Comp. Biochem. Physiol. Part D Genomics Proteomics [JOURNAL]
Sun
200 papers
Transcriptomics reveals the temporal responses of sea cucumber (Apostichopus japonicus) to the challenge by bacterial peptidoglycans.
Gao S, Jiang P, Zhao Z … +10 more , Zhang F, Liu Y, Sun H, Li P, Xiao Y, Pan Y, Zhang G, Yue D, Jiang J, Zhou Z
Comp Biochem Physiol Part D Genomics Proteomics · 2026 Jun · PMID 41655475 · Publisher ↗
Sea cucumber (Apostichopus japonicus) is of considerable commercial and ecological value, yet disease outbreaks substantially constrain the sustainable development of its aquaculture industry. The molecular mechanisms un...
Sea cucumber (Apostichopus japonicus) is of considerable commercial and ecological value, yet disease outbreaks substantially constrain the sustainable development of its aquaculture industry. The molecular mechanisms underlying A. japonicus's response to pathogenic bacterial invasion remain incompletely elucidated to date, particularly with respect to its differential response to peptidoglycans derived from distinct Gram-specific bacteria. In this study, the transcriptomes of A. japonicus coelomocytes were analyzed in response to challenges involving two different peptidoglycans: one from Gram-negative Escherichia coli (named "EK") and the other from Gram-positive Bacillus subtilis (named "BS"). Signal transduction, post-translational modification, and immune pathways were recognized as the dominant functions related to the identified transcripts. Significant variations in gene expression profiles were observed during the challenges, with tens of thousands of genes being expressed differently between the challenged and control groups. Further KEGG enrichment analyses revealed that the alternative complement pathway and apoptosis were the primary immune pathways, which were greatly up-regulated at 72 h after both challenges. Additionally, the enriched pathways revealed a distinct initial response of A. japonicus to different challenges, characterized by the upregulation of signal transduction pathways in the BS treatment group and stronger lipid and energy metabolism in the EK group. Furthermore, cell adhesion-related pathways were found to be enriched in A. japonicus at 96 h after the challenges. Moreover, according to the Venn diagram, the cytochrome c oxidase subunit I (CO1) and gag-pro-pol polyprotein transcripts were down-regulated throughout both challenges. Preliminary investigation of the function of the A. japonicus gag-pro-pol polyprotein was conducted using RNAi combined with RNA-Seq analysis. This revealed that four functional gene groups, including those responsible for vitamin transport, antioxidation and inflammation, cell adhesion, and complement activation, were positively regulated by this gene. Therefore, it can be speculated that the peptidoglycans from Gram-negative and -positive bacteria not only triggered differentiated immune reactions in A. japonicus, but also suppressed some immune response, nutrition absorption and energy delivery via the negative regulation of CO1 and gag-pro-pol polyprotein gene expression.
miR-182-5p affects melanin formation in Crassostrea gigas by regulating the MITF gene.
Li Y, Wang W, Liu W … +7 more , Zhao J, Zhang X, Han Y, Zhang H, Jia X, YangLi J, Wang X
Comp Biochem Physiol Part D Genomics Proteomics · 2026 Jun · PMID 41653664 · Publisher ↗
MicroRNAs (miRNAs) contribute to diverse biological functions and physiological mechanisms through the intricate regulation of their target genes. In this study, we investigated the influence of miR-182-5p on pigmentatio...
MicroRNAs (miRNAs) contribute to diverse biological functions and physiological mechanisms through the intricate regulation of their target genes. In this study, we investigated the influence of miR-182-5p on pigmentation in Crassostrea gigas. Differentially expressed miR-182-5p associated with melanin formation was successfully screened using small RNA sequencing. qRT-PCR revealed a higher expression level of miR-182-5p in the white mantle and lower expression in hemocytes and the black mantle across diverse tissues of C. gigas. Target prediction analyses identified microphthalmia-associated transcription factor (MITF) as a potential target of miR-182-5p. The relationship between MITF and miR-182-5p was further verified via the overexpression and inhibition of miRNAs, as well as by a dual-luciferase reporter assay. Masson-Fontana melanin staining revealed a marked decrease in pigment granules after injections of miR-182-5p mimics. Western blotting analyses revealed that changes in miR-182-5p levels could regulate MITF protein expression. Upon miR-182-5p overexpression, genes associated with melanin synthesis were markedly downregulated in the mantle tissue. In summary, miR-182-5p participates in the regulation of melanin formation in C. gigas through the regulation of MITF. These results are significant for elucidating the regulatory role of miRNAs in mollusk melanin synthesis and promoting comprehension of the molecular mechanisms underlying mollusk melanin formation.
Genome-wide association analysis to identify novel candidate genes and genomic model optimization to predict acute low-temperature stress resilience in olive flounder (Paralichthys olivaceus).
Hanchapola HACR, Kim G, Omeka WKM … +14 more , Gong P, Liyanage DS, Udayantha HMV, Kodagoda YK, Dilshan MAH, Rodrigo DCG, Ganepola GANP, Jo Y, Lee J, Massault C, Jerry DR, Lee J, Kim J, Lee J
Comp Biochem Physiol Part D Genomics Proteomics · 2026 Jun · PMID 41653663 · Publisher ↗
The Republic of Korea is the global leading producer of olive flounder (Paralichthys olivaceus), accounting for approximately 49% of national aquaculture production. Acute low-temperature stress poses a major challenge t...
The Republic of Korea is the global leading producer of olive flounder (Paralichthys olivaceus), accounting for approximately 49% of national aquaculture production. Acute low-temperature stress poses a major challenge to this industry, causing substantial economic losses through impaired growth, increased mortality, and compromised immune function. This study aimed to identify genetic markers associated with acute low-temperature stress tolerance using a genome-wide association study (GWAS) and determine optimal genomic prediction parameters. A total of 576 healthy olive flounders (average weight 419.57 ± 9.56 g) were subjected to acute low-temperature stress at 9 °C for 20 min. Serum cortisol levels were measured and caudal fin samples were collected from 384 individuals for genomic DNA isolation. Genotyping using a 70 K single-nucleotide polymorphism (SNP) chip yielded 57,638 high-quality SNPs from 375 individuals, which were analyzed using a linear mixed model. Eighteen putative SNPs exhibiting suggestive significance level (p < 1 × 10) were identified on chromosomes 8, 20, and 21; however, none surpassed the Bonferroni-corrected genome-wide significance threshold (p < 8.6 × 10). These suggestive associations, therefore, require validation in independent populations. Among them, SNPs AX-419197258 and AX-419200963 explained 3.44% and 3.25% of the phenotypic variance, respectively. Functional annotation indicated that putative candidate genes, including gbe1, serta, lpgat1, and il20ra, are involved in key biological and immune-related pathways. Genomic prediction analyses demonstrated that the random forest model achieved the highest accuracy for predicting serum cortisol levels. Moreover, GWAS-based marker selection outperformed random marker selection, with approximately 1000 markers identified as optimal for reliable prediction. Collectively, these findings provide insights into the genetic architecture of low-temperature stress tolerance in olive flounder and support the application of genomic approaches in selective breeding programs to enhance resilience and sustainability in aquaculture.
Molecular responses to high temperature in the intestine of the sea urchin Strongylocentrotus intermedius.
Huang J, Liu X, Fan Y … +5 more , Xu H, Tian Y, Han L, Zhao C, Ding J
Comp Biochem Physiol Part D Genomics Proteomics · 2026 Jun · PMID 41650490 · Publisher ↗
The sea urchin Strongylocentrotus intermedius is a commercially cold-water species in China, and is highly sensitive to temperature fluctuation. High temperatures from global warming pose a major threat to its survival a...
The sea urchin Strongylocentrotus intermedius is a commercially cold-water species in China, and is highly sensitive to temperature fluctuation. High temperatures from global warming pose a major threat to its survival and physiological homeostasis in summer. However, little is known about the molecular regulatory mechanisms of the heat stress response in the intestine of adult S. intermedius. In this study, RNA sequencing and data-independent acquisition (DIA)-based proteomics were applied to investigate intestinal transcriptomic and proteomic responses of adult S. intermedius following a 15 day high-temperature exposure (25 °C), compared with a control group maintained at 15 °C. Transcriptomic profiles showed that heat stress significantly suppressed the expression of COX and ATPase subunits in the oxidative phosphorylation pathway, potentially reducing energy synthesis efficiency. Meanwhile, the expression of heat shock proteins and molecular chaperones was upregulated to enhance misfolded protein repair. In the proteomic profile, high temperature upregulated LC3C and STK11 in autophagy pathway, which may promote the clearance of damaged components, while caspase-3 mediated apoptosis was also enhanced. Integrative analysis identified 20 co-upregulated DEGs/DEPs, mostly enriched in protein processing in the endoplasmic reticulum pathway, highlighting its key role in high temperature response. Additionally, cathepsins involved in immune-related pathways were downregulated, potentially affecting intestinal immunity. The present study enriches the current knowledge of the high temperature response in adult S. intermedius, and provides important insights into heat stress regulation in S. intermedius and other echinoderms.
Comprehensive identification, phylogenetic analysis, and sex-biased expression of the Sox gene family in Spinibarbus hollandi.
Yang W, Zhou J, Li S … +6 more , Lai J, Zhang M, Xie Z, Han C, Li Q, Huang J
Comp Biochem Physiol Part D Genomics Proteomics · 2026 Jun · PMID 41643345 · Publisher ↗
The Sox gene family plays a fundamental role in vertebrate reproductive processes, including sex determination, gonadal development, and steroidogenesis. In this study, 42 Sox genes were systematically identified in the...
The Sox gene family plays a fundamental role in vertebrate reproductive processes, including sex determination, gonadal development, and steroidogenesis. In this study, 42 Sox genes were systematically identified in the genome of Spinibarbus hollandi and categorized into seven subfamilies (B1, B2, C, D, E, F, and H) based on phylogenetic and conserved domain analyses.Comparative genomics and gene structure evaluations demonstrated high evolutionary conservation alongside functional diversification, likely driven by teleost-specific whole-genome duplication (TS-WGD). Quantitative real-time PCR (qRT-PCR) across eight adult tissues revealed distinct expression profiles: 14 genes exhibited brain-predominant expression, with eight of these being the most abundant across all tissues. Notably, significant sexual dimorphism was observed in the gonads; Sox-3 and Sox-11b were characterized as female-biased (ovary-enriched), while Sox-9a/9b and Sox-30 were identified as male-biased (testis-enriched). Masculinization experiments induced by 17α-methyltestosterone (MT) demonstrated that exogenous androgens suppress female-biased Sox genes and activate male-biased ones, facilitating ovarian transformation into testis-like tissue via an androgen receptor-mediated regulatory cascade. Interestingly, Sox-17 and Sox-10 maintained stable expression across different gonadal states, suggesting their involvement in cellular homeostasis independent of hormonal fluctuations. Collectively, these findings elucidate the functional plasticity and endocrine-regulatory roles of Sox genes in teleost gonadal differentiation, providing a molecular basis for understanding sex determination mechanisms and enhancing sex-control technologies in aquaculture.
Comprehensive transcriptome analysis of somatic and gonadal tissues for identification of sex-biased genes in spotted scat (Scatophagus argus).
Lin X, Wu T, Jiang D … +5 more , Shi H, Tian C, Chen H, Li G, Deng S
Comp Biochem Physiol Part D Genomics Proteomics · 2026 Jun · PMID 41637829 · Publisher ↗
The spotted scat (Scatophagus argus), an economically valuable aquaculture species in southern China, exhibits a pronounced sexual dimorphism in growth performance, with females growing significantly faster than males. N...
The spotted scat (Scatophagus argus), an economically valuable aquaculture species in southern China, exhibits a pronounced sexual dimorphism in growth performance, with females growing significantly faster than males. Nevertheless, progress in sex-controlled breeding remains limited due to limited understanding of its sex determination and differentiation mechanisms. To investigate sex-biased gene expression in this species, a comprehensive transcriptomic analysis was performed. A total of 62 transcriptomic libraries were analyzed, comprising 18 newly sequenced libraries derived from female gill, muscle, stomach, heart, and adipose tissue, and male adipose tissue, integrated with 44 publicly available libraries covering the brain, pituitary gland, liver, kidney, gonads, and other tissues. The analysis identified 33,214 unigenes, including 8958 novel genes, with 1724 receiving functional annotation. Principal component analysis (PCA) and heatmap clustering revealed distinct expression profiles in gonadal (ovary and testis) and somatic tissues. Differential expression analysis identified 2951 ovary-highly expressed and 1660 testis-highly expressed genes. Functional annotation revealed genes essential for folliculogenesis, spermatogenesis, and meiosis, including figla, gdf9, mos, amhr2, spata22, and dmc1. Additionally, 23 ovary-specific and 75 testis-specific genes were identified. KEGG enrichment analysis revealed significantly enriched pathways in the gonads, including oocyte meiosis, cell cycle, and DNA replication. RT-PCR and qRT-PCR validations confirmed the RNA-seq results, demonstrating consistent tissue-specific expression patterns of these genes. These findings advance the understanding of the molecular mechanisms of sex differentiation and gametogenesis in spotted scat and provided a foundation for studies of reproductive regulation and gonadal development in this species.
Proteomic analysis of spermathecal fluid in Amphioctopus fangsiao: molecular insights into long-term sperm storage.
Yao J, Sun X, Huang Z … +11 more , Li Y, Luo Q, Wang W, Sun G, Xu X, Li Z, Li B, Cui C, Wang Q, Yang J, Feng Y
Comp Biochem Physiol Part D Genomics Proteomics · 2026 Jun · PMID 41619580 · Publisher ↗
Amphioctopus fangsiao is an economically important cephalopod species in northern China. A notable reproductive adaptation of this species is the prolonged storage of sperm in the female spermatheca for up to 8 months po...
Amphioctopus fangsiao is an economically important cephalopod species in northern China. A notable reproductive adaptation of this species is the prolonged storage of sperm in the female spermatheca for up to 8 months post-mating, until oocyte maturation and release. Spermathecal fluid, as a critical component of the microenvironment directly interacting with stored sperm, is essential for maintaining sperm long-term viability and fertilizing capacity. To explore the regulatory mechanism of the A. fangsiao spermathecal microenvironment during sperm storage, this study employed data-independent acquisition (DIA)-based quantitative proteomic to compare changes in protein expression between spermathecal fluid with stored sperm and without stored sperm. A total number of 3195 proteins were identified in the two groups, and 200 differentially expressed proteins were screened - 94 upregulated, 106 downregulated in spermathecal fluid with stored sperm. Functional enrichment analysis revealed that these DEPs were mainly involved in metabolic processes, antioxidant activity, and immune system processes, with significant enrichment in the glycolysis/gluconeogenesis and TCA cycle pathways. After sperm storage, glycolysis-related enzymes (PGK1, PGM1, ADPGK, ENO1) in the spermathecal fluid were significantly upregulated, while TCA cycle-related enzymes (SUCLG, IDH3) and dephosphorylases (ACP1) were significantly downregulated. This suggests that the energy supply mode in the spermatheca may shift from TCA cycle to glycolysis-dominated anaerobic metabolism to reduce the production of reactive oxygen species. Meanwhile, the dynamic expression of antioxidant proteins (TALDO1, PHGDH, UROD) may synergistically protect sperm from oxidative stress, and the downregulation of immune factors (IL17, PNP) may inhibit local immune responses to prevent stored sperm from being attacked. This study demonstrates that spermathecal fluid may ensure sperm viability through three aspects: altering energy metabolism modes, providing antioxidant defense, and suppressing immune responses. These results contribute to a deeper understanding of the sperm storage mechanism of A. fangsiao and provide a scientific basis for developing sperm storage technology in vitro.
Transcriptomic analysis of the mantle of Manila clam Ruditapes philippinarum reveals the molecular basis of biomineralization during shell regeneration.
Zhang Y, Li Y, Nie H
Comp Biochem Physiol Part D Genomics Proteomics · 2026 Jun · PMID 41616418 · Publisher ↗
Biomineralization in mollusks, particularly shell formation and repair, is a dynamic process mediated by shell matrix proteins and tightly regulated gene expression. In this study, we investigated the temporal transcript...
Biomineralization in mollusks, particularly shell formation and repair, is a dynamic process mediated by shell matrix proteins and tightly regulated gene expression. In this study, we investigated the temporal transcriptomic profiles of mantle tissue in the Manila clam (Ruditapes philippinarum) during shell repair. Experimental shells were artificially damaged in a V-shaped pattern, and regeneration was monitored at short-term (48 h), long-term (18 d), and control group (cn) using RNA-seq and qPCR analysis. Scanning electron microscopy (SEM) revealed a sequential reconstruction of the periostracum, prismatic, and nacreous layer, reflecting the temporal organization of mineral deposition. Transcriptomic analysis identified stage-specific differentially expressed genes (350 in m48h vs cn, 163 in m18d vs cn, and 119 in m48h vs m18d) enriched in pathways associated with tyrosine metabolism, chitin biosynthesis, and extracellular matrix (ECM) regulation. Early-stage repair was characterized by rapid upregulation of Pif, Tem, and chitin-binding domain genes, facilitating the formation of organic scaffolds for CaCO₃ crystallization. In later stages, DPT downregulation and reduced ECM-related gene expression, alongside sustained Pif activity, suggest a regulatory mechanism to balance ECM assembly and mineralization. Additionally, upregulation of Pax7 and tyrosine metabolism genes indicates an integration of biomineralization processes with shell structural repair. These findings provide new insights into the molecular networks orchestrating bivalve shell regeneration and identify potential genetic targets for strengthening shell robustness in aquaculture and enhancing resilience to environmental stressors such as ocean acidification.
Corrigendum to "Integrated transcriptomic and proteomic insights into low-salinity stress adaptation in Penaeus monodon" [Comp. Biochem. Physiol. Part D Genomics Proteomics (2025) 101699].
Diao H, Shi J, Jiang S … +7 more , Yang Q, Li W, Li Y, Huang J, Yang L, Ding Y, Zhou F
Comp Biochem Physiol Part D Genomics Proteomics · 2026 Jun · PMID 41611608 · Publisher ↗
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A multi-omics investigation reveals the hepatic response to salinity stress in grass carp (Ctenopharyngodon idella).
Fang X, Wang Y, Yu R … +4 more , Tang D, Li Z, Qin Q, Wei S
Comp Biochem Physiol Part D Genomics Proteomics · 2026 Jun · PMID 41610786 · Publisher ↗
In the context of increasing freshwater scarcity and the effects of climate change on aquatic environments, developing salt-tolerant fish strains has become a critical strategy for sustainable aquaculture. The limited av...
In the context of increasing freshwater scarcity and the effects of climate change on aquatic environments, developing salt-tolerant fish strains has become a critical strategy for sustainable aquaculture. The limited availability of suitable species for saline-water aquaculture poses a significant challenge, severely impacting the development of the fishery economy. This study investigated the effects of 24 h exposure to freshwater, and seawater at salinities of 4, 9 ppt and 12 ppt, on juvenile grass carp (Ctenopharyngodon idella). Following these exposures, liver tissues were collected to assess physiological and biochemical indicators, as well as transcriptional and metabolic responses. Histological examination revealed that liver structure was compromised after 24 h of exposure to 9 ppt and 12 ppt salt stress. Concurrently, we observed a decrease in the levels of Superoxide Dismutase (SOD), whereas the levels of Malondialdehyde (MDA) exhibited an increase. Salinity exposure significantly altered the levels of 120 metabolic products (67% of which were lipid and lipophilic molecules) and the transcriptional expression of 1005 genes. Metabolomic analysis indicated that most of the significantly different metabolites were associated with the metabolism of lipids and amino acids. Transcriptome analysis revealed significant enrichment of 20 metabolic pathways, including glutathione metabolism, lipid digestion and absorption, bile secretion, glycerolipid metabolism, and the tricarboxylic acid cycle. Comprehensive multi-omics analysis revealed significant alterations in key metabolic pathways, including glycerophospholipid metabolism, α-linolenic acid metabolism, histidine metabolism, and β-alanine metabolism, along with several vital genes such as HO-1, NQO1, GCLM, and GSS, under salt stress. These changes closely correlate with variations in cellular membrane lipid composition and antioxidant activity. Further analysis demonstrated that acute salt stress induces oxidative damage in the liver, leading to lipid imbalance and oxidative stress. This is evidenced by impaired antioxidant function and disruptions in amino acid and fatty acid metabolism. Moreover, carnosine synthesis in liver tissue occurs via the activation of histidine and β-alanine metabolic pathways, leading to the upregulation of CNDP2. This process plays a crucial role in regulating lipid metabolism and redox homeostasis, effectively mitigating the damage caused by acute salinity stress. In summary, these findings provide a deeper understanding of the molecular mechanisms underlying salt stress responses in grass carp and offer valuable insights for the breeding of salt-tolerant strains of grass carp.
Genome-wide identification of lipases in the oriental armyworm, Mythimna separata Walker (Lepidoptera: Noctuidae).
Liu Y, Han Z, Chen X … +5 more , Fan X, Ren S, Yang Q, Li G, Li B
Comp Biochem Physiol Part D Genomics Proteomics · 2026 Jun · PMID 41610785 · Publisher ↗
Lipases are indispensable for animal digestion. Insects rely on lipases to catabolize lipids from food in immature stages, and to break down TAGs in adults that accumulated earlier in fat body to supply flight and reprod...
Lipases are indispensable for animal digestion. Insects rely on lipases to catabolize lipids from food in immature stages, and to break down TAGs in adults that accumulated earlier in fat body to supply flight and reproduction. The oriental armyworm, Mythimna separata Walker (Lepidoptera: Noctuidae), is a migratory moth that damages crops and pastures in East Asia. We identified 85 lipases from the genome of M. separata, including 56 neutral lipases, 22 acid lipases, one lipase 3, one hormone-sensitive lipase (HSL), one lipase with Gly-Asp-Ser-Leu motif (GDSL), and four adipose-triglyceride lipases (ATGLs). The phylogeny, catalytic capacity, and expression of neutral and acid lipases were investigated. The majority of neutral and acid lipases contain the conserved GXLXG nucleophilic elbow, a Ser-Asp-His triad, and an active lid/flap, although the length of active site lids from neutral lipases was short (< 18 residues) compared to pancreatic lipases from mammals. The results of expression analyses indicated that about half of neutral lipases and 35% of acid lipases were highly expressed in 3rd instar larvae compared to egg, pre-pupal, pupal and adult stage. Our findings could contribute to a better understanding of the lipase family gene in moth species.
Transcriptomic and WGCNA analysis of immune and antioxidant responses in Meretrix meretrix under combined thermal and residual chlorine stress.
Han S, Zhu Y, Fan Y … +7 more , Zhang X, Hu H, Wang F, Liu L, Bao J, Li L, Jiang M
Comp Biochem Physiol Part D Genomics Proteomics · 2026 Jun · PMID 41605099 · Publisher ↗
As the social economy develops and living standards improve, electricity use by businesses and residents has steadily increased, resulting in more and larger thermal and nuclear power plants. Thermal discharge from coast...
As the social economy develops and living standards improve, electricity use by businesses and residents has steadily increased, resulting in more and larger thermal and nuclear power plants. Thermal discharge from coastal power plants not only introduced residual chlorine but also elevated the temperature of adjacent seawater, thereby threatening marine ecosystems, particularly benthic mollusks. However, studies investigating the molecular mechanisms associated with immunity and antioxidation in clams (Meretrix meretrix) under the combined thermal and residual chlorine stress remained scarce. Hence, a comparative transcriptomic approach with multiple stress gradients was used to detect the potential molecular mechanism. In this study, the control group was maintained at 26 °C without residual chlorine, while M. meretrix were exposed to combined stress of different temperatures (27 °C, 28 °C, 30 °C) and 0.02 mg/L residual chlorine for 30 days, and the hepatopancreas were subjected to transcriptomic analysis. The results identified 654 differentially expressed genes (DEGs), which were primarily enriched in amino acid metabolism, metabolism of cofactors and vitamins, lipid metabolism, carbohydrate metabolism, and energy pathways, including metabolism, transport and catabolism, and signal transduction. Thermal and residual chlorine stress significantly downregulated the expression of immune-related genes across all groups, including those involved in signal transduction, prophenoloxidase cascade, apoptosis, and pattern recognition proteins/receptors. Furthermore, thermal and residual chlorine stress significantly influenced the expression of antioxidant-related genes, including glutathione S-transferase (GST) and heat shock protein 70 (HSP70). Moreover, a weighted co-expression network analysis (WGCNA) analysis was conducted to detect DEGs, involving Hspa12b, CASP3, Prdx1, CYP10, CYP2C16, and txn. Generally, this study provided valuable insights into the effects of combined thermal and residual chlorine stress on the immune and antioxidant functions of the M. meretrix, laying a foundation for understanding its adaptive mechanisms and guiding ecological risk mitigation in coastal aquaculture.
Different degrees of environmental high temperature induce varying endoplasmic reticulum stress responses in Apostichopus japonicus.
Wang Q, Li S, Yang Y … +5 more , Xie R, Wang L, Wang W, Yang J, Sun G
Comp Biochem Physiol Part D Genomics Proteomics · 2026 Jun · PMID 41592379 · Publisher ↗
Heat temperature caused by changes in the global environment have significant impacts on marine organisms. Apostichopus japonicus (A. japonicus) is an economically important benthic species in China's shallow-sea aquacul...
Heat temperature caused by changes in the global environment have significant impacts on marine organisms. Apostichopus japonicus (A. japonicus) is an economically important benthic species in China's shallow-sea aquaculture. However, its growth and survival are easily affected by rising seawater temperatures. Therefore, it is necessary to explore its response to environmental high temperature. Endoplasmic reticulum (ER)stressserves as an important regulatory strategy for organisms to respond to environmental changes. It acts as the core hub connecting stress and immunity. In this study, we analyzed the histology, ultrastructure, and transcriptome of the digestive tract of A. japonicus at three temperatures: normal (18 °C), aestivation (25 °C), and lethal (32 °C) temperatures, to explore the role of ER stress in response to high temperature. Histological and ultrastructural results indicate that high temperature caused morphological changes in the digestive tract and that the structure and morphology of the ER exhibit alterations and even varying degrees of damage. A total of 603 and 4615 differentially expressed genes (DEGs) were identified by transcriptome sequencing in the T25-vs-T18 and the T32-vs-T25 group comparisons, respectively. The GO results showed that DEGs were significantly enriched in GO terms related to protein folding, such as chaperone-mediated protein folding in both comparison groups. Additionally, KEGG enrichment analysis showed that both groups activated the pathway of protein processing in the ER and induced the ER stress response. The ER molecular chaperones, including BiP, GRP94, and HSP70, were all upregulated in expression. In addition to the aforementioned ER molecular chaperones, downstream factors in the unfolded protein response, such as S1P, TRAF2, and XBP, were also significantly upregulated in T32-vs-T25 group comparisons, indicating that UPR signaling pathways had enhanced expression. Our findings have characterized the internal molecular regulatory process of A. japonicus under high temperature from the perspective of ER stress and provides clues regarding immune response and homeostatic regulation in invertebrates under environment stress. These findings can provide a reference for the formulation of management measures to mitigate the impact of climate change on aquaculture.
Identification of candidate hub genes and key pathways related to growth rate of the red swamp crayfish based on WGCNA analysis.
Sheng N, Li Y, Wang Y … +5 more , Chen Z, Li X, Tao X, Li J, Feng J
Comp Biochem Physiol Part D Genomics Proteomics · 2026 Jun · PMID 41579847 · Publisher ↗
The red swamp crayfish, Procambarus clarkii, is a commercially significant crustacean species for aquaculture globally. Growth traits are of great importance for economic efficiency in the aquaculture of the species. How...
The red swamp crayfish, Procambarus clarkii, is a commercially significant crustacean species for aquaculture globally. Growth traits are of great importance for economic efficiency in the aquaculture of the species. However, the molecular mechanisms of regulating growth rate in P. clarkii remain poorly understood. Here, to identify the hub genes and key pathways related to growth rate, transcriptome sequencing and Weighted Gene Co-expression Network Analysis (WGCNA) were conducted on the gill, heart, hepatopancreas, intestine, and muscle from P. clarkii with different growth rate in three full-sib families. A total of 906 differentially expressed genes (DEGs) in the gill (95 up-regulated and 811 down-regulated), 1042 DEGs in the heart (45 up-regulated and 997 down-regulated), 257 DEGs in the hepatopancreas (80 up-regulated and 177 down-regulated), 691 DEGs in the intestine (174 up-regulated and 517 down-regulated), and 158 DEGs in the muscle (30 up-regulated and 128 down-regulated) were identified, respectively. The DEGs were annotated into 101 GO terms, which mainly involved in chitin binding, structural components of the stratum corneum, extracellular region and extracellular space. Nine key pathways including the Wnt signaling pathway, autophagy-animal, phagosome, amino sugar and nucleotide sugar metabolism, TGF-β signaling pathway, drug metabolism-other enzymes, mTOR signaling pathway, lysine degradation, and lysosome pathway were identified based on the KEGG enrichment analysis. A hub module was identified by WGCNA analysis. The hub genes related to structural composition, such as cuticle protein 7-like and pro-resilin, as well as genes involved in various cellular processes, like ataxin-2 homolog were identified based on the PPI network analysis. Overall, the results would provide valuable insights into understanding the molecular regulatory mechanisms of growth rate of P. clarkii.
Response mechanisms of hepatopancreatic metabolism and gut microbiota in Chinese mitten crab (Eriocheir sinensis) under chronic high-pH stress.
Liu Y, Yang Z, Zhang M … +2 more , Chen X, Jiang X
Comp Biochem Physiol Part D Genomics Proteomics · 2026 Jun · PMID 41579846 · Publisher ↗
The Chinese mitten crab (Eriocheir sinensis) is a commercially important aquaculture species in China, with its survival highly vulnerable to abnormal water pH. This study subjected E. sinensis to chronic high-pH stress...
The Chinese mitten crab (Eriocheir sinensis) is a commercially important aquaculture species in China, with its survival highly vulnerable to abnormal water pH. This study subjected E. sinensis to chronic high-pH stress (control: pH = 8; experimental groups: pH = 9 and pH = 10) and integrated hepatopancreas transcriptomic/metabolomic analyses with intestinal microbiota 16S rRNA sequencing to explore its adaptive mechanisms. The results revealed distinct adaptive strategies across stress phases: under short-term (15 days) high-pH stress, E. sinensis maintained somatic homeostasis mainly via rapid regulation of carbohydrate, lipid, protein metabolism, and energy allocation. In contrast, long-term (30 days) stress drove a strategic shift toward accelerated lipid catabolism, enhanced energy metabolism, and activated immune-related pathways. Additionally, high-pH stress significantly altered the intestinal microbiota community structure, marked by increased abundances of Proteobacteria and Pseudomonas, indicating a potential risk of microbial dysbiosis. Collectively, these findings elucidate the physiological adaptation mechanisms of E. sinensis to high-pH environments and lay a theoretical foundation for improving the sustainability of its aquaculture under extreme pH conditions.
Transcriptomics analysis provides insights into the molecular response of the clam Cyclina sinensis to Vibrio infection under heat stress.
Sun D, Ouyang X, Zheng R … +4 more , Cao J, Wei L, Xu M, Wang G
Comp Biochem Physiol Part D Genomics Proteomics · 2026 Jun · PMID 41576620 · Publisher ↗
The heat stress and Vibrio infection are considered as the key factors contributing to the mass mortality of clams in summer. In this study, we explored the combined effects of high temperature and Vibrio infection on th...
The heat stress and Vibrio infection are considered as the key factors contributing to the mass mortality of clams in summer. In this study, we explored the combined effects of high temperature and Vibrio infection on the survival of the clam Cyclina sinensis. The clams C. sinensis were separately cultivated at 26 °C (low temperature) or 30 °C (high temperature) and subjected to Vibrio infection experiment. The results showed that dual challenges aggravated the mortality of clam. To further investigate the underlying mechanisms, the hepatopancreas of clam C. sinensis under varying thermal conditions were separately sampled at different infection phases, including pre-infection, 8 days post-infection (dpi) and 12 dpi. Transcriptomic analysis revealed that the dual challenges significantly decreased the expression level of genes related to immunity, antioxidation, and energy metabolism, while upregulating genes associated with apoptosis and endoplasmic reticulum stress compared to the control group (26 °C and non-infection). The functional analysis indicated that downregulated differentially expressed genes (DEGs), identified in the dual challenges groups compared with the control group, were primarily involved in lysosome, phagosome, peroxisome, carbohydrate metabolism and regulation of oxidoreductase activity. The qRT-PCR validation of 15 DEGs corroborated the RNA-seq findings. We further demonstrated that the combined stress increased the content of MDA and decreased the activity of antioxidant enzymes (SOD, CAT) and immune enzymes (ACP, LZM) in hepatopancreas. Taken together, these findings suggest that immunosuppression, oxidative damage and deficiencies in carbohydrate metabolism were potential contributors to the mass summer mortality of clams. This study provides valuable data resources and critical information for revealing the molecular response of C. sinensis to combined stress of high temperature and Vibrio infection.
Identification and expression of transient receptor potential (TRP) genes in Urechis unicinctus and the role of TRPC5 in immune response.
Yang Z, Zhang W, Lai W
Comp Biochem Physiol Part D Genomics Proteomics · 2026 Jun · PMID 41576619 · Publisher ↗
Transient receptor potential (TRP) ion channels play crucial roles in mediating responses to environmental stimuli. In this study, we identified 64 TRP genes from 6 subfamilies in the Urechis unicinctus genome and charac...
Transient receptor potential (TRP) ion channels play crucial roles in mediating responses to environmental stimuli. In this study, we identified 64 TRP genes from 6 subfamilies in the Urechis unicinctus genome and characterized their genomic locations, gene structures, and basic physicochemical properties. We also analyzed their expression across various developmental stages, tissues, and environmental conditions. The results revealed that TRP gene expression varied throughout development and exhibited distinct tissue-specific patterns. Notably, we identified 20 TRP genes as putative transcriptional memory genes following sulfide stress and another 7 as temperature-sensitive. We also found that both short-term drought and ultraviolet radiation affected the expression of TRP genes in U. unicinctus. Our pharmacological experiments suggested that TRPC5 is positively involved in the immune response of U. unicinctus. Furthermore, TRPC5-mediated immunoenhancement correlated with increased weight gain and a higher visceral index. Collectively, our findings provide a valuable foundation for future research into the functional roles of TRP channels in U. unicinctus.
Hepatic physiological and transcriptomic responses of grass carp (Ctenopharyngodon idella) to long-term salinity stress.
Zhu T, Zhu Z, Li S … +4 more , Tian J, Lei C, Du J, Song H
Comp Biochem Physiol Part D Genomics Proteomics · 2026 Jun · PMID 41570637 · Publisher ↗
Salinity profoundly impacts fish survival, distribution, and physiological functions. Grass carp (Ctenopharyngodon idella), a vital aquaculture species, offers a representative model to investigate salinity adaptation me...
Salinity profoundly impacts fish survival, distribution, and physiological functions. Grass carp (Ctenopharyngodon idella), a vital aquaculture species, offers a representative model to investigate salinity adaptation mechanisms, providing crucial theoretical support for aquaculture practices. While the liver is a key metabolic organ in fish salinity adaptation, its specific regulatory role in the high-salinity tolerance of grass carp remains unclear. In this study, we investigated the effects of long-term salinity stress (0parts per thousand [ppt], 4 ppt, and 8 for one month) on grass carp liver. At 4 ppt salinity, mild hepatocyte edema and acinar cell hyperplasia were observed, while at 8 ppt salinity, irregular hepatocyte shapes, dilated hepatic sinusoids, and focal inflammatory cell infiltration were detected. Transcriptome sequencing showed that increasing salinity led to significant upregulation of genes involved in steroid synthesis, lipid metabolism, and cholesterol synthesis, while immune-related gene expression trended downward. Notably, LOC127523424 (carbonic anhydrase 4), igfbp7 (insulin-like growth factor-binding protein 7), and taurine transporter genes (slc6a6b, slc6a6a) all increased with rising salinity, suggesting their involvement in enhancing hyperosmotic stress adaptation. In conclusion, our findings confirm a significant impact of salinity on the grass carp liver. Long-term high-salinity adaptation appears to reduce immunity, while the liver enhances high-salinity tolerance through increased steroid synthesis and metabolism.
Transcription dynamics and regulation of heat shock protein genes during stress and development in the estuarine cnidarian Nematostella vectensis.
Bhalodi JA, Surm JM, Reitzel AM
Comp Biochem Physiol Part D Genomics Proteomics · 2026 Jun · PMID 41564688 · Publisher ↗
Heat shock proteins (HSPs) are molecular chaperones that function in protecting cells from proteotoxicity. Eukaryotes have multiple HSPs that localize in the cytoplasm, endoplasmic reticulum (ER), and mitochondria. In cn...
Heat shock proteins (HSPs) are molecular chaperones that function in protecting cells from proteotoxicity. Eukaryotes have multiple HSPs that localize in the cytoplasm, endoplasmic reticulum (ER), and mitochondria. In cnidarian species, where HSPs are often used as biomarkers of environmental stress, little is known about how particular HSPs vary in copy number, expression, inducibility, and regulation within a species. Here, we characterized the full repertoire of HSP70 and HSP90 genes in an emerging model cnidarian, Nematostella vectensis. We identified five HSP70 and three HSP90 genes, with at least one homolog from each family belonging to the three primary clades based on subcellular localization. Although transcriptional induction remained insignificant by a 10 °C temperature change, two cytosolic HSP70s and one cytosolic HSP90 were significantly upregulated with a 20 °C temperature increase. Most HSPs exhibited similar developmental expression patterns, with elevated expression during the early larval stage followed by reduced expression in the juvenile stage. HSPs showed evidence for differential expression across cell types, with multiple cytosolic and ER HSPs being highly expressed in neuronal and cnidocyte populations. Moreover, the putative promoters of N. vectensis HSPs differed in both the abundance and sequences of regulatory heat shock element motifs, providing a potential mechanism of functional diversification in response to temperature and development. By characterizing expression of all HSP70 and HSP90 genes in this cnidarian, we reveal distinct roles of these core chaperones in the proteostasis response, providing a foundation for future functional studies on contributions of HSPs to cnidarian life cycle and stress resilience.
Multi-omics dissection of large-size formation in Eriocheir sinensis: Insights from RNA, metabolite profiling, and ceRNA regulatory networks.
Xuan F, Zhang X, Hu J … +10 more , Li X, Chen Y, Zhang A, Wang R, Ren Q, Wu T, Guan W, Cheng Y, Zhou J, Liu R
Comp Biochem Physiol Part D Genomics Proteomics · 2026 Jun · PMID 41548390 · Publisher ↗
Eriocheir sinensis (Chinese mitten crab) is a key economic species in China's freshwater aquaculture industry. Individual body size is a critical trait that determines both market price and production profitability. Larg...
Eriocheir sinensis (Chinese mitten crab) is a key economic species in China's freshwater aquaculture industry. Individual body size is a critical trait that determines both market price and production profitability. Large-sized crabs exhibit substantial commercial advantages; however, the underlying molecular mechanisms regulating size formation remain poorly understood. In this study, we conducted an integrative multi-omics analysis combining whole-transcriptome data (mRNA, miRNA, and lncRNA) and untargeted metabolomics across two aquaculture cohorts (cohort2023 and cohort2024). Our results revealed a systemic downregulation of glycolysis, the tricarboxylic acid (TCA) cycle, fatty acid oxidation, and glycerol metabolism in large-sized crabs, suggesting a "low consumption-high storage" metabolic strategy. In contrast, pathways related to organismal development, exoskeleton reconstruction, steroid hormone biosynthesis, and nutrient absorption were significantly upregulated, indicating enhanced growth potential and nutrient assimilation efficiency. ceRNA network modeling and cis-acting lncRNA analysis identified multiple core regulatory genes (e.g., PTGS1, TPI1, POR) as targets of complex non-coding RNA interactions involved in body size regulation. Enzyme activity assays for key rate-limiting steps in carbohydrate and lipid catabolism, along with extensive qPCR validation, further corroborated the transcriptomic findings. Taken together, our study provides the first comprehensive multi-omics perspective on the molecular basis of body size differentiation in E. sinensis, proposing a tripartite mechanism involving suppressed catabolism, stimulated growth and morphogenesis, and improved nutrient acquisition. These findings offer theoretical insight into crustacean growth regulation and provide molecular targets to support selective breeding of high-value, large-sized mitten crab strains.
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