Comp. Biochem. Physiol. Part D Genomics Proteomics [JOURNAL]
Sun
200 papers
Serine proteases and serine protease inhibitors identified from the venom gland transcriptome of Rhitymna verruca.
Li Z, Zhang M, Yin W … +4 more , Zheng Y, Liu H, Zhao Y, Yang Z
Comp Biochem Physiol Part D Genomics Proteomics · 2026 Jun · PMID 41435494 · Publisher ↗
Rhitymna verruca is a large nocturnal wandering spider and an important natural predator of agricultural and forestry pests, with its venom playing a key role in prey capture. However, systematic studies on the compositi...
Rhitymna verruca is a large nocturnal wandering spider and an important natural predator of agricultural and forestry pests, with its venom playing a key role in prey capture. However, systematic studies on the composition of its venom remain scarce. In this study, we performed an integrated analysis of the venom gland and venom samples using high-throughput transcriptome sequencing combined with quantitative proteomics. The transcriptome yielded 43,244 representative unigene sequences, among which 102 toxin-like sequences were identified through functional annotation, encompassing 13 peptide toxin superfamilies and 7 protein toxin families. Proteomic analysis identified 35 venom components, including 14 peptide toxins and 21 functional proteins. The most abundantly expressed toxin families, Superfamily IX and VII, were highly expressed at both transcriptomic and proteomic levels, suggesting central roles in prey paralysis and neuroregulation. Most peptide toxins possessed ICK or Kunitz domains, indicating high structural stability and potential target specificity. In addition, the venom was rich in auxiliary components such as CAP protein superfamily, hyaluronidases, and metalloproteases, which may contribute to toxin synergy, diffusion, and tissue disruption. This study provides the first comprehensive characterization of the venom composition of R. verruca, offering fundamental insights into its functional mechanisms, evolutionary patterns, and potential applications in the development of novel bioactive agents.
Molecular mechanisms of quercetin in regulating antioxidant defense and pyroptosis pathways in the redclaw crayfish (Cherax quadricarinatus).
Zhou Z, Lv W, Si Q … +6 more , Zhang B, Hwai ATS, Tay YJ, Han M, Zhan Z, Jiang Q
Comp Biochem Physiol Part D Genomics Proteomics · 2026 Jun · PMID 41421238 · Publisher ↗
As a principal species in freshwater aquaculture, the redclaw crayfish (Cherax quadricarinatus) depends on a competent immune system to mitigate environmental and pathogenic challenges. Quercetin, a ubiquitous plant-deri...
As a principal species in freshwater aquaculture, the redclaw crayfish (Cherax quadricarinatus) depends on a competent immune system to mitigate environmental and pathogenic challenges. Quercetin, a ubiquitous plant-derived flavonoid, has garnered scientific attention due to its pleiotropic bioactivities, including antioxidant, anti-inflammatory, and immunomodulatory properties. This study investigated the effects of waterborne quercetin exposure on transcriptional regulation and antioxidant capacity in C. quadricarinatus. Over a 28-day period, crayfish were subjected to five quercetin concentrations (0, 1.0, 2.5, 5.0, and 10.0 mg/L), with outcomes evaluated against an untreated control. At the concentration of 5.0 mg/L, which showed the most pronounced effects among the tested concentrations, quercetin exposure was associated with significant downregulation of key transcripts in the NLRP3 inflammasome pathway (NLRP3, GSDMD, Caspase-1), as evidenced by the downregulation of NLRP3, GSDMD, and Caspase-1. Simultaneously, the transcriptional changes were consistent with the modulation/activation of the Nrf2 signaling axis, upregulating the expression of Nrf2, NQO1, and Keap1. These transcriptional changes indicate that quercetin attenuates pyroptosis and augments cellular antioxidant defenses via the Nrf2-Keap1 cascade. Correspondingly, the hepatopancreas displayed markedly elevated activities of SOD, CAT, and GSH-Px, accompanied by a significant reduction in MDA levels, indicating enhanced antioxidative capacity and diminished lipid peroxidation. This study provides valuable toxicological insights and elucidates part of the molecular basis for quercetin's immunomodulatory and antioxidant roles in freshwater crustaceans.
Knockout of zebrafish Clec3bb does cause vertebra density reduction.
Shi F, Wang X, Chen Y … +5 more , Xiao Z, Xiong X, Wang J, Gao Z, Nie C
Comp Biochem Physiol Part D Genomics Proteomics · 2026 Jun · PMID 41421237 · Publisher ↗
C-type lectin domain family 3 member B (Clec3b) is widely involved in various biological processes, including bone mineralization, cell proliferation, and pathogenesis of diseases. While clec3b association with skeletal...
C-type lectin domain family 3 member B (Clec3b) is widely involved in various biological processes, including bone mineralization, cell proliferation, and pathogenesis of diseases. While clec3b association with skeletal development has been well characterized in mammals, its role in fish skeletal development remains unclear. Due to genome duplication in teleosts, zebrafish possess two paralogous genes of clec3b, namely clec3ba and clec3bb, whose functional divergence remains unclear. The amino acid sequence similarity between zebrafish clec3ba and clec3bb was 55.61 %. Tissue-specific expression analysis revealed distinct expression patterns of clec3ba and clec3bb across multiple tissues (brain, gonads, fin, skin, vertebra, eyes, ribs, muscle, kidney, liver, gills) and embryonic stages. Mutants of clec3ba and clec3bb were generated using CRISPR/Cas9 system. Micro-CT analysis revealed that vertebral bone density was significantly reduced in clec3bb/ mutants compared to wild type, whereas no significant change was observed in clec3ba/ mutants. Comparative transcriptome was used to analyze gene expression differences of vertebrae in clec3bb and clec3bb/ zebrafish and identified 3316 differentially expressed genes were in vertebral tissues of clec3bb mutants, which were mainly enriched in the MAPK, TGF-β, Calcium and Wnt signaling pathways. RT-qPCR validated results showed that 10 skeletal-related genes (col1a1a, entpd5a, fgf23, bmp6, aspn, bglapl, tnmd, scxa, sp7, tnc) had a lower expression in vertebrae of clec3bb mutant. The above results highlight the critical role of clec3bb in zebrafish bone mineralization, providing insights into the functional specialization of clec3b paralogs and a theoretical basis for understanding skeletal development mechanisms in teleosts.
Comparative transcriptome analysis provides novel insights into the evolution of enhanced cold tolerance in the northward invasion of the eel goby, Taenioides sp.
Liu J, Xu A, Liu T … +9 more , Huang K, Zhu W, Yu J, Yang Y, Li F, Zhu D, Gong L, Liu L, Lü Z
Comp Biochem Physiol Part D Genomics Proteomics · 2026 Jun · PMID 41418498 · Publisher ↗
Invasive species serve as an ideal model for investigating adaptation, since they are typically introduced to unfamiliar environments where adaptation is essential for survival. Taenioides sp. is a typical invasive eel g...
Invasive species serve as an ideal model for investigating adaptation, since they are typically introduced to unfamiliar environments where adaptation is essential for survival. Taenioides sp. is a typical invasive eel goby that originally inhabited the tropical and subtropical coasts of Southeast China but has recently expanded into the temperate regions of North China due to the implementation of ESNT Project. However, the molecular basis underlying how the invasive population adapted to the climate of northern China during the invasion remains largely unknown. Here, we compared the cold tolerance and transcriptomic changes to cold stress in source (Yangtze River estuary) and northernmost invasive (Zhaoyang Lake) populations to elucidate the possible molecular mechanisms underlying this climate adaptation. Our results revealed significantly enhanced cold tolerance in the invasive compared to the source population (CT: 7.11 °C vs 10.66 °C). Transcriptome analysis revealed 56 differentially expressed genes (DEGs) with similar expression patterns across all tissues and populations, suggesting their core roles in the cold response of Taenioides sp. Meanwhile, multiple DEGs exhibit population-specific expression profiles, indicating their involvement in divergent cold tolerance. Further WGCNA analyses revealed a subset of cold-response hub genes associated with muscle structure and thermogenesis (e.g., MYO18B) exhibiting a distinct expression profile in the invasive population under cold stress, highlighting their roles in the evolution of enhanced cold tolerance. Our findings provided novel insights into the molecular basis of thermal adaptation underpinning the northward invasion of Taenioides sp. in a hydraulic-project-facilitating context, thus had important implications for predicting their invasive potential and developing management strategies for their effective control. Further analyses regarding how genetic and epigenetic forces have driven population-distinct gene expression regulation and, hence, divergent thermal adaptation will be necessary in the future.
Integrated transcriptomic and proteomic insights into low-salinity stress adaptation in Penaeus monodon.
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 41406502 · Publisher ↗
Salinity is a critical environmental factor affecting the growth of crustaceans. As an economically important aquaculture species, the farming of Penaeus monodon is currently facing challenges from salinity fluctuations...
Salinity is a critical environmental factor affecting the growth of crustaceans. As an economically important aquaculture species, the farming of Penaeus monodon is currently facing challenges from salinity fluctuations caused by climate change. However, studies utilizing multi-omics approaches to elucidate its molecular adaptation mechanisms to low salinity remain limited. This study systematically investigated the molecular regulatory mechanisms of P. monodon under low salinity stress (3 ‰) at different time points (6 h, 24 h, 96 h) using transcriptomic and proteomic technologies. A total of 927 DEGs and 928 DEPs were identified compared to the control group. This study revealed a dynamic adaptive strategy. At 6 h, P. monodon exhibited disruptions in energy metabolism and immune suppression, alongside the activation of immediate compensatory pathways. As the stress continued to 24 h, P. monodon showed a broad enhancement of metabolic activity, indicating a systemic effort to mitigate stress damage. After 96 h of exposure, P. monodon demonstrated a sustained upregulation of energy metabolism and the activation of detoxification systems, facilitating stable adaptive regulation. Furthermore, transcriptome-proteome integration analysis uncovered coordinated gene-protein regulatory patterns. This study provides the first multi-omics atlas of P. monodon's response to low salinity, which delineates a time-resolved molecular adaptation strategy. Our findings not only offer novel insights into osmoregulation but also deliver valuable molecular targets for breeding stress-resistant strains, presenting scientific basis for sustainable aquaculture facing environmental challenges.
Transcriptomic analysis of Cuvierian Organs regeneration in the sea cucumber Holothuria leucospilota.
Zhang X, Liu R, Ge H … +8 more , Chen T, Ren X, Long C, Huang J, Pan W, Qin H, Yuan L, Yan A
Comp Biochem Physiol Part D Genomics Proteomics · 2026 Jun · PMID 41406501 · Publisher ↗
Sea cucumbers are renowned for their regenerative capabilities, making them ideal models for studying tissue and organ regeneration. Holothuria leucospilota possesses a unique defensive structure, the Cuvierian organ (CO...
Sea cucumbers are renowned for their regenerative capabilities, making them ideal models for studying tissue and organ regeneration. Holothuria leucospilota possesses a unique defensive structure, the Cuvierian organ (CO), which is ejected upon threat and regenerates within weeks. However, the molecular mechanisms underlying CO regeneration remain poorly understood. In this study, we induced CO expulsion in H. leucospilota by mechanical stimulation and examined the regeneration process over 31 days. Histological analysis revealed that regeneration initiated with mesothelium formation, followed by connective tissue and epithelium development. Transcriptomic analysis identified numerous differentially expressed genes during regeneration. Key extracellular matrix (ECM)-related genes were upregulated, while matrix protease genes were downregulated. Signaling pathways including Wnt and Hippo were suppressed, whereas apoptosis and cell cycle pathways were activated. Additionally, several structural outer-layer proteins showed altered expression. These results indicate that ECM reorganization and coordinated regulation of cell proliferation and apoptosis are central to CO regeneration. This study provides important insights into the molecular mechanisms of organ regeneration in echinoderms and offers valuable clues for regenerative studies in higher animals.
Physiological effects of long-term saline-alkaline stress on the gills of Acanthopagrus latus: A combined analysis of transcriptomics and metabolomics.
Huang W, Zhou F, Lian Z … +2 more , Lin Z, Zhang Z
Comp Biochem Physiol Part D Genomics Proteomics · 2026 Jun · PMID 41406500 · Publisher ↗
Saline-alkaline stress poses a significant environmental challenge to fish in aquaculture, yet the molecular mechanisms underlying adaptation remain poorly understood. In this study, we integrated transcriptomic, metabol...
Saline-alkaline stress poses a significant environmental challenge to fish in aquaculture, yet the molecular mechanisms underlying adaptation remain poorly understood. In this study, we integrated transcriptomic, metabolomic, physiological, and histological analyses to elucidate the adaptive mechanisms of Acanthopagrus latus gills under saline-alkaline water (SAW) exposure. After 40 days of treatment, SAW caused evident histological alterations in gill structures but did not significantly affect growth performance. Physiological assays showed that glutathione peroxidase (GSH-Px), acid phosphatase (ACP) and alkaline phosphatase (ALP) activities showed no significant change, while malondialdehyde (MDA) levels increased, indicating oxidative stress and metabolic disturbance. Transcriptomic analysis identified 2539 differentially expressed genes (DEGs), mainly enriched in immune-related pathways such as T-cell receptor signaling, Th17 cell differentiation, and IL-17 signaling. Metabolomic profiling detected 892 differentially expressed metabolites (DEMs), primarily involved in energy metabolism pathways, including arachidonic acid, α-linolenic acid, and linoleic acid metabolism. Integrated multi-omics analysis further revealed a significant co-enrichment in platelet activation, phospholipase D signaling, and glutathione metabolism pathways. Notably, 29 DEGs and 4 key metabolites (ATP, prostaglandin H₂, cyclic AMP, and ADP) were significantly altered in the platelet activation pathway. Among them, upregulated genes such as p2ry12, LOC119021196, and LOC119027230 were linked to energy metabolism, while lyn, fynb, pik3r1, pik3cd, and akt1 were associated with apoptosis and immune regulation. Overall, this study provides comprehensive molecular and physiological evidence of how A. latus adapts to saline-alkaline stress through coordinated immune regulation and energy metabolism. These findings enhance our understanding of fish adaptive mechanisms and offer theoretical support for the sustainable utilization of saline-alkaline water resources in aquaculture.
Epitranscriptomic variation in banded newts (Ommatotriton vittatus) across life stages and sexes in the semi-arid habitat in northern Israel.
Meerson A, Almozlino M, Degani G … +1 more , Bercovich D
Comp Biochem Physiol Part D Genomics Proteomics · 2026 Jun · PMID 41391324 · Publisher ↗
The banded newt, Ommatotriton vittatus, is considered endangered in Israel, which is the southern border of its distribution and requires adaptation to highly unstable habitats. Banded newts have both aquatic and terrest...
The banded newt, Ommatotriton vittatus, is considered endangered in Israel, which is the southern border of its distribution and requires adaptation to highly unstable habitats. Banded newts have both aquatic and terrestrial forms, going through metamorphosis and various phenotypic changes during their life. Our group has previously reported on the extensive transcriptomic remodeling based on sex and especially the life stage of the newt. These dramatic changes in gene expression are likely accompanied by extensive epitranscriptomic regulation, which remains poorly understood. In this study, direct RNA sequencing was used to characterize mA RNA modifications in 12 newts from the Nehalit population. We focused on 127 genes with >30 differentially modified regions (DMRs, with a differential modification score > 5) in their transcripts, involved in structural, translational, and extracellular matrix processes. Among them, 18 genes showed clustering of methylation patterns according to life stage, particularly keratins and translation-related proteins, suggesting that mA plays a regulatory role in structural remodeling and developmental transitions. In contrast, the majority of DMR genes were associated with housekeeping and stress-response functions and did not show life-stage-specific clustering. Cross-analysis with differential expression data further indicated that muscle, immune, and connective tissue pathways are co-regulated at both the transcriptional and epitranscriptomic levels. These findings provide the first evidence of mA methylation patterns in O. vittatus and highlight their role in developmental transitions. The results advance understanding of transcriptomic-epitranscriptomic regulation in amphibian plasticity, and more generally, in vertebrate development.
Transcriptomic profiling of Helice tientsinensis reveals its adaptation mechanisms to different salinity levels.
Cui L, Hao S, Guan Y … +3 more , Chen Z, Wang Y, Wang Z
Comp Biochem Physiol Part D Genomics Proteomics · 2026 Jun · PMID 41389579 · Publisher ↗
Helice tientsinensis is a typical species in the intertidal ecosystem, which is easily affected by fluctuations in salinity. This study systematically investigated the physiological and molecular responses of H. tientsin...
Helice tientsinensis is a typical species in the intertidal ecosystem, which is easily affected by fluctuations in salinity. This study systematically investigated the physiological and molecular responses of H. tientsinensis under freshwater (0 ‰), low-salinity (15 ‰, control group), and high salinity (30 ‰) stress conditions at 24 and 48 h, using histological observation, enzyme activity detection, and transcriptome sequencing. The results showed that there were relatively few differentially expressed genes between different salinity groups, indicating that H. tientsinensis has a certain degree of adaptability to salinity fluctuations, which is consistent with its intertidal lifestyle. The gill tissue shows structural damage in the freshwater environment, and immune-related genes were downregulated, indicating that freshwater stress damages the gill tissue and suppresses the immune response. At the same time, H. tientsinensis responds to salinity stress through strategies related to energy metabolism, such as enhancing glycolysis, lipid metabolism, and purine synthesis. The study further reveals that H. tientsinensis adopts a tissue-specific osmoregulation strategy: osmoregulation-related genes (e.g., SLC34A, nptA) are significantly upregulated in gill tissue to enhance ion transport efficiency; in contrast, ion transport-related osmoregulation genes (e.g., ABCA1, ABCC2, ABCC3) are downregulated in the hepatopancreas to reduce metabolic load by saving energy consumption. The gene expression patterns of the two tissues act synergistically to maintain the overall osmotic balance homeostasis of the organism. The purpose of this study was to systematically elucidate the physiological and molecular mechanisms underlying the adaptation of H. tientsinensis to different salinity stresses, thereby filling the gap in current research on its molecular response to salinity changes and providing molecular evidence for the environmental adaptation of intertidal crustaceans.
Multomics decipher the mechanisms of bisphenol S-induced oxidative stress and inflammation in Pseudobagrus ussuriensis.
Wang L, Pu C, Li Y … +4 more , Zhu J, Ommati MM, Wang B, Zhang C
Comp Biochem Physiol Part D Genomics Proteomics · 2026 Jun · PMID 41386215 · Publisher ↗
Bisphenol S (BPS), a widespread environmental endocrine-disrupting chemical, has raised growing concerns regarding its ecotoxicological effects. In this study, we systematically investigated the integrated toxicity of BP...
Bisphenol S (BPS), a widespread environmental endocrine-disrupting chemical, has raised growing concerns regarding its ecotoxicological effects. In this study, we systematically investigated the integrated toxicity of BPS exposure using Pseudobagrus ussuriensis as a model aquatic species. Three hundred sixty fish (mean initial weight: 30.42 ± 0.62 g) were randomly allocated into four groups and exposed to 0 (control), 1, 10, or 100 μg/L BPS for 14 days. Histopathological examination revealed significant tissue damage, including gill filament edema, intestinal epithelial desquamation, and hepatic vacuolization. Oxidative stress assessment showed a concentration-dependent elevation in malondialdehyde (MDA) levels (p < 0.05). 16S rRNA sequencing analysis demonstrated that 10 μg/L BPS exposure markedly altered gut microbial composition, with significant enrichment of Achromobacter and Acinetobacter. Liver transcriptome profiling identified substantial differential expression of immune-related genes (hmgb1, nfκb, and nfκbiα) in the 100 μg/L exposure group. Importantly, Pearson correlation analysis established a significant association between gut microbiota perturbation and hepatic immune-inflammatory responses (p < 0.05). To our knowledge, this study provides the first evidence that environmentally relevant concentrations (10 μg/L) of BPS can induce significant physiological impairments in P. ussuriensis, offering novel insights into the ecological risks of BPS contamination.
Differential expression miRNAs in the gonad of sea cucumber Holothuria leucospilota.
Zhang J, Fu XQ, Lin RX … +3 more , Zhang Y, Zheng PM, Li H
Comp Biochem Physiol Part D Genomics Proteomics · 2026 Jun · PMID 41380583 · Publisher ↗
MicroRNAs are defined as a class of short noncoding RNAs, which play important function in cell differentiation, developmental process and gender determination. The sea cucumber Holothuria leucospilota is a member of the...
MicroRNAs are defined as a class of short noncoding RNAs, which play important function in cell differentiation, developmental process and gender determination. The sea cucumber Holothuria leucospilota is a member of the Echinodermata, known for its excellent nutritional and economic value. Breeding efficiency of sea cucumbers is low due to the difficulty in distinguishing between male and female individuals. Discovering molecular markers that distinguish between genders will provide a robust strategy for elucidating the genetic mechanisms governing gender determination and differentiation. In this investigation, high-throughput sequencing was utilized to compare miRNA expression patterns in the gonadal tissues of male and female specimens of H. leucospilota. A total of 584 known miRNAs and 404 novel miRNAs were identified, of which 97 miRNAs were identified as significantly differentially expressed miRNAs (DEMs) between male and female sea cucumbers. These findings enabled the construction of a miRNA-mRNA regulatory network. Pathway analysis of target genes highlighted the potential roles of neuroactive ligand-receptor interactions, calcium signaling, Salmonella infection, endocytosis, and MAPK signaling in governing gender differentiation processes. The expression results of high-throughput sequencing were validated in sc-miR121, sc-miR41, sc-miR67, sc-miR90, sc-miR104 and sc-miR189 by quantitative real-time quantity polymerase chain reaction (RT-qPCR). In summary, our results will provide a foundation for future studies of miRNA regulation in gender differentiation of sea cucumber H. leucospilota.
Profiling and functional validation of LPS-responsive miRNAs in the giant freshwater prawn, Macrobrachium rosenbergii.
Pangeson T, Thammason R, Ongvarrasopone C … +2 more , Wiengnak N, Phetrungnapha A
Comp Biochem Physiol Part D Genomics Proteomics · 2026 Jun · PMID 41380582 · Publisher ↗
MicroRNAs (miRNAs) are key post-transcriptional regulators involved in crustacean immune responses, yet their roles during pattern recognition receptor activation remain poorly understood. In this study, we investigated...
MicroRNAs (miRNAs) are key post-transcriptional regulators involved in crustacean immune responses, yet their roles during pattern recognition receptor activation remain poorly understood. In this study, we investigated the miRNA response of Macrobrachium rosenbergii to lipopolysaccharide (LPS), a conserved bacterial pathogen-associated molecular pattern (PAMP). High-throughput small RNA sequencing identified 155 differentially expressed miRNAs (DEMs) in the hepatopancreas following LPS injection. Pathway enrichment analysis revealed that target genes of these DEMs were significantly associated with immune pathways, including the ubiquitin-proteasome pathway (UPP) and endocytosis. Network analysis highlighted mro-miR-365-1-5p as a central regulator targeting key genes such as Rpn10, Rab11, Vps2, and ArfGAP3. Temporal expression profiling revealed rapid downregulation of mro-miR-365-1-5p after LPS exposure. The regulatory role of mro-miR-365-1-5p was validated by dual-luciferase reporter assays and an in vivo challenge experiment. In vivo overexpression of mro-miR-365-1-5p significantly increased mortality in prawns challenged with Vibrio harveyi, indicating impaired immune defense. These findings provide novel insights into the regulatory roles of LPS-responsive miRNAs in crustaceans and suggest that modulation of specific miRNAs may be crucial for effective immune activation during bacterial infection.
Incorporating GWAS-derived prior information enhances genomic prediction for body size traits in the mud crab (Scylla paramamosain).
Zhang W, Luo J, Shih Y … +7 more , Zhang Y, Zhou S, Qin Q, Huang K, Wang Q, Wang X, Ye H
Comp Biochem Physiol Part D Genomics Proteomics · 2026 Jun · PMID 41371055 · Publisher ↗
Scylla paramamosain is an economically important marine crab species in Asia, yet the genetic architecture of its growth traits remains poorly characterized. This study employed an integrated approach combining genome-wi...
Scylla paramamosain is an economically important marine crab species in Asia, yet the genetic architecture of its growth traits remains poorly characterized. This study employed an integrated approach combining genome-wide association studies (GWAS) and genomic prediction to dissect the genetic basis of four body size traits (carapace width, carapace length, posterior width of carapace, and body height) in 346 individuals genotyped at 3.9 million high-confidence SNPs. GWAS identified five pleiotropic loci and six candidate genes (including Exportin-5 and FANCI) shared among traits, with KEGG enrichment analysis underscoring the importance of metabolic pathways, particularly the citrate cycle. We further evaluated the genomic prediction performance of the GFBLUP model using two types of prior biological knowledge: functionally annotated SNPs derived from the top-enriched KEGG pathways, and trait-associated SNPs selected under varying GWAS significance thresholds. GFBLUP using trait-associated SNPs significantly outperformed standard GBLUP, with prediction accuracy gains of 0.528-0.888. Prediction accuracy increased with SNP panel size, exceeding 0.819 for all traits with the top 1000 SNPs and stabilizing beyond 5000 SNPs (0.837-0.865). An FDR threshold of 0.05 offered an optimal balance, achieving high accuracy (0.840-0.862) with a practical number of SNPs (7980-9302). In contrast, functionally informed GFBLUP provided only modest improvements (0.020-0.197), likely due to the inclusion of non-causal variants. These results demonstrate that low-density SNP panels informed by GWAS prior knowledge substantially enhance genomic prediction for body size traits in S. paramamosain, providing a practical breeding strategy and valuable insights into the genetic mechanisms of growth in non-model crustaceans.
Astral-based DIA proteomics explored the cold response mechanism in the liver of juvenile greenfin horse-faced filefish (Thamnaconus septentrionalis).
Zang X, Liu Y, Wang Z … +4 more , Wu Y, Qin B, Yin S, Wang T
Comp Biochem Physiol Part D Genomics Proteomics · 2026 Jun · PMID 41365212 · Publisher ↗
Thamnaconus septentrionalis, a high-value commercial fish, exhibits significant sensitivity to low temperatures. Understanding its cold response mechanism is vital for the aquaculture industry development. This study ana...
Thamnaconus septentrionalis, a high-value commercial fish, exhibits significant sensitivity to low temperatures. Understanding its cold response mechanism is vital for the aquaculture industry development. This study analyzed the hepatic response of T. septentrionalis to 24-h exposure at four temperature (10 °C, 15 °C, 20 °C, and 25 °C) using histology, biochemical parameters, and proteomics. Results showed that decreased temperature exacerbated hepatic damage, increased ROS accumulation, and induced oxidative stress. The cold-induced ROS accumulation was further validated by primary T. septentrionalis hepatocyte. Low-temperature groups (10 °C, 15 °C) exhibited elevated oxidative stress enzyme activities (SOD, CAT, GSH-Px), and the MDA level and decreased hepatic triglycerides compared to the control group (25 °C). Proteomic result revealed significant enrichment in energy metabolism pathways. It is hypothesized that cold stress tended to inhibited aerobic respiration and oxidative phosphorylation but enhanced fatty acid catabolism and potentially ketone body utilization as alternative fuels. The proteomic data also suggesting that liver also maintains cellular function by modulating lipid metabolism, activating autophagy, and suppressing apoptosis. This study reveals the physiological and proteomic response of T. septentrionalis to temperature variation, providing insights into its cold tolerance.
Aberrant body coloration in captive Yellow River carp (Cyprinus carpio haematopterus): A genomic perspective from whole-genome resequencing and bulk segregant analysis.
Liu Y, Chang L, Wang L … +3 more , Liu C, Feng D, Wang L
Comp Biochem Physiol Part D Genomics Proteomics · 2026 Jun · PMID 41352308 · Publisher ↗
To elucidate the genetic mechanism underlying body color variation within a single breeding family of captive Yellow River carp (Cyprinus carpio haematopterus), individuals exhibiting normal and aberrant pigmentation fro...
To elucidate the genetic mechanism underlying body color variation within a single breeding family of captive Yellow River carp (Cyprinus carpio haematopterus), individuals exhibiting normal and aberrant pigmentation from the same concrete pond were selected for analysis. Using bulked segregant analysis combined with whole-genome resequencing, DNA pools were constructed from progeny with extreme phenotypes for sequencing. SNP variation detection followed by linkage analysis identified a candidate region on chromosome 25, spanning approximately 10.1 Mb (from 15,881,284 bp to 26,645,798 bp). Gene Ontology (GO) enrichment analysis revealed four candidate genes potentially associated with aberrant pigmentation: dkk1, kndc1, lyst, and opn3. Based on the candidate genes' mutation sites, certain primers were created, and the PCR products were then sequenced. Notably, a mutation was detected at the 8th bp of the opn3 cDNA corresponding to transcript HHLG25g0668 in the aberrant-color offspring. At this position, 81.25 % of wild-type individuals carried the cytosine (C) allele, whereas all mutant individuals carried an adenine (A) substitution, resulting in an amino acid change from serine to tyrosine at position 3 of the protein. This suggests that opn3 may play a key role in the development of abnormal pigmentation in Yellow River carp. These findings provide a theoretical foundation for further functional studies of pigmentation-related genes and the genetic improvement of novel germplasm in Yellow River carp.
Transcriptomic analysis of gill tissues in blunt snout bream (Megalobrama amblycephala) under hypoxia and bacterial infection.
Sany APM, Chen S, Qin Q … +6 more , Luo J, Wang H, Foning LK, Kerebih A, Zheng G, Zou S
Comp Biochem Physiol Part D Genomics Proteomics · 2026 Jun · PMID 41352307 · Publisher ↗
Blunt snout bream (Megalobrama amblycephala) is an important commercial freshwater fish species in China's aquaculture system. It is unknown how the interaction of bacterial infections and dissolved oxygen concentration...
Blunt snout bream (Megalobrama amblycephala) is an important commercial freshwater fish species in China's aquaculture system. It is unknown how the interaction of bacterial infections and dissolved oxygen concentration affects the gene expression and physiological function of the gill tissues in this fish species. Therefore, fish were exposed to hypoxic conditions and challenged with Aeromonas hydrophila. Then, fish were classified into resistant (H-RMA) and sensitive (H-SMA) groups based on their survival outcomes. Gill tissues were collected for RNA-Seq and functional analysis. A total of 36,774 expressed genes, encompassing 33,852 known genes and 2922 novel genes were identified and around 93 % of these genes were correctly mapped to the reference genome. A comparative expression analysis between H-RMA and H-SMA fish revealed 5482 differentially expressed genes (DEGs) encompassing 2557 up-regulated and 2925 down-regulated genes. The examination of KEGG pathways revealed significant enrichment in DNA replication, proteasome, cell cycle, mismatch repair, oxidative phosphorylation and cellular senescence. Obviously structural alterations were observed in the gill tissues, resulting from the compounded impact of hypoxic stress and bacterial infection. Moreover, antioxidant enzymes (SOD, CAT) and immune enzyme activity modulation (ACP and AKP) were significantly (p < 0.05) changed between H-RMA and H-SMA groups. Our findings suggest a strong connection between cell cycle arrest and cellular senescence, indicating that resistance to these environmental stresses may depend on the capacity of the cellular senescence pathway to coordinate an immune response localized in the gills.
Unveiling the roles of oxidative stress defense and energy metabolism adjustment in low-temperature stress responses of Apostichopus japonicus: An integrated physiological, transcriptomic and metabolomic analysis.
He X, Li S, Wang S … +8 more , Wang Q, Xu X, Feng Y, Wang W, Li Z, Yang J, Luo Q, Sun G
Comp Biochem Physiol Part D Genomics Proteomics · 2026 Jun · PMID 41352306 · Publisher ↗
Sea cucumber Apostichopus japonicus is an important aquaculture species along the North Pacific coast. Its farming efficiency faces a growing threat from the impacts of global climate change, which characterized by eithe...
Sea cucumber Apostichopus japonicus is an important aquaculture species along the North Pacific coast. Its farming efficiency faces a growing threat from the impacts of global climate change, which characterized by either extreme low-temperature events or extended periods of cold stress. This study employed integrated physiological, transcriptomic, and metabolomic analyses to investigate A. japonicus responses to low temperatures (7.5 °C and 2.5 °C). When the temperature decreased to 7.5 °C and 2.5 °C, both significantly increased the activities of antioxidant enzymes (superoxide dismutase, SOD; catalase, CAT; glutathione peroxidase, GPX), thereby alleviating oxidative damage. Transcriptomic data showed that at 7.5 °C, genes related to antioxidant defense (e.g., ALDH7A1) were significantly upregulated, as were genes associated with lipid metabolism, such as SCP2. At 2.5 °C, the number of differentially expressed genes increased significantly, including the upregulation of lipid metabolism-related gene acox1, antioxidant defense-related genes (gclm, pdxk), and the downregulation of lipid metabolism-related gene hmgcr. Metabolomic profiling revealed enrichment of unsaturated fatty acids (e.g., linoleic acid) and primary bile acid biosynthesis at 7.5 °C, enhancing membrane fluidity and lipid utilization. Key metabolites at 2.5 °C (e.g., glutathione, L-aspartic acid) were involved in amino acid metabolism pathways. Integrated analyses highlighted co-enrichment of genes and metabolites linked to bile acid synthesis and fatty acid metabolism at 7.5 °C, supporting membrane stability and energy balance, while 2.5 °C induced pathways related to vitamin B6 metabolism, the TCA cycle, oxidative phosphorylation, and fatty acid degradation. These results indicate that A. japonicus primarily counters cold stress through antioxidant defense and energy homeostasis regulation. The findings provide a theoretical basis for understanding temperature adaptation in echinoderms and establish a foundation for developing precise cultivation strategies and breeding novel stress-resistant strains of A. japonicus to mitigate the impacts of global climate change.
A multi-omics atlas of testicular development in Leiocassis longirostris: dynamic regulation of spermatogenesis.
Qin F, Liu F, Cao Q … +9 more , Wei Z, Gao H, Zheng W, Ke Z, Xiong Y, Luo H, Wu R, Wang Z, Ye H
Comp Biochem Physiol Part D Genomics Proteomics · 2026 Jun · PMID 41349461 · Publisher ↗
The Chinese longsnout catfish (Leiocassis longirostris) is a commercially valuable freshwater species in China. We elucidated molecular mechanisms underlying testicular development of L. longirostris across five stages (...
The Chinese longsnout catfish (Leiocassis longirostris) is a commercially valuable freshwater species in China. We elucidated molecular mechanisms underlying testicular development of L. longirostris across five stages (stages I to V) through integrated transcriptomic and proteomic analyses, which is crucial for enhancing its sperm quality and efficient reproduction. Enrichment analyses identified several key pathways as essential for testicular development, including TGF-β signaling, Wnt signaling, ECM-receptor interaction, ferroptosis, cell cycle regulation, and ubiquitin-mediated proteolysis. Gene Ontology (GO) enrichment highlighted core biological processes such as germ cell proliferation, differentiation, meiotic progression, and spermatogenesis regulation involved in development. Notably, qPCR validation showed peak expression levels of wnt7a, pax6, and kiss1r at distinct spermatogenic phases (p < 0.01), suggesting their potential as temporal biomarkers for identification of development stages. Furthermore, protein-protein interaction (PPI) analyses revealed C-type lysozyme (LysC) as a potential regulatory factor, with peak expression at stages I and III, possibly linking testicular immunity and reproductive processes. These findings elucidate the molecular mechanisms of testicular development and provide insights for developing efficient artificial breeding strategies for L. longirostris.
Estrone exposure-induced feminization in male Siniperca chuatsi: A multidimensional study on sex reversal, liver damage, and changes in gene expression.
Chen K, Li W, Chen W … +5 more , Lin S, Deng Z, Cai G, Li Q, Han C
Comp Biochem Physiol Part D Genomics Proteomics · 2026 Jun · PMID 41349460 · Publisher ↗
Estrone (E1) is one of the primary natural estrogens found in aquatic environments and has the potential to impact the reproductive and endocrine systems of fish. To evaluate the impact of E1 on Siniperca chuatsi, in thi...
Estrone (E1) is one of the primary natural estrogens found in aquatic environments and has the potential to impact the reproductive and endocrine systems of fish. To evaluate the impact of E1 on Siniperca chuatsi, in this study, male S. chuatsi were exposed to E1 at concentrations of 0.0, 0.01, 0.1, and 1.0 μg/L for 60 consecutive days. Subsequently, we analyzed the gonadal histology, hepatic histology, antioxidant enzyme activities, and transcriptomic analysis of the fish. Histological examination of the gonads revealed that high concentrations of E1 can induce the transformation of testes into ovaries in male S.chuatsi, with an induction rate of 80 %. Moreover, significant changes in the levels of the androgen 11-ketotestosterone and the estrogen were observed at high concentrations. Hepatic histology revealed that E1 exposure led to vacuolization of hepatocytes, pyknosis, and inflammation in the liver. Additionally, exposure to 1.0 μg/L E1 significantly increased the activities of SOD (superoxide dismutase) and T-AOC (total antioxidant capacity) in the liver. Transcriptomic analysis of the liver identified several genes significantly associated with sex differentiation, including vtg1, cyp19a, hsd17β3, and esr1, among others. GO and KEGG enrichment analyses suggested that E1 exposure significantly altered the level of lipid metabolism in the liver of male S. chuatsi. In summary, these results indicate that E1 exposure not only causes oxidative damage to the liver but also induces alterations in hepatic steroid hormone synthesis and lipid metabolism pathways, which are indicative of feminizing endocrine effects, thereby leading to the feminization of male S.chuatsi.
Evolution of the animal globin superfamily: Insights from the blood clam Anadara granosa.
Zhang W, Chen T, Hu Y … +2 more , Shi X, Bao Y
Comp Biochem Physiol Part D Genomics Proteomics · 2026 Mar · PMID 41338068 · Publisher ↗
In recent decades, various globin groups have been identified and characterized in vertebrates, while studies on invertebrates remain limited. Therefore, we conducted this study to explore the repertoire, evolution, and...
In recent decades, various globin groups have been identified and characterized in vertebrates, while studies on invertebrates remain limited. Therefore, we conducted this study to explore the repertoire, evolution, and functions of globin genes in the blood clam Anadara granosa, an economically significant bivalve known for its hemoglobin. A total of 31 globin genes were identified, driven by tandem gene duplications that played a pivotal role in their expansion. Phylogenetic analysis identifies two previously unreported basal clades, provisionally named cluster A and B, alongside the well-known ancient globin groups neuroglobin, androglobin, globin X, and globin X-like. This suggests that invertebrates may have retained a more complete ancestral globin gene repertoire compared to vertebrates, and that the globin gene repertoire in the last common ancestor of vertebrates and invertebrates was more diverse than previously hypothesized. Protein structural analyses indicate that evolutionary changes in hemoglobin's oxygen-transport function may be driven by structural alterations in the CD region and EF helices or substitutions at select residues therein. Furthermore, the ancient globin groups exhibit widespread N-myristoylation and 3C-palmitoylation modifications, indicating their potential membrane-associated ancestral functions. Transcriptome analysis and hypoxia stress experiments indicate that globins are involved in the development and hypoxia tolerance of A. granosa. The pentacoordinate heme in animal globins likely switched from a hexacoordinate form, possibly associated with the evolution of oxygen-carrying functionality. This study expands our understanding of the globin superfamily's structure, function, and evolution, particularly in mollusks.
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