Comparative Biochemistry and Physiology D-Genomics & Proteomics最新文献_第3页

Integrated multi-omics analyses reveals physiological and gut microbiota responses of Litopenaeus vannamei to graded levels of dietary bile acids 综合多组学分析揭示了凡纳滨对虾（Litopenaeus vannamei）对膳食胆汁酸水平的生理和肠道微生物群反应。

IF 2.2 2区生物学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY

Comparative Biochemistry and Physiology D-Genomics & Proteomics

Pub Date : 2026-01-06 DOI: 10.1016/j.cbd.2026.101744

Peng Tan , Lei Zhang , Jinzhi Zhang , Aizhi Cao , Dongdong Xu , Aijun Zhu , Zhili Ding , Qingjun Shao

Despite being sterol auxotrophs that lack de novo steroid synthesis pathways, the specific physiological roles of exogenous bile acids (BAs) in crustaceans remain to be fully elucidated. This study investigated the effects of dietary BAs on the antioxidant capacity, immune regulation, and intestinal microbiota of the Pacific white shrimp, Litopenaeus vannamei. Shrimp were fed diets supplemented with graded levels of BAs (0–1000 mg kg⁻¹) for 56 days. Integrated multi-omics analyses were employed, where the 200 mg kg⁻¹ physiological optimum was used for transcriptomic profiling to decipher signaling pathways, while the 1000 mg kg⁻¹ group was analyzed to assess high-dose tolerance and microbial composition changes. Results showed that dietary BAs significantly enhanced non-specific immune parameters, specifically hemolymph lysozyme activity and total antioxidant capacity, without inducing histological damage to the hepatopancreas or intestine even at the highest dosage. Transcriptomic analysis showed an upregulation of antioxidant-related genes, such as sod1, gst and nos1, suggesting that BAs enhance the host's transcriptional potential to cope with oxidative stress. Furthermore, dietary BAs modulated immune signaling by upregulating the NF-κB inhibitor gene nfkbia and downregulating the adaptor myd88, indicating a potential mechanism for maintaining immune homeostasis and suppressing pro-inflammatory responses. In the intestine, BAs significantly increased the Shannon diversity index by promoting community evenness rather than species richness, and reduced the relative abundance of the opportunistic pathogen Vibrio while enriching beneficial genera such as Ruegeria. These findings indicate that exogenous BAs exert a protective role in L. vannamei by priming antioxidant defenses, modulating inflammatory signaling pathways, and stabilizing the intestine microbial ecosystem. These results suggest that BAs can be used as effective feed additives to improve health and intestine stability in shrimp farming.

尽管胆汁酸是缺乏新生类固醇合成途径的甾醇营养缺陷，但外源性胆汁酸在甲壳类动物中的具体生理作用仍有待充分阐明。本试验研究了饲料中添加ba对凡纳滨对虾（Litopenaeus vannamei）抗氧化能力、免疫调节和肠道菌群的影响。在饲料中添加不同水平的ba (0 ~ 1000 mg kg-1)，饲喂56 d。采用综合多组学分析，其中200 mg kg-1生理最佳值用于转录组学分析以破译信号通路，而1000 mg kg-1组用于评估高剂量耐受性和微生物组成变化。结果表明，饲料中添加ba显著提高了非特异性免疫参数，特别是血淋巴溶菌酶活性和总抗氧化能力，即使在最高剂量下也未对肝胰腺和肠道造成组织学损伤。转录组学分析显示，抗氧化相关基因如sod1、gst和nos1上调，表明BAs增强了宿主应对氧化应激的转录潜力。此外，饮食中的ba通过上调NF-κB抑制剂基因nfkbia和下调受体myd88来调节免疫信号，表明其可能是维持免疫稳态和抑制促炎反应的一种机制。在肠道中，BAs通过促进群落均匀度而非物种丰富度显著提高了Shannon多样性指数，降低了条件致病菌弧菌的相对丰度，同时丰富了鲁氏菌等有益菌属。这些发现表明外源性BAs通过启动抗氧化防御、调节炎症信号通路和稳定肠道微生物生态系统发挥保护作用。综上所述，ba可作为有效的饲料添加剂，改善对虾养殖的健康状况和肠道的稳定性。

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引用次数: 0

Metabolomic insights into fish osmoregulation: Unveiling adaptive mechanisms to salinity change 代谢组学对鱼类渗透调节的见解：揭示盐度变化的适应机制

IF 2.2 2区生物学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY

Comparative Biochemistry and Physiology D-Genomics & Proteomics

Pub Date : 2026-01-03 DOI: 10.1016/j.cbd.2025.101742

Xiaoli Chen , Youdi Tang , Xue Du , Ivone Giffard-Mena , Quanquan Cao

Salinity fluctuation is a major environmental driver influencing fish physiology and aquaculture performance. Metabolomics offers a systems perspective on the small molecule networks underlying osmoregulation. This review synthesizes studies across fish species to identify conserved metabolic responses to salinity change, including shifts in energy metabolism, amino acid turnover, and organic osmolyte synthesis. We evaluate the strengths and limitations of current analytical platforms (NMR, LC–MS, GC–MS) in metabolite coverage and identification, and highlight emerging approaches such as spatial metabolomics, multi-omics integration, and machine learning. By linking metabolic patterns to physiological and aquacultural outcomes, this work clarifies the molecular basis of salinity adaptation and offers actionable guidance for improving salinity tolerance in aquaculture.

盐度波动是影响鱼类生理和养殖性能的主要环境驱动因素。代谢组学为渗透调节背后的小分子网络提供了系统视角。本文综述了鱼类对盐度变化的保守代谢反应，包括能量代谢、氨基酸转换和有机渗透物合成的变化。我们评估了当前分析平台（NMR, LC-MS, GC-MS）在代谢物覆盖和鉴定方面的优势和局限性，并重点介绍了空间代谢组学，多组学集成和机器学习等新兴方法。通过将代谢模式与生理和养殖结果联系起来，本研究阐明了盐度适应的分子基础，并为提高水产养殖的耐盐性提供了可行的指导。

引用次数: 0

Diversity of ligand-gated ion channels in free-living and parasitic copepods (Crustacea) 自由生活和寄生桡足类（甲壳类）配体门控离子通道的多样性。

IF 2.2 2区生物学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY

Comparative Biochemistry and Physiology D-Genomics & Proteomics

Pub Date : 2026-01-03 DOI: 10.1016/j.cbd.2025.101741

F. Neptalí Morales-Serna , Ivana Ramos-de la Cruz , Alejandra García-Gasca , Miguel Betancourt-Lozano , Jesús Briones-Mendoza , Josué Pinto-Gualpa , Luis A. Yañez-Guerra , Víctor Hugo Caña-Bozada

Ligand-gated ion channels (LGICs) are essential mediators of synaptic transmission and sensory processing in animals, yet their diversity and evolution in copepods remain poorly understood. Copepods are among the most abundant metazoans in marine ecosystems and also occur across a wide range of salinity regimes, including freshwater habitats. They play central roles in food webs, biogeochemical cycling, and host-parasite interactions, with some parasitic taxa having significant impacts on aquaculture. In this study, we conducted a comprehensive analysis of LGICs across 20 copepod species (13 free-living and 7 parasitic) spanning four orders, Calanoida, Cyclopoida, Harpacticoida, and Siphonostomatoida, using transcriptomic and expressed sequence tag (EST) datasets. We identified 6456 putative LGICs belonging to four major families: Cys-loop, ionotropic glutamate receptors (iGluRs), P2X, and ASIC/Deg/ENaC. Phylogenetic and clustering analyses revealed both conserved and lineage-specific patterns, with approximately 20 % of LGICs showing taxonomic restriction to copepods, particularly within the ASIC/Deg/ENaC family. Notably, P2X receptors, previously reported as largely absent in arthropods, were consistently detected across copepod species, suggesting that this family is comparatively well represented in the group. We also identified multiple receptors associated with environmental sensing, including ionotropic receptors (IRs), shared across free-living species, as well as potential pharmacological targets such as GluCl and GABA receptors in parasitic taxa. Our findings highlight the evolutionary complexity of LGICs in copepods and provide a foundation for future research on their roles in environmental adaptation, and chemosensory biology, with potential pharmacological applications in aquaculture.

配体门控离子通道（lgic）是动物突触传递和感觉加工的重要介质，但其在桡足类动物中的多样性和进化尚不清楚。桡足类是海洋生态系统中最丰富的后生动物之一，也出现在各种盐度环境中，包括淡水栖息地。它们在食物网、生物地球化学循环和宿主-寄生虫相互作用中发挥着核心作用，其中一些寄生类群对水产养殖具有重要影响。在这项研究中，我们利用转录组和表达序列标签（EST）数据集对包括Calanoida、Cyclopoida、Harpacticoida和Siphonostomatoida四目在内的20种桡足动物（13种自由生活和7种寄生）的lgic进行了综合分析。我们确定了6456个推定的lgic，属于四个主要家族：Cys-loop、嗜离子性谷氨酸受体（iGluRs）、P2X和ASIC/Deg/ENaC。系统发育和聚类分析显示了保守的和谱系特异性的模式，大约20%的LGICs显示出桡足类的分类限制，特别是在ASIC/Deg/ENaC家族中。值得注意的是，先前报道在节肢动物中基本不存在的P2X受体，在桡足动物物种中一致检测到，这表明该家族在该群体中具有相对较好的代表性。我们还发现了多种与环境感知相关的受体，包括在自由生活物种中共享的嗜离子受体（IRs），以及寄生类群中潜在的药理靶点，如葡萄糖和GABA受体。我们的研究结果突出了桡足类动物lgic的进化复杂性，并为未来研究它们在环境适应、化学感觉生物学和潜在的水产养殖药理应用中的作用奠定了基础。

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引用次数: 0

Genome and transcriptome mining of the corazonin (Crz)-like peptide and gonadotropin-releasing hormone (GnRH)-like peptides in the spotted Babylon, Babylonia areolata 斑点巴比伦鱼中corazonin （Crz）样肽和促性腺激素释放激素（GnRH）样肽的基因组和转录组挖掘。

IF 2.2 2区生物学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY

Comparative Biochemistry and Physiology D-Genomics & Proteomics

Pub Date : 2026-01-02 DOI: 10.1016/j.cbd.2025.101738

Uraipan Saetan , Napamanee Kornthong , Supawadee Duangprom , Supita Tanasawet , Wanida Sukketsiri , Montakan Tamtin , Phetcharat Phanthong , Amornrat Sanprick , Narainrit Chinfak , Jirawat Saetan

The Spotted Babylon (Babylonia areolata) is an economically marine species in Thailand and other Asian countries. Due to the high demand for its meat, improving aquaculture practices for this species is essential. Regarding the lack of neuroendocrine control of reproduction in this species, we performed transcriptome analysis of the central nervous system and ovaries, and we searched against the reported genome of this animal species to find out the neurohormones. Here, we reported the identification of corazonin (ba-Crz)-like and gonadotropin-releasing hormone (ba-GnRH)-like mRNAs in B. areolata. The ba-Crz-like mRNA encoded mature ba-Crz-like peptide as QNYHYSNGWHP. Two ba-GnRH-like mRNAs encoded ba-GnRH-I-, and ba-GnRH-II-like peptides containing active peptides as QIHFSPTWGT and QIHFSHSWGT. Two introns were found in the ba-Crz-like gene while one intron was present in each ba-GnRH-like gene. These three peptides were phylogenetically placed in the molluscan Crz and GnRH clades. RT-PCR of these three mRNAs revealed their ubiquitous expressions across various organs, with all three predominantly expressed in ganglia, which was further confirmed by in situ hybridization of the cerebral ganglia. Immunohistochemistry showed positive signals for the Crz-like peptide in both the CNS and ovaries. To examine expression across ovarian cycle, the ba-Crz-like, and ba-GnRH-I-like mRNAs were consistently expressed in the CNS and ovaries of both immature and mature female snails, while the ba-GnRH-II-like mRNA significantly reduced its expression in the CNS of mature snails. Conclusively, this study was preliminary to report on the existence of GnRH/AKH/Crz peptides in the B. areolata, Further characterization of their receptors and biological functions is ongoing to ensure the GnRH, AKH, and Crz identification in this species.

斑点巴比伦是泰国和其他亚洲国家的经济海洋物种。由于对其肉的高需求，改进该物种的水产养殖方法至关重要。针对该物种缺乏神经内分泌对生殖的控制，我们对该动物的中枢神经系统和卵巢进行了转录组分析，并对该动物物种的已报道基因组进行了检索，以找出神经激素。在这里，我们报道了在乳状蛙中鉴定出corazonin （ba-Crz）样mrna和促性腺激素释放激素（ba-GnRH）样mrna。ba-Crz-like mRNA编码成熟的ba-Crz-like肽为QNYHYSNGWHP。两个ba- gnrh样mrna编码含有活性肽的ba-GnRH-I-和ba- gnrh - ii样肽，分别为QIHFSPTWGT和QIHFSHSWGT。在ba- crz样基因中发现两个内含子，而在每个ba- gnrh样基因中发现一个内含子。这三个肽在系统发育上被放置在软体动物Crz和GnRH分支中。RT-PCR结果显示，这三种mrna在各器官中均有普遍表达，且均以神经节为主表达，脑神经节原位杂交进一步证实了这一点。免疫组化显示crz样肽在中枢神经系统和卵巢均呈阳性。为了检测整个卵巢周期的表达情况，未成熟和成熟雌螺的CNS和卵巢中ba- crz样mRNA和ba- gnrh - i样mRNA的表达一致，而成熟螺的CNS中ba- gnrh - ii样mRNA的表达显著降低。总之，本研究初步报道了乳状蛙中GnRH/AKH/Crz肽的存在，其受体和生物学功能的进一步表征正在进行中，以确保该物种的GnRH， AKH和Crz的鉴定。

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引用次数: 0

Hypoxia and reoxygenation induce changes in oxidative stress, histological structure, and transcriptome in the liver of mandarin fish (Siniperca chuatsi) 缺氧和复氧诱导鳜鱼肝脏氧化应激、组织结构和转录组的变化

IF 2.2 2区生物学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY

Comparative Biochemistry and Physiology D-Genomics & Proteomics

Pub Date : 2025-12-31 DOI: 10.1016/j.cbd.2025.101740

Dingbin Gong, Lin Zhou, Xiaoru Hong, Mingyang Yao, Zeting Huang, Wanting Yu, Yan Wu, Minmin Chen, Daoping Yu, Yaling Song, Liming Wang, Yuxi Lian, Xiaohuan Zhang, Pingping Wang

The mandarin fish (Siniperca chuatsi, MD) is a highly valued freshwater economic fish species in China, but it exhibits a notably low tolerance to a hypoxic environment. However, the underlying regulatory mechanisms in response to environmental hypoxia and reoxygenation stress remain poorly understood. Therefore, we examined liver biochemical parameters and transcriptomes of MD under normoxic, hypoxic, and reoxygenation conditions, aiming to illuminate the dynamic changes in molecular regulatory mechanisms and oxidative stress responses. This study revealed that the enzymatic antioxidant systems acted in a coordinated manner to alleviate oxidative stress injury caused by hypoxia. In RNA-seq analysis, we identified differentially expressed genes (DEGs) and conducted enrichment analysis. Among the Gene Ontology (GO) functional categories, several critical hypoxia-related genes (nfkbia, vegfa, aplnr) in biological processes were observed. Furthermore, based on the Kyoto Encyclopedia of Genes and Genomes (KEGG) functional enrichment analyses, the finding revealed that many DEGs were involved in the HIF-1 signaling pathway (gln, epo, vegfa, pfka, ldh), AMPK signaling pathway (pfka, eef2k, gys), p53 signaling pathway (ccne, gtse1), PI3K-Akt signaling pathway (ddit4, egf, gh, ghr, vwf, gys), and NOD-like receptor signaling pathway (atg8, sharpin, ifnar1), among others. This study offers crucial insights into elucidating the molecular regulatory mechanisms underlying hypoxia stress, and holds the potential to facilitate the development of effective strategies for coping with environmental hypoxia and reoxygenation stress in MD. This is valuable for fish genetic improvement.

鳜鱼（sininiperca chuatsi， MD）是中国一种非常有价值的淡水经济鱼类，但它对缺氧环境的耐受性明显较低。然而，对环境缺氧和再氧化应激的潜在调节机制仍然知之甚少。因此，我们在常氧、低氧和再氧条件下检测了MD的肝脏生化参数和转录组，旨在阐明分子调控机制和氧化应激反应的动态变化。本研究揭示了酶促抗氧化系统协同作用以减轻缺氧引起的氧化应激损伤。在RNA-seq分析中，我们鉴定了差异表达基因（DEGs）并进行了富集分析。在基因本体（Gene Ontology， GO）功能类别中，观察到几个与生物过程相关的关键缺氧相关基因（nfkbia, vegfa, applnr）。此外，基于京都基因与基因组百科全书（KEGG）功能富集分析，发现许多deg参与HIF-1信号通路（gln, epo, vegfa, pfka, ldh）， AMPK信号通路（pfka, eef2k, gys）， p53信号通路（ccne, gtse1）， PI3K-Akt信号通路（ddit4, egf, gh, ghr, vwf, gys）和nod样受体信号通路（atg8, sharpin, ifnar1）等。该研究为阐明缺氧胁迫的分子调控机制提供了重要的见解，并有可能促进MD应对环境缺氧和再氧化应激的有效策略的发展，这对鱼类遗传改良具有重要价值。

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引用次数: 0

Transcriptional responses to DHA-induced lipid droplet accumulation in primary adherent mantle cells of Sinonovacula constricta (Lamarck, 1818) dha诱导的缢蛏原代贴壁套细胞脂滴积累的转录反应（Lamarck, 1818）。

IF 2.2 2区生物学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY

Comparative Biochemistry and Physiology D-Genomics & Proteomics

Pub Date : 2025-12-29 DOI: 10.1016/j.cbd.2025.101737

Bowen Yan , Zhaoshou Ran , Qiang Zhou , Jiaxin Zhu , Fei Kong , Jilin Xu

Docosahexaenoic acid (DHA), an essential omega-3 long-chain polyunsaturated fatty acid, is crucial for the development of marine mollusks. Despite its importance, the molecular mechanisms of DHA action in these organisms are poorly understood, primarily due to the lack of reliable in vitro models. This study utilizes the razor clam Sinonovacula constricta as a model organism, establishing a primary adherent cell culture from various tissues, with mantle tissue identified as the optimal source for its rapid migration and low contamination risk. Cells incubated with varying concentrations of DHA (0–400 μM) for 6 h exhibited a concentration-dependent accumulation of lipid droplets (LDs), highlighting the model's suitability for investigating lipid metabolism. Transcriptomic analysis of cells treated with 50 μM DHA identified 848 differentially expressed genes (DEGs), with 747 upregulated and 101 downregulated, indicating the complex effects of DHA. The top 20 significantly upregulated and downregulated DEGs revealed significant involvement in cell signaling transduction, extracellular matrix organization, and substance transport and metabolism. Particularly, lipid metabolism genes, including perilipin 2 and abhydrolase domain containing 2, as well as pathways such as the PPAR signaling pathway and sphingolipid metabolism, were significantly altered, suggesting a reprograming of fatty acid metabolism contributing to LD accumulation. Additionally, pathways related to immune response were notably affected, potentially enhancing cellular health. Collectively, this study provides the first comprehensive insights into the molecular mechanisms underlying DHA-induced LD accumulation in a marine mollusk model at the cellular level, laying a foundation for developing precise nutritional strategies involving DHA in S. constricta aquaculture.

二十二碳六烯酸（DHA）是一种必需的omega-3长链多不饱和脂肪酸，对海洋软体动物的发育至关重要。尽管它很重要，但由于缺乏可靠的体外模型，人们对DHA在这些生物中的作用的分子机制知之甚少。本研究以蛏子缢蛏（Sinonovacula constricta）为模型生物，建立了不同组织的原代贴壁细胞培养，并确定了套膜组织为其快速迁移和低污染风险的最佳来源。在不同浓度的DHA （0-400 μM）中培养6小时的细胞显示出脂滴（ld）的浓度依赖性积累，这表明该模型适合研究脂质代谢。经50 μM DHA处理的细胞转录组学分析发现848个差异表达基因（deg），其中747个上调，101个下调，表明DHA的复杂作用。前20个显著上调和下调的deg表明，它们显著参与细胞信号转导、细胞外基质组织、物质运输和代谢。特别是脂质代谢基因，包括perilippin 2和abhydrolase domain containing 2，以及PPAR信号通路和鞘脂代谢等途径，都发生了显著的改变，表明脂肪酸代谢的重编程导致了LD的积累。此外，与免疫反应相关的途径受到显著影响，可能增强细胞健康。总的来说，本研究首次在细胞水平上全面了解了DHA在海洋软体动物模型中诱导LD积累的分子机制，为制定涉及DHA的缢蛏养殖精确营养策略奠定了基础。

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引用次数: 0

Transcriptomic analysis under the stress of insecticides and the functional role of three genes related to host finding behavior of Scleroderma sichuanensis 杀虫剂胁迫下四川硬皮病找宿主行为相关基因的转录组学分析及功能作用。

IF 2.2 2区生物学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY

Comparative Biochemistry and Physiology D-Genomics & Proteomics

Pub Date : 2025-12-29 DOI: 10.1016/j.cbd.2025.101734

Sumbul Mureed Mastoi , Yang Hua , Waqar Ali Chandio , Paras Mureed Mastoi , Yang Wei

The female parasitoid wasp Scleroderma sichuanensis (Hymenoptera: Bethylidae) utilizes various intricate behavior strategies, including host detection, learning, and memory, to enhance its survival and reproductive success. RNA-Seq analysis conducted under sublethal insecticide stress identified three differentially expressed genes, SsOR5, SsGRIN2B, and SsPDE8A, selected for functional validation due to their likely roles in host searching behavior. The SsOR5, an odorant receptor, is believed to interact with other olfactory receptors and downstream signaling molecules to improve host detection. In contrast, SsGRIN2B, an NMDA-type glutamate receptor, may influence synaptic plasticity and neural transmission, thereby affecting leering behavior. Additionally, SsPDE8A modulates cAMP-dependent signaling pathways, which are crucial for memory consolidation and behavioral response. This research investigates these genes in S. sichuanensis using RNA interference (RNAi) to assess changes in host finding efficiency. Adult female wasp received dsRNA treatments at doses of (0.5 μL, 1 μL, and 3 μL) and time durations (12, 24, 48, and 72 h), with the most significant gene silencing observed at 3 μL for 48–72 h. Behavioral assays conducted with a Y-tube olfactometer revealed that knockdown of SsOR5 significantly reduced host attraction, while knockdown of SsGRIN2B and SsPDE8A led to moderate reeducations, highlighting the varying contributions of these genes to olfactory drive behavior. This study demonstrates that insecticides induced changes in gene expression can disrupt neural and olfactory pathways essential for host location, and emphasizes the potential of RNAi-based approaches to target behaviorally significant genes, offering new strategies for parasitoid-mediated pest management.

摘要四川硬皮蜂（Scleroderma sichuanensis，膜翅目：硬皮蜂科）利用多种复杂的行为策略，包括识别寄主、学习和记忆，以提高其生存和繁殖的成功率。在亚致死杀虫剂胁迫下进行的RNA-Seq分析鉴定出三个差异表达基因SsOR5、SsGRIN2B和SsPDE8A，由于它们可能在宿主搜索行为中发挥作用，因此被选中进行功能验证。SsOR5是一种气味受体，被认为与其他嗅觉受体和下游信号分子相互作用，以提高对宿主的检测。相反，nmda型谷氨酸受体SsGRIN2B可能影响突触可塑性和神经传递，从而影响抛媚眼行为。此外，SsPDE8A调节camp依赖的信号通路，这对记忆巩固和行为反应至关重要。本研究利用RNA干扰（RNAi）技术对这些基因进行了研究，以评估其在四川葡萄中寻宿主效率的变化。在不同剂量（0.5 μL、1 μL和3 μL）和不同时间（12、24、48和72 h）的dsRNA处理下，3 μL处理下48-72 h的dsRNA基因沉默最显著。用y管嗅觉仪进行的行为分析显示，敲低SsOR5显著降低寄主吸引力，而敲低SsGRIN2B和SsPDE8A导致中度的再教育，突出了这些基因对嗅觉驱动行为的不同贡献。该研究表明，杀虫剂诱导的基因表达变化可以破坏宿主定位所必需的神经和嗅觉通路，并强调了基于rnai的方法靶向行为重要基因的潜力，为寄生虫介导的害虫管理提供了新的策略。

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引用次数: 0

Comprehensive identification and expression profiling of piRNA pathway genes in the Pacific oyster Crassostrea gigas 太平洋牡蛎长牡蛎piRNA通路基因的综合鉴定及表达谱分析

IF 2.2 2区生物学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY

Comparative Biochemistry and Physiology D-Genomics & Proteomics

Pub Date : 2025-12-29 DOI: 10.1016/j.cbd.2025.101739

Xuan Zhao , Yaru Zhou , Hong Yu , Qi Li

PIWI-interacting RNAs (piRNAs) and their associated proteins are key regulators of germline development and genome defense, but their roles in mollusks remain largely unexplored. In this study, we systematically identified 28 piRNA pathway genes in the Pacific oyster Crassostrea gigas and characterized their genomic composition and expression profiles. The oyster piRNA gene repertoire exhibits a mosaic-like architecture, combining deeply conserved components with lineage-specific features, including the presence of vertebrate-type transcription factors such as A-MYB, the absence of the insect-specific RDC complex, and the retention of the exonuclease MUT7, which has been lost in several vertebrate and insect lineages. Transcriptome analyses revealed pronounced tissue-, stage-, and sex-biased expression patterns, consistent with this composite regulatory configuration. Several key factors, including CgPiwil1, CgGtsf1, and CgTdrd5 exhibit female-biased expression peaking at the maturation stage of the gonads, whereas CgYthdc2, CgMyb, and CgHsp83 show preferential expression in male gonads. Furthermore, CgHsp83 displays high expression in gills, suggesting potential multifunctional roles beyond germline regulation. qPCR validation of representative genes confirmed the transcriptome-based patterns. These findings provide the first comprehensive overview of the piRNA pathway in mollusks, reveal both conserved and divergent features compared to model animals, and establish a foundation for future functional studies on germline regulation in bivalves.

piwi相互作用rna （pirna）及其相关蛋白是种系发育和基因组防御的关键调节因子，但它们在软体动物中的作用仍未得到充分研究。在这项研究中，我们系统地鉴定了太平洋牡蛎长牡蛎中28个piRNA通路基因，并对其基因组组成和表达谱进行了分析。牡蛎piRNA基因库呈现出一种花叶状结构，结合了深度保守的成分和谱系特异性特征，包括存在脊椎动物类型的转录因子，如a - myb，缺乏昆虫特异性RDC复合物，以及保留在一些脊椎动物和昆虫谱系中丢失的外切酶MUT7。转录组分析揭示了明显的组织、阶段和性别偏向的表达模式，与这种复合调控配置一致。包括CgPiwil1、CgGtsf1和CgTdrd5在内的几个关键因子在性腺成熟阶段表现出雌性偏向性表达，而CgYthdc2、CgMyb和CgHsp83在雄性性腺中表现出优先表达。此外，CgHsp83在鳃中表现出高表达，这表明除了种系调节外，CgHsp83还具有潜在的多功能作用。代表性基因的qPCR验证证实了基于转录组的模式。这些发现提供了软体动物中piRNA通路的第一个全面概述，揭示了与模型动物相比的保守性和差异性特征，并为未来双壳类动物生殖系调控的功能研究奠定了基础。

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引用次数: 0

Divergent mechanisms of hypoxia tolerance in zebrafish (Danio rerio) and Nile tilapia (Oreochromis niloticus) 斑马鱼和尼罗罗非鱼耐缺氧机制的差异

IF 2.2 2区生物学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY

Comparative Biochemistry and Physiology D-Genomics & Proteomics

Pub Date : 2025-12-25 DOI: 10.1016/j.cbd.2025.101735

Ruiming Ren , Xingxing Hu , Shouwen Jiang , Jiulin Chan , Yan Zhou , Wanying Zhai , Qianghua Xu

Hypoxia is a critical environmental stressor that differentially impacts aquatic species. To investigate interspecific variations in hypoxia tolerance, we compared zebrafish (Danio rerio) and tilapia (Oreochromis niloticus) exposed to progressively decreasing oxygen levels. Behavioral observations revealed that zebrafish exhibited aquatic surface respiration and rapid mortality at 0.7 mg/L dissolved oxygen (DO), whereas tilapia maintained bottom-oriented swimming and higher survival, indicating stronger hypoxia tolerance. Transcriptomic analyses of zebrafish identified heart- and liver-specific gene modules strongly associated with acute hypoxia, with functional enrichment pointing to impaired cell proliferation, heme biosynthesis, and energy metabolism. TUNEL assays further confirmed severe apoptosis in zebrafish liver, underscoring its vulnerability to hypoxic damage. Comparative transcriptomics revealed divergent regulation of ribosome-related pathways: tilapia suppressed ribosomal gene expression and enhanced translation initiation factor activity, while zebrafish maintained protein biosynthesis, potentially exacerbating energy deficits. Metabolic assays showed increased hepatic phosphofructokinase (PFK) activity in zebrafish, suggesting reliance on glycolysis, whereas tilapia exhibited consistently higher basal PFK activity and reduced oxygen consumption under hypoxia, indicating metabolic suppression as an adaptive strategy. Antioxidant analysis revealed a significant decline in superoxide dismutase (SOD) activity in zebrafish but not tilapia, further reflecting species-specific oxidative stress responses. Together, these findings demonstrate that zebrafish and tilapia employ distinct hypoxia-coping strategies, with tilapia favoring metabolic suppression and oxidative stability, while zebrafish rely on glycolysis but suffer greater oxidative and apoptotic damage under acute hypoxia. These findings also provide new insights into divergent hypoxia adaptation strategies among teleosts.

缺氧是一种重要的环境应激源，对水生物种有不同的影响。为了研究缺氧耐受性的种间差异，我们比较了暴露于逐渐降低的氧气水平下的斑马鱼（Danio rerio）和罗非鱼（Oreochromis niloticus）。行为观察表明，在0.7 mg/L溶解氧（DO）条件下，斑马鱼表现出水体表面呼吸和快速死亡，而罗非鱼则保持了向底游和较高存活率，表现出较强的缺氧耐受性。斑马鱼的转录组学分析发现，心脏和肝脏特异性基因模块与急性缺氧密切相关，功能富集指向细胞增殖、血红素生物合成和能量代谢受损。TUNEL实验进一步证实斑马鱼肝脏存在严重的细胞凋亡，表明其易受缺氧损伤。比较转录组学揭示了核糖体相关途径的不同调控：罗非鱼抑制核糖体基因表达并增强翻译起始因子活性，而斑马鱼维持蛋白质生物合成，可能加剧能量不足。代谢实验显示，斑马鱼的肝磷酸果糖激酶（PFK）活性增加，表明其依赖糖酵解，而罗非鱼在缺氧条件下表现出更高的基础PFK活性和更低的氧消耗，表明代谢抑制是一种适应性策略。抗氧化分析显示，斑马鱼的超氧化物歧化酶（SOD）活性显著下降，而罗非鱼没有，进一步反映了物种特异性氧化应激反应。总之，这些研究结果表明，斑马鱼和罗非鱼采用不同的缺氧应对策略，罗非鱼倾向于代谢抑制和氧化稳定性，而斑马鱼依赖糖酵解，但在急性缺氧下遭受更大的氧化和凋亡损伤。这些发现也为硬骨鱼不同的缺氧适应策略提供了新的见解。

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引用次数: 0

Comparative transcriptomics identifies key genes and pathways underlying the early skin coloration in leopard coral grouper (Plectropomus leopardus) 比较转录组学鉴定了豹珊瑚石斑鱼（plectroomus leopardus）早期皮肤颜色的关键基因和途径。

IF 2.2 2区生物学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY

Comparative Biochemistry and Physiology D-Genomics & Proteomics

Pub Date : 2025-12-25 DOI: 10.1016/j.cbd.2025.101736

Lei Pang , Dan Sheng , Simin Wen , Lei Fang , Mouyan Jiang , Changxu Tian , Dayan Zhou , Huapu Chen , Guangli Li , Chunhua Zhu

The leopard coral grouper (Plectropomus leopardus) is a valuable marine economic fish, whose body color (especially red coloration) is a key trait determining its economic value. During early development, the body color of this fish transitions from transparent to red, providing an ideal model for elucidating the molecular mechanisms of body color formation. This study selected two critical time points, 26 dph(transparent)and 30 dph(red) post-hatching, to collect transparent skin (TC) and red skin (RC) tissues for comparative transcriptome analysis. Using the thresholds of |Fold Change| ≥ 2 and FDR < 0.05, a total of 1747 differentially expressed genes (DEGs) were identified, including 1213 up-regulated and 534 down-regulated genes, indicating that the formation of red body color involves the coordinated action of multiple genes. Further analysis revealed differential expression of several genes related to body color formation, including carotenoid metabolism-related genes (e.g., scarb1, ttc39b, bco2, fabp2, fabp3, apod, stard9) and melanin synthesis-related genes (e.g., tyr, tyrp1, dct, foxd3a). KEGG enrichment analysis showed significant enrichment of pathways related to lipid metabolism (e.g., steroid biosynthesis, cholesterol metabolism, arachidonic acid metabolism), melanin synthesis pathways (e.g., the Wnt signaling pathway and melanogenesis), and other potentially related pathways (e.g., retinol metabolism, insulin signaling pathway, purine metabolism), suggesting these pathways may collectively participate in the regulation of the body color transition. Furthermore, validation of 11 genes by qPCR confirmed the reliability of the RNA-seq data. This study highlights key molecular features during the early transition from transparent to red body color in the leopard coral grouper, providing new experimental evidence and a theoretical basis for a deeper understanding of its body color formation mechanisms.

豹珊瑚石斑鱼（plectroomus leopardus）是一种珍贵的海洋经济鱼类，其体色（尤其是红色）是决定其经济价值的关键特征。在发育早期，这种鱼的身体颜色从透明转变为红色，为阐明身体颜色形成的分子机制提供了理想的模型。本研究选取孵化后26 dph（透明）和30 dph（红色）两个关键时间点，采集透明皮肤（TC）和红色皮肤（RC）组织进行比较转录组分析。使用阈值|Fold Change|≥2和FDR

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引用次数: 0