Comparative Biochemistry and Physiology D-Genomics & Proteomics最新文献_第2页

Transcription dynamics and regulation of heat shock protein genes during stress and development in the estuarine cnidarian Nematostella vectensis 河口刺胞线虫应激和发育过程中热休克蛋白基因的转录动力学和调控。

IF 2.2 2区生物学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY

Comparative Biochemistry and Physiology D-Genomics & Proteomics

Pub Date : 2026-01-16 DOI: 10.1016/j.cbd.2026.101754

Janki A. Bhalodi , Joachim M. Surm , Adam M. Reitzel

Heat shock proteins (HSPs) are molecular chaperones that function in protecting cells from proteotoxicity. Eukaryotes have multiple HSPs that localize in the cytoplasm, endoplasmic reticulum (ER), and mitochondria. In cnidarian species, where HSPs are often used as biomarkers of environmental stress, little is known about how particular HSPs vary in copy number, expression, inducibility, and regulation within a species. Here, we characterized the full repertoire of HSP70 and HSP90 genes in an emerging model cnidarian, Nematostella vectensis. We identified five HSP70 and three HSP90 genes, with at least one homolog from each family belonging to the three primary clades based on subcellular localization. Although transcriptional induction remained insignificant by a 10 °C temperature change, two cytosolic HSP70s and one cytosolic HSP90 were significantly upregulated with a 20 °C temperature increase. Most HSPs exhibited similar developmental expression patterns, with elevated expression during the early larval stage followed by reduced expression in the juvenile stage. HSPs showed evidence for differential expression across cell types, with multiple cytosolic and ER HSPs being highly expressed in neuronal and cnidocyte populations. Moreover, the putative promoters of N. vectensis HSPs differed in both the abundance and sequences of regulatory heat shock element motifs, providing a potential mechanism of functional diversification in response to temperature and development. By characterizing expression of all HSP70 and HSP90 genes in this cnidarian, we reveal distinct roles of these core chaperones in the proteostasis response, providing a foundation for future functional studies on contributions of HSPs to cnidarian life cycle and stress resilience.

热休克蛋白（HSPs）是一种具有保护细胞免受蛋白质毒性作用的分子伴侣蛋白。真核生物有多种热休克蛋白，它们分布在细胞质、内质网和线粒体中。在刺胞动物物种中，热休克蛋白经常被用作环境胁迫的生物标志物，但人们对特定热休克蛋白在一个物种内的拷贝数、表达、诱导和调控方面的变化知之甚少。在这里，我们鉴定了一种新型刺胞动物——线虫病的HSP70和HSP90基因的全部序列。我们鉴定了5个HSP70和3个HSP90基因，根据亚细胞定位，每个家族至少有一个同源基因属于三个初级分支。虽然在10℃温度下转录诱导不显著，但在20℃温度升高时，两种细胞质hsp70和一种细胞质HSP90显著上调。大多数热休克蛋白表现出相似的发育表达模式，在幼虫早期表达升高，然后在幼年期表达降低。热休克蛋白在不同细胞类型中表现出差异表达，多种胞质热休克蛋白和内质热休克蛋白在神经元和刺胞细胞群体中高度表达。此外，这些推测的启动子在调节热休克元件的丰度和序列上都存在差异，这为温度和发育下的功能多样化提供了潜在的机制。通过表征所有HSP70和HSP90基因在该刺胞动物中的表达，我们揭示了这些核心伴侣蛋白在蛋白质停滞反应中的不同作用，为进一步研究热休克蛋白对刺胞动物生命周期和应激恢复能力的贡献奠定了基础。

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引用次数: 0

Proteomic analysis reveals the mechanism of cold tolerance in black porgy (Acanthopagrus schlegelii) via ribosome hibernation, metabolic remodeling, and antioxidant coordination 蛋白质组学分析揭示了黑棘虫（Acanthopagrus schlegelii）的耐寒机制，包括核糖体冬眠、代谢重塑和抗氧化协调

IF 2.2 2区生物学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY

Comparative Biochemistry and Physiology D-Genomics & Proteomics

Pub Date : 2026-01-15 DOI: 10.1016/j.cbd.2026.101748

Jingyang Li , Ruijian Sun , Tongxuan Zhao , Xiaojian Tang , Bo Gao , Guangping Xu , Yue Wang , Han Yu , Qian Meng , Zhiwei Zhang

Low-temperature stress poses a critical challenge to the overwintering survival of black porgy (Acanthopagrus schlegelii), a commercially important marine fish distributed across the coastal waters of West Pacific region, including the continental shelves of China, Japan, and the Korean Peninsula. To unravel the molecular mechanisms underlying cold adaptation, this study employed quantitative proteomics was employed to analyze hepatic protein profiles of black porgy between three groups: control group (CG, 15 °C), cold-sensitive group (CS, 3.8 °C), and cold-tolerant group (CT, 2.8 °C). A total of 4437 proteins were identified, with 1616 differentially expressed protein (DEPs) detected among the groups. Bioinformatics analyses, including Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment, Gene Set Enrichment Analysis (GSEA), and trend analysis, revealed distinct adaptive strategies between CT and CS groups. The CT group exhibited a coordinated “energy conservation - metabolic remodeling - antioxidation” strategy: (1) significant downregulation of ribosomal subunits and protein export pathways to reduce Adenosine Triphosphate (ATP) consumption from protein synthesis (called “ribosomal hibernation”); (2) upregulation of Peroxisome Proliferator-Activated Receptor (PPAR) signaling pathway and peroxisomal functions to enhance fatty acid β-oxidation and ketone body production, facilitating efficient energy supply; (3) activation of antioxidant systems to mitigate damage induced by reactive oxygen species (ROS). In contrast, the CS group showed dysregulated energy metabolism, characterized by enhanced but inefficient glycolysis, impaired endoplasmic reticulum function, and excessive inflammatory responses, which may contribute to protential proteotoxic stress and metabolic dysfunction. Key DEPs and pathways, such as ribosomal proteins, PPAR family proteins, and peroxisomal enzymes, were identified as protential core regulators of cold tolerance in black porgy. This study provides the first comprehensive proteomic insights into the molecular mechanisms of cold tolerance in black porgy, highlighting the evolutionary significance of energy allocation and metabolic plasticity in teleosts. These findings offer potential molecular markers for breeding cold-tolerant strains, addressing critical challenges in aquaculture sustainability.

黑porgy （Acanthopagrus schlegelii）是一种重要的商业海鱼，分布在西太平洋地区的沿海水域，包括中国、日本和朝鲜半岛的大陆架，低温胁迫对黑porgy的越冬生存构成了严峻的挑战。为了揭示冷适应的分子机制，本研究采用定量蛋白质组学方法分析了三组黑porgy肝脏蛋白谱：对照组（CG, 15°C）、冷敏感组（CS, 3.8°C）和耐寒组（CT, 2.8°C）。共鉴定出4437个蛋白，组间检测到1616个差异表达蛋白（DEPs）。生物信息学分析，包括基因本体（GO）、京都基因与基因组百科全书（KEGG）富集、基因集富集分析（GSEA）和趋势分析，揭示了CT组和CS组之间不同的适应策略。CT组表现出协调的“能量节约-代谢重塑-抗氧化”策略：(1)显著下调核糖体亚基和蛋白质输出途径，以减少蛋白质合成中三磷酸腺苷（ATP）的消耗（称为“核糖体冬眠”）；(2)上调过氧化物酶体增殖激活受体（PPAR）信号通路和过氧化物酶体功能，促进脂肪酸β-氧化和酮体生成，促进高效能量供应；(3)激活抗氧化系统以减轻活性氧（ROS）引起的损伤。相比之下，CS组表现出能量代谢失调，表现为糖酵解增强但效率低下，内质网功能受损，炎症反应过度，可能导致潜在的蛋白质毒性应激和代谢功能障碍。核糖体蛋白、PPAR家族蛋白和过氧化物酶体酶等关键dep及其通路被确定为黑豆耐寒性的潜在核心调控因子。本研究首次从蛋白质组学角度全面揭示了硬骨鱼耐冷性的分子机制，强调了硬骨鱼能量分配和代谢可塑性的进化意义。这些发现为培育耐寒菌株提供了潜在的分子标记，解决了水产养殖可持续性的关键挑战。

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引用次数: 0

Comprehensive transcriptomic analysis reveals detoxification gene expansion and adaptive genetic variation in the emerging pest Acanthotomicus suncei 综合转录组学分析揭示了新兴害虫棘虫的解毒基因扩增和适应性遗传变异

IF 2.2 2区生物学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY

Comparative Biochemistry and Physiology D-Genomics & Proteomics

Pub Date : 2026-01-13 DOI: 10.1016/j.cbd.2026.101749

Lulu Dai, Jiao Li, Weiyi Pan, Fangyuan Shen, Dejun Hao

The bark beetle Acanthotomicus suncei is an emerging destructive pest of the introduced American sweetgum (Liquidambar styraciflua) in China. The molecular mechanisms underlying its successful adaptation to this exotic host, particularly its ability to overcome plant chemical defenses, remain largely unknown. We conducted a comprehensive transcriptomic analysis of A. suncei. Our assembly yielded 30,557 unigenes (N50 = 2175 bp). We identified a significant expansion of genes within three major detoxification enzyme families: 122 cytochrome P450 monooxygenases (P450s), 75 carboxylesterases (COEs), and 47 glutathione S-transferases (GSTs). This repertoire is notably larger than that of many compared curculionid beetles. Phylogenetic analyses revealed complex evolutionary relationships, with A. suncei clustering closely with Dendroctonus species in some P450 and GST clades, while showing considerable divergence in others. Furthermore, we uncovered abundant genetic variation, with single nucleotide polymorphisms (SNPs) being highly prevalent within the coding sequences of these detoxification genes, especially P450s. Simple sequence repeat (SSR) analysis indicated a predominance of A/T-rich motifs. The remarkable expansion and substantial genetic variation observed in the detoxification gene families of A. suncei provide a compelling molecular basis for its potent detoxification capacity. These findings suggest that an enriched and highly adaptable detoxification system likely facilitates this beetle's successful colonization of the exotic host L. styraciflua. This study offers crucial insights into the molecular mechanisms of host adaptation in an emerging forest pest and identifies potential genetic targets for future management strategies.

suncei树皮甲虫是中国引进的美洲甜（Liquidambar styraciflua）的一种新出现的破坏性害虫。其成功适应这种外来寄主的分子机制，特别是其克服植物化学防御的能力，在很大程度上仍然未知。我们进行了一项全面的转录组学分析。我们的组装得到30,557个unigenes （N50 = 2175 bp）。我们在三个主要的解毒酶家族中发现了显著的基因扩增：122个细胞色素P450单加氧酶（P450s）， 75个羧酯酶（COEs）和47个谷胱甘肽s转移酶（GSTs）。这一技能明显比许多相比较的曲头甲虫要大。系统发育分析揭示了复杂的进化关系，在一些P450和GST分支中，suncei与Dendroctonus物种密切聚集，而在其他分支中则表现出相当大的差异。此外，我们发现了丰富的遗传变异，单核苷酸多态性（snp）在这些解毒基因的编码序列中非常普遍，尤其是p450。SSR （Simple sequence repeat）分析表明，a / t富集基序居多。解毒基因家族的显著扩展和大量遗传变异为其强大的解毒能力提供了令人信服的分子基础。这些发现表明，一个丰富和高度适应性的解毒系统可能有助于这种甲虫成功定植外来寄主L. styraciflua。这项研究为新出现的森林害虫宿主适应的分子机制提供了重要见解，并为未来的管理策略确定了潜在的遗传靶点。

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引用次数: 0

Transcriptomics analysis provides insights into the molecular response of the clam Cyclina sinensis to Vibrio infection under heat stress 转录组学分析揭示了热应激条件下中华环蚌对弧菌感染的分子反应

IF 2.2 2区生物学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY

Comparative Biochemistry and Physiology D-Genomics & Proteomics

Pub Date : 2026-01-13 DOI: 10.1016/j.cbd.2026.101752

Dehui Sun , Xiuke Ouyang , Ruili Zheng , Jing Cao, Lisha Wei, Meng Xu, Guxin Wang

The heat stress and Vibrio infection are considered as the key factors contributing to the mass mortality of clams in summer. In this study, we explored the combined effects of high temperature and Vibrio infection on the survival of the clam Cyclina sinensis. The clams C. sinensis were separately cultivated at 26 °C (low temperature) or 30 °C (high temperature) and subjected to Vibrio infection experiment. The results showed that dual challenges aggravated the mortality of clam. To further investigate the underlying mechanisms, the hepatopancreas of clam C. sinensis under varying thermal conditions were separately sampled at different infection phases, including pre-infection, 8 days post-infection (dpi) and 12 dpi. Transcriptomic analysis revealed that the dual challenges significantly decreased the expression level of genes related to immunity, antioxidation, and energy metabolism, while upregulating genes associated with apoptosis and endoplasmic reticulum stress compared to the control group (26 °C and non-infection). The functional analysis indicated that downregulated differentially expressed genes (DEGs), identified in the dual challenges groups compared with the control group, were primarily involved in lysosome, phagosome, peroxisome, carbohydrate metabolism and regulation of oxidoreductase activity. The qRT-PCR validation of 15 DEGs corroborated the RNA-seq findings. We further demonstrated that the combined stress increased the content of MDA and decreased the activity of antioxidant enzymes (SOD, CAT) and immune enzymes (ACP, LZM) in hepatopancreas. Taken together, these findings suggest that immunosuppression, oxidative damage and deficiencies in carbohydrate metabolism were potential contributors to the mass summer mortality of clams. This study provides valuable data resources and critical information for revealing the molecular response of C. sinensis to combined stress of high temperature and Vibrio infection.

热应激和弧菌感染被认为是夏季蛤蜊大量死亡的关键因素。在本研究中，我们探讨了高温和弧菌感染对中华圆蛤存活的联合影响。分别在26°C（低温）和30°C（高温）条件下培养中华蛤，进行弧菌感染实验。结果表明，双重攻毒加重了蛤蜊的死亡率。为了进一步研究其潜在机制，我们在不同的感染阶段（感染前、感染后8天和12天）分别采集了不同温度条件下的中华蛤肝胰脏。转录组学分析显示，与对照组（26°C和未感染）相比，双重刺激显著降低了与免疫、抗氧化和能量代谢相关的基因表达水平，同时上调了与凋亡和内质网应激相关的基因表达水平。功能分析表明，与对照组相比，双重刺激组差异表达基因（DEGs）的下调主要涉及溶酶体、吞噬体、过氧化物酶体、碳水化合物代谢和氧化还原酶活性的调节。15个deg的qRT-PCR验证证实了RNA-seq的发现。结果表明，复合应激增加了肝胰腺MDA含量，降低了抗氧化酶（SOD、CAT）和免疫酶（ACP、LZM）活性。综上所述，这些发现表明免疫抑制、氧化损伤和碳水化合物代谢不足是夏季蛤蜊大量死亡的潜在原因。本研究为揭示中华梭菌对高温和弧菌感染联合胁迫的分子响应提供了宝贵的数据资源和关键信息。

{"title":"Transcriptomics analysis provides insights into the molecular response of the clam Cyclina sinensis to Vibrio infection under heat stress","authors":"Dehui Sun , Xiuke Ouyang , Ruili Zheng , Jing Cao, Lisha Wei, Meng Xu, Guxin Wang","doi":"10.1016/j.cbd.2026.101752","DOIUrl":"10.1016/j.cbd.2026.101752","url":null,"abstract":"<div><div>The heat stress and <em>Vibrio</em> infection are considered as the key factors contributing to the mass mortality of clams in summer. In this study, we explored the combined effects of high temperature and <em>Vibrio</em> infection on the survival of the clam <em>Cyclina sinensis</em>. The clams <em>C. sinensis</em> were separately cultivated at 26 °C (low temperature) or 30 °C (high temperature) and subjected to <em>V</em>ibrio infection experiment. The results showed that dual challenges aggravated the mortality of clam. To further investigate the underlying mechanisms, the hepatopancreas of clam <em>C. sinensis</em> under varying thermal conditions were separately sampled at different infection phases, including pre-infection, 8 days post-infection (dpi) and 12 dpi. Transcriptomic analysis revealed that the dual challenges significantly decreased the expression level of genes related to immunity, antioxidation, and energy metabolism, while upregulating genes associated with apoptosis and endoplasmic reticulum stress compared to the control group (26 °C and non-infection). The functional analysis indicated that downregulated differentially expressed genes (DEGs), identified in the dual challenges groups compared with the control group, were primarily involved in lysosome, phagosome, peroxisome, carbohydrate metabolism and regulation of oxidoreductase activity. The qRT-PCR validation of 15 DEGs corroborated the RNA-seq findings. We further demonstrated that the combined stress increased the content of MDA and decreased the activity of antioxidant enzymes (SOD, CAT) and immune enzymes (ACP, LZM) in hepatopancreas. Taken together, these findings suggest that immunosuppression, oxidative damage and deficiencies in carbohydrate metabolism were potential contributors to the mass summer mortality of clams. This study provides valuable data resources and critical information for revealing the molecular response of <em>C. sinensis</em> to combined stress of high temperature and <em>Vibrio</em> infection.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"58 ","pages":"Article 101752"},"PeriodicalIF":2.2,"publicationDate":"2026-01-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146022425","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Multi-omics dissection of large-size formation in Eriocheir sinensis: Insights from RNA, metabolite profiling, and ceRNA regulatory networks 中华绒螯蟹大尺寸结构的多组学解剖：来自RNA、代谢物谱和ceRNA调控网络的见解

IF 2.2 2区生物学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY

Comparative Biochemistry and Physiology D-Genomics & Proteomics

Pub Date : 2026-01-12 DOI: 10.1016/j.cbd.2026.101750

Fujun Xuan , Xinyue Zhang , Jinghao Hu , Xuguang Li , Yuchen Chen , Aiming Zhang , Ruifang Wang , Qian Ren , Tao Wu , Weibing Guan , Yongxu Cheng , Jun Zhou , Rongchen Liu

Eriocheir sinensis (Chinese mitten crab) is a key economic species in China's freshwater aquaculture industry. Individual body size is a critical trait that determines both market price and production profitability. Large-sized crabs exhibit substantial commercial advantages; however, the underlying molecular mechanisms regulating size formation remain poorly understood. In this study, we conducted an integrative multi-omics analysis combining whole-transcriptome data (mRNA, miRNA, and lncRNA) and untargeted metabolomics across two aquaculture cohorts (cohort2023 and cohort2024). Our results revealed a systemic downregulation of glycolysis, the tricarboxylic acid (TCA) cycle, fatty acid oxidation, and glycerol metabolism in large-sized crabs, suggesting a “low consumption–high storage” metabolic strategy. In contrast, pathways related to organismal development, exoskeleton reconstruction, steroid hormone biosynthesis, and nutrient absorption were significantly upregulated, indicating enhanced growth potential and nutrient assimilation efficiency. ceRNA network modeling and cis-acting lncRNA analysis identified multiple core regulatory genes (e.g., PTGS1, TPI1, POR) as targets of complex non-coding RNA interactions involved in body size regulation. Enzyme activity assays for key rate-limiting steps in carbohydrate and lipid catabolism, along with extensive qPCR validation, further corroborated the transcriptomic findings. Taken together, our study provides the first comprehensive multi-omics perspective on the molecular basis of body size differentiation in E. sinensis, proposing a tripartite mechanism involving suppressed catabolism, stimulated growth and morphogenesis, and improved nutrient acquisition. These findings offer theoretical insight into crustacean growth regulation and provide molecular targets to support selective breeding of high-value, large-sized mitten crab strains.

中华绒螯蟹（Eriocheir sinensis）是中国淡水养殖业的重要经济物种。个体尺寸是决定市场价格和生产利润的关键特征。大型螃蟹具有显著的商业优势；然而，调节尺寸形成的潜在分子机制仍然知之甚少。在本研究中，我们结合两个水产养殖队列（cohort2023和cohort2024）的全转录组数据（mRNA， miRNA和lncRNA）和非靶向代谢组学进行了综合多组学分析。我们的研究结果揭示了大蟹糖酵解、三羧酸（TCA）循环、脂肪酸氧化和甘油代谢的系统性下调，表明了一种“低消耗-高储存”的代谢策略。相比之下，与机体发育、外骨骼重建、类固醇激素生物合成和营养吸收相关的途径显著上调，表明生长潜力和营养同化效率增强。ceRNA网络建模和顺式作用lncRNA分析发现，多个核心调控基因（如PTGS1、TPI1、POR）是参与体型调节的复杂非编码RNA相互作用的靶点。碳水化合物和脂质分解代谢中关键限速步骤的酶活性测定，以及广泛的qPCR验证，进一步证实了转录组学的发现。综上所述，我们的研究首次从多组学的角度全面研究了中华赤霉素体型分化的分子基础，提出了抑制分解代谢、促进生长和形态发生以及改善营养获取的三重机制。这些发现为研究甲壳类动物的生长调控提供了理论依据，并为高价值、大型绒螯蟹品系的选择性育种提供了分子靶点。

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引用次数: 0

Comparative transcriptome analysis reveals molecular mechanism of temperature effect on body color of red swamp crayfish (Procambarus clarkii) 比较转录组分析揭示温度对克氏原螯虾体色影响的分子机制

IF 2.2 2区生物学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY

Comparative Biochemistry and Physiology D-Genomics & Proteomics

Pub Date : 2026-01-10 DOI: 10.1016/j.cbd.2026.101751

Guoliang Chang , Fanqian Kong , Songyue Gao , Huajie Cai , Long Wang , Huaiyu Ding , Yongxu Cheng , Jiayao Li

The carapace coloration is of great significance to Procambarus clarkii, and the molecular mechanism of temperature affecting carapace color has not yet been reported. In this study, comparative transcriptome was used to study molecular mechanism of temperature-induced changes in carapace coloration of P. clarkii. This study identified many genes (such as tyrosinase, APOD) and signaling pathways (such as tyrosine metabolism) related to pigment accumulation. As an important environmental factor, temperature can change metabolism and accumulation of pigment in P. clarkii by changing expression patterns of related genes and pathways. High temperature can damage transport of related proteins (such as ABC transporters), thus affecting the metabolism of carotenoids and melanin, and finally lead to the change of body color of P. clarkii. Oxidative stress caused by high temperature can destroy pigment metabolism and accumulation, resulting in changes in body color. The results of this study revealed molecular mechanism of temperature affecting body color of P. clarkii, provided basic data for subsequent selective breeding and practical production, and provided new insights for crustacean body color formation and change.

甲壳着色对克氏原螯虾具有重要意义，温度影响甲壳着色的分子机制尚未见报道。本研究采用比较转录组学方法研究温度诱导克氏假单胞菌甲壳颜色变化的分子机制。本研究发现了许多与色素积累相关的基因（如酪氨酸酶、APOD）和信号通路（如酪氨酸代谢）。温度作为一个重要的环境因子，可以通过改变相关基因和途径的表达模式来改变克氏疟原虫色素的代谢和积累。高温会破坏相关蛋白（如ABC转运蛋白）的运输，从而影响类胡萝卜素和黑色素的代谢，最终导致克氏杆菌体色的变化。高温引起的氧化应激会破坏色素的代谢和积累，导致身体颜色的变化。本研究结果揭示了温度影响克拉氏疟原虫体色的分子机制，为后续的选育和实际生产提供了基础数据，并为甲壳类动物体色的形成和变化提供了新的见解。

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引用次数: 0

Comparative transcriptomic analysis across ovarian developmental stages in Sepiella japonica provides novel insights into its molecular regulatory mechanisms 比较转录组学分析在整个卵巢发育阶段的日本海蛾提供了新的见解，其分子调控机制

IF 2.2 2区生物学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY

Comparative Biochemistry and Physiology D-Genomics & Proteomics

Pub Date : 2026-01-09 DOI: 10.1016/j.cbd.2026.101746

An Xu , Zhenming Lü , Jing Liu , Tianwei Liu , Jing Yu , Yijing Yang , Kun Huang , Li Gong , Fenghui Li , Denghui Zhu , Hongling Ping , Huilai Shi , Liqin Liu

Sepiella japonica is a cephalopod of significant commercial value, commonly found throughout China's coastal waters, ranging from southern Hong Kong to the Korean Peninsula and western regions of Japan. However, under captive conditions, S. japonica frequently exhibits precocious sexual maturation, which can result in reduced adult body size and severely limit aquaculture development. Therefore, elucidating the molecular mechanisms on ovarian development has become a critical priority. In this study, RNA sequencing was performing of the ovary tissue of female S. japonica collected across four key ovarian developmental stages: oogonium production (stage I), protoplasmic growth (stage II), interstitial growth (stage III), and trophoplasmic growth (stage IV). A total of 354,393,214 clean reads (Q20>98.58%) were obtained from 16 samples. Pairwise comparative analyses of I vs II, II vs III, and III vs IV identified 10050, 2564, 2278 differentially expressed genes (DEGs), respectively. Through differential expression analysis, we identified 13,319 differentially expressed genes (DEGs), among of which exhibited consistently high expression across four developmental stages, such as FOXL2, HSD17B2, and BMP1, suggesting their critical roles in regulating ovarian development in S. japonica. Gene Ontology (GO) enrichment analysis showed that these DEGs were significantly enriched in processes including protein targeting to the ER, response to estradiol, oxidative phosphorylation, and female pregnancy. KEGG pathway analysis revealed that DEGs were significantly enriched in key functional pathways, such as Ribosome, Prolactin signaling, FOXO signaling, and Lysosome. Furthermore, the “response to estradiol” pathway was consistently enriched across multiple developmental stage comparisons, suggesting that genes associated with steroid-related signaling may play conserved roles during ovarian development in S. japonica. This study clarified the regulation of transcript expression and molecular mechanisms in the ovary of S. japonica at different ovarian development stages, thereby offering theoretical guidance for enhancing reproductive efficiency in mollusk aquaculture.

日本Sepiella japonica是一种具有重要商业价值的头足类动物，常见于中国沿海水域，从香港南部到朝鲜半岛和日本西部地区。然而，在圈养条件下，粳稻经常表现出性成熟早熟，这可能导致成虫体型缩小，严重限制了水产养殖的发展。因此，阐明卵巢发育的分子机制已成为当务之急。在本研究中，对采集的日本粳稻雌性卵巢的四个关键发育阶段进行了RNA测序：卵母细胞产生（阶段I）、原生质生长（阶段II）、间质生长（阶段III）和滋养质生长（阶段IV）。16份样本共获得354,393,214个clean reads （Q20>98.58%）。I与II、II与III和III与IV的两两比较分析分别鉴定出10050、2564和2278个差异表达基因（DEGs）。通过差异表达分析，我们鉴定出13319个差异表达基因（deg），其中FOXL2、HSD17B2和BMP1在四个发育阶段均保持高表达，表明它们在调控粳稻卵巢发育中起着关键作用。基因本体（Gene Ontology， GO）富集分析显示，这些deg在内质网蛋白靶向、雌二醇应答、氧化磷酸化和女性妊娠等过程中显著富集。KEGG通路分析显示，deg在核糖体、催乳素信号、FOXO信号和溶酶体等关键功能通路中显著富集。此外，“对雌二醇的反应”通路在多个发育阶段的比较中都持续丰富，这表明与类固醇相关的信号传导相关的基因可能在粳稻卵巢发育过程中发挥保守作用。本研究阐明了粳稻卵巢不同发育阶段转录物的表达调控及其分子机制，为提高软体动物养殖的繁殖效率提供理论指导。

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引用次数: 0

Transcriptome analysis revealed the effects of dietary faba bean (Vicia faba L.) on muscle quality of Nile tilapia (Oreochromis niloticus) 转录组分析揭示了饲料中添加蚕豆对尼罗罗非鱼肌肉品质的影响

IF 2.2 2区生物学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY

Comparative Biochemistry and Physiology D-Genomics & Proteomics

Pub Date : 2026-01-08 DOI: 10.1016/j.cbd.2026.101747

Qingqing Li , Yao Huang , Xi Xie , Shaowen Liang , Li Lin

Nile tilapia (Oreochromis niloticus) is a widely farmed freshwater fish. Feeding with faba bean (Vicia faba L.) for 90–120 days can improve the muscle quality of tilapia. However, the underlying mechanism remain unclear. In the present study, tilapia were fed a faba bean–based diet for 120 days to induce muscle crisped, and ordinary tilapia fed a conventional diet were used as controls. Muscle histological characteristics were evaluated using hematoxylin and eosin staining, and transcriptome sequencing was conducted to explore molecular changes associated with the crisped muscle phenotype. The results showed that, as compared to ordinary tilapia, the fiber diameter and area were significantly reduced in crisped tilapia (p < 0.05), while the muscle fiber density was significantly increased (p < 0.05). In total, 576 differentially expressed genes (DEGs) were identified (FDR < 0.05), of which 211 were significantly up-regulated and 365 significantly down-regulated. Further analysis showed that DEGs associated with myofibroblast proliferation were up-regulated in crisped tilapia, while the glycolytic pathway was inhibited. The expression levels of muscle-related genes (i.e., actc1, myo7a, cib2, abcf2, and pfkfb2) were significantly higher in crisped tilapia than ordinary tilapia (p < 0.05), whereas the expression levels of gapdh, pgam2, eno3, and g6pi were significantly decreased (p < 0.05). Several DEGs and signaling pathways were identified. These findings provide transcriptomic evidence linking dietary faba bean feeding to muscle fiber remodeling and metabolic modulation in tilapia, offering a molecular basis for improving fillet quality through nutritional strategies.

尼罗罗非鱼（Oreochromis niloticus）是广泛养殖的淡水鱼。罗非鱼投喂蚕豆（Vicia faba L.） 90 ~ 120 d可提高其肌肉品质。然而，其潜在机制尚不清楚。本试验采用以蚕豆为主的饲料饲喂罗非鱼120 d，诱导其肌肉脆化，以饲喂常规饲料的普通罗非鱼为对照。使用苏木精和伊红染色评估肌肉组织学特征，并进行转录组测序以探索与卷曲肌肉表型相关的分子变化。结果表明，与普通罗非鱼相比，脆皮罗非鱼的纤维直径和面积显著减少（p < 0.05），肌纤维密度显著增加（p < 0.05）。共鉴定出576个差异表达基因（deg）（FDR < 0.05），其中211个显著上调，365个显著下调。进一步分析表明，与肌成纤维细胞增殖相关的DEGs在脆罗非鱼中上调，而糖酵解途径被抑制。脆皮罗非鱼肌肉相关基因actc1、myo7a、cib2、abcf2、pfkfb2的表达量显著高于普通罗非鱼（p < 0.05），而gapdh、pgam2、eno3、g6pi的表达量显著降低（p < 0.05）。确定了几个deg和信号通路。这些发现为罗非鱼饲料中蚕豆喂养与肌纤维重塑和代谢调节之间的联系提供了转录组学证据，为通过营养策略改善鱼片质量提供了分子基础。

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引用次数: 0

Genome-wide identification and characterization of HSP90, HSP60 and HSP40 family genes in Riptortus pedestris (Hemiptera: Alydidae) 徒步梨蝇HSP90、HSP60和HSP40家族基因的全基因组鉴定与特征分析（半翅目：叶蝉科）

IF 2.2 2区生物学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY

Comparative Biochemistry and Physiology D-Genomics & Proteomics

Pub Date : 2026-01-08 DOI: 10.1016/j.cbd.2026.101745

Wenhao Dong , Huaijun Xue , Yipeng Ren

To the best of our knowledge, heat shock proteins (HSPs) serve as molecular chaperones and play vital roles in providing protection under numerous physiological processes and environmental stressors, such as temperature, mechanical injury, chemical agents, and so on. Although their functional roles in hemipteran insects have been identified, comprehensive genome-wide identification and characterization of HSP family genes remain poorly understood in heteropteran pests, especially in R. pedestris, which has led to significant and widespread issues with soybean quality and yield through its sucking stylet, thus inducing a staygreen-like syndrome. In this study, four HSP90, fourteen HSP60 and twenty-six HSP40 family genes were obtained from the R. pedestris genome. Next, phylogenetic analysis, combined with conserved and domain characterization, supported our classification results. Chromosomal mapping indicated that all these HSP genes are distributed across the six chromosomes of R. pedestris, and a Ka/Ks ratio of <1 provides essential information for purifying selection acting on two duplicated Hsp90 genes in R. pedestris. Through data mining of transcriptome data, we obtained the expression patterns of three HSP family genes across all developmental stages and analyzed their expression differences during changes in feeding conditions in the whole body and gut of R. pedestris, respectively. Finally, a miRNA–mRNA interaction network of four significantly differentially expressed (DE) HSPs and corresponding regulatory miRNAs was constructed, of which one miRNA, novel-miRNA-927-3p, exhibited significant downregulation and combined with significantly DE Hsp60a and DnaJA1 in one comparison group, suggesting their underlying relationships in response to antibiotic feeding in the R. pedestris gut. Overall, these findings provide valuable insights into how the three types of HSP genes in R. pedestris are involved in developmental and environmental adaptation at the transcriptional and posttranscriptional levels.

据我们所知，热休克蛋白（HSPs）作为分子伴侣，在许多生理过程和环境应激源（如温度、机械损伤、化学试剂等）下提供保护发挥着重要作用。尽管HSP家族基因在半翅目昆虫中的功能作用已经被确定，但在异翅目昆虫中，特别是在黄豆中，对HSP家族基因的全基因组鉴定和表征仍然知之甚少，这导致了大豆质量和产量的重大和广泛问题，通过其吸柱头，从而诱发了一种类似于待绿的综合征。本研究共获得4个HSP90、14个HSP60和26个HSP40家族基因。其次，系统发育分析，结合保守和结构域表征，支持我们的分类结果。染色体定位结果表明，这些HSP基因均分布在6条染色体上，Ka/Ks比值为<；1，为纯化选择作用于两条重复的Hsp90基因提供了重要信息。通过转录组数据的数据挖掘，我们获得了3个HSP家族基因在各发育阶段的表达模式，并分别分析了它们在摄食条件变化时在步行鼠全身和肠道中的表达差异。最后，构建了由4个显著差异表达（DE）的HSPs及其调控miRNA组成的miRNA- mrna互作网络，其中一个miRNA （novel-miRNA-927-3p）在一个对照组中表现出显著下调，并与显著DE Hsp60a和DnaJA1结合，提示它们在步行鼠肠道中对抗生素喂养的反应中存在潜在关系。总的来说，这些发现为了解三种HSP基因在转录和转录后水平上如何参与发育和环境适应提供了有价值的见解。

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引用次数: 0

Molecular insights into hydrogen sulfide defense: A tissue-resolved transcriptomic study in the crab Eriocheir sinensis 硫化氢防御的分子洞察：蟹的组织分辨转录组学研究

IF 2.2 2区生物学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY

Comparative Biochemistry and Physiology D-Genomics & Proteomics

Pub Date : 2026-01-06 DOI: 10.1016/j.cbd.2026.101743

Jian Tian , Zihan Zhou , Mingming Han , Yi Juin Tay , Mengyu Bao , Longlong Fu , Qichen Jiang

The increasing prevalence of multiple abiotic stressors in aquatic ecosystems has raised significant ecological concerns. While molecular responses to hydrogen sulfide (H₂S) have been investigated in some aquatic species, the tissue-specific regulatory mechanisms in the Chinese mitten crab (Eriocheir sinensis) remain poorly understood. Following a 48-h exposure to varying concentrations of H₂S (0, 0.1, and 5 mg/L), four key tissues—hepatopancreas, gill, muscle, and intestine—were collected for an integrated analysis of transcriptomic sequencing and physiological/biochemical assays. Our results demonstrated significant enrichment of pathways related to serine endopeptidase activity and tyrosine metabolism in affected tissues, highlighting their potential role in mitigating H₂S-induced damage. Furthermore, high-concentration H₂S exposure substantially elevated the activities of antioxidant enzymes (SOD, CAT, GSH-PX) and up-regulated the expression of associated genes (SOD1, GPX1, HO-1), while simultaneously suppressing cytochrome c oxidase expression. These coordinated changes indicate that H₂S toxicity triggers pronounced oxidative stress alongside disrupted energy metabolism. The present study provides novel experimental insights into the molecular mechanisms of H₂S toxicity in crustaceans and offers a scientific foundation for ecological risk assessment and sustainable aquaculture management.

多种非生物应激源在水生生态系统中日益普遍，引起了重大的生态问题。虽然一些水生物种对硫化氢（H₂S）的分子反应已经被研究过，但中华绒螯蟹（Eriocheir sinensis）的组织特异性调节机制尚不清楚。在暴露于不同浓度的h2s(0、0.1和5 mg/L) 48小时后，收集四个关键组织——肝胰腺、鳃、肌肉和肠道，进行转录组测序和生理/生化分析。我们的研究结果表明，在受影响的组织中，与丝氨酸内肽酶活性和酪氨酸代谢相关的途径显著富集，突出了它们在减轻h2s诱导的损伤中的潜在作用。此外，高浓度h2s暴露显著提高抗氧化酶（SOD、CAT、GSH-PX）的活性，上调相关基因（SOD1、GPX1、HO-1）的表达，同时抑制细胞色素c氧化酶的表达。这些协调的变化表明，H₂S毒性引发了明显的氧化应激，同时破坏了能量代谢。本研究为甲壳类动物H₂S毒性的分子机制提供了新的实验见解，为生态风险评价和水产养殖可持续管理提供了科学依据。

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引用次数: 0