Comparative Biochemistry and Physiology D-Genomics & Proteomics最新文献_第6页

Comparative transcriptome analysis provides novel insights into the evolution of enhanced cold tolerance in the northward invasion of the eel goby, Taenioides sp. 比较转录组分析为北侵鳗鱼虾虎鱼（Taenioides sp.）耐寒性增强的进化提供了新的见解。

IF 2.2 2区生物学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY

Comparative Biochemistry and Physiology D-Genomics & Proteomics

Pub Date : 2025-12-11 DOI: 10.1016/j.cbd.2025.101709

Jing Liu, An Xu, Tianwei Liu, Kun Huang, Weihu Zhu, Jing Yu, Yijing Yang, Fenghui Li, Denghui Zhu, Li Gong, Liqin Liu, Zhenming Lü

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_min: 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.

入侵物种是研究适应的理想模型，因为它们通常被引入不熟悉的环境，在那里适应是生存所必需的。Taenioides sp.是一种典型的入侵性虾虎鱼，最初栖息在中国东南部的热带和亚热带海岸，最近由于ESNT项目的实施而扩展到华北温带地区。然而，入侵种群在入侵期间如何适应中国北方气候的分子基础仍不清楚。本研究比较了长江口源种群和最北端入侵种群对冷胁迫的耐寒性和转录组学变化，以阐明这种气候适应的可能分子机制。我们的研究结果显示，与源种群相比，侵入性种群的耐寒性显著增强（CTmin: 7.11°C vs 10.66°C）。转录组分析发现56个差异表达基因（DEGs）在所有组织和群体中表达模式相似，表明它们在Taenioides sp.的冷响应中起核心作用。同时，多个DEGs表现出群体特异性表达谱，表明它们参与了不同的抗寒性。进一步的WGCNA分析显示，与肌肉结构和产热相关的冷反应中枢基因子集（例如MYO18B）在寒冷胁迫下的入侵种群中表现出不同的表达谱，突出了它们在增强耐寒性进化中的作用。本研究结果为水工程环境下带蚊北侵的热适应分子机制提供了新的见解，对预测其入侵潜力和制定有效控制策略具有重要意义。关于遗传和表观遗传力量如何驱动种群不同的基因表达调控，因此，不同的热适应将在未来进行进一步的分析。

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引用次数: 0

Epitranscriptomic variation in banded newts (Ommatotriton vittatus) across life stages and sexes in the semi-arid habitat in northern Israel 以色列北部半干旱地区带状蝾螈（Ommatotriton vittatus）跨生命阶段和性别的表转录组变异

IF 2.2 2区生物学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY

Comparative Biochemistry and Physiology D-Genomics & Proteomics

Pub Date : 2025-12-09 DOI: 10.1016/j.cbd.2025.101727

Ari Meerson , Monika Almozlino , Gad Degani , Dani Bercovich

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 m⁶A 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 m⁶A 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 m⁶A 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.

带状蝾螈（Ommatotriton vittatus）在以色列被认为是濒危物种，以色列是其分布的南部边界，需要适应高度不稳定的栖息地。带状蝾螈有水栖和陆生两种形态，在其一生中经历了蜕变和各种表型变化。我们的团队之前已经报道了基于性别的广泛转录组重塑，特别是蝾螈的生命阶段。这些基因表达的戏剧性变化可能伴随着广泛的表转录组调控，这仍然知之甚少。在这项研究中，使用直接RNA测序来表征来自Nehalit种群的12只蝾螈的m6A RNA修饰。我们重点研究了127个转录本中有30个差异修饰区（DMRs，差异修饰评分为5）的基因，这些基因参与了结构、翻译和细胞外基质过程。其中，18个基因显示出不同生命阶段的甲基化模式聚类，尤其是角蛋白和翻译相关蛋白，提示m6A在结构重塑和发育转变中发挥调控作用。相比之下，大多数DMR基因与管家和压力反应功能有关，没有表现出生命阶段特异性聚类。与差异表达数据的交叉分析进一步表明，肌肉、免疫和结缔组织通路在转录和表转录组水平上共同调控。这些发现提供了m6A甲基化模式在O. vittatus中的第一个证据，并强调了它们在发育转变中的作用。这些结果促进了对两栖动物可塑性的转录组-表转录组调控的理解，更广泛地说，是对脊椎动物发育的理解。

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引用次数: 0

Profiling and functional validation of LPS-responsive miRNAs in the giant freshwater prawn, Macrobrachium rosenbergii 罗氏沼虾lps应答mirna的分析与功能验证

IF 2.2 2区生物学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY

Comparative Biochemistry and Physiology D-Genomics & Proteomics

Pub Date : 2025-12-09 DOI: 10.1016/j.cbd.2025.101724

Tanapat Pangeson , Rattikon Thammason , Chalermporn Ongvarrasopone , Nalinnipa Wiengnak , Amnat Phetrungnapha

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.

MicroRNAs （miRNAs）是甲壳类动物免疫应答的关键转录后调节因子，但其在模式识别受体激活过程中的作用仍知之甚少。在这项研究中，我们研究了罗氏沼虾（Macrobrachium rosenbergii）对脂多糖（LPS）的miRNA反应，脂多糖是一种保守的细菌病原体相关分子模式（PAMP）。高通量小RNA测序鉴定了LPS注射后肝胰腺中155个差异表达的mirna （dem）。途径富集分析显示，这些dem的靶基因与免疫途径显著相关，包括泛素-蛋白酶体途径（UPP）和内吞作用。网络分析表明，mir -365-1-5p是一个针对关键基因如Rpn10、Rab11、Vps2和ArfGAP3的中央调控因子。时间表达谱显示，LPS暴露后，mir -365-1-5p快速下调。通过双荧光素酶报告基因检测和体内激发实验验证了mir - mir -365-1-5p的调控作用。在体内，mir -365-1-5p的过表达显著增加了哈威弧菌攻击对虾的死亡率，表明免疫防御受损。这些发现为甲壳类动物lps反应性mirna的调节作用提供了新的见解，并表明特定mirna的调节可能对细菌感染期间有效的免疫激活至关重要。

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引用次数: 0

Physiological effects of long-term saline-alkaline stress on the gills of Acanthopagrus latus: A combined analysis of transcriptomics and metabolomics 长期盐碱胁迫对棘鱼鳃的生理影响：转录组学和代谢组学的联合分析。

IF 2.2 2区生物学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY

Comparative Biochemistry and Physiology D-Genomics & Proteomics

Pub Date : 2025-12-08 DOI: 10.1016/j.cbd.2025.101701

Weiqing Huang , Fengfang Zhou , Zongqiang Lian , Zhideng Lin , Zipeng Zhang

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.

盐碱胁迫对水产养殖鱼类构成了重大的环境挑战，但其适应盐碱胁迫的分子机制尚不清楚。在这项研究中，我们综合了转录组学、代谢组学、生理学和组织学分析来阐明棘鱼鳃在盐碱水（SAW）暴露下的适应机制。处理40天后，SAW引起了鳃结构的明显组织学改变，但对生长性能没有显著影响。生理分析显示，谷胱甘肽过氧化物酶（GSH-Px）、酸性磷酸酶（ACP）和碱性磷酸酶（ALP）活性无显著变化，丙二醛（MDA）水平升高，提示氧化应激和代谢紊乱。转录组学分析鉴定出2539个差异表达基因（DEGs），主要富集于免疫相关通路，如t细胞受体信号传导、Th17细胞分化和IL-17信号传导。代谢组学分析检测到892种差异表达代谢物（DEMs），主要参与能量代谢途径，包括花生四烯酸、α-亚麻酸和亚油酸代谢。综合多组学分析进一步揭示了血小板活化、磷脂酶D信号转导和谷胱甘肽代谢途径中显著的共富集。值得注意的是，29个DEGs和4个关键代谢物（ATP、前列腺素H₂、环AMP和ADP）在血小板活化途径中显著改变。其中，p2ry12、LOC119021196和LOC119027230等上调基因与能量代谢相关，lyn、fynb、pik3r1、pik3cd和akt1等上调基因与细胞凋亡和免疫调节相关。综上所述，本研究提供了水杨如何通过协调免疫调节和能量代谢来适应盐碱胁迫的分子和生理证据。这些发现增强了我们对鱼类适应机制的认识，为盐碱水资源在水产养殖中的可持续利用提供了理论支持。

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引用次数: 0

Multomics decipher the mechanisms of bisphenol S-induced oxidative stress and inflammation in Pseudobagrus ussuriensis 多组学揭示了双酚s诱导的乌苏里假袋氧化应激和炎症的机制

IF 2.2 2区生物学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY

Comparative Biochemistry and Physiology D-Genomics & Proteomics

Pub Date : 2025-12-08 DOI: 10.1016/j.cbd.2025.101725

Lu Wang , Changchang Pu , Yimin Li , Jiaxiang Zhu , Mohammad Mehdi Ommati , Bingke Wang , Chunnuan Zhang

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.

双酚S （BPS）是一种广泛存在的环境内分泌干扰化学物质，其生态毒理学效应引起了人们越来越多的关注。本研究以乌苏里假bagrus为模型水生物种，系统研究了BPS暴露的综合毒性。360尾鱼（平均初始体重：30.42±0.62 g）随机分为4组，分别暴露于0（对照）、1、10和100 μg/L BPS中14 d。组织病理学检查显示明显的组织损伤，包括鳃丝水肿、肠上皮脱屑和肝脏空泡化。氧化应激评估显示丙二醛（MDA）水平呈浓度依赖性升高（p < 0.05）。16S rRNA测序分析表明，10 μg/L BPS暴露显著改变了肠道微生物组成，无色杆菌和不动杆菌显著富集。肝脏转录组分析发现，在100 μg/L暴露组中，免疫相关基因（hmgb1、nfκb和nfκbiα）的表达存在显著差异。重要的是，Pearson相关分析建立了肠道菌群扰动与肝脏免疫炎症反应之间的显著关联（p < 0.05）。据我们所知，本研究首次证明了环境相关浓度（10 μg/L）的BPS可引起乌苏里江拟南鲷的显著生理损伤，为研究BPS污染的生态风险提供了新的视角。

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引用次数: 0

Knockout of zebrafish Clec3bb does cause vertebra density reduction 敲除斑马鱼的Clec3bb确实会导致椎骨密度降低

IF 2.2 2区生物学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY

Comparative Biochemistry and Physiology D-Genomics & Proteomics

Pub Date : 2025-12-08 DOI: 10.1016/j.cbd.2025.101726

Feilong Shi , Xudong Wang , Yulong Chen , Zhengyu Xiao , Xuemei Xiong , Jianbo Wang , Zexia Gao , Chunhong Nie

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.

c型凝集素结构域家族3成员B （Clec3b）广泛参与多种生物过程，包括骨矿化、细胞增殖和疾病的发病机制。虽然在哺乳动物中已经很好地描述了cle3b与骨骼发育的关系，但它在鱼类骨骼发育中的作用仍不清楚。由于硬骨鱼基因组的重复，斑马鱼具有两个类似的clec3b基因，即clec3ba和clec3bb，其功能分化尚不清楚。斑马鱼clec3ba与clec3bb氨基酸序列相似性为55.61%。组织特异性表达分析显示，clec3ba和clec3bb在多个组织（脑、性腺、鳍、皮肤、脊椎、眼睛、肋骨、肌肉、肾脏、肝脏、鳃）和胚胎期的表达模式不同。利用CRISPR/Cas9系统生成了clec3ba和clec3bb突变体。Micro-CT分析显示，与野生型相比，clec3bb - / -突变体的椎体骨密度显著降低，而clec3ba - / -突变体的椎体骨密度没有明显变化。采用比较转录组分析clec3bb+/+和clec3bb−/−斑马鱼椎体基因表达差异，发现clec3bb突变体椎组织中存在3316个差异表达基因，主要富集于MAPK、TGF-β、钙和Wnt信号通路。RT-qPCR验证结果显示，10个骨骼相关基因（col1a1a、entpd5a、fgf23、bmp6、aspn、bglap、tnmd、scxa、sp7、tnc）在cle3bb−/−突变体的椎骨中表达量较低。上述结果突出了clec3bb在斑马鱼骨矿化中的关键作用，为了解clec3b类似物的功能专门化提供了见解，并为理解硬骨鱼骨骼发育机制提供了理论基础。

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引用次数: 0

Differential expression miRNAs in the gonad of sea cucumber Holothuria leucospilota 细鳞海参生殖腺mirna的差异表达

IF 2.2 2区生物学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY

Comparative Biochemistry and Physiology D-Genomics & Proteomics

Pub Date : 2025-12-04 DOI: 10.1016/j.cbd.2025.101711

Jing Zhang , Xiao-qin Fu , Run-xin Lin , Yang Zhang , Pei-ming Zheng , Huo Li

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.

MicroRNAs是一类短链非编码rna，在细胞分化、发育过程和性别决定中发挥重要作用。海参Holothuria leucospilota是棘皮科的一员，以其优良的营养和经济价值而闻名。由于雌雄个体难以区分，海参的繁殖效率较低。发现区分性别的分子标记将为阐明控制性别决定和分化的遗传机制提供强有力的策略。本研究利用高通量测序技术，比较了雄性和雌性标本的雄性和雌性标本性腺组织中miRNA的表达模式。共鉴定出584个已知mirna和404个新mirna，其中97个mirna在雄性和雌性海参之间被鉴定为显著差异表达mirna （dem）。这些发现使得构建miRNA-mRNA调控网络成为可能。靶基因的通路分析强调了神经活性配体-受体相互作用、钙信号、沙门氏菌感染、内吞作用和MAPK信号在调节性别分化过程中的潜在作用。采用实时定量聚合酶链反应（RT-qPCR）对高通量测序结果在sc-miR121、sc-miR41、sc-miR67、sc-miR90、sc-miR104和sc-miR189中的表达进行验证。综上所述，我们的研究结果将为进一步研究miRNA在海参性别分化中的调控作用提供基础。

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引用次数: 0

Astral-based DIA proteomics explored the cold response mechanism in the liver of juvenile greenfin horse-faced filefish (Thamnaconus septentrionalis) 基于星体的DIA蛋白质组学研究了绿鳍马面鱼幼鱼肝脏的冷反应机制。

IF 2.2 2区生物学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY

Comparative Biochemistry and Physiology D-Genomics & Proteomics

Pub Date : 2025-12-04 DOI: 10.1016/j.cbd.2025.101710

Xuechun Zang , Yuxi Liu , Zijiao Wang , Yanqing Wu , Bo Qin , Shaowu Yin , Tao Wang

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.

作为一种高价值的商品鱼，Thamnaconus septentrionalis对低温表现出显著的敏感性。了解其冷反应机制对水产养殖业的发展具有重要意义。本研究使用组织学、生化参数和蛋白质组学分析了在4种温度（10°C、15°C、20°C和25°C）下暴露24小时的七毛绦虫的肝脏反应。结果表明，温度降低会加重肝损伤，增加ROS积累，诱导氧化应激。低温诱导的ROS积累在原代七爪绦虫肝细胞中得到进一步验证。低温组（10°C, 15°C）与对照组（25°C）相比，氧化应激酶（SOD， CAT, GSH-Px）活性升高，MDA水平升高，肝脏甘油三酯降低。蛋白质组学结果显示能量代谢途径显著富集。假设冷应激倾向于抑制有氧呼吸和氧化磷酸化，但增强脂肪酸分解代谢和潜在的酮体利用作为替代燃料。蛋白质组学数据还表明肝脏还通过调节脂质代谢、激活自噬和抑制细胞凋亡来维持细胞功能。本研究揭示了七斑绦虫对温度变化的生理和蛋白质组反应，为其耐寒性提供了新的认识。

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引用次数: 0

Incorporating GWAS-derived prior information enhances genomic prediction for body size traits in the mud crab (Scylla paramamosain) 结合gwas衍生的先验信息，增强了泥蟹（Scylla paramamosain）体型性状的基因组预测。

IF 2.2 2区生物学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY

Comparative Biochemistry and Physiology D-Genomics & Proteomics

Pub Date : 2025-12-02 DOI: 10.1016/j.cbd.2025.101704

Weiren Zhang , Jun Luo , Yijia Shih , Yaodong Zhang , Siyi Zhou , Qionghui Qin , Kewei Huang , Qi Wang , Xiaopeng Wang , Haihui Ye

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.

Scylla paramosain是亚洲重要的海洋蟹品种，但其生长性状的遗传结构尚不清楚。本研究采用全基因组关联研究（GWAS）和基因组预测相结合的综合方法，以390万个高置信度SNPs对346个个体进行基因分型，分析了四个体型性状（甲壳宽度、甲壳长度、甲壳后宽度和身高）的遗传基础。GWAS鉴定出性状间共有的5个多效位点和6个候选基因（包括Exportin-5和FANCI）， KEGG富集分析强调了代谢途径，特别是柠檬酸循环的重要性。我们使用两种类型的先验生物学知识进一步评估了GFBLUP模型的基因组预测性能：来自顶部富集的KEGG通路的功能注释snp，以及在不同GWAS显著性阈值下选择的性状相关snp。使用性状相关snp的GFBLUP显著优于标准GBLUP，预测精度提高0.528-0.888。预测精度随SNP面板大小的增加而增加，SNP前1000位性状的预测精度均超过0.819，超过5000位性状的预测精度稳定（0.837 ~ 0.865）。FDR阈值为0.05提供了最佳平衡，实现了高准确度（0.840-0.862）和实际snp数量（7980-9302）。相比之下，功能知情的GFBLUP只提供了适度的改善（0.020-0.197），可能是由于包含了非因果变量。这些结果表明，基于GWAS先验知识的低密度SNP面板大大增强了S. paramamosain体型性状的基因组预测，为非模式甲壳类动物的生长遗传机制提供了实用的育种策略和有价值的见解。

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引用次数: 0

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 揭示氧化应激防御和能量代谢调节在刺参低温胁迫响应中的作用：生理、转录组学和代谢组学综合分析

IF 2.2 2区生物学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY

Comparative Biochemistry and Physiology D-Genomics & Proteomics

Pub Date : 2025-12-02 DOI: 10.1016/j.cbd.2025.101706

Xiaohua He , Siyi Li , Shuhai Wang , Qiang Wang , Xiaohui Xu , Yanwei Feng , Weijun Wang , Zan Li , Jianmin Yang , Qihao Luo , Guohua Sun

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.

Apostichopus japonicus是北太平洋沿岸重要的水产养殖品种。由于全球气候变化的影响，其农业效率面临着越来越大的威胁，其特征要么是极端低温事件，要么是长时间的寒冷压力。本研究采用综合生理学、转录组学和代谢组学分析来研究日本刺参对低温（7.5°C和2.5°C）的反应。当温度降低到7.5℃和2.5℃时，抗氧化酶（超氧化物歧化酶，SOD，过氧化氢酶，CAT，谷胱甘肽过氧化物酶，GPX）的活性均显著升高，从而减轻氧化损伤。转录组学数据显示，在7.5°C时，与抗氧化防御相关的基因（如ALDH7A1）和与脂质代谢相关的基因（如SCP2）显著上调。2.5℃时，差异表达基因数量显著增加，包括脂质代谢相关基因acox1上调、抗氧化防御相关基因（gclm、pdxk）下调、脂质代谢相关基因hmgcr下调。代谢组学分析显示，在7.5°C时，不饱和脂肪酸（如亚油酸）和初级胆汁酸的生物合成富集，增强了膜流动性和脂质利用。2.5℃下的关键代谢物（如谷胱甘肽、l -天冬氨酸）参与氨基酸代谢途径。综合分析显示，在7.5°C时，胆汁酸合成和脂肪酸代谢相关的基因和代谢物共同富集，支持膜稳定性和能量平衡，而2.5°C诱导的与维生素B6代谢、TCA循环、氧化磷酸化和脂肪酸降解相关的途径。这些结果表明，刺参主要通过抗氧化防御和能量稳态调节来对抗冷胁迫。研究结果为深入了解棘皮动物的温度适应性提供了理论依据，并为制定精准的栽培策略和选育抗逆性新品系以减轻全球气候变化的影响奠定了基础。

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引用次数: 0