biofilm formation. Overall, this study demonstrates pronounced sex-associated differences in both the taxonomic composition and functional potential of epidermal mucus microbiota in humphead wrasse, highlighting the importance of host sex in shaping host-microbiome interactions and providing new insights for health management and conservation of coral reef fishes.
Proteomic profiling reveals matrix remodeling and metabolic homeostasis in sea cucumber mutable collagenous tissue.
Wu Q, Su F, Jiang C … +2 more , Cui W, Sun L
Comp Biochem Physiol Part D Genomics Proteomics · 2026 Sep · PMID 41887040 · Publisher ↗
Mutable Collagenous Tissue (MCT) is an echinoderm-specific connective tissue, capable of rapidly altering its mechanical properties under neural regulation. Although several potential effector proteins have been identifi...
Mutable Collagenous Tissue (MCT) is an echinoderm-specific connective tissue, capable of rapidly altering its mechanical properties under neural regulation. Although several potential effector proteins have been identified, the overall molecular network governing the transition between the stiffened and softened states of MCT remains unclear. To uncover potential mechanisms, we performed iTRAQ-based quantitative proteomics on MCT from Stichopus chloronotus under stiffened and softened conditions. A total of 1653 proteins were identified, with 160 differentially abundant proteins detected between stiffened and softened tissues. Functional enrichment analysis revealed that the stiffened state was significantly associated with upregulation of vesicle-mediated transport systems and glycosaminoglycan metabolism, supporting the hypothesis of secretion-driven matrix remodeling. The softened state was characterized by enrichment in protein synthesis, ribosome biosynthesis, and oxidative phosphorylation pathways. Additionally, enrichment of Hippo signaling and DNA damage response terms was observed in the softened condition. Collectively, these data provide a proteomic resource for MCT state transitions and suggest that stiffening is associated with matrix remodeling. In contrast, softening is accompanied by shifts in metabolic homeostasis and stress-response programs. This research provides a systematic understanding of MCT's rapid reversibility and may inform the design of bioinspired mechanically adaptable materials.
Transcriptome analysis reveals the effect of fermented feed on the growth, antioxidant capacity, and immune function in juvenile Eriocheir sinensis.
Ma Y, Li Y, Yan Z … +6 more , Liu B, Xie S, Gu Y, Wan Z, Ding S, Li X
Comp Biochem Physiol Part D Genomics Proteomics · 2026 Sep · PMID 41880898 · Publisher ↗
The capacity of fermented feed to improve the nutrient consumption, water quality, and immunological health of cultured species has drawn increased interest in aquaculture. This study aimed to establish the ideal supplem...
The capacity of fermented feed to improve the nutrient consumption, water quality, and immunological health of cultured species has drawn increased interest in aquaculture. This study aimed to establish the ideal supplementation ratio of fermented feed by analyzing its effects on growth metrics, antioxidative potential, and immunological function in juvenile Eriocheir sinensis. Five trial diets containing 0, 10, 20, 30, and 40% fermented feed were administered for 60 days under controlled pond conditions. Growth indices, hepatopancreas histology, antioxidant enzyme activities, immune parameters, and transcriptomic profiles were analyzed. Crabs fed 30% fermented feed exhibited the highest final weight, weight gain rate, and specific growth rate, accompanied by improved hepatopancreas structure characterized by increased fibrillar cells. The expression levels and activities of enzymes and genes linked to antioxidants and immunity were markedly upregulated in this group relative to the control group. Transcriptome sequencing of hepatopancreas showed 148 differentially expressed genes, mainly enriched in steroid hormone biosynthesis, Hippo, TGF, and Toll and Imd signaling pathways, indicating activation of immune and antioxidant mechanisms. Feeding with 30% fermented feed upregulated key immune genes such as Relish, MyD88, and DREDD while downregulating Cactus, confirming stimulation of Toll and Imd signaling. Overall, an appropriate proportion of fermented feed, particularly 30%, improved growth, enhanced antioxidant defense, and strengthened innate immunity in juvenile E. sinensis. These results demonstrate that optimized fermented feed can promote health and sustainability in crab aquaculture through nutritional and immunological enhancement.
Integrative transcriptome and metabolome analyses reveal molecular mechanisms of tail resorption in Fejervarya multistriata.
Li W, Zhang J, Wang D … +3 more , He J, Zhou X, Wang H
Comp Biochem Physiol Part D Genomics Proteomics · 2026 Sep · PMID 41875788 · Publisher ↗
Tail resorption is a hallmark of amphibian metamorphosis, yet the underlying molecular mechanisms remain incompletely understood. To address these deficiencies, we integrated morphological, histological, transcriptomic,...
Tail resorption is a hallmark of amphibian metamorphosis, yet the underlying molecular mechanisms remain incompletely understood. To address these deficiencies, we integrated morphological, histological, transcriptomic, and metabolomic analyses to explore tail resorption in Fejervarya multistriata. Tadpole tail regressed during metamorphosis, whereas the limbs gradually developed to maturity. Correspondingly, the expression levels of genes encoding motor proteins were lower in the tail than in the hindlimbs, supporting a functional shift from tail to limb locomotion. Tail resorption is driven by three cellular processes: MMP mediated ECM degradation, autophagy, and apoptosis. Our transcriptomic analysis revealed key regulatory genes involved in these processes, including ECM-related genes (mmp9, mmp14, and mmp18), autophagy-related genes (atg4, gabarap, atg12, and atg16l), and apoptosis-related genes (bid, bax, apaf1, casp7, and casp9). Metabolomic data indicated palmitoylcarnitine and pAzPC as potential apoptosis indicators. Overall, our findings offer insights into the molecular basis of tail resorption and provide a multi-omics resource that will facilitate future studies of this process.
Genome-wide association study identifies loci and candidate genes associated with growth traits in Siniperca scherzeri.
Xu H, Huang R, Jin J … +6 more , Wu Y, Cheng Z, Wang M, Ye X, Lai M, Zhang D
Comp Biochem Physiol Part D Genomics Proteomics · 2026 Sep · PMID 41875787 · Publisher ↗
Growth performance is a key economic trait that determines aquaculture productivity and profitability, and elucidating its genetic mechanisms is of great importance for germplasm improvement and molecular breeding in aqu...
Growth performance is a key economic trait that determines aquaculture productivity and profitability, and elucidating its genetic mechanisms is of great importance for germplasm improvement and molecular breeding in aquaculture species. Siniperca scherzeri, an important freshwater cultured species in East Asia, exhibits significant individual variation in growth rate. In this study, a genome-wide association study (GWAS) based on a linear mixed model (LMM) was conducted for five major growth traits in S. scherzeri-body weight (BW), extended length (EL), body length (BL), body thickness (BTH), and body height (BH). A total of 17 significant loci associated with growth traits were identified across nine chromosomes. Among them, 13 loci showed significant or suggestive associations with two or more traits, indicating that growth traits in S. scherzeri exhibit polygenic, small-effect, and cross-trait shared genetic characteristics. Genotype-phenotype association analysis confirmed the presence of specific genotypes conferring growth advantages, among which, the AA genotypes at loci Chr13_5825730 and Chr13_5825731 were significantly associated with increased body weight, extended length, and body length in S. scherzeri. Further annotation of candidate genes within the ±50 kb regions surrounding the significant loci identified a total of 55 candidate genes. GO and KEGG enrichment analyses revealed that these genes were significantly enriched in several biological pathways related to energy metabolism and growth regulation, including the insulin signaling pathway, AMPK signaling pathway, mTOR signaling pathway, FoxO signaling pathway, and carbohydrate digestion and absorption. These genes and their associated signaling pathways provide important molecular insights into the genetic basis of individual growth differences in S. scherzeri, offering theoretical support and potential targets for marker-assisted selection (MAS) and precision molecular breeding.
Identification and sex-specific expression profiles of chemosensory genes from tarsi and antennae in the dead leaf butterfly Kallima inachus.
Wu YH, Dong ZW, He JW … +2 more , Wang W, Li XY
Comp Biochem Physiol Part D Genomics Proteomics · 2026 Sep · PMID 41875786 · Publisher ↗
Chemical sensation plays important roles in insect life history, such as host recognition and intraspecific identification, which in turn are key drivers of speciation processes. Kallima butterflies mimic dead leaves to...
Chemical sensation plays important roles in insect life history, such as host recognition and intraspecific identification, which in turn are key drivers of speciation processes. Kallima butterflies mimic dead leaves to camouflage themselves under shady forest habitat. However, the lack of knowledge about the Kallima chemosensory system has hindered our understanding of how they adapt to host and shady habitat which influence speciation processes. In this study, chemosensory genes of Kallima inachus were identified based on transcriptome data combined with genomic data, including 107 gustatory receptors (GRs), 55 odorant receptors (ORs) and 34 ionotropic receptors (IRs). K. inachus exhibits a higher GR copy number compared to those of other Lepidopteran species, especially for the bitter receptors. Interestingly, among 36 copies in an expanded clade, 17 GRs clustered into a 0.5 Mb window of chromosome 7, suggesting serial tandem duplication events occurred. These GRs such as KinGR14, KinGR39, KinGR42, KinGR45 showed female-specific expression pattern in tarsi, indicating that the duplication events were possibly driven by female-specific biological behaviors such as host recognition and oviposition. One of the ORs in K. inachus (KinOR3) was found to be clustered with Bombyx mori pheromone receptor, and quantitative real-time PCR (qPCR) confirmed its male-biased expression pattern in antennae, which coordinates with expression pattern of moth sex pheromone receptor. Taken together, this study yields a robust dataset of K. inachus chemosensory genes and reveals their expression profile between sexes and organs, providing fundamental insights into host recognition and intraspecific identification in K. inachus and other butterflies.
Identification of pheromone-binding protein genes in Dioryctria abietella Denis & Schiffermüller (Lepidoptera: Pyralidae), a major pest of pine cones.
Han JH, Jung MH, Lee SC … +1 more , Park IK
Comp Biochem Physiol Part D Genomics Proteomics · 2026 Sep · PMID 41865499 · Publisher ↗
The spruce cone worm, Dioryctria abietella (Lepidoptera: Pyralidae), is a major conifer pest that threatens forest regeneration and seed production. To investigate the molecular basis of sex pheromone perception, we perf...
The spruce cone worm, Dioryctria abietella (Lepidoptera: Pyralidae), is a major conifer pest that threatens forest regeneration and seed production. To investigate the molecular basis of sex pheromone perception, we performed antennal transcriptome analysis and molecular investigation of candidate pheromone-binding proteins (PBPs). Transcriptome profiling identified diverse olfactory-related genes, including five candidate PBPs, some of which showed high sequence similarity to previously reported Lepidopteran PBPs. Phylogenetic analysis revealed distinct evolutionary relationships among these proteins, with several clustering with known PBPs while others formed separate lineages within the OBP/PBP family. Structural modeling combined with molecular docking suggested differential binding potentials of selected PBPs to two sex pheromone components of D. abietella. Quantitative RT-PCR analysis showed that three PBPs exhibited male head-enriched expression patterns consistent with roles in male pheromone detection, whereas one candidate displayed comparable expression in both sexes, suggesting possible involvement in female olfactory perception. Together, these findings provide integrative molecular evidence linking predicted pheromone interactions with expression patterns, contributing to our understanding of olfactory mechanisms in D. abietella and providing a basis for future functional validation and species-specific pheromone-based pest management strategies.
Transcriptome was utilized to unravel the liver tissue changes of the successful recovery from freezing in the Perccottus glenii.
Zhao X, Wang Z, Guo B … +6 more , Chang Y, Cheng M, Ning Z, Wang W, Tan R, Mu W
Comp Biochem Physiol Part D Genomics Proteomics · 2026 Sep · PMID 41864116 · Publisher ↗
The Amur sleeper (Perccottus glenii) exhibits remarkable tolerance to freezing conditions, yet the molecular and physiological mechanisms underlying its recovery from cold stress remain poorly understood. This study inve...
The Amur sleeper (Perccottus glenii) exhibits remarkable tolerance to freezing conditions, yet the molecular and physiological mechanisms underlying its recovery from cold stress remain poorly understood. This study investigated the recovery process in P. glenii following freezing by integrating transcriptomic, histological, and biochemical analyses. Fish were subjected to a freezing experiment at -2 °C for 24 h, followed by a recovery phase at 4 °C. Liver transcriptome sequencing revealed 5622 differentially expressed genes (DEGs) across comparison groups (DEA vs. CK, SUR vs. CK, and DEA vs. SUR). KEGG enrichment analysis highlighted the significant upregulation of genes involved in the pancreatic secretion pathway and in the metabolism of xenobiotics by cytochrome P450 and steroid biosynthesis pathways in successfully resuscitated individuals. Histological examination showed restored liver architecture in the successful recovery group, contrasting with vacuolation and structural disorganization in the death group. Biochemically, successful recovery was associated with significantly elevated activities of antioxidant enzymes and digestive enzymes (lipase), alongside increased triglyceride (TG) content. These findings demonstrate that the successful post-freezing recovery in P. glenii is underpinned by the coordinated upregulation of genes facilitating the restoration of digestive function, enhancement of detoxification capacity, regulation of steroid biosynthesis, and mitigation of oxidative stress. This study provides comprehensive insights into the adaptive molecular mechanisms that confer exceptional freezing tolerance and recovery capability in this vertebrate model.
Protein signatures of aging in the hemolymph of marbled crayfish: Insights into crustacean immune aging.
Mengal K, Siino V, Buřič M … +2 more , Levander F, Niksirat H
Comp Biochem Physiol Part D Genomics Proteomics · 2026 Sep · PMID 41844002 · Publisher ↗
Aging is accompanied by progressive physiological declines in body functions. However, the molecular mechanisms of aging remain poorly understood in decapod crustaceans, a diverse group of invertebrates. We investigated...
Aging is accompanied by progressive physiological declines in body functions. However, the molecular mechanisms of aging remain poorly understood in decapod crustaceans, a diverse group of invertebrates. We investigated age-related differences in the hemolymph proteomes of marbled crayfish using label-free protein quantification (LC-MS/MS), applying a significance threshold of p < 0.05 and a fold change >2 to elucidate molecular mechanisms underpinning aging. Two groups including young (n = 6) and old (n = 7) crayfish were used. Results showed a downregulation of superoxide dismutase in the hemolymph of older individuals. At the same time, glutathione peroxidase and transketolase were upregulated, which may reflect age-dependent changes in oxidative stress regulation and potential compensatory responses. Aging crayfish exhibited changes in levels of the ProPO system and phagocytosis-related proteins that suggest a possible shift from melanization to phagocytosis in the aging immune system. Additionally, the lower levels of some other immune-related proteins in the old individuals may be consistent with a decline in the crayfish immune system with age. Proteins associated with wound healing and regeneration were higher in young individuals, which may suggest an age-based decline in regenerative capacity. Cytoskeletal and extracellular matrix proteins were upregulated in older crayfish, which could potentially influence immune cell functions. Age-related alterations in the quantities of vitellogenins, hemocyanins, and metabolic enzymes maybe associated with changes in reproductive investment, respiratory capacity, and energy metabolism. Together, these findings highlight the complex molecular basis by which aging reshapes the hemolymph composition and alters immune system characteristics in an invertebrate, revealing molecular signatures that may represent aging mechanisms. Data are available via ProteomeXchange with identifier PXD065434.
Resveratrol alleviates heat-stress intestinal barrier dysfunction in Siberian sturgeon by activating PPAR/NF-kB-mediated antioxidant capacity and microbiota homeostasis.
Wang H, Zhang Y, Chen X … +9 more , Zhang Z, Xu Z, Xu W, Chen X, Xiong Y, Jiang M, Wei Z, Du X, Yang S
Comp Biochem Physiol Part D Genomics Proteomics · 2026 Sep · PMID 41844001 · Publisher ↗
Heat stress impairs intestinal barrier function and microbial balance in cold-water fish like Siberian sturgeon. Resveratrol improves aquatic animal growth and intestinal homeostasis, but its protective mechanism in heat...
Heat stress impairs intestinal barrier function and microbial balance in cold-water fish like Siberian sturgeon. Resveratrol improves aquatic animal growth and intestinal homeostasis, but its protective mechanism in heat-stressed Siberian sturgeon remains unclear. This study found resveratrol maintains intestinal integrity, enhances antioxidant capacity, and regulates gut microbiota in heat-stressed Siberian sturgeon: the HRH group showed higher Cetobacterium and lower pathogenic Rhodococcus, Acinetobacter, and Pseudomonas than the HC group. Transcriptomic analysis suggested that heat stress might induce uncoupling protein 1 (UCP1)-mediated uncoupling of ATP synthesis from oxidative phosphorylation, which could in turn reduce mitochondrial energy production and cause intestinal villus damage. Resveratrol regulates duodenal lipid metabolism via the PPAR pathway to boost energy supply, and modulates valvular intestinal immune response through the NF-κB pathway. Meanwhile, the protective effect of the resveratrol-supplemented group remained significantly superior to that of the control group. These findings indicate resveratrol mitigates heat stress by preserving villi integrity, alleviating oxidative stress and pathogenic proliferation, and regulating lipid metabolism/immunity via PPAR/NF-κB, clarifying its protective mechanism for Siberian sturgeon intestinal homeostasis and providing a theoretical basis for heat stress mitigation in aquatic animals.
Hypersaline transplantation promotes oyster fattening partially through the Caand Cl regulation.
He G, Jiang Z, Liu Y … +1 more , Zhao L
Comp Biochem Physiol Part D Genomics Proteomics · 2026 Sep · PMID 41830898 · Publisher ↗
Oysters are a major source of high-quality protein, and their contribution to global food production has driven the rapid expansion of oyster aquaculture. Yet, intensified farming density and degraded environmental condi...
Oysters are a major source of high-quality protein, and their contribution to global food production has driven the rapid expansion of oyster aquaculture. Yet, intensified farming density and degraded environmental conditions have greatly affected oyster meat yield. While hypersaline transplantation can partially tackle this issue through rapid fattening, underlying processes remain poorly understood. Here, we found that hypersaline transplantation of oysters (Crassostrea sikamea) from a salinity of 18 to 30 significantly enhanced meat yield, but further increase to 42 resulted in a significant decrease. Moderately elevated salinity at 30 increased gill Ca and Cl fluxes compared with salinity 18, while remaining significantly lower than those at 42. Transcriptomic analyses revealed that gene networks associated with Ca and Cl transport mediated oyster fattening. Moderately elevated salinity activated calcium signaling pathway and associated Ca-responsive genes (CaM, CaBPs). Concurrently, Ca signaling activated Cl transport-related genes (CLCs) to preserve osmotic balance and enhance fattening. Extremely elevated salinity at 42 suppressed apoptosis and calcium signaling pathway, indicating stress-induced membrane damage which ultimately constrained soft tissue growth. Our findings make a leap forward in understanding mechanisms underpinning hypersaline transplantation induced increases in oyster meat yield, with widespread implications for oyster fattening and aquaculture.
Revealing the transcriptional profile of fish muscle cells in vitro and in vivo: Insights to improve fish muscle culture.
Zanella BTT, Perez ÉS, Dos Santos Barbosa MF … +3 more , Valente JS, Duran BOS, Dal-Pai-Silva M
Comp Biochem Physiol Part D Genomics Proteomics · 2026 Sep · PMID 41812377 · Publisher ↗
In vitro experiments have contributed to numerous fields of knowledge, including fish skeletal muscle. Despite improved strategies, in vitro assays still show discrepancies with in vivo systems, especially for non-model...
In vitro experiments have contributed to numerous fields of knowledge, including fish skeletal muscle. Despite improved strategies, in vitro assays still show discrepancies with in vivo systems, especially for non-model organisms. In this sense, we characterized the transcriptional profile of pacu (Piaractus mesopotamicus) muscle cells in vitro and in vivo. Processes related to proliferation, glycolytic metabolism, and extracellular matrix were enriched in vitro, while energy production, muscle contraction, and amino acid processing were enriched in vivo. Through qPCR, the genes fn1a (fibronectin 1a), hk1 (hexokinase 1), and ctnnb1 (catenin beta 1), respectively related to extracellular matrix, glycolytic metabolism, and cell proliferation and differentiation, were highly expressed in vitro. The genes ckma (creatine kinase, muscle a), acat1 (acetyl-CoA acetyltransferase 1), mdh2 (malate dehydrogenase 2), and pkmb (pyruvate kinase M1/2b), respectively associated with ATP production, fatty acid oxidation, oxidative and glycolytic metabolism, and the genes musk (muscle, skeletal, receptor tyrosine kinase), chrna1 (cholinergic receptor, nicotinic, alpha 1) and clu (clusterin), involved in cell signaling, were highly expressed in vivo. Overall, our results indicate that the main limitation of in vitro muscle cell model is the maintenance of an embryonic-like molecular state, whereas in vivo muscle displays a mature transcriptional profile, providing a molecular basis to guide future strategies for improving fish muscle cell culture systems and supporting advances in sustainable aquaculture and in vitro meat production.
Transcriptome-based identification and expression profiling of olfaction-related genes in the semi-aquatic firefly Pygoluciola qingyu (Coleoptera: Lampyridae).
Chen X, Li Y, Cao C
Comp Biochem Physiol Part D Genomics Proteomics · 2026 Sep · PMID 41806589 · Publisher ↗
The semi-aquatic firefly Pygoluciola qingyu, a bioluminescent insect inhabiting stream and wetland environments, is closely associated with the ecological quality of semi-aquatic habitats and wetland biodiversity. Its un...
The semi-aquatic firefly Pygoluciola qingyu, a bioluminescent insect inhabiting stream and wetland environments, is closely associated with the ecological quality of semi-aquatic habitats and wetland biodiversity. Its unique glow, combined with its ornamental value, also makes it a potential candidate for special aquaculture and ecological landscape enhancement. In this study, transcriptome sequencing of adult antennae and larval heads was performed using the Illumina platform. A total of 35,178 unigenes were obtained, and 8432 differential expression genes were revealed. The assembled unigenes were functionally annotated against the NR, GO, and KEGG databases. Also, 66 olfaction-related genes were identified, including 28 odorant receptors (ORs), 16 gustatory receptors (GRs), 8 ionotropic receptors (IRs), 12 odorant-binding proteins (OBPs), and 2 sensory neuron membrane proteins (SNMPs). OBP relative expression analysis based on RT-qPCR showed that PqinOBPs exhibited differential expression between sexes and among different tissues in adults, with some genes showing relatively higher expression levels in legs. In larval samples, several PqinOBPs displayed significant expression differences between head and body, with generally higher expression in the head. These results clarify the composition and expression profiles of olfaction-related genes in P. qingyu and provide a molecular basis for understanding olfactory perception mechanisms and ecological adaptation in this semi-aquatic firefly.
Multi-omics analysis reveals molecular disruption in mouse testes following cumulative heat stress.
Baibrus MA, Nazir F, Zhou R … +6 more , Xiong H, Liang Q, Huang A, Majeed A, Zhou G, Yu G
Comp Biochem Physiol Part D Genomics Proteomics · 2026 Sep · PMID 41795304 · Publisher ↗
Rising global temperatures threaten male fertility, yet the molecular mechanisms by which heat stress disrupts spermatogenesis remain incompletely understood. We employed an integrative multi-omics approach incorporating...
Rising global temperatures threaten male fertility, yet the molecular mechanisms by which heat stress disrupts spermatogenesis remain incompletely understood. We employed an integrative multi-omics approach incorporating transcriptomics, proteomics, and metabolomics to examine the impact of sub-lethal HS (Heat stress) on the testes and spermatozoa of male mice. Our results demonstrated that HS significantly diminished sperm motility and compromised the architecture of seminiferous tubules. Multi-omics integration demonstrated a synchronized downregulation of pathways regulating glycolysis, flagellar assembly, and antioxidant defense, as well as disruptions in steroid hormone production and redox equilibrium. These systemic changes collectively contribute to defective energy metabolism, aberrant sperm viability, and diminished tolerance to oxidative stress, ultimately leading to reduced reproductive potential. This study provides an integrated multi-omics view of heat stress-associated molecular disruptions in mouse testes and highlights convergent pathways linked to impaired male reproductive function.
Dual-layered epigenetic regulation links water body size constraints to somatic growth in an allotetraploid fish.
Zeng Y, Zhang J, Wang Q … +7 more , Han X, Liu L, Yang K, Zhang R, Luo K, Ren L, Liu S
Comp Biochem Physiol Part D Genomics Proteomics · 2026 Sep · PMID 41795303 · Publisher ↗
Polyploidy endows fish with genomic plasticity to colonize restricted environments, yet the molecular mechanisms linking ecological constraints to somatic growth remain elusive. Here, we investigated the adaptive respons...
Polyploidy endows fish with genomic plasticity to colonize restricted environments, yet the molecular mechanisms linking ecological constraints to somatic growth remain elusive. Here, we investigated the adaptive response of an allotetraploid lineage (Carassius auratus × Cyprinus carpio) to contrasting water body sizes using multi-omics approaches. We found that spatial constraints triggered targeted transcriptional remodeling specifically in the eye and muscle. This response effectively links sensory perception to growth regulation. Meanwhile, we identified a dual-layered epigenetic strategy. Environmental stress forced a reduction in the active gene pool via promoter silencing, while concurrently depressing the expression levels of growth-related structural genes through enhancer inhibition. Interestingly, this plasticity exhibited striking subgenome asymmetry. The Cyprinus subgenome displayed higher epigenetic responsiveness and acted as the primary adaptive buffer, exemplified by the targeted repression of a Cyprinus-derived enhancer regulating the mTOR gene rps6kb1a. Our findings demonstrate how subgenome-biased epigenetic remodeling aligns growth phenotypes with ecological constraints, offering molecular insights into the evolutionary success of polyploids in fragmented habitats.
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