Comparative Biochemistry and Physiology D-Genomics & Proteomics最新文献

{"title":"Comparative transcriptomic analysis across ovarian developmental stages in Sepiella japonica provides novel insights into its molecular regulatory mechanisms","authors":"An Xu ,&nbsp;Zhenming Lü ,&nbsp;Jing Liu ,&nbsp;Tianwei Liu ,&nbsp;Jing Yu ,&nbsp;Yijing Yang ,&nbsp;Kun Huang ,&nbsp;Li Gong ,&nbsp;Fenghui Li ,&nbsp;Denghui Zhu ,&nbsp;Hongling Ping ,&nbsp;Huilai Shi ,&nbsp;Liqin Liu","doi":"10.1016/j.cbd.2026.101746","DOIUrl":"10.1016/j.cbd.2026.101746","url":null,"abstract":"<div><div><em>Sepiella japonica</em> 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, <em>S. japonica</em> 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 <em>S. japonica</em> 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&gt;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 <em>FOXL2</em>, <em>HSD17B2</em>, and <em>BMP1</em>, suggesting their critical roles in regulating ovarian development in <em>S. japonica</em>. 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 <em>S. japonica</em>. This study clarified the regulation of transcript expression and molecular mechanisms in the ovary of <em>S. japonica</em> at different ovarian development stages, thereby offering theoretical guidance for enhancing reproductive efficiency in mollusk aquaculture.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"58 ","pages":"Article 101746"},"PeriodicalIF":2.2,"publicationDate":"2026-01-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145977218","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}

{"title":"Transcriptome analysis revealed the effects of dietary faba bean (Vicia faba L.) on muscle quality of Nile tilapia (Oreochromis niloticus)","authors":"Qingqing Li ,&nbsp;Yao Huang ,&nbsp;Xi Xie ,&nbsp;Shaowen Liang ,&nbsp;Li Lin","doi":"10.1016/j.cbd.2026.101747","DOIUrl":"10.1016/j.cbd.2026.101747","url":null,"abstract":"<div><div>Nile tilapia (<em>Oreochromis niloticus</em>) is a widely farmed freshwater fish. Feeding with faba bean (<em>Vicia faba</em> 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 (<em>p</em> &lt; 0.05), while the muscle fiber density was significantly increased (<em>p</em> &lt; 0.05). In total, 576 differentially expressed genes (DEGs) were identified (FDR &lt; 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 (<em>p</em> &lt; 0.05), whereas the expression levels of gapdh, pgam2, eno3, and g6pi were significantly decreased (<em>p</em> &lt; 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.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"58 ","pages":"Article 101747"},"PeriodicalIF":2.2,"publicationDate":"2026-01-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145925915","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}

{"title":"Genome-wide identification and characterization of HSP90, HSP60 and HSP40 family genes in Riptortus pedestris (Hemiptera: Alydidae)","authors":"Wenhao Dong ,&nbsp;Huaijun Xue ,&nbsp;Yipeng Ren","doi":"10.1016/j.cbd.2026.101745","DOIUrl":"10.1016/j.cbd.2026.101745","url":null,"abstract":"<div><div>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 <em>HSP</em> family genes remain poorly understood in heteropteran pests, especially in <em>R. pedestris</em>, 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 <em>HSP90</em>, fourteen <em>HSP60</em> and twenty-six <em>HSP40</em> family genes were obtained from the <em>R. pedestris</em> genome. Next, phylogenetic analysis, combined with conserved and domain characterization, supported our classification results. Chromosomal mapping indicated that all these <em>HSP</em> genes are distributed across the six chromosomes of <em>R. pedestris</em>, and a Ka/Ks ratio of &lt;1 provides essential information for purifying selection acting on two duplicated <em>Hsp90</em> genes in <em>R. pedestris</em>. Through data mining of transcriptome data, we obtained the expression patterns of three <em>HSP</em> family genes across all developmental stages and analyzed their expression differences during changes in feeding conditions in the whole body and gut of <em>R. pedestris</em>, respectively. Finally, a miRNA–mRNA interaction network of four significantly differentially expressed (DE) <em>HSPs</em> and corresponding regulatory miRNAs was constructed, of which one miRNA, novel-miRNA-927-3p, exhibited significant downregulation and combined with significantly DE <em>Hsp60a</em> and <em>DnaJA1</em> in one comparison group, suggesting their underlying relationships in response to antibiotic feeding in the <em>R. pedestris</em> gut. Overall, these findings provide valuable insights into how the three types of <em>HSP</em> genes in <em>R. pedestris</em> are involved in developmental and environmental adaptation at the transcriptional and posttranscriptional levels.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"58 ","pages":"Article 101745"},"PeriodicalIF":2.2,"publicationDate":"2026-01-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145925935","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}

{"title":"Molecular insights into hydrogen sulfide defense: A tissue-resolved transcriptomic study in the crab Eriocheir sinensis","authors":"Jian Tian ,&nbsp;Zihan Zhou ,&nbsp;Mingming Han ,&nbsp;Yi Juin Tay ,&nbsp;Mengyu Bao ,&nbsp;Longlong Fu ,&nbsp;Qichen Jiang","doi":"10.1016/j.cbd.2026.101743","DOIUrl":"10.1016/j.cbd.2026.101743","url":null,"abstract":"<div><div>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 (<em>Eriocheir sinensis</em>) 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 (<em>SOD1</em>, <em>GPX1</em>, <em>HO-1</em>), while simultaneously suppressing cytochrome <em>c</em> 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.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"58 ","pages":"Article 101743"},"PeriodicalIF":2.2,"publicationDate":"2026-01-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145925936","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}

{"title":"Integrated multi-omics analyses reveals physiological and gut microbiota responses of Litopenaeus vannamei to graded levels of dietary bile acids","authors":"Peng Tan ,&nbsp;Lei Zhang ,&nbsp;Jinzhi Zhang ,&nbsp;Aizhi Cao ,&nbsp;Dongdong Xu ,&nbsp;Aijun Zhu ,&nbsp;Zhili Ding ,&nbsp;Qingjun Shao","doi":"10.1016/j.cbd.2026.101744","DOIUrl":"10.1016/j.cbd.2026.101744","url":null,"abstract":"<div><div>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, <em>Litopenaeus vannamei</em>. 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 <em>sod1</em>, <em>gst</em> and <em>nos1</em>, 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 <em>nfkbia</em> and downregulating the adaptor <em>myd88</em>, 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 <em>Vibrio</em> while enriching beneficial genera such as <em>Ruegeria</em>. These findings indicate that exogenous BAs exert a protective role in L. <em>vannamei</em> 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.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"58 ","pages":"Article 101744"},"PeriodicalIF":2.2,"publicationDate":"2026-01-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145968045","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}

{"title":"Metabolomic insights into fish osmoregulation: Unveiling adaptive mechanisms to salinity change","authors":"Xiaoli Chen ,&nbsp;Youdi Tang ,&nbsp;Xue Du ,&nbsp;Ivone Giffard-Mena ,&nbsp;Quanquan Cao","doi":"10.1016/j.cbd.2025.101742","DOIUrl":"10.1016/j.cbd.2025.101742","url":null,"abstract":"<div><div>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.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"58 ","pages":"Article 101742"},"PeriodicalIF":2.2,"publicationDate":"2026-01-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145925934","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}

{"title":"Diversity of ligand-gated ion channels in free-living and parasitic copepods (Crustacea)","authors":"F. Neptalí Morales-Serna ,&nbsp;Ivana Ramos-de la Cruz ,&nbsp;Alejandra García-Gasca ,&nbsp;Miguel Betancourt-Lozano ,&nbsp;Jesús Briones-Mendoza ,&nbsp;Josué Pinto-Gualpa ,&nbsp;Luis A. Yañez-Guerra ,&nbsp;Víctor Hugo Caña-Bozada","doi":"10.1016/j.cbd.2025.101741","DOIUrl":"10.1016/j.cbd.2025.101741","url":null,"abstract":"<div><div>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.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"58 ","pages":"Article 101741"},"PeriodicalIF":2.2,"publicationDate":"2026-01-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145914212","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}

{"title":"Genome and transcriptome mining of the corazonin (Crz)-like peptide and gonadotropin-releasing hormone (GnRH)-like peptides in the spotted Babylon, Babylonia areolata","authors":"Uraipan Saetan ,&nbsp;Napamanee Kornthong ,&nbsp;Supawadee Duangprom ,&nbsp;Supita Tanasawet ,&nbsp;Wanida Sukketsiri ,&nbsp;Montakan Tamtin ,&nbsp;Phetcharat Phanthong ,&nbsp;Amornrat Sanprick ,&nbsp;Narainrit Chinfak ,&nbsp;Jirawat Saetan","doi":"10.1016/j.cbd.2025.101738","DOIUrl":"10.1016/j.cbd.2025.101738","url":null,"abstract":"<div><div>The Spotted Babylon (<em>Babylonia areolata</em>) 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 <em>B. areolata</em>. 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 <em>ba-Crz</em>-like gene while one intron was present in each <em>ba-GnRH</em>-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 <em>B. areolata</em>, Further characterization of their receptors and biological functions is ongoing to ensure the GnRH, AKH, and Crz identification in this species.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"58 ","pages":"Article 101738"},"PeriodicalIF":2.2,"publicationDate":"2026-01-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145968043","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}

{"title":"Hypoxia and reoxygenation induce changes in oxidative stress, histological structure, and transcriptome in the liver of mandarin fish (Siniperca chuatsi)","authors":"Dingbin Gong,&nbsp;Lin Zhou,&nbsp;Xiaoru Hong,&nbsp;Mingyang Yao,&nbsp;Zeting Huang,&nbsp;Wanting Yu,&nbsp;Yan Wu,&nbsp;Minmin Chen,&nbsp;Daoping Yu,&nbsp;Yaling Song,&nbsp;Liming Wang,&nbsp;Yuxi Lian,&nbsp;Xiaohuan Zhang,&nbsp;Pingping Wang","doi":"10.1016/j.cbd.2025.101740","DOIUrl":"10.1016/j.cbd.2025.101740","url":null,"abstract":"<div><div>The mandarin fish (<em>Siniperca chuatsi</em>, 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 (<em>nfkbia</em>, <em>vegfa</em>, <em>aplnr</em>) 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 (<em>gln</em>, <em>epo</em>, <em>vegfa</em>, <em>pfka</em>, <em>ldh</em>), AMPK signaling pathway (<em>pfka</em>, <em>eef2k</em>, <em>gys</em>), p53 signaling pathway (<em>ccne</em>, <em>gtse1</em>), PI3K-Akt signaling pathway (<em>ddit4</em>, <em>egf</em>, <em>gh</em>, <em>ghr</em>, <em>vwf</em>, <em>gys</em>), and NOD-like receptor signaling pathway (<em>atg8</em>, <em>sharpin</em>, <em>ifnar1</em>), 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.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"58 ","pages":"Article 101740"},"PeriodicalIF":2.2,"publicationDate":"2025-12-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145884357","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}

{"title":"Transcriptional responses to DHA-induced lipid droplet accumulation in primary adherent mantle cells of Sinonovacula constricta (Lamarck, 1818)","authors":"Bowen Yan ,&nbsp;Zhaoshou Ran ,&nbsp;Qiang Zhou ,&nbsp;Jiaxin Zhu ,&nbsp;Fei Kong ,&nbsp;Jilin Xu","doi":"10.1016/j.cbd.2025.101737","DOIUrl":"10.1016/j.cbd.2025.101737","url":null,"abstract":"<div><div>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 <em>in vitro</em> models. This study utilizes the razor clam <em>Sinonovacula constricta</em> 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 <em>S. constricta</em> aquaculture.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"58 ","pages":"Article 101737"},"PeriodicalIF":2.2,"publicationDate":"2025-12-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145879667","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}