Comparative Biochemistry and Physiology D-Genomics & Proteomics比较生物化学与生理学 D 辑：基因组学与蛋白质组学
Comparative Biochemistry and Physiology D-Genomics & Proteomics(英文缩写 COMP BIOCHEM PHYS D),ISSN 1744-117X,eISSN 1878-0407,中文译名:比较生物化学与生理学 D 辑：基因组学与蛋白质组学 是一本学术期刊。本页汇总该期刊的最新影响因子、分区信息以及最新收录于 PubMed 的文献,帮助您快速了解期刊全貌。
发文量统计区间：2025-10-01 至 2026-09-30，按本站收录文献的发表日期统计。
期刊介绍
历年影响因子趋势
| JCR 数据年份 | 影响因子 | JCR 分区 |
|---|---|---|
| 2021 | 3.306 | Q3 |
| 2022 | 3.000 | Q3 |
| 2023 | 2.200 | Q3 |
| 2024 | 2.400 | Q3 |
| 2025 | 2.900 | Q2 |
Comparative Biochemistry and Physiology D-Genomics & Proteomics 最新收录文献
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1. Transcriptome and metabolome integration reveals molecular mechanisms underlying divergent cold tolerance in geographically distinct Procambarus clarkii populations.
PMID:日期:2026-10-01Low temperature is a major environmental stressor that constrains the survival and distribution of Procambarus clarkii. To explore the cold adaptation mechanisms of geographically differentiated populations, we exposed P. clarkii from Northeast China, Hubei and Anhui to continuous cold stress at 4 °C, while crayfish maintained at 20 °C serving as the control group. After 10 days of stress exposure, tail-muscle tissues were collected for transcriptomic and metabolomic analyses. Phenotypic observation revealed distinct cold tolerance among populations: the Northeast population had the highest cold tolerance while the Anhui population was the most cold-sensitive. Transcriptomic screening identified population-specific differentially expressed genes (DEGs), with 598, 113, and 193 DEGs detected in the Anhui, Hubei, and Northeast populations, respectively. Meanwhile, metabolomic analysis yielded 76, 456, and 176 differentially expressed metabolites (DEMs) in the Anhui, Hubei, and Northeast populations respectively. In this study, we performed integrated KEGG enrichment analysis of transcriptomes and metabolomes to delineate cold adaptive signatures across three geographically distinct P. clarkii populations. The Northeast population exhibited the most distinct adaptive reprogramming, with specific enrichment of pathways related to cell junction, phagocytosis, estrogen signaling, glutathione metabolism and D-amino acid metabolism, which may confer superior cold tolerance by reinforcing cellular structural integrity, enhancing innate immune defense and improving antioxidant capacity. The Hubei population was characterized by enriched tricarboxylic acid cycle, AMPK-mediated energy signaling, MAPK signaling and protein processing pathways, reflecting a strategy of energy homeostasis coupling with cellular stress response. The Anhui population mainly enriched basal metabolic pathways including carbohydrate metabolism, purine metabolism and aminoacyl-tRNA biosynthesis, suggesting a relatively basal metabolic maintenance strategy. Notably, basal energy and substance metabolism pathways such as sulfur metabolism, HIF-1 signaling and purine metabolism were conserved across all three populations. Collectively, the differential metabolic and transcriptional pathway reprogramming contributes to the cold adaptive differentiation of geographically separated P. clarkii populations, providing a comprehensive theoretical basis for exploring stress resistance mechanisms in crustaceans.
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2. Integrative ATAC-seq and RNA-seq reveal chromatin remodeling as a hub of immune, oxidative, and metabolic reprogramming under heat and hypoxia stress in Apostichopus japonicus.
PMID:日期:2026-09-28The sea cucumber Apostichopus japonicus holds significant economic importance in China's marine aquaculture. However, climate change-particularly extreme summer temperatures and hypoxia-has caused substantial economic losses in major production regions. These stressors impair the physiological, immunological, and survival ability of A. japonicus, with compounded high temperature and low oxygen stress exerting particularly severe effects. Using enzyme activity assays, RNA-seq, and ATAC-seq, we investigated how elevated temperature and hypoxia affect immune, antioxidant, and metabolic responses in A. japonicus (mean body weight 106 ± 15.3 g) under three conditions: optimal growth, low oxygen, and combined high temperature with low oxygen. Integrative analysis of transcriptomic and epigenomic data identified key co-expression modules and pathways associated with stress responses. Notably, the NF-κB signaling pathway emerged as a central regulator of immune and inflammatory responses under combined stress. Furthermore, genes involved in immune function (Orct2, bmp2), epigenetic regulation (DNMT), and protein homeostasis (ST8SIA1) exhibited coordinated changes in both chromatin accessibility and expression, revealing that chromatin remodeling underpins stress-induced transcriptional reprogramming. These findings demonstrate that A. japonicus responds to escalating environmental stress through hierarchical layers of signal transduction, epigenetic remodeling, and physiological output, with important implications for climate-adaptive aquaculture management.
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3. Genome-wide identification of the LLTP superfamily in three cuttlefish species and expression profiling in Sepiella japonica.
PMID:日期:2026-09-28The large lipid transfer protein (LLTP) superfamily, characterized by a conserved LPD_N domain, plays important roles not only in lipid transport but also in diverse physiological processes, including animal development, reproduction, and immunity. However, comprehensive characterization of the LLTP gene family in cuttlefish remains limited. In this study, a total of 15 LLTP genes were identified in three cuttlefish species, Sepiella japonica, Sepia officinalis, and S. esculenta, using bioinformatic approaches. Phylogenetic analysis revealed that these genes clustered into three distinct families: VTG, Apo, and MTP. Analyses of motif patterns and gene structures revealed distinct yet conserved features among LLTP families. Chromosomal localization and synteny analyses revealed conserved organization with species-specific variations among LLTP genes. Tissue expression profiling of LLTP genes in S. japonica revealed distinct expression patterns among the three families, with VTG genes showing ovary-biased expression, whereas Apo and MTP genes exhibited broader tissue distribution patterns. Our findings advance the understanding of LLTP evolutionary diversification in cuttlefish and provide insights into their potential roles in lipid transport and other physiological processes.
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4. Evolutionary diversification and Vibrio-responsive regulation of NF-κB signaling in bivalves: Evidence from Mimachlamys nobilis and comparative datasets.
PMID:日期:2026-09-25The nuclear factor kappa B (NF-κB) pathway is a central regulator of innate immunity in animals, yet its evolutionary diversification in bivalve molluscs remains incompletely understood. Here, we analyzed NF-κB/Rel genes across 29 representative bivalve species from 11 families. Our analyses revealed substantial variation in observed annotated copy number and a conserved separation between Rel-type and NF-κB-type proteins, both of which possess the Rel homology domain (RHD), whereas ankyrin (ANK) repeats were predominantly associated with NF-κB-type members. Notably, McoRel_1 clustered within the NF-κB-type lineage but lacked detectable ANK-associated motifs in its predicted 355-aa protein model, while complementary ANK-containing sequence information was identified in an immediately adjacent 891-aa model, consistent with possible local annotation fragmentation. In Mimachlamys nobilis, RNA-seq of 27 independent libraries from nine tissues of six individuals and qRT-PCR after Vibrio parahaemolyticus challenge revealed tissue- and time-dependent transcriptional patterns of NF-κB/IKK-related genes. Together, these results provide an integrated evolutionary and transcriptional framework for understanding NF-κB/Rel diversification in bivalves and highlight lineage-associated structural variation and Vibrio-responsive genes as priorities for future functional investigation.
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5. Transcriptome profiling of mantle tissue reveals candidate genes associated with growth variation in Asian hard clam (Meretrix meretrix).
PMID:日期:2026-09-25Growth rate is an important economic trait in the Asian hard clam Meretrix meretrix, yet the molecular basis underlying growth variation remains poorly understood. In this study, fast- and slow-growing individuals from the same breeding cohort and cultured under identical pond conditions were selected for comparative transcriptomic analysis of mantle tissue. Differential expression and functional enrichment analyses identified genes and biological pathways potentially associated with growth variation. The identified differentially expressed genes were mainly involved in muscle development, shell formation, extracellular matrix remodeling, biomineralization, energy metabolism, iron transport, and immune-related processes. Representative genes, including myosin heavy chain, chitinase3, cathepsin K, tyrosinase, carbohydrate sulfotransferase 11, pantetheinase-like protein, and hephaestin, showed distinct expression patterns between fast- and slow-growing clams and may contribute to differences in growth performance. Several representative genes were further validated by RT-qPCR, and the expression trends were generally consistent with the RNA-seq results. Overall, this study provides a mantle transcriptomic resource for M. meretrix and identifies candidate genes and pathways potentially associated with growth variation, providing useful molecular information for understanding growth regulation and future genetic improvement and selective breeding of this species.
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6. Structural, biochemical, transcriptomic, and metabolomic changes in the body wall of sea cucumber (Stichopus monotuberculatus) across different stages of autolysis.
PMID:日期:2026-09-25Stichopus monotuberculatus is a highly prized marine delicacy that undergoes post-harvest autolysis at a rate exceptionally faster than common species like Apostichopus japonicus. Driven by this pronounced phenotypic difference, we hypothesized that the autolysis of S. monotuberculatus is governed by an exceptionally accelerated cascade of oxidative and lipid disruptions, which rapidly overwhelms the classical protease and apoptosis mechanisms. To test this hypothesis, a trauma induced degradation model was established by incision and air exposure, and body-wall samples across seven time points were examined using histological, biochemical, metabolomic, and transcriptomic analyses. The autolytic process featured four distinct morphological and molecular stages, with temporal changes in Cathepsin B content and glycosaminoglycan solubilization accompanying progressive tissue disintegration. Integrated multi-omics strongly suggested that oxidative stress and lipid metabolism disruption are central events highly associated with the autolytic cascade. While oxidative injury is a ubiquitous cellular stress response, the rapid early molecular changes observed in this species appear to differ from patterns previously reported for A. japonicus, although direct interspecific comparisons under identical experimental conditions are still required. Overall, these findings support our hypothesis. By identifying oxidative stress and lipid metabolic disruption as the prominent biochemical processes associated with autolysis, this study provides a basis for future functional studies to determine whether modulation of these processes can influence post-harvest degradation.
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7. Tract-wide transcriptomic and metabolomic profiling reveals gastrointestinal regionalization in Jiekarzi semi-fine wool sheep.
PMID:日期:2026-09-23Jiekarzi semi-fine-wool sheep are indigenous to the Qinghai-Tibet Plateau, and may face substantial demands on digestive efficiency under low temperatures, hypoxia and seasonal forage limitation. However, the molecular organization of the gastrointestinal tract in this breed remains insufficiently characterized. Here, we profiled mucosal transcriptomes and digestive-fluid metabolomes from 10 gastrointestinal segments collected from six 12-month-old male Jiekarzi. The segments were grouped into four digestive regions: forestomach, true stomach, small intestine and large intestine. Transcriptomes analysis separated clearly by regions, with PC1 and PC2 explaining 40.82% and 15.00% of the variation, respectively. Pairwise differential expression analysis identified 4,941-9,598 differentially expressed genes, with the largest difference between the small intestine and forestomach. Region-specific enrichment indicated differences in immune processes, epithelial organization, transmembrane transport, digestion and absorption, lipid metabolism and xenobiotic associated pathways. Untargeted LC-MS detected 1,757 metabolites in positive-ion mode and 1547 metabolites in negative-ion mode. Integrated transcriptome and metabolomic patterns suggested region associated immune function, nutrient transport and metabolic specialization. These results provide a baseline molecular map of gastrointestinal regionalization for a wider area of the tract, and a reference resource for future research on digestive physiology, nutrient utilization and environmental resilience in plateau-adapted ruminants.
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8. Proteasomal and lysosomal protein signatures in surviving Meretrix meretrix after acute ammonia exposure.
PMID:日期:2026-09-23Ammonia stress can disturb cellular protein homeostasis, but the coordinated response of protein quality-control systems in the bivalve hepatopancreas is not well understood. Hard clams (Meretrix meretrix) were exposed for 96 h to nominal total ammonia nitrogen (TAN) concentrations of 0 (Ctrl), 1.17 (Low), or 11.7 mg L (High). The High concentration was based on an extrapolated 96 h median lethal concentration estimate: the estimate of 11.7 mg L was below the lowest non-control concentration tested (12.5 mg L). The experimental unit was the tank (n = 3 per treatment), and hepatopancreata from five survivors in each tank were pooled. TAN was measured during exposure, but the numerical records were not retained; actual TAN and unionized-ammonia (NH) exposures are therefore unknown. diaPASEF-based data-independent acquisition proteomics identified 9437 proteins. Exploratory criteria identified 417, 613, and 625 differentially abundant proteins (DAPs) in Low versus Ctrl, High versus Ctrl, and High versus Low, respectively, whereas 2, 10, and 13 proteins remained significant after false-discovery-rate (FDR) correction. KEGG gene-set enrichment analysis showed positive proteasomal enrichment and negative lysosomal enrichment in both comparisons involving the High group. These comparisons share the same High samples and are not independent. Protein processing in the endoplasmic reticulum was also enriched in High versus Ctrl. GPX3 was lower in High than in Low (0.52-fold; FDR = 0.0104), but requires independent validation. The results describe protein-abundance patterns in 96 h survivors, not changes in pathway activity or degradation flux. The High-group profile may include both treatment responses and selection of more tolerant individuals.
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9. Time-resolved transcriptomics reveals sex-specific programs of gametogenesis and post-spawning gonadal remodeling in the sea cucumber Apostichopus japonicus.
PMID:日期:2026-09-23The sea cucumber Apostichopus japonicus is an important mariculture species in East Asia, yet the temporal programs that distinguish female and male gonadal development remain incompletely resolved. Histological staging and RNA sequencing were combined to profile female and male gonads across five histologically defined gonadal developmental stages (stages a-e), spanning recovery/resting, proliferation/early differentiation, growth/vitellogenesis, maturation, and post-spawning degeneration/remodeling. Thirty libraries were generated from ten sex-by-stage groups, with three pooled biological replicates per group. Male gonads underwent extensive transcriptional remodeling after stage a, whereas the largest female shift occurred between the recovery and post-spawning stages. Stage-matched comparisons identified 1310, 609, 1436, 4733, and 7578 differentially expressed genes at stages a, b, c, d, and e, respectively, showing that sex-biased expression expanded sharply during maturation and after spawning. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment, together with gene set enrichment analysis (GSEA), associated female development with DNA replication, cell-cycle progression, oocyte maturation, lysosomal degradation, glycosaminoglycan turnover, and extracellular-matrix remodeling. Male development was characterized by cytoskeletal reorganization, microtubule and axoneme assembly, ciliary/flagellar movement, motor proteins, lipid metabolism, and energy metabolism. Short Time-series Expression Miner (STEM) and weighted gene co-expression network analysis (WGCNA) resolved distinct temporal profiles and complementary co-expression modules associated with early/recovery, female stage-e remodeling, and male stage-e axoneme/motility patterns. Representative genes associated with these patterns included vasa/DDX4, PIWIL1, nanos1, CDK1, CCNB2, CCNB3, PLK1, TEKT3, CFAP61, DNAH5, CTSF, and ITGB1. These data provide a stage-resolved transcriptomic framework for gametogenesis and post-spawning gonadal remodeling in A. japonicus.
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10. Effects of black soldier fly larvae meal on hepatic metabolism and intestinal health in juvenile southern catfish (Silurus meridionalis): Insights from non-targeted metabolomics.
PMID:日期:2026-09-22To investigate the effects of replacing fishmeal (FM) with black soldier fly larvae meal (BSFLM) on hepatic metabolism and intestinal health in juvenile southern catfish (Silurus meridionalis), six isonitrogenous and isoenergetic diets were formulated with graded replacement levels of 0%, 10%, 20%, 30%, 40%, and 50% and fed to fish for 8 weeks. Intestinal antioxidant parameters, serum immune factors, hepatic free amino acids, and non-targeted hepatic metabolomics were analyzed. No significant differences were observed among groups in intestinal superoxide dismutase (SOD), glutaredoxin (GSH-PX), total antioxidant capacity (T-AOC), or malondialdehyde (MDA) (ANOVA, all P > 0.05). Serum interleukin-10 (IL-10) showed a significant linear increase with increasing BSFLM inclusion (P = 0.021), indicating dose-dependent anti-inflammatory immunomodulation. Hepatic free amino acid profiling revealed that ornithine decreased significantly with increasing replacement (P = 0.012), S-adenosylmethionine (SAM) peaked in the H50 group (36.59 vs. 24.00 in H0, P = 0.006), proline decreased significantly (P = 0.030), taurine and cysteine were significantly elevated in the H50 group (P = 0.007 and 0.022, respectively), and gamma-aminobutyric acid (GABA) declined significantly (P = 0.004). Non-targeted metabolomics revealed a three-phase metabolic trajectory: 10-20% replacement represented an adaptation phase characterized by decoupling of central nitrogen metabolism from anabolism; 30% constituted a transition phase with synergistic integration of energy metabolism, carbohydrate utilization, and glucuronidation detoxification; 40-50% represented a stress/dysregulation phase, marked by a coordinated stress module containing norepinephrine and pyroglutamic acid, with 2-furoic acid emerging as a potential stress biomarker at 50% inclusion. The number of differentially abundant metabolites increased from 7 in the H10 group to over 60 in the H50 group. KEGG pathway enrichment confirmed activation of amino acid and secondary metabolite biosynthesis at low levels, while high levels enriched oxidative stress-related pathways including glutathione metabolism, ferroptosis, and ABC transporters. Collectively, these findings indicate that BSFLM replacement should not exceed 30% in juvenile southern catfish diets to balance sustainable protein utilization with maintenance of metabolic homeostasis and overall health.