Comp. Biochem. Physiol. Part D Genomics Proteomics [JOURNAL]
Sun
200 papers
Mechanisms of heat and hypoxia defense in the sea cucumber Apostichopus japonicus: Insights from ubiquitination regulation.
Xia B, Song J, Xin Q … +6 more , Wang C, Yu W, Liu J, Yu G, Wang F, Xu D
Comp Biochem Physiol Part D Genomics Proteomics · 2026 Sep · PMID 41795302 · Publisher ↗
Sea cucumbers Apostichopus japonicus are valuable resources for nature and food. High temperature and hypoxia are main kinds of stress factors for A. japonicus. Our study showed proteins from three stress-treatment group...
Sea cucumbers Apostichopus japonicus are valuable resources for nature and food. High temperature and hypoxia are main kinds of stress factors for A. japonicus. Our study showed proteins from three stress-treatment groups (HT, LO and HT_LO) had high ubiquitin-conjugate levels. The mRNA expression of 6 ubiquitinating enzymes had a significant response, especially in HT_LO group. The global ubiquitinomes quantified a total of 1594 lysine ubiquitination sites on 924 proteins. Quantification values of 523, 387 and 804 Kub sites were differentially changed in HT, LO and HT_LO respectively. The top 3 up-regulated DUSs in HT vs C comparison were located in glyceraldehyde-3-phosphate dehydrogenase (GADPH), putative fatty acid-binding protein type 3-like (FABP3), heat shock protein 90-alpha (HSP90α). Some up-regulated DUSs were shared both in HT vs C comparison and LO vs C comparison, such as K(101) in FABP3 and K(104) in HSP90α. The ubiquitination quantitative level of sites in profilin (PFN), molecule interacting with CasL 3 (MICAL3), cytochrome P450 (CYP450) and HSP90α in HT_LO group markedly higher than those in the Control group. GO items associated with membrane and ribosome proteins, and KEGG pathways involved cellular degradation and ribosome, were significantly enriched in all stress-treatment groups. It was worth noting that mTOR signaling pathway, FoxO signaling pathway and TGF-β signaling pathway were significantly enriched only in HT_LO group compared with the Control group. Integrated analysis between ubiquitinome and transcriptomics data highlighted a variety of genes dysregulated in both the ubiquitination and the mRNA level. Our research may further help reveal the mechanism of stress response from the perspective of protein ubiquitination.
Navigating salt gradients: Transcriptomic strategies of bivalves for surviving salinity stress in aquatic systems.
Alba MM, Mello FT, Capeletti J … +3 more , Gutiérrez JM, Marroni S, D'Anatro A
Comp Biochem Physiol Part D Genomics Proteomics · 2026 Sep · PMID 41793930 · Publisher ↗
Salinity fluctuations are among the most pervasive abiotic stressors in coastal and estuarine ecosystems, shaping the physiology, distribution, and resilience of bivalves. Over the past decade, more than thirty transcrip...
Salinity fluctuations are among the most pervasive abiotic stressors in coastal and estuarine ecosystems, shaping the physiology, distribution, and resilience of bivalves. Over the past decade, more than thirty transcriptomic studies have examined the molecular responses of oysters, clams, and mussels to salinity change. However, the diversity of experimental designs, tissues analysed, and genome annotation quality has limited cross-species synthesis and has hindered the identification of conserved molecular signatures that define the evolutionary transition between different salinity regimes. In this review, we integrate evidence from 32 transcriptomic datasets encompassing 18 bivalve species to identify convergent molecular processes associated with salinity stress. Across taxa, hyposalinity consistently induces antioxidant defences, osmolyte biosynthesis, and chaperone-mediated protein stabilization, while optimal salinity maintains active mitochondrial metabolism, translation, and ion transport. To illustrate these conserved patterns under standardized analysis, we reanalyzed two representative species, Crassostrea gigas and Mercenaria mercenaria, revealing 217 shared Gene Ontology (GO), including antioxidant defence systems, osmolyte metabolic processes (specifically amino acid transport), and chaperone-mediated protein folding, representing a conserved molecular toolkit for hyposaline acclimation. Beyond these biological insights, our results highlight major methodological disparities among studies, including variable biological replication, analytical frameworks, and annotation completeness, which strongly influence DEG counts and functional interpretations. Addressing these sources of technical heterogeneity through standardized comparative frameworks, rigorous reporting of metadata, and improved genomic resources will be essential to fully resolve the molecular architecture of salinity tolerance across the bivalve tree of life. This framework integrates transcriptomic data to reveal divergent adaptive trajectories along a salinity gradient, providing a molecular perspective on the evolutionary colonization of estuarine and freshwater habitats by bivalve lineages. Several bivalve families, including Unionidae, Margaritiferidae, Tridacnidae, and Pharidae, remain markedly underrepresented, particularly in freshwater environments where transcriptomic resources are scarce compared with marine and estuarine taxa. Expanding coverage across these neglected lineages and regions will be essential for building a more comprehensive picture of salinity adaptation.
Genome-wide analysis and expression profile of the thioester-containing proteins (TEP) in Micropterus salmoides.
Chen Y, Jiang M, Tang S … +4 more , Xian Y, Wen J, Zou Z, Wang Y
Comp Biochem Physiol Part D Genomics Proteomics · 2026 Sep · PMID 41785564 · Publisher ↗
Thioester-containing proteins (TEPs) play vital roles in the innate immune responses to biotic and abiotic stresses. However, comprehensive genome-wide identification and expression analyses of the TEP gene family in Mic...
Thioester-containing proteins (TEPs) play vital roles in the innate immune responses to biotic and abiotic stresses. However, comprehensive genome-wide identification and expression analyses of the TEP gene family in Micropterus salmoides (M. salmoides) are lacking. In this study, 21 TEP genes were identified in the genome of M. salmoides, including 7 copies in A2M, two in CD109, five in C3, four in C4, and single copies of C5, A2ML1, and CPAMD8. Functional analyses and evolutionary relationships indicated a high level of homology with other teleost TEPs. Transcript sequence variants analysis identified numerous non-synonymous single nucleotide variants (nsSNVs) in TEP gene transcripts, with MsA2ML1, MsC3, and MsC4 being among the most affected. These variants, while potentially reflecting genomic diversity, require further validation to distinguish true polymorphisms from transcriptional or technical artifacts. Alternative splicing (AS) analysis has revealed multiple splicing sites and events in the TEPs of M. salmoides. Differential alternative splicing (DAS) analysis showed a significant induction of MsA2ML1 variants after infection with Aeromonas. Analysis of the gene structure and multiple sequence alignments revealed that these variants were produced through AS of the 18th exon. Both transcriptome quantification and qRT-PCR validation confirmed TEP gene responsiveness to Aeromonas infection in M. salmoides. Our study provides the first comprehensive characterization of the TEPs repertoire in largemouth bass, and reveals infection-induced AS as a novel layer of regulatory complexity in teleost innate immunity.
High-dose ginsenoside Rg5 induces tissue-specific metabolic and transcriptional responses in muscle and liver of grass carp (Ctenopharyngodon idella).
Ren L, Han X, Wang Q … +9 more , Yang K, Zhang J, Zhang R, Wang Y, Zeng Y, Liu L, Liu W, Li W, Liu S
Comp Biochem Physiol Part D Genomics Proteomics · 2026 Sep · PMID 41785563 · Publisher ↗
Optimizing growth efficiency in grass carp (Ctenopharyngodon idella) is a key objective in aquaculture, yet the broader physiological responses to intensive growth-promoting treatments remain incompletely characterized....
Optimizing growth efficiency in grass carp (Ctenopharyngodon idella) is a key objective in aquaculture, yet the broader physiological responses to intensive growth-promoting treatments remain incompletely characterized. In this study, whole-genome resequencing, transcriptomics, and targeted metabolomics were integrated to assess tissue-specific responses to high-dose ginsenoside Rg5 administration. Whole-genome resequencing suggested highly comparable genetic backgrounds among experimental groups. High-dose Rg5 treatment was associated with marked myofiber hypertrophy and increased expression of igf1r and muscle structural genes, while hepatic igf1 expression was reduced. In muscle tissue, nicotinamide abundance increased by 20.8-fold, accompanied by elevated nampt expression. In the liver, 3-hydroxypropionic acid (3-HP) levels were strongly reduced, together with increased expression of gluconeogenic enzymes (g6pc and pc). In addition, expression of the endoplasmic reticulum stress marker hspa5 was substantially elevated, and transcripts of circadian regulators (clock and arntl) were reduced across tissues. These observations indicate that high-dose Rg5-induced growth is accompanied by coordinated metabolic and transcriptional adjustments in muscle and liver, highlighting potential physiological considerations associated with pharmacological growth enhancement.
Structural diversity and evolutionary dynamics of the neuropeptide Y receptor Y8b across various teleosts.
Yu XZ, Chen HT, Liu ZY
Comp Biochem Physiol Part D Genomics Proteomics · 2026 Sep · PMID 41785562 · Publisher ↗
The Neuropeptide Y receptor Y8b plays a crucial role in regulating physiological processes in teleosts, yet its structural evolution remains underexplored. This study performed a comprehensive bioinformatic analysis of t...
The Neuropeptide Y receptor Y8b plays a crucial role in regulating physiological processes in teleosts, yet its structural evolution remains underexplored. This study performed a comprehensive bioinformatic analysis of the Y8b receptor across 15 representative teleost species. Multiple sequence alignment revealed high conservation in core regions, underscoring the functional criticality of Y8b, while significant divergence in the N- and C-termini suggested species-specific adaptations. Secondary structure prediction highlighted variations in α-helix and β-sheet composition, potentially influencing conformational dynamics. Furthermore, 3D modeling and RMSD analysis demonstrated strict maintenance of the tertiary fold (RMSD <2.0 Å) even among distantly related orders. Phylogenetic analysis largely mirrored taxonomic classification but identified unique divergence in Oreochromis niloticus, implying distinct evolutionary trajectories. Collectively, these findings elucidate a conserved core, variable termini architecture for Y8b, providing a structural framework for understanding its functional diversification and ligand-binding mechanisms in aquatic vertebrates.
Explosive expansion and functional specialization of SCP genes associated with "drifting" behavior in the hard clam Meretrix meretrix.
Fu LL, Shi HM, Jin DD … +5 more , Yao HH, He L, Lin ZH, Chen HM, Dong YH
Comp Biochem Physiol Part D Genomics Proteomics · 2026 Sep · PMID 41740426 · Publisher ↗
Sarcoplasmic calcium-binding proteins (SCPs), key intracellular regulators of Ca homeostasis in invertebrates, display evolutionary dynamics that are tightly associated with species-specific physiological functions. Howe...
Sarcoplasmic calcium-binding proteins (SCPs), key intracellular regulators of Ca homeostasis in invertebrates, display evolutionary dynamics that are tightly associated with species-specific physiological functions. However, how SCP family expansion influences organismal physiological behaviors remains unclear. In this study, phylogenetic and genomic analyses revealed that the SCP gene family has undergone explosive expansions driven by extensive tandem duplications, particularly in lineages subject to extreme physiological demands, such as chitons and venerid clams. Transcriptomic profiling revealed that these expanded SCP genes have undergone significant subfunctionalization, with specialized expression across the adductor muscle, foot, mantle and hemolymph in Veneridae. This "functional amplification" may provide a general molecular basis for venerid clams to cope with intertidal environments, potentially facilitating traits such as rapid burrowing and immune defense. Against this background, the hard clam Meretrix meretrix exhibits a lineage-specific mechanism that supports its specialized "drifting" behavior. We identified a key paralog, MmerSCP14, which was specifically and highly expressed in drifting tissue and was significantly upregulated during the drifting stage (DI). Biochemical assays confirmed that the encoded protein binds Ca but not Mg. Acting as a high-fidelity Ca-responsive switch, MmerSCP14 may function as an important regulator that helps sustain Ca-dependent mucus secretion during drifting. Together, these findings link genomic expansion, tissue-level subfunctionalization and behavior-associated neofunctionalization, and are consistent with the idea that large-scale gene duplications can provide a basis for novel regulatory mechanisms contributing to complex behavioral phenotypes in marine invertebrates.
Molecular characterization of ionotropic receptors of a parasitic copepod Caligus fugu (Crustacea: Copepoda).
Rana KMS, Junji Z, Kotani T … +1 more , Tasumi S
Comp Biochem Physiol Part D Genomics Proteomics · 2026 Sep · PMID 41740425 · Publisher ↗
Chemosensation regulates behavioral responses of copepods to environmental stimuli and in parasitic species, to host-derived cues. Ionotropic receptors (IRs) are believed to play roles in chemosensory signal transduction...
Chemosensation regulates behavioral responses of copepods to environmental stimuli and in parasitic species, to host-derived cues. Ionotropic receptors (IRs) are believed to play roles in chemosensory signal transduction, especially in species, such as Caligus fugu that lack odorant and gustatory receptors. This study aimed to characterize C. fugu IR genes through Sanger sequencing using de novo assembled transcriptomic data as reference. Sanger sequencing confirmed at least one functional copy from each of four IRs (IR21a, IR25a, IR40a, and IR93a) by the retention of intact open reading frames. We performed evolutionary and structural characterization of the sequences confirmed through Sanger sequencing using phylogenetic analysis, protein homology search, and conserved domain prediction. Phylogenetic analysis showed that IR25a and IR93a clustered clearly with copepod orthologs, whereas IR21a exhibits lineage-specific divergence. Nevertheless, IR40a did not cluster with the available copepod IR40a sequences, indicating that its placement may be constrained by the limited representation of IR40a in publicly available copepod databases. However, all four C. fugu IRs contained characteristic ligand-binding and transmembrane domains, showing strong sequence similarity to crustacean homologs. The relative expression of C. fugu IRs depicted significant dominance in the infective copepod I stage compared with the free-living nauplius II stage. The combined approach of de novo assembled transcriptome analysis and Sanger sequencing yielded functional sequences of the four C. fugu IRs and will be useful for further characterizing the chemosensory mechanisms, including host-finding, of the parasite.
Postbiotics from Saccharomyces cerevisiae fermentation protect the Chinese mitten crab (Eriocheir sinensis) against hypoxia-thermal stress through metabolic regulation and antioxidant defense.
Wang S, Li E, Luo Z … +3 more , Wang X, Qin JG, Chen L
Comp Biochem Physiol Part D Genomics Proteomics · 2026 Sep · PMID 41734532 · Publisher ↗
This study investigated the protective mechanisms of postbiotics from the Saccharomyces cerevisiae fermentation product (SCFP) against combined hypoxia-thermal stress in Chinese mitten crabs. Juvenile crabs were randomly...
This study investigated the protective mechanisms of postbiotics from the Saccharomyces cerevisiae fermentation product (SCFP) against combined hypoxia-thermal stress in Chinese mitten crabs. Juvenile crabs were randomly allocated into four treatment groups (n = 4 tanks/group, 40 crabs/tank) and fed diets with 0 g/kg SCFP (control and nonsupplemented stress groups), 3.2, or 6.4 g/kg SCFP for 56 days. SCFP supplementation significantly increased weight gain compared with the control group (p < 0.05). Following the feeding trial, the control group remained under optimal conditions (24 °C, 7.0 mg/L dissolved oxygen), whereas the three stress groups (0, 3.2, and 6.4 g/kg SCFP) were exposed to acute hypoxia-thermal stress (30 °C, 1.0 mg/L dissolved oxygen, 24 h). Under stress conditions, oxygen consumption rates were significantly elevated in nonsupplemented crabs, whereas SCFP supplementation maintained rates comparable to those of the control (p < 0.05). Integrated transcriptomic and WGCNA analyses revealed that hypoxia-thermal stress significantly upregulated stress response pathways while suppressing energy metabolism pathways. SCFP supplementation modulated key metabolic pathways, particularly oxidative phosphorylation and amino acid metabolism. Biochemical and cellular analyses confirmed that 6.4 g/kg SCFP restored the NADPH-dependent redox balance and maintained integrity of the mitochondrial membrane potential, effectively counteracting stress-related metabolic imbalances. This improved metabolic state was supported by enhanced antioxidant capacity. Specifically, SCFP supplementation reduced cellular reactive oxygen species levels, decreased malondialdehyde content (p < 0.05), and improved glutathione/oxidized glutathione ratio. These findings demonstrate that SCFP supplementation protects crabs against hypoxia-thermal stress through integrated metabolic and antioxidant mechanisms, offering a promising nutritional strategy for intensive aquaculture.
Transcriptomic insights into the molecular basis of brachyurization of the mud crab Scylla paramamosain.
Ke W, Zhu Z, Liang M … +3 more , Wan Y, Liu A, Ye H
Comp Biochem Physiol Part D Genomics Proteomics · 2026 Sep · PMID 41734531 · Publisher ↗
The development of megalopa into the first juvenile crab (C1) in brachyuran species involves a key morphological event known as brachyurization metamorphosis. To date, the molecular mechanism underling brachyurization in...
The development of megalopa into the first juvenile crab (C1) in brachyuran species involves a key morphological event known as brachyurization metamorphosis. To date, the molecular mechanism underling brachyurization in crabs remains poorly understood. To shed new light on this process, this study performed comparative transcriptomic analysis of intact individuals and abdominal tissues from the mud crab Scylla paramamosain at the megalopa and C1 stages. It revealed 2317 DEGs in the intact individuals and 4864 DEGs in the abdominal tissues during brachyurization, in which 3514 DEGs were unique to the abdomen. Gene Ontology (GO) and KEGG enrichment analyses further elucidated distinctly functional preferences in different tissues during larval development. DEGs in the intact individuals were enriched in the pathways related to exoskeleton development, such as chitin metabolism and cuticle structure. In contrast, DEGs in the abdominal tissues showed significant enrichment in proteasomes, membrane components, cell junctions, and various signaling pathways (e.g., MAPK, mTOR, Hippo, Wnt), suggesting active roles in cellular remodeling, apoptosis, and signal transduction. In addition, the up-regulated transcription factor genes in the abdominal tissues, including zf-C2H2, Homeobox, and bHLH, are involed in the regulation of developmental processes. The expression profiles of 16 tissue-specific DEGs were further validated by qPCR, confirming the reliability of the transcriptomic data. Our study provides new insights into the molecular basis of brachyurization, revealing that this synergistic process-comprising exoskeleton remodeling, abdominal tissue degradation, and metabolic reprogramming-is precisely regulated by an intricate molecular network.
Integrative transcriptomic and metabolomic analysis of body color formation in transparent goldfish (Carassius auratus).
Lu F, Huang J, Wen B … +1 more , Chen ZZ
Comp Biochem Physiol Part D Genomics Proteomics · 2026 Sep · PMID 41734530 · Publisher ↗
The mechanism underlying the transparent body coloration in goldfish (Carassius auratus) remains unclear. This study employed untargeted metabolomics and transcriptomics analyses of scales, skin, and muscle tissues from...
The mechanism underlying the transparent body coloration in goldfish (Carassius auratus) remains unclear. This study employed untargeted metabolomics and transcriptomics analyses of scales, skin, and muscle tissues from transparent goldfish (T) and common goldfish (L), revealing that the transparent phenotype stems from systemic disruption of the purine metabolism network. Metabolomic analysis revealed significant downregulation of guanine and its precursor guanosine across all tissues. Correspondingly, transcriptomic analysis further demonstrated tissue-specific dysregulation of key genes involved in purine synthesis and conversion (mpv17 and pnp4a), collectively preventing iridophore cells from synthesizing sufficient reflector granules and resulting in the loss of structural coloration. Beyond iridophores, this purine metabolic abnormality triggered cascading dysfunctions across the pigment cell network. In melanocytes, the differentiation driver mitfb was upregulated while the synthesis executor tyrp1 was silenced, exemplifying a pattern of enhanced signaling but blocked execution. Compensatory upregulation of the carotenoid transport gene scarb1 also failed to complete pigment deposition. This study, for the first time through integrated metabolomic and transcriptomic analyses, systematically reveals the cascade effects triggered by purine metabolic dysregulation in transparent goldfish and elucidates the molecular mechanism by which purine metabolism disruption impairs iridophore function and further leads to abnormalities in the entire pigment cell system. It offers a new theoretical framework for understanding the evolution and artificial regulation of fish coloration.
The genome-wide identification and gonad-specific expression analysis of the PfTSSK gene family in Pinctada fucata.
Guo T, Guo Y, Wang P … +7 more , Sang X, Chen W, Zhu R, Wang H, Pan C, Bai L, Yu D
Comp Biochem Physiol Part D Genomics Proteomics · 2026 Jun · PMID 41722232 · Publisher ↗
Pinctada fucata is a crucial marine pearl oyster species for pearl culture, and the regulation of gonadal maturation is essential for pearl oyster breeding. This study investigates the genetic characteristics and express...
Pinctada fucata is a crucial marine pearl oyster species for pearl culture, and the regulation of gonadal maturation is essential for pearl oyster breeding. This study investigates the genetic characteristics and expression patterns of the testis-specific serine/threonine kinase family (PfTSSK) in this species. A total of six PfTSSK genes were identified, namely PfTSSK1, PfTSSK1-like, PfTSSK3, PfTSSK4, PfTSSK5, and PfTSSK7, among which PfTSSK1-like is a newly reported member in P. fucata. Phylogenetic and conserved motif analyses indicated that these genes are highly conserved among bivalves, but exhibit evolutionary divergence compared to those in mammals. The cis-regulatory element analysis suggests that this gene family may influence growth and developmental processes through gene regulation. Expression profile analysis revealed that PfTSSK genes are most highly expressed in the testes, particularly during testicular maturation, while their expression in the ovaries is lower but synchronized with female gametogenesis. In situ hybridization results demonstrated that PfTSSK are expressed in various cells within both the testes and ovaries, suggesting their involvement in the development of both male and female gametes. This study provides new insights into the molecular mechanisms underlying bivalve reproductive development and lays a theoretical foundation for the molecular regulatory network governing gonadal development and gametogenesis.
Sex-biased transcriptome dynamics during embryogenesis of the Eriocheir sinensis.
Liu Y, Shao S, Yang Y … +6 more , Ni M, Xue X, Zheng J, Zhang Y, Li B, Cui Z
Comp Biochem Physiol Part D Genomics Proteomics · 2026 Jun · PMID 41702304 · Publisher ↗
The embryonic stages of Eriocheir sinensis are critical for establishing early sex-differentiation signals, yet the molecular mechanisms remain unclear, partly due to the long-standing lack of effective techniques for se...
The embryonic stages of Eriocheir sinensis are critical for establishing early sex-differentiation signals, yet the molecular mechanisms remain unclear, partly due to the long-standing lack of effective techniques for sex identification in embryos. In this study, sex was distinguished using a sex-specific molecular marker available exclusively in our research group. Transcriptome sequencing combined with weighted gene co-expression network analysis (WGCNA) was then employed to compare sex-biased gene expression across three embryonic stages (blastula, gastrula, and egg-nauplius). Results showed a "development-dominated, sex-emerging" transcriptional pattern. WGCNA identified 19 co-expression modules in which the gene expression was mainly different among developmental stages. Only a clear sex bias was showed at the blastula stage with green and light-yellow modules. Combined with differentially expressed genes (DEGs), the germline and reproduction related genes (VASA, WNT7, FTZ-F1, and GATA4) were upregulated at the male blastula. Notably, the marked sex regulators (Sxl, tra-2c, fem-1b, runt1a, FoxL2, and Sox-14) showed stage-dependent expression and peaked at the gastrula stage, as supported by both DEG analysis and Mfuzz trend clustering. This gastrula-peaked pattern was accompanied by enrichment of spliceosome and nucleocytoplasmic transport pathways in both sexes. It is suggested that sex differences during embryo genesis may partly be shaped at the RNA/splicing level. These findings reveal the connection between developmental and sex-regulatory programs in E. sinensis embryo stages, providing new molecular insights into crustacean sex differentiation.
Population-specific phenotypic plasticity of endangered bivalves in response to extreme events.
Gomes-Dos-Santos A, Lopes-Lima M, Silva B … +15 more , Machado AM, Pinto R, Österling M, Wallerius ML, Urbańska M, Golski J, Runowski S, Kaźmierczak S, Teixeira A, Sousa R, C Castro LF, Castro P, Carvalho F, Fonseca E, Froufe E
Comp Biochem Physiol Part D Genomics Proteomics · 2026 Jun · PMID 41690096 · Publisher ↗
Freshwater mussels are among the most endangered animal groups, highly sensitive to climate change due to their strict dependence on freshwater habitats. While freshwater mussels are often considered ecologically strict,...
Freshwater mussels are among the most endangered animal groups, highly sensitive to climate change due to their strict dependence on freshwater habitats. While freshwater mussels are often considered ecologically strict, their distribution across broad environmental gradients raises the possibility of population-specific adaptations mediated by phenotypic plasticity. This study investigates whether geographically and climatically distinct populations of two freshwater mussel species (Unio pictorum and Unio delphinus) exhibit different transcriptomic responses to prolonged heat stress and whether these responses reveal signs of local adaptation. We exposed northern and southern populations of both species to gradually increasing temperatures in controlled laboratory conditions, simulating a prolonged thermal extreme event, and RNA-seq was used to quantify differential gene expression. Results showed strong differences between northern and southern populations of the two species, both in the magnitude and functional composition of transcriptomic responses. Southern populations exhibited intense expression shifts involving classical stress pathways, heat shock proteins, detoxification (cytochrome P450s), apoptosis, and energy metabolism, while northern populations, particularly U. delphinus, showed a markedly subdued response. Notably, U. pictorum's northern population relied heavily on the cytochrome P450 family even at moderate temperatures, while the southern populations of both species activated broader proteostasis and immune responses at higher stress thresholds. These findings demonstrate clear population-specific phenotypic plasticity, shaped by environmental conditions rather than phylogenetic proximity. They underscore the need for conservation strategies to move beyond species-level management, embracing intraspecific variation as a buffer against climate impacts. As climate change accelerates, safeguarding the evolutionary potential encoded within populations, not just species, is essential to preserving biodiversity resilience.
Comparison of transcriptomics and proteomics revealed distinct molecular mechanisms underlying egg development of Culter alburnus between northern and southern China.
Chen H, Guo Z, Zhang Z … +4 more , Cai S, Wang J, Chen X, Wang C
Comp Biochem Physiol Part D Genomics Proteomics · 2026 Jun · PMID 41687135 · Publisher ↗
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 C...
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.
Transcriptomic profiling reveals the mechanisms underlying growth divergence in Apostichopus japonicus.
Chang S, Abulizi A, Huang X … +3 more , Cong J, Sun Z, Wang Y
Comp Biochem Physiol Part D Genomics Proteomics · 2026 Jun · PMID 41687134 · Publisher ↗
Sea cucumber (Apostichopus japonicus) displays considerable variation in growth rates under the same cultivation conditions, with a subset of individuals displaying a "growth stagnation" phenotype. After one year of labo...
Sea cucumber (Apostichopus japonicus) displays considerable variation in growth rates under the same cultivation conditions, with a subset of individuals displaying a "growth stagnation" phenotype. After one year of laboratory cultivation from the same breeding population, normally growing (NG) individuals of A. japonicus averaged 38.02 ± 3.36 g, whereas stunted-growing (SG) individuals averaged 2.02 ± 0.360 g. To investigate the molecular basis of this growth divergence, transcriptomic profiling was performed on the body wall tissues of NG and SG individuals. A total of 816 differentially expressed genes (DEGs) were identified, including key genes related to growth, muscle function, motility, and cytoskeletal organization. NG individuals showed upregulation of growth-promoting genes such as HGFR and RAS. Whereas SG individuals exhibited significant upregulation of genes associated with muscle and cytoskeletal structure, including ACTG1, MYHC, TITIN, and FLNB, reflecting compensatory or disordered activation rather than productive growth, as further supported by histological observations of abnormal muscle tissue. Furthermore, traditional Chinese medicine compounds, including Imperatae Rhizoma and Hedysarum multijugum Maxim, were identified as potential modulators of HGFR and RAS signaling. These findings provide new insights into the regulation of growth in A. japonicus and may lay the foundation for developing herbal-based strategies to mitigate growth retardation.
Physiological response and transcriptomics study of three Litopenaeus vannamei populations to alkaline stress and recovery.
Xu R, Hou Y, Lei Y … +2 more , Liu J, Dilorakhon Rasuljon Kizi D
Comp Biochem Physiol Part D Genomics Proteomics · 2026 Jun · PMID 41678992 · Publisher ↗
The development of alkali-tolerant shrimp strains is crucial for sustainable aquaculture in saline-alkaline waters. However, the population-specific genetic basis of alkali tolerance remains poorly understood. This study...
The development of alkali-tolerant shrimp strains is crucial for sustainable aquaculture in saline-alkaline waters. However, the population-specific genetic basis of alkali tolerance remains poorly understood. This study investigated the immuno-physiological and transcriptomic responses of three Litopenaeus vannamei populations (DF, XH and SIS) to alkaline stress (AG, 15 mmol/L alkalinity for 72 h), and recovery (AR, post-stress return to 1.2 mmol/L for 72 h). Alkaline stress induced significant gill and hepatopancreas damage, characterized by structural distortion and vacuolization. Physiologically, stress suppressed antioxidant capacity (SOD, CAT, GSH-Px) and elevated lipid peroxidation (MDA), while simultaneously activating immune defenses (increased ACP and ALP activities) and disturbing osmoregulation (altered NKA and CA activities). During recovery, tissue integrity and antioxidant capacity improved, and immune/osmoregulatory indicators partially recovered, though not fully to control levels. Transcriptomic analysis revealed population-specific response strategies: The XH (4932 and 4435 DEGs during stress and recovery, respectively) maintains homeostasis via synergistic activation of oxidative phosphorylation and glutathione metabolism across both stages to mitigate oxidative stress; The DF (13,047 and 2579 DEGs) activates innate immunity through pathways like C-type lectin receptor signaling under stress and relied on arachidonic acid metabolism-involved metabolic adaptation during recovery; The SIS population (11,842 and 3351 DEGs) potentially undergoes insulin-PI3K-Akt-mTOR-driven immunometabolic reprogramming under alkaline stress, and may mediate epithelial barrier repair via, for example, the Rap1 signaling pathway and other related pathways during the recovery phase. WGCNA identified 23 hub genes (e.g., APOD, ARSB, RPS15/19/5, SORD) that coordinate stress adaptation by immune responses, oxidative damage alleviation, and regulating energy metabolism. This study reveals dynamic changes in gene expression profiles and regulatory networks of different L. vannamei populations during acute alkaline stress and short-term recovery, providing key theoretical basis for elucidating their alkali tolerance molecular mechanisms.
Identification of genes involved in the development of Weberian apparatus in rohu, Labeo rohita (Hamilton, 1822), as revealed by comparative transcriptome analyses.
Priyadarshini N, Nandanpawar P, Sahoo B … +3 more , Mahapatra PK, Sahoo L, Das P
Comp Biochem Physiol Part D Genomics Proteomics · 2026 Jun · PMID 41671962 · Publisher ↗
Ostariophysi has a history of successful adaptation to freshwater environments due to the evolution of a unique morphological structure, i.e. Weberian apparatus (WA). This structure transfers sound waves from the swim bl...
Ostariophysi has a history of successful adaptation to freshwater environments due to the evolution of a unique morphological structure, i.e. Weberian apparatus (WA). This structure transfers sound waves from the swim bladder to the inner ear by forming a physical linkage that leads to enhanced hearing sensitivity. However, there are very few reports on genes specifically linked to this modified structure in fish. In this study, we compared Weberian ossicles, the modified vertebrae, and unmodified vertebrae transcriptomes of representative species from ostariophysi and non-ostariophysi by mRNA sequencing. A total of 21 and 25 million high-quality reads were generated from Labeo rohita and Oreochromis niloticus, respectively, and differential expression analysis identified 161 upregulated and 98 down-regulated transcripts (>2 fold change) between modified and unmodified vertebrae. Functional annotation revealed their significant involvement in biological functions such as energy metabolism, osteoblast proliferation, differentiation, and matrix mineralization related to bone development. A total of 41 miRNA target interactions were found to be associated with differentially expressed transcripts (p < 0.05). Fourteen hub genes were identified and categorized into six major GO terms: endoplasmic reticulum, large ribosomal subunit, rRNA binding, translation and metabolic process. Ontogenic expression of selected genes linked to ossification showed elevated expression till 3 days post-hatch (dph). A novel gene, LrOSSP1 (Ossicle Secretory Signal Protein 1), reported for the first time, exclusively found in ostariophysi, demonstrated significant up-regulation in the earliest stages of larval development in this study. This is the first report of its kind in Labeo rohita and will be helpful in understanding the molecular underplay of modified vertebrae in ostariophysans.
The SoxE gene family in Siniperca scherzeri: Systematic characterization, spatiotemporal expression, and sexual dimorphism in early gonads.
Deng B, Chen D, Lin S … +8 more , Li J, Yang H, Cai G, Deng Z, Xie Z, Zhan L, Han C, Li Q
Comp Biochem Physiol Part D Genomics Proteomics · 2026 Jun · PMID 41666563 · Publisher ↗
This study systematically identified all six members of the soxE gene family (sox8a, sox8b, sox9a, sox9b, sox10a, sox10b) in Siniperca scherzeri for the first time. Their conserved HMG-box domains were confirmed through...
This study systematically identified all six members of the soxE gene family (sox8a, sox8b, sox9a, sox9b, sox10a, sox10b) in Siniperca scherzeri for the first time. Their conserved HMG-box domains were confirmed through bioinformatics analysis. The expression patterns of these genes were analyzed across different tissues of adult fish and during various stages of gonad development. Additionally, the effects of 17α-methyltestosterone (MT) immersion treatment during the critical period of sex differentiation on soxE genes expression and gonad development were investigated. The results revealed that the expression levels of all soxE genes were significantly higher in male individuals, particularly in the testes, compared to females, indicating pronounced sexual dimorphism. Specifically, MT treatment significantly upregulated the expression of sox9a and sox9b, accompanied by an increase in the expression of the male-related gene dmrt1 and a decrease in the expression of the female-related gene cyp19a1a, thereby inducing sex reversal in genetic females. These findings suggest that the soxE gene family, particularly the two isoforms of sox9, may play crucial roles in male sex determination, gonad development, and the regulatory network of sex differentiation in Siniperca scherzeri, providing an important molecular foundation for understanding its sex determination mechanisms.
Comparative metabolomic analysis reveals sex differences and heat stress responses in germ cells of Sipunculus nudus.
Feng W, He M, Li W
Comp Biochem Physiol Part D Genomics Proteomics · 2026 Jun · PMID 41666562 · Publisher ↗
The sipunculid worm Sipunculus nudus is a dioecious marine invertebrate with ecological and aquaculture importance. To investigate the metabolic features underlying gamete specialization and thermal response, we performe...
The sipunculid worm Sipunculus nudus is a dioecious marine invertebrate with ecological and aquaculture importance. To investigate the metabolic features underlying gamete specialization and thermal response, we performed untargeted metabolomic analysis of spermatozeugmata and oocytes under control conditions, as well as oocytes exposed to acute heat stress (37 °C for 24 h; n = 6 males, 6 females, and 4 heat-stressed females) using ultra-high-performance liquid chromatography-mass spectrometry (UHPLC-MS). Combined multivariate and univariate statistical analyses, applied with fold-change and significance thresholds, revealed 894 putatively annotated metabolites that differed between oocytes and spermatozeugmata, and 1749 that changed significantly under heat stress. Oocytes were enriched in lipid species (e.g., phospholipids such as PI and LPC) and nucleotide derivatives (e.g., putatively annotated uridine monophosphate, deoxynucleosides), whereas spermatozeugmata showed higher levels of lipids (e.g., PE and PC species), amino acid derivatives (e.g., putatively annotated N-acetyl-DL-serine), and small peptides. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis indicated that metabolites mapped to neurotransmitter and energy metabolism pathways were more prominent in oocytes, while metabolites associated with antioxidant and nucleotide biosynthesis pathways were comparatively enriched in spermatozeugmata. Under heat stress, oocytes exhibited significant metabolic changes, with increased organic acids and lipid metabolites (fatty acids and glycerophospholipids) and decreased nucleotide- and amino acid-related compounds. Most KEGG-mapped metabolic pathways showed an overall reduction in associated metabolites, including amino sugar, nucleotide, and amino acid metabolism, whereas metabolites mapped to Fc epsilon RI signaling and bile secretion KEGG pathways were relatively enriched. This study provides the first comprehensive metabolomic profile of S. nudus germ cells, revealing sex-specific metabolic patterns and heat-induced reprogramming of oocyte metabolism. These findings enhance our understanding of gamete physiology and acute thermal stress responses in marine invertebrates and may contribute to the development of reproductive health biomarkers.
Integrated ATAC-seq and RNA-seq analyses reveal epigenetic regulation of body color variation in the leopard coral grouper (Plectropomus leopardus).
Zhang D, Li H, Li L … +9 more , Long H, Yang S, Hao R, Wang C, Hu Q, Deng Q, Ru X, Huang Y, Zhu C
Comp Biochem Physiol Part D Genomics Proteomics · 2026 Jun · PMID 41666561 · Publisher ↗
The leopard coral grouper (Plectropomus leopardus) is a reef-dwelling fish that is highly valued for its striking coloration. This coloration is affected by the expression of genes, which is, in turn, governed by chromat...
The leopard coral grouper (Plectropomus leopardus) is a reef-dwelling fish that is highly valued for its striking coloration. This coloration is affected by the expression of genes, which is, in turn, governed by chromatin structure. In this study, we characterized chromatin accessibility in black and red morphs to identify regulatory elements associated with pigmentation. Most accessible chromatin regions (ACRs) were located in non-coding regions, especially distal intergenic regions; the number of ACRs was 7.26% and 8.01% greater in distal intergenic regions than in promoters (≤1 kb) in black and red groups, respectively. Comparative analysis uncovered 3480 differentially accessible regions (DARs), including 2926 with increased and 554 with decreased accessibility. 1764 genes annotated from the identified DARs were subjected to functional enrichment analysis. Gene Ontology (GO) enrichment analysis of these genes derived from DARs revealed significant associations with pigmentation-related processes, including pigment granule formation, pigment biosynthesis, and melanin metabolism. Meanwhile, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis indicated that these genes were significantly enriched in multiple pathways, such as melanogenesis, the MAPK signaling pathway, lipid metabolism pathways (fatty acid, α-linolenic acid, and linoleic acid metabolism), and immune-related signaling pathways (TNF, IL-17, and C-type lectin receptor pathways). Integrated analysis of ATAC-seq and RNA-seq data revealed a positive association between chromatin accessibility and differential gene expression. Overall, these findings shed light on the regulatory landscape underlying body color variation in P. leopardus and provide valuable insights with implications for enhancing the coloration of fish via genetic approaches and selective breeding.
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