Comp. Biochem. Physiol. Part D Genomics Proteomics [JOURNAL]
Sun
200 papers
Comprehensive transcriptomic analysis reveals detoxification gene expansion and adaptive genetic variation in the emerging pest Acanthotomicus suncei.
Dai L, Li J, Pan W … +2 more , Shen F, Hao D
Comp Biochem Physiol Part D Genomics Proteomics · 2026 Jun · PMID 41546977 · Publisher ↗
The bark beetle Acanthotomicus suncei is an emerging destructive pest of the introduced American sweetgum (Liquidambar styraciflua) in China. The molecular mechanisms underlying its successful adaptation to this exotic h...
The bark beetle Acanthotomicus suncei is an emerging destructive pest of the introduced American sweetgum (Liquidambar styraciflua) in China. The molecular mechanisms underlying its successful adaptation to this exotic host, particularly its ability to overcome plant chemical defenses, remain largely unknown. We conducted a comprehensive transcriptomic analysis of A. suncei. Our assembly yielded 30,557 unigenes (N50 = 2175 bp). We identified a significant expansion of genes within three major detoxification enzyme families: 122 cytochrome P450 monooxygenases (P450s), 75 carboxylesterases (COEs), and 47 glutathione S-transferases (GSTs). This repertoire is notably larger than that of many compared curculionid beetles. Phylogenetic analyses revealed complex evolutionary relationships, with A. suncei clustering closely with Dendroctonus species in some P450 and GST clades, while showing considerable divergence in others. Furthermore, we uncovered abundant genetic variation, with single nucleotide polymorphisms (SNPs) being highly prevalent within the coding sequences of these detoxification genes, especially P450s. Simple sequence repeat (SSR) analysis indicated a predominance of A/T-rich motifs. The remarkable expansion and substantial genetic variation observed in the detoxification gene families of A. suncei provide a compelling molecular basis for its potent detoxification capacity. These findings suggest that an enriched and highly adaptable detoxification system likely facilitates this beetle's successful colonization of the exotic host L. styraciflua. This study offers crucial insights into the molecular mechanisms of host adaptation in an emerging forest pest and identifies potential genetic targets for future management strategies.
Proteomic analysis reveals the mechanism of cold tolerance in black porgy (Acanthopagrus schlegelii) via ribosome hibernation, metabolic remodeling, and antioxidant coordination.
Li J, Sun R, Zhao T … +7 more , Tang X, Gao B, Xu G, Wang Y, Yu H, Meng Q, Zhang Z
Comp Biochem Physiol Part D Genomics Proteomics · 2026 Jun · PMID 41544486 · Publisher ↗
Low-temperature stress poses a critical challenge to the overwintering survival of black porgy (Acanthopagrus schlegelii), a commercially important marine fish distributed across the coastal waters of West Pacific region...
Low-temperature stress poses a critical challenge to the overwintering survival of black porgy (Acanthopagrus schlegelii), a commercially important marine fish distributed across the coastal waters of West Pacific region, including the continental shelves of China, Japan, and the Korean Peninsula. To unravel the molecular mechanisms underlying cold adaptation, this study employed quantitative proteomics was employed to analyze hepatic protein profiles of black porgy between three groups: control group (CG, 15 °C), cold-sensitive group (CS, 3.8 °C), and cold-tolerant group (CT, 2.8 °C). A total of 4437 proteins were identified, with 1616 differentially expressed protein (DEPs) detected among the groups. Bioinformatics analyses, including Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment, Gene Set Enrichment Analysis (GSEA), and trend analysis, revealed distinct adaptive strategies between CT and CS groups. The CT group exhibited a coordinated "energy conservation - metabolic remodeling - antioxidation" strategy: (1) significant downregulation of ribosomal subunits and protein export pathways to reduce Adenosine Triphosphate (ATP) consumption from protein synthesis (called "ribosomal hibernation"); (2) upregulation of Peroxisome Proliferator-Activated Receptor (PPAR) signaling pathway and peroxisomal functions to enhance fatty acid β-oxidation and ketone body production, facilitating efficient energy supply; (3) activation of antioxidant systems to mitigate damage induced by reactive oxygen species (ROS). In contrast, the CS group showed dysregulated energy metabolism, characterized by enhanced but inefficient glycolysis, impaired endoplasmic reticulum function, and excessive inflammatory responses, which may contribute to protential proteotoxic stress and metabolic dysfunction. Key DEPs and pathways, such as ribosomal proteins, PPAR family proteins, and peroxisomal enzymes, were identified as protential core regulators of cold tolerance in black porgy. This study provides the first comprehensive proteomic insights into the molecular mechanisms of cold tolerance in black porgy, highlighting the evolutionary significance of energy allocation and metabolic plasticity in teleosts. These findings offer potential molecular markers for breeding cold-tolerant strains, addressing critical challenges in aquaculture sustainability.
Comparative transcriptomic analysis across ovarian developmental stages in Sepiella japonica provides novel insights into its molecular regulatory mechanisms.
Xu A, Lü Z, Liu J … +10 more , Liu T, Yu J, Yang Y, Huang K, Gong L, Li F, Zhu D, Ping H, Shi H, Liu L
Comp Biochem Physiol Part D Genomics Proteomics · 2026 Jun · PMID 41544485 · Publisher ↗
Sepiella japonica is a cephalopod of significant commercial value, commonly found throughout China's coastal waters, ranging from southern Hong Kong to the Korean Peninsula and western regions of Japan. However, under ca...
Sepiella japonica is a cephalopod of significant commercial value, commonly found throughout China's coastal waters, ranging from southern Hong Kong to the Korean Peninsula and western regions of Japan. However, under captive conditions, S. japonica frequently exhibits precocious sexual maturation, which can result in reduced adult body size and severely limit aquaculture development. Therefore, elucidating the molecular mechanisms on ovarian development has become a critical priority. In this study, RNA sequencing was performing of the ovary tissue of female S. japonica collected across four key ovarian developmental stages: oogonium production (stage I), protoplasmic growth (stage II), interstitial growth (stage III), and trophoplasmic growth (stage IV). A total of 354,393,214 clean reads (Q20>98.58%) were obtained from 16 samples. Pairwise comparative analyses of I vs II, II vs III, and III vs IV identified 10050, 2564, 2278 differentially expressed genes (DEGs), respectively. Through differential expression analysis, we identified 13,319 differentially expressed genes (DEGs), among of which exhibited consistently high expression across four developmental stages, such as FOXL2, HSD17B2, and BMP1, suggesting their critical roles in regulating ovarian development in S. japonica. Gene Ontology (GO) enrichment analysis showed that these DEGs were significantly enriched in processes including protein targeting to the ER, response to estradiol, oxidative phosphorylation, and female pregnancy. KEGG pathway analysis revealed that DEGs were significantly enriched in key functional pathways, such as Ribosome, Prolactin signaling, FOXO signaling, and Lysosome. Furthermore, the "response to estradiol" pathway was consistently enriched across multiple developmental stage comparisons, suggesting that genes associated with steroid-related signaling may play conserved roles during ovarian development in S. japonica. This study clarified the regulation of transcript expression and molecular mechanisms in the ovary of S. japonica at different ovarian development stages, thereby offering theoretical guidance for enhancing reproductive efficiency in mollusk aquaculture.
Comparative transcriptome analysis reveals molecular mechanism of temperature effect on body color of red swamp crayfish (Procambarus clarkii).
Chang G, Kong F, Gao S … +5 more , Cai H, Wang L, Ding H, Cheng Y, Li J
Comp Biochem Physiol Part D Genomics Proteomics · 2026 Jun · PMID 41544484 · Publisher ↗
The carapace coloration is of great significance to Procambarus clarkii, and the molecular mechanism of temperature affecting carapace color has not yet been reported. In this study, comparative transcriptome was used to...
The carapace coloration is of great significance to Procambarus clarkii, and the molecular mechanism of temperature affecting carapace color has not yet been reported. In this study, comparative transcriptome was used to study molecular mechanism of temperature-induced changes in carapace coloration of P. clarkii. This study identified many genes (such as tyrosinase, APOD) and signaling pathways (such as tyrosine metabolism) related to pigment accumulation. As an important environmental factor, temperature can change metabolism and accumulation of pigment in P. clarkii by changing expression patterns of related genes and pathways. High temperature can damage transport of related proteins (such as ABC transporters), thus affecting the metabolism of carotenoids and melanin, and finally lead to the change of body color of P. clarkii. Oxidative stress caused by high temperature can destroy pigment metabolism and accumulation, resulting in changes in body color. The results of this study revealed molecular mechanism of temperature affecting body color of P. clarkii, provided basic data for subsequent selective breeding and practical production, and provided new insights for crustacean body color formation and change.
Genome and transcriptome mining of the corazonin (Crz)-like peptide and gonadotropin-releasing hormone (GnRH)-like peptides in the spotted Babylon, Babylonia areolata.
Saetan U, Kornthong N, Duangprom S … +7 more , Tanasawet S, Sukketsiri W, Tamtin M, Phanthong P, Sanprick A, Chinfak N, Saetan J
Comp Biochem Physiol Part D Genomics Proteomics · 2026 Jun · PMID 41529500 · Publisher ↗
The Spotted Babylon (Babylonia areolata) is an economically marine species in Thailand and other Asian countries. Due to the high demand for its meat, improving aquaculture practices for this species is essential. Regard...
The Spotted Babylon (Babylonia areolata) is an economically marine species in Thailand and other Asian countries. Due to the high demand for its meat, improving aquaculture practices for this species is essential. Regarding the lack of neuroendocrine control of reproduction in this species, we performed transcriptome analysis of the central nervous system and ovaries, and we searched against the reported genome of this animal species to find out the neurohormones. Here, we reported the identification of corazonin (ba-Crz)-like and gonadotropin-releasing hormone (ba-GnRH)-like mRNAs in B. areolata. The ba-Crz-like mRNA encoded mature ba-Crz-like peptide as QNYHYSNGWHP. Two ba-GnRH-like mRNAs encoded ba-GnRH-I-, and ba-GnRH-II-like peptides containing active peptides as QIHFSPTWGT and QIHFSHSWGT. Two introns were found in the ba-Crz-like gene while one intron was present in each ba-GnRH-like gene. These three peptides were phylogenetically placed in the molluscan Crz and GnRH clades. RT-PCR of these three mRNAs revealed their ubiquitous expressions across various organs, with all three predominantly expressed in ganglia, which was further confirmed by in situ hybridization of the cerebral ganglia. Immunohistochemistry showed positive signals for the Crz-like peptide in both the CNS and ovaries. To examine expression across ovarian cycle, the ba-Crz-like, and ba-GnRH-I-like mRNAs were consistently expressed in the CNS and ovaries of both immature and mature female snails, while the ba-GnRH-II-like mRNA significantly reduced its expression in the CNS of mature snails. Conclusively, this study was preliminary to report on the existence of GnRH/AKH/Crz peptides in the B. areolata, Further characterization of their receptors and biological functions is ongoing to ensure the GnRH, AKH, and Crz identification in this species.
Integrated multi-omics analyses reveals physiological and gut microbiota responses of Litopenaeus vannamei to graded levels of dietary bile acids.
Tan P, Zhang L, Zhang J … +5 more , Cao A, Xu D, Zhu A, Ding Z, Shao Q
Comp Biochem Physiol Part D Genomics Proteomics · 2026 Jun · PMID 41529499 · Publisher ↗
Despite being sterol auxotrophs that lack de novo steroid synthesis pathways, the specific physiological roles of exogenous bile acids (BAs) in crustaceans remain to be fully elucidated. This study investigated the effec...
Despite being sterol auxotrophs that lack de novo steroid synthesis pathways, the specific physiological roles of exogenous bile acids (BAs) in crustaceans remain to be fully elucidated. This study investigated the effects of dietary BAs on the antioxidant capacity, immune regulation, and intestinal microbiota of the Pacific white shrimp, Litopenaeus vannamei. Shrimp were fed diets supplemented with graded levels of BAs (0-1000 mg kg) for 56 days. Integrated multi-omics analyses were employed, where the 200 mg kg physiological optimum was used for transcriptomic profiling to decipher signaling pathways, while the 1000 mg kg group was analyzed to assess high-dose tolerance and microbial composition changes. Results showed that dietary BAs significantly enhanced non-specific immune parameters, specifically hemolymph lysozyme activity and total antioxidant capacity, without inducing histological damage to the hepatopancreas or intestine even at the highest dosage. Transcriptomic analysis showed an upregulation of antioxidant-related genes, such as sod1, gst and nos1, suggesting that BAs enhance the host's transcriptional potential to cope with oxidative stress. Furthermore, dietary BAs modulated immune signaling by upregulating the NF-κB inhibitor gene nfkbia and downregulating the adaptor myd88, indicating a potential mechanism for maintaining immune homeostasis and suppressing pro-inflammatory responses. In the intestine, BAs significantly increased the Shannon diversity index by promoting community evenness rather than species richness, and reduced the relative abundance of the opportunistic pathogen Vibrio while enriching beneficial genera such as Ruegeria. These findings indicate that exogenous BAs exert a protective role in L. vannamei by priming antioxidant defenses, modulating inflammatory signaling pathways, and stabilizing the intestine microbial ecosystem. These results suggest that BAs can be used as effective feed additives to improve health and intestine stability in shrimp farming.
Transcriptome analysis revealed the effects of dietary faba bean (Vicia faba L.) on muscle quality of Nile tilapia (Oreochromis niloticus).
Li Q, Huang Y, Xie X … +2 more , Liang S, Lin L
Comp Biochem Physiol Part D Genomics Proteomics · 2026 Jun · PMID 41520454 · Publisher ↗
Nile tilapia (Oreochromis niloticus) is a widely farmed freshwater fish. Feeding with faba bean (Vicia faba L.) for 90-120 days can improve the muscle quality of tilapia. However, the underlying mechanism remain unclear....
Nile tilapia (Oreochromis niloticus) is a widely farmed freshwater fish. Feeding with faba bean (Vicia faba L.) for 90-120 days can improve the muscle quality of tilapia. However, the underlying mechanism remain unclear. In the present study, tilapia were fed a faba bean-based diet for 120 days to induce muscle crisped, and ordinary tilapia fed a conventional diet were used as controls. Muscle histological characteristics were evaluated using hematoxylin and eosin staining, and transcriptome sequencing was conducted to explore molecular changes associated with the crisped muscle phenotype. The results showed that, as compared to ordinary tilapia, the fiber diameter and area were significantly reduced in crisped tilapia (p < 0.05), while the muscle fiber density was significantly increased (p < 0.05). In total, 576 differentially expressed genes (DEGs) were identified (FDR < 0.05), of which 211 were significantly up-regulated and 365 significantly down-regulated. Further analysis showed that DEGs associated with myofibroblast proliferation were up-regulated in crisped tilapia, while the glycolytic pathway was inhibited. The expression levels of muscle-related genes (i.e., actc1, myo7a, cib2, abcf2, and pfkfb2) were significantly higher in crisped tilapia than ordinary tilapia (p < 0.05), whereas the expression levels of gapdh, pgam2, eno3, and g6pi were significantly decreased (p < 0.05). Several DEGs and signaling pathways were identified. These findings provide transcriptomic evidence linking dietary faba bean feeding to muscle fiber remodeling and metabolic modulation in tilapia, offering a molecular basis for improving fillet quality through nutritional strategies.
Genome-wide identification and characterization of HSP90, HSP60 and HSP40 family genes in Riptortus pedestris (Hemiptera: Alydidae).
Dong W, Xue H, Ren Y
Comp Biochem Physiol Part D Genomics Proteomics · 2026 Jun · PMID 41518682 · Publisher ↗
To the best of our knowledge, heat shock proteins (HSPs) serve as molecular chaperones and play vital roles in providing protection under numerous physiological processes and environmental stressors, such as temperature,...
To the best of our knowledge, heat shock proteins (HSPs) serve as molecular chaperones and play vital roles in providing protection under numerous physiological processes and environmental stressors, such as temperature, mechanical injury, chemical agents, and so on. Although their functional roles in hemipteran insects have been identified, comprehensive genome-wide identification and characterization of HSP family genes remain poorly understood in heteropteran pests, especially in R. pedestris, which has led to significant and widespread issues with soybean quality and yield through its sucking stylet, thus inducing a staygreen-like syndrome. In this study, four HSP90, fourteen HSP60 and twenty-six HSP40 family genes were obtained from the R. pedestris genome. Next, phylogenetic analysis, combined with conserved and domain characterization, supported our classification results. Chromosomal mapping indicated that all these HSP genes are distributed across the six chromosomes of R. pedestris, and a Ka/Ks ratio of <1 provides essential information for purifying selection acting on two duplicated Hsp90 genes in R. pedestris. Through data mining of transcriptome data, we obtained the expression patterns of three HSP family genes across all developmental stages and analyzed their expression differences during changes in feeding conditions in the whole body and gut of R. pedestris, respectively. Finally, a miRNA-mRNA interaction network of four significantly differentially expressed (DE) HSPs and corresponding regulatory miRNAs was constructed, of which one miRNA, novel-miRNA-927-3p, exhibited significant downregulation and combined with significantly DE Hsp60a and DnaJA1 in one comparison group, suggesting their underlying relationships in response to antibiotic feeding in the R. pedestris gut. Overall, these findings provide valuable insights into how the three types of HSP genes in R. pedestris are involved in developmental and environmental adaptation at the transcriptional and posttranscriptional levels.
Metabolomic insights into fish osmoregulation: Unveiling adaptive mechanisms to salinity change.
Chen X, Tang Y, Du X … +2 more , Giffard-Mena I, Cao Q
Comp Biochem Physiol Part D Genomics Proteomics · 2026 Jun · PMID 41506122 · Publisher ↗
Salinity fluctuation is a major environmental driver influencing fish physiology and aquaculture performance. Metabolomics offers a systems perspective on the small molecule networks underlying osmoregulation. This revie...
Salinity fluctuation is a major environmental driver influencing fish physiology and aquaculture performance. Metabolomics offers a systems perspective on the small molecule networks underlying osmoregulation. This review synthesizes studies across fish species to identify conserved metabolic responses to salinity change, including shifts in energy metabolism, amino acid turnover, and organic osmolyte synthesis. We evaluate the strengths and limitations of current analytical platforms (NMR, LC-MS, GC-MS) in metabolite coverage and identification, and highlight emerging approaches such as spatial metabolomics, multi-omics integration, and machine learning. By linking metabolic patterns to physiological and aquacultural outcomes, this work clarifies the molecular basis of salinity adaptation and offers actionable guidance for improving salinity tolerance in aquaculture.
Molecular insights into hydrogen sulfide defense: A tissue-resolved transcriptomic study in the crab Eriocheir sinensis.
Tian J, Zhou Z, Han M … +4 more , Tay YJ, Bao M, Fu L, Jiang Q
Comp Biochem Physiol Part D Genomics Proteomics · 2026 Jun · PMID 41506121 · Publisher ↗
The increasing prevalence of multiple abiotic stressors in aquatic ecosystems has raised significant ecological concerns. While molecular responses to hydrogen sulfide (H₂S) have been investigated in some aquatic species...
The increasing prevalence of multiple abiotic stressors in aquatic ecosystems has raised significant ecological concerns. While molecular responses to hydrogen sulfide (H₂S) have been investigated in some aquatic species, the tissue-specific regulatory mechanisms in the Chinese mitten crab (Eriocheir sinensis) remain poorly understood. Following a 48-h exposure to varying concentrations of H₂S (0, 0.1, and 5 mg/L), four key tissues-hepatopancreas, gill, muscle, and intestine-were collected for an integrated analysis of transcriptomic sequencing and physiological/biochemical assays. Our results demonstrated significant enrichment of pathways related to serine endopeptidase activity and tyrosine metabolism in affected tissues, highlighting their potential role in mitigating H₂S-induced damage. Furthermore, high-concentration H₂S exposure substantially elevated the activities of antioxidant enzymes (SOD, CAT, GSH-PX) and up-regulated the expression of associated genes (SOD1, GPX1, HO-1), while simultaneously suppressing cytochrome c oxidase expression. These coordinated changes indicate that H₂S toxicity triggers pronounced oxidative stress alongside disrupted energy metabolism. The present study provides novel experimental insights into the molecular mechanisms of H₂S toxicity in crustaceans and offers a scientific foundation for ecological risk assessment and sustainable aquaculture management.
Transcriptomic analysis under the stress of insecticides and the functional role of three genes related to host finding behavior of Scleroderma sichuanensis.
Mastoi SM, Hua Y, Chandio WA … +2 more , Mastoi PM, Wei Y
Comp Biochem Physiol Part D Genomics Proteomics · 2026 Jun · PMID 41500007 · Publisher ↗
The female parasitoid wasp Scleroderma sichuanensis (Hymenoptera: Bethylidae) utilizes various intricate behavior strategies, including host detection, learning, and memory, to enhance its survival and reproductive succe...
The female parasitoid wasp Scleroderma sichuanensis (Hymenoptera: Bethylidae) utilizes various intricate behavior strategies, including host detection, learning, and memory, to enhance its survival and reproductive success. RNA-Seq analysis conducted under sublethal insecticide stress identified three differentially expressed genes, SsOR5, SsGRIN2B, and SsPDE8A, selected for functional validation due to their likely roles in host searching behavior. The SsOR5, an odorant receptor, is believed to interact with other olfactory receptors and downstream signaling molecules to improve host detection. In contrast, SsGRIN2B, an NMDA-type glutamate receptor, may influence synaptic plasticity and neural transmission, thereby affecting leering behavior. Additionally, SsPDE8A modulates cAMP-dependent signaling pathways, which are crucial for memory consolidation and behavioral response. This research investigates these genes in S. sichuanensis using RNA interference (RNAi) to assess changes in host finding efficiency. Adult female wasp received dsRNA treatments at doses of (0.5 μL, 1 μL, and 3 μL) and time durations (12, 24, 48, and 72 h), with the most significant gene silencing observed at 3 μL for 48-72 h. Behavioral assays conducted with a Y-tube olfactometer revealed that knockdown of SsOR5 significantly reduced host attraction, while knockdown of SsGRIN2B and SsPDE8A led to moderate reeducations, highlighting the varying contributions of these genes to olfactory drive behavior. This study demonstrates that insecticides induced changes in gene expression can disrupt neural and olfactory pathways essential for host location, and emphasizes the potential of RNAi-based approaches to target behaviorally significant genes, offering new strategies for parasitoid-mediated pest management.
Diversity of ligand-gated ion channels in free-living and parasitic copepods (Crustacea).
Morales-Serna FN, Ramos-de la Cruz I, García-Gasca A … +5 more , Betancourt-Lozano M, Briones-Mendoza J, Pinto-Gualpa J, Yañez-Guerra LA, Caña-Bozada VH
Comp Biochem Physiol Part D Genomics Proteomics · 2026 Jun · PMID 41494232 · Publisher ↗
Ligand-gated ion channels (LGICs) are essential mediators of synaptic transmission and sensory processing in animals, yet their diversity and evolution in copepods remain poorly understood. Copepods are among the most ab...
Ligand-gated ion channels (LGICs) are essential mediators of synaptic transmission and sensory processing in animals, yet their diversity and evolution in copepods remain poorly understood. Copepods are among the most abundant metazoans in marine ecosystems and also occur across a wide range of salinity regimes, including freshwater habitats. They play central roles in food webs, biogeochemical cycling, and host-parasite interactions, with some parasitic taxa having significant impacts on aquaculture. In this study, we conducted a comprehensive analysis of LGICs across 20 copepod species (13 free-living and 7 parasitic) spanning four orders, Calanoida, Cyclopoida, Harpacticoida, and Siphonostomatoida, using transcriptomic and expressed sequence tag (EST) datasets. We identified 6456 putative LGICs belonging to four major families: Cys-loop, ionotropic glutamate receptors (iGluRs), P2X, and ASIC/Deg/ENaC. Phylogenetic and clustering analyses revealed both conserved and lineage-specific patterns, with approximately 20 % of LGICs showing taxonomic restriction to copepods, particularly within the ASIC/Deg/ENaC family. Notably, P2X receptors, previously reported as largely absent in arthropods, were consistently detected across copepod species, suggesting that this family is comparatively well represented in the group. We also identified multiple receptors associated with environmental sensing, including ionotropic receptors (IRs), shared across free-living species, as well as potential pharmacological targets such as GluCl and GABA receptors in parasitic taxa. Our findings highlight the evolutionary complexity of LGICs in copepods and provide a foundation for future research on their roles in environmental adaptation, and chemosensory biology, with potential pharmacological applications in aquaculture.
Comprehensive identification and expression profiling of piRNA pathway genes in the Pacific oyster Crassostrea gigas.
Zhao X, Zhou Y, Yu H … +1 more , Li Q
Comp Biochem Physiol Part D Genomics Proteomics · 2026 Jun · PMID 41483596 · Publisher ↗
PIWI-interacting RNAs (piRNAs) and their associated proteins are key regulators of germline development and genome defense, but their roles in mollusks remain largely unexplored. In this study, we systematically identifi...
PIWI-interacting RNAs (piRNAs) and their associated proteins are key regulators of germline development and genome defense, but their roles in mollusks remain largely unexplored. In this study, we systematically identified 28 piRNA pathway genes in the Pacific oyster Crassostrea gigas and characterized their genomic composition and expression profiles. The oyster piRNA gene repertoire exhibits a mosaic-like architecture, combining deeply conserved components with lineage-specific features, including the presence of vertebrate-type transcription factors such as A-MYB, the absence of the insect-specific RDC complex, and the retention of the exonuclease MUT7, which has been lost in several vertebrate and insect lineages. Transcriptome analyses revealed pronounced tissue-, stage-, and sex-biased expression patterns, consistent with this composite regulatory configuration. Several key factors, including CgPiwil1, CgGtsf1, and CgTdrd5 exhibit female-biased expression peaking at the maturation stage of the gonads, whereas CgYthdc2, CgMyb, and CgHsp83 show preferential expression in male gonads. Furthermore, CgHsp83 displays high expression in gills, suggesting potential multifunctional roles beyond germline regulation. qPCR validation of representative genes confirmed the transcriptome-based patterns. These findings provide the first comprehensive overview of the piRNA pathway in mollusks, reveal both conserved and divergent features compared to model animals, and establish a foundation for future functional studies on germline regulation in bivalves.
Hypoxia and reoxygenation induce changes in oxidative stress, histological structure, and transcriptome in the liver of mandarin fish (Siniperca chuatsi).
Gong D, Zhou L, Hong X … +11 more , Yao M, Huang Z, Yu W, Wu Y, Chen M, Yu D, Song Y, Wang L, Lian Y, Zhang X, Wang P
Comp Biochem Physiol Part D Genomics Proteomics · 2026 Jun · PMID 41483595 · Publisher ↗
The mandarin fish (Siniperca chuatsi, MD) is a highly valued freshwater economic fish species in China, but it exhibits a notably low tolerance to a hypoxic environment. However, the underlying regulatory mechanisms in r...
The mandarin fish (Siniperca chuatsi, MD) is a highly valued freshwater economic fish species in China, but it exhibits a notably low tolerance to a hypoxic environment. However, the underlying regulatory mechanisms in response to environmental hypoxia and reoxygenation stress remain poorly understood. Therefore, we examined liver biochemical parameters and transcriptomes of MD under normoxic, hypoxic, and reoxygenation conditions, aiming to illuminate the dynamic changes in molecular regulatory mechanisms and oxidative stress responses. This study revealed that the enzymatic antioxidant systems acted in a coordinated manner to alleviate oxidative stress injury caused by hypoxia. In RNA-seq analysis, we identified differentially expressed genes (DEGs) and conducted enrichment analysis. Among the Gene Ontology (GO) functional categories, several critical hypoxia-related genes (nfkbia, vegfa, aplnr) in biological processes were observed. Furthermore, based on the Kyoto Encyclopedia of Genes and Genomes (KEGG) functional enrichment analyses, the finding revealed that many DEGs were involved in the HIF-1 signaling pathway (gln, epo, vegfa, pfka, ldh), AMPK signaling pathway (pfka, eef2k, gys), p53 signaling pathway (ccne, gtse1), PI3K-Akt signaling pathway (ddit4, egf, gh, ghr, vwf, gys), and NOD-like receptor signaling pathway (atg8, sharpin, ifnar1), among others. This study offers crucial insights into elucidating the molecular regulatory mechanisms underlying hypoxia stress, and holds the potential to facilitate the development of effective strategies for coping with environmental hypoxia and reoxygenation stress in MD. This is valuable for fish genetic improvement.
A comparative transcriptomics reveals stage-specific molecular mechanisms during early zoeal development in the Chinese mitten crab, Eriocheir sinensis.
Huang P, Yao Y, Gao J … +5 more , Du J, Zhu H, Chen D, Chen W, Xu G
Comp Biochem Physiol Part D Genomics Proteomics · 2026 Jun · PMID 41483594 · Publisher ↗
This study systematically analyzed the molecular expression patterns across the zoeal stages (ZI to ZV) of the Chinese mitten crab (Eriocheir sinensis) using comparative transcriptomics. It focused on core biological pro...
This study systematically analyzed the molecular expression patterns across the zoeal stages (ZI to ZV) of the Chinese mitten crab (Eriocheir sinensis) using comparative transcriptomics. It focused on core biological processes, including metabolism, organelle structure, and signal transduction, to reveal the molecular mechanisms underlying the crab's early development. Based on trend analysis, the differentially expressed genes (DEGs) profile of the ZI stage was significantly distinct from that of the other four developmental stages. Genes enriched and highly expressed in ZI were primarily associated with transmembrane signaling and calcium signaling pathways, which support the transition of early larvae from embryonic development to a free-living life. Meanwhile, enzyme activity analysis indicated that ZI activated the body's antioxidant defense system and nonspecific immune capacity. In the ZII-ZIII stages, DEGs were mainly related to endoplasmic reticulum (ER) structural components and pathways (e.g., ER protein processing and proteasome), suggesting the activation of ER-associated degradation to maintain protein homeostasis during morphological and dietary transitions. In the ZIV-ZV stages, DEGs were predominantly enriched in metabolic pathways (e.g., organic acid metabolism, tyrosine metabolism) and peroxisome/lysosome pathways, which enhance energy supply, exoskeleton sclerotization, immunity, and cell remodeling to facilitate megalopa metamorphosis. Overall, this study sheds new light on the molecular mechanisms underlying zoeal development in E. sinensis and provides theoretical support for aquaculture practices.
Transcriptional responses to DHA-induced lipid droplet accumulation in primary adherent mantle cells of Sinonovacula constricta (Lamarck, 1818).
Yan B, Ran Z, Zhou Q … +3 more , Zhu J, Kong F, Xu J
Comp Biochem Physiol Part D Genomics Proteomics · 2026 Jun · PMID 41475309 · Publisher ↗
Docosahexaenoic acid (DHA), an essential omega-3 long-chain polyunsaturated fatty acid, is crucial for the development of marine mollusks. Despite its importance, the molecular mechanisms of DHA action in these organisms...
Docosahexaenoic acid (DHA), an essential omega-3 long-chain polyunsaturated fatty acid, is crucial for the development of marine mollusks. Despite its importance, the molecular mechanisms of DHA action in these organisms are poorly understood, primarily due to the lack of reliable in vitro models. This study utilizes the razor clam Sinonovacula constricta as a model organism, establishing a primary adherent cell culture from various tissues, with mantle tissue identified as the optimal source for its rapid migration and low contamination risk. Cells incubated with varying concentrations of DHA (0-400 μM) for 6 h exhibited a concentration-dependent accumulation of lipid droplets (LDs), highlighting the model's suitability for investigating lipid metabolism. Transcriptomic analysis of cells treated with 50 μM DHA identified 848 differentially expressed genes (DEGs), with 747 upregulated and 101 downregulated, indicating the complex effects of DHA. The top 20 significantly upregulated and downregulated DEGs revealed significant involvement in cell signaling transduction, extracellular matrix organization, and substance transport and metabolism. Particularly, lipid metabolism genes, including perilipin 2 and abhydrolase domain containing 2, as well as pathways such as the PPAR signaling pathway and sphingolipid metabolism, were significantly altered, suggesting a reprograming of fatty acid metabolism contributing to LD accumulation. Additionally, pathways related to immune response were notably affected, potentially enhancing cellular health. Collectively, this study provides the first comprehensive insights into the molecular mechanisms underlying DHA-induced LD accumulation in a marine mollusk model at the cellular level, laying a foundation for developing precise nutritional strategies involving DHA in S. constricta aquaculture.
Comparative transcriptomics identifies key genes and pathways underlying the early skin coloration in leopard coral grouper (Plectropomus leopardus).
Pang L, Sheng D, Wen S … +7 more , Fang L, Jiang M, Tian C, Zhou D, Chen H, Li G, Zhu C
Comp Biochem Physiol Part D Genomics Proteomics · 2026 Jun · PMID 41475308 · Publisher ↗
The leopard coral grouper (Plectropomus leopardus) is a valuable marine economic fish, whose body color (especially red coloration) is a key trait determining its economic value. During early development, the body color...
The leopard coral grouper (Plectropomus leopardus) is a valuable marine economic fish, whose body color (especially red coloration) is a key trait determining its economic value. During early development, the body color of this fish transitions from transparent to red, providing an ideal model for elucidating the molecular mechanisms of body color formation. This study selected two critical time points, 26 dph(transparent)and 30 dph(red) post-hatching, to collect transparent skin (TC) and red skin (RC) tissues for comparative transcriptome analysis. Using the thresholds of |Fold Change| ≥ 2 and FDR < 0.05, a total of 1747 differentially expressed genes (DEGs) were identified, including 1213 up-regulated and 534 down-regulated genes, indicating that the formation of red body color involves the coordinated action of multiple genes. Further analysis revealed differential expression of several genes related to body color formation, including carotenoid metabolism-related genes (e.g., scarb1, ttc39b, bco2, fabp2, fabp3, apod, stard9) and melanin synthesis-related genes (e.g., tyr, tyrp1, dct, foxd3a). KEGG enrichment analysis showed significant enrichment of pathways related to lipid metabolism (e.g., steroid biosynthesis, cholesterol metabolism, arachidonic acid metabolism), melanin synthesis pathways (e.g., the Wnt signaling pathway and melanogenesis), and other potentially related pathways (e.g., retinol metabolism, insulin signaling pathway, purine metabolism), suggesting these pathways may collectively participate in the regulation of the body color transition. Furthermore, validation of 11 genes by qPCR confirmed the reliability of the RNA-seq data. This study highlights key molecular features during the early transition from transparent to red body color in the leopard coral grouper, providing new experimental evidence and a theoretical basis for a deeper understanding of its body color formation mechanisms.
Divergent mechanisms of hypoxia tolerance in zebrafish (Danio rerio) and Nile tilapia (Oreochromis niloticus).
Ren R, Hu X, Jiang S … +4 more , Chan J, Zhou Y, Zhai W, Xu Q
Comp Biochem Physiol Part D Genomics Proteomics · 2026 Jun · PMID 41455309 · Publisher ↗
Hypoxia is a critical environmental stressor that differentially impacts aquatic species. To investigate interspecific variations in hypoxia tolerance, we compared zebrafish (Danio rerio) and tilapia (Oreochromis nilotic...
Hypoxia is a critical environmental stressor that differentially impacts aquatic species. To investigate interspecific variations in hypoxia tolerance, we compared zebrafish (Danio rerio) and tilapia (Oreochromis niloticus) exposed to progressively decreasing oxygen levels. Behavioral observations revealed that zebrafish exhibited aquatic surface respiration and rapid mortality at 0.7 mg/L dissolved oxygen (DO), whereas tilapia maintained bottom-oriented swimming and higher survival, indicating stronger hypoxia tolerance. Transcriptomic analyses of zebrafish identified heart- and liver-specific gene modules strongly associated with acute hypoxia, with functional enrichment pointing to impaired cell proliferation, heme biosynthesis, and energy metabolism. TUNEL assays further confirmed severe apoptosis in zebrafish liver, underscoring its vulnerability to hypoxic damage. Comparative transcriptomics revealed divergent regulation of ribosome-related pathways: tilapia suppressed ribosomal gene expression and enhanced translation initiation factor activity, while zebrafish maintained protein biosynthesis, potentially exacerbating energy deficits. Metabolic assays showed increased hepatic phosphofructokinase (PFK) activity in zebrafish, suggesting reliance on glycolysis, whereas tilapia exhibited consistently higher basal PFK activity and reduced oxygen consumption under hypoxia, indicating metabolic suppression as an adaptive strategy. Antioxidant analysis revealed a significant decline in superoxide dismutase (SOD) activity in zebrafish but not tilapia, further reflecting species-specific oxidative stress responses. Together, these findings demonstrate that zebrafish and tilapia employ distinct hypoxia-coping strategies, with tilapia favoring metabolic suppression and oxidative stability, while zebrafish rely on glycolysis but suffer greater oxidative and apoptotic damage under acute hypoxia. These findings also provide new insights into divergent hypoxia adaptation strategies among teleosts.
Identification of genes expressed in the pectoral fins and skin of Takifugu rubripes to reveal candidate genes involved in host recognition by the crustacean ectoparasite Caligus fugu.
Rana KMS, Matsunaga R, Sato Y … +5 more , Suetake H, Kikuchi K, Ohtsuka S, Kotani T, Tasumi S
Comp Biochem Physiol Part D Genomics Proteomics · 2026 Jun · PMID 41435496 · Publisher ↗
The initial detection of host-derived chemical cues is a key physiological event that strongly influences infection success in parasitic copepods such as Caligus fugu. Although ionotropic receptors were previously identi...
The initial detection of host-derived chemical cues is a key physiological event that strongly influences infection success in parasitic copepods such as Caligus fugu. Although ionotropic receptors were previously identified in C. fugu as potential host-sensing molecules, their ligands and specific roles in host recognition remain unknown. Since the infective copepodid I stage preferentially attaches to the fins of the puffer host, genes expressed at higher levels in fins may contribute to host recognition by C. fugu. In this study, differentially expressed genes between the pectoral fins and skin of Takifugu rubripes were comprehensively identified through RNA-seq to expand the list of candidate host-recognition genes beyond those detected earlier. To refine this list, genes expressed at higher levels in pectoral fins that were annotated with the gene ontology term "extracellular region" (Gene Ontology:0005576) were examined for predicted protein features, with emphasis on secreted, soluble molecules that the parasite could encounter in the surrounding water. From an initial set of 126 genes, intracellular and membrane-associated proteins were removed, and those possessing signal peptides or globular domains were retained. The remaining 92 proteins were considered likely secreted, water-soluble host-derived ligands. Relative qPCR analysis highlighted col10a1a, stc2a, mmp9, fibinb, bmp5, c4b, bmp6, and lipg as potential secreted cues for C. fugu. Antimicrobial peptides such as hamp and db1 were also identified as candidates. Overall, this study expands the pool of molecules that may function as chemoattractants for C. fugu and provides targets for future experimental validation.
Identification of the mapk gene family in large yellow croaker (Larimichthys crocea): Involvement in immune response to Pseudomonas plecoglossicida infection and hypoxia exposure.
Wang Z, Han P, Xue Y … +3 more , Chen J, Liu X, Wang X
Comp Biochem Physiol Part D Genomics Proteomics · 2026 Jun · PMID 41435495 · Publisher ↗
Mitogen-activated protein kinases (MAPKs) are a family of evolutionarily conserved serine/threonine protein kinases that can be activated by diverse stimuli. They transmit signals from the cell membrane to the nucleus, r...
Mitogen-activated protein kinases (MAPKs) are a family of evolutionarily conserved serine/threonine protein kinases that can be activated by diverse stimuli. They transmit signals from the cell membrane to the nucleus, regulating various biological processes such as apoptosis, hormone signaling, and immune responses. Members of the MAPK family have been extensively studied in multiple species and have been confirmed as a central hub for regulating antibacterial immunity and hypoxia adaptation in perciform fishes, such as Asian seabass and groupers. Given that the large yellow croaker, as an important mariculture species within this order, faces serious threats from Pseudomonas plecoglossicida infection and hypoxic stress, deciphering the functions of its MAPK family is of significant importance. To this end, this study identified 16 mapk genes in the large yellow croaker. Phylogenetic analysis revealed that these mapk genes were classified into three major subfamilies: ERK, JNK, and p38 MAPK. Comparative analyses of gene structures and conserved protein motifs demonstrated high conservation among MAPK family members. Meanwhile, RNA-seq data following bacterial and hypoxic stress revealed distinct expression patterns of mapk genes. mapk7, mapk10, and mapk14a exhibited significant differential expression in response to P. plecoglossicida challenge, and mapk7, mapk8b, and mapk14a were significantly induced under hypoxia stress, implying their potential involvement in stress adaptation. The protein-protein interaction (PPI) network analysis revealed that MAPK family members (including MAPK3, MAPK7, MAPK8b, MAPK12a, MAPK13, and MAPK14a) in Larimichthys crocea exhibit close interactions with key signaling proteins (such as MAP2K1, c-Fos, AP-1, and MAPKAPK2). These interactions suggested the potential formation of a complex signal transduction network involved in the immune stress response, collectively mediating the immune stress regulation in Larimichthys crocea. These findings enhanced the understanding of environmental adaptation mechanisms in large yellow croaker, and provided crucial candidate target genes and a theoretical basis for in-depth analysis of its molecular responses to pathogen infection and hypoxic stress.
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