Comparative biochemistry and physiology. Part D, Genomics & proteomics最新文献

{"title":"Integrated transcriptomic and co-expression analyses reveal hypoxia-responsive patterns in the gills of Mytilus coruscus.","authors":"Rui Zhao, Jichun Li, Hongfei Li, Yingying Ye, Jiji Li","doi":"10.1016/j.cbd.2026.101861","DOIUrl":"https://doi.org/10.1016/j.cbd.2026.101861","url":null,"abstract":"<p><p>Hypoxia is a significant environmental stressor that negatively affects the growth, survival, and overall health of marine bivalves. This study aimed to investigate the physiological and molecular responses of Mytilus coruscus (thick-shell mussel) to hypoxic stress by integrating histological analysis, enzyme activity assays, whole-transcriptome sequencing, and Weighted Gene Co-expression Network Analysis (WGCNA) of gill tissues. The results revealed marked structural damage to gill filaments under prolonged hypoxia, including epithelial swelling, exfoliation, and lamellar fusion. Enzyme activities, including acid phosphatase (ACP), alkaline phosphatase (AKP), superoxide dismutase (SOD), catalase (CAT), and glutathione peroxidase (GSH-Px), exhibited distinct temporal fluctuations, with an initial decrease followed by partial recovery at later time points. WGCNA identified four gene co-expression modules associated with hypoxia exposure, and these modules were enriched in pathways related to metabolic regulation, stress response, and antioxidant defense. Transcriptome sequencing identified 56 differentially expressed miRNAs, 1393 mRNAs, 392 lncRNAs, and 21 circRNAs, and RT-qPCR validation confirmed the consistency of the expression trends of selected mRNAs. Functional enrichment analysis indicated that hypoxia-responsive coding and non-coding transcripts were associated with signaling pathways involved in stress response, energy metabolism, and antioxidant defense. Together, these findings support a transcriptome-based working model in which FOXO and HIF-1-related pathways may participate in hypoxia-associated metabolic and antioxidant adjustment in M. coruscus. These results provide candidate targets for future functional validation and may offer a basis for aquaculture management strategies aimed at improving stress resilience.</p>","PeriodicalId":93949,"journal":{"name":"Comparative biochemistry and physiology. Part D, Genomics & proteomics","volume":"59 ","pages":"101861"},"PeriodicalIF":2.4,"publicationDate":"2026-05-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147876951","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Role of Activin A in regulating ovarian development during vitellogenesis in Japanese eel (Anguilla japonica).","authors":"Chenpeng Zuo, Yonghang Zhang, Yuting Ci, Xuanhan Zhang, Xiao Jing, Ziyi Zhao, Xin Qi","doi":"10.1016/j.cbd.2026.101863","DOIUrl":"https://doi.org/10.1016/j.cbd.2026.101863","url":null,"abstract":"<p><p>Activin A, a member of the TGF-β superfamily, plays pivotal roles in vertebrate reproductive regulation. This research investigated the biological functions and potential regulatory mechanisms of Activin A during vitellogenesis in Japanese eel. Analysis of the structural characteristics and evolutionary relationships confirmed that Japanese eel Activin A is highly conserved, providing a molecular basis for elucidating its role in ovarian development. Using a prokaryotic expression system, recombinant Japanese eel Activin A protein was successfully produced, and a series of in vitro functional assays were subsequently conducted. Results demonstrated that Activin A significantly promoted vitellogenin uptake by oocytes and enhanced the efficiency of gonadotropin-mediated downstream signaling by upregulating receptor expression during vitellogenesis. Transcriptomic analysis of ovarian cells revealed that Activin A is involved in multiple physiological processes closely associated with ovarian development, including substance transport, energy metabolism, steroid receptor activity, and key reproductive signaling pathways. These findings indicate that Activin A orchestrates ovarian development during vitellogenesis in Japanese eel.</p>","PeriodicalId":93949,"journal":{"name":"Comparative biochemistry and physiology. Part D, Genomics & proteomics","volume":"59 ","pages":"101863"},"PeriodicalIF":2.4,"publicationDate":"2026-05-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147876962","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Population genomics and GWAS reveal genetic basis of shell traits in Manila clam (Ruditapes philippinarum).","authors":"Jiakang Wang, Di Wei, Zhihong Liu, Liqing Zhou, Biao Wu, Xiujun Sun","doi":"10.1016/j.cbd.2026.101859","DOIUrl":"https://doi.org/10.1016/j.cbd.2026.101859","url":null,"abstract":"<p><p>The Manila clam (Ruditapes philippinarum) is a key aquaculture species in China's intertidal zones, where body size and growth rates strongly influence market preference and commercial value. Nevertheless, the genetic basis of shell traits and population structure of coastal stocks remain poorly understood. Here, we performed RAD-seq sequencing of 301 individuals from 10 populations along the Chinese coast to analyze population genetics and conduct a genome-wide association study (GWAS). Population genetic analyses revealed nucleotide diversity (π) ranging from 0.259 to 0.273, with the Haiyang population showing the highest diversity. The Hongdao population exhibited the highest inbreeding coefficient (F_IS = 0.469) and lowest observed heterozygosity (H_o = 0.144), whereas the Sanya population had the lowest inbreeding (F_IS = 0.235) and highest heterozygosity (H_o = 0.199). Genetic differentiation (F_ST) was greatest between the Rizhao and Donggang populations (F_ST = 0.0484). In contrast, unexpectedly low differentiation between the geographically distant Donggang and Beihai populations (F_ST = 0.0122) suggests the possible anthropogenic translocation and gene flow. Using a mixed linear model (MLM) for GWAS, we identified 142 significant SNPs associated with shell traits after Bonferroni correction. Notably, 139 SNPs distributed across chromosomes from 1 to 19 were linked to shell thickness, while only three SNPs on chromosome 13 were associated with shell width. Within 50 kb flanking regions of these loci, 453 candidate genes were annotated. Functional enrichment analyses (GO and KEGG) highlighted seven candidate genes (e.g., Calml3, MC1R, and TBXT) that may be associated with biomineralization, calcium signaling, and shell-related trait variation. Additionally, a selective sweep analysis comparing Beihai and Hongdao populations identified 118 candidate genes located in putative outlier regions (top 1% of F_ST and π ratio). Enrichment of these regions revealed three candidate genes (Acp5, SLC6A1, and FNTA) related to metabolism and cellular transport, potentially reflecting local adaptation or artificial selection. Together, these findings provide important insights into the germplasm resources of R. philippinarum and offer valuable genomic targets for marker-assisted selection to improve shell traits in aquaculture breeding programs.</p>","PeriodicalId":93949,"journal":{"name":"Comparative biochemistry and physiology. Part D, Genomics & proteomics","volume":"59 ","pages":"101859"},"PeriodicalIF":2.4,"publicationDate":"2026-05-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147876975","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Transcriptome profiling to decipher molecular mechanisms of diapause in Chilo partellus (Swinhoe) (Lepidoptera: Crambidae).","authors":"Mukesh K Dhillon, Sanjay Kumar Singh, Sarika Jaiswal, Aditya K Tanwar, Karuppannasamy Ashok, Mogili Ramaiah, Mir Asif Iquebal, Dinesh Kumar","doi":"10.1016/j.cbd.2026.101857","DOIUrl":"https://doi.org/10.1016/j.cbd.2026.101857","url":null,"abstract":"<p><p>Diapause is a critical adaptive strategy in insects to survive unfavourable environmental conditions. The present study investigated molecular mechanisms underlying diapause in Chilo partellus, using high-throughput RNA sequencing and de novo transcriptome assembly. Six transcriptome libraries from diapause and non-diapause larvae yielded over 50 million reads per sample, with >98% mapping efficiency. The Evidential Gene-refined assembly produced 67,116 high-quality transcripts, and BUSCO analysis confirmed its completeness. DEG analysis identified 1204 DEGs, including 660 upregulated and 544 downregulated in diapause larvae. GO enrichment revealed significant activation of stress response pathways, including heat shock proteins, protein folding, and redox homeostasis. Hormone-related genes such as juvenile hormone epoxide hydrolase and juvenile hormone esterase-like transcripts that are associated primarily with hormone degradation or early steps of ecdysteroidogenesis rather than direct synthesis of active ecdysteroids, were upregulated, suggesting endocrine regulation of diapause. Conversely, downregulation of insulin-like peptides, mitochondrial respiratory genes, and ribosomal proteins reflected suppressed metabolic and translational activity, hallmarks of diapause. PCA and hierarchical clustering confirmed clear transcriptional separation between diapause and non-diapause stages. Ten representative DEGs were validated using qRT-PCR, demonstrating strong concordance with RNA-seq. Notably, upregulated genes included Hsp70-like proteins, cytochrome P450s, and cuticle proteins, while insulin signaling and oxidative phosphorylation were downregulated. This study provides a comprehensive molecular framework for diapause in C. partellus, highlighting stress tolerance, metabolic suppression, and hormonal control as key regulatory themes. The identified genes offer potential targets for disrupting diapause, contributing to improved pest management strategies against this economically important insect.</p>","PeriodicalId":93949,"journal":{"name":"Comparative biochemistry and physiology. Part D, Genomics & proteomics","volume":"59 ","pages":"101857"},"PeriodicalIF":2.4,"publicationDate":"2026-05-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147876996","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Histological and transcriptomic analysis of the white hepatopancreas in Amphioctopus fangsiao.","authors":"Zexin Huang, Jiayu Liu, Meng Chen, Ruihua Li, Weijun Wang, Guohua Sun, Xiaohui Xu, Zan Li, Bin Li, Yanwei Feng, Jianmin Yang","doi":"10.1016/j.cbd.2026.101858","DOIUrl":"https://doi.org/10.1016/j.cbd.2026.101858","url":null,"abstract":"<p><p>Ink production and release is one of the most important defense strategies in cephalopods. Previous studies have shown that ink production and release are closely associated with the hepatopancreas. In octopuses, the ink sac is embedded within the hepatopancreas, and the surrounding hepatopancreatic tissue appears white. To explore the differences between the white hepatopancreas and normal hepatopancreas, as well as the potential function of the white hepatopancreas, this study took Amphioctopus fangsiao as the research object and conducted histological and transcriptomic studies on white hepatopancreas and normal hepatopancreas tissues. Histological analysis revealed clear structural differences between the two tissues, with lipid droplets absent in the white hepatopancreas. Transcriptomic analysis identified 6530 differentially expressed genes (DEGs). Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and protein-protein interaction (PPI) analyses found that oxidative phosphorylation and the Apelin signaling pathways were significantly enriched in white hepatopancreas, suggesting an increase in ATP production and the alleviation of oxidative stress. Members of the ABHD gene family enriched may regulate lipid droplet metabolism. TAT, SLC6A6, Dop1R1 and Dop2R could potentially influence the levels of tyrosine, taurine and dopamine in the white hepatopancreas. Considering that these substances are involved in the main components of ink, we speculate that these genes may be related to the precursor supply for ink production. Our study demonstrates that the white hepatopancreas is structurally distinct from the normal hepatopancreas, and may be functionally related to the ink sac to some extent.</p>","PeriodicalId":93949,"journal":{"name":"Comparative biochemistry and physiology. Part D, Genomics & proteomics","volume":"59 ","pages":"101858"},"PeriodicalIF":2.4,"publicationDate":"2026-05-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147877001","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Evolutionary analysis of ghrelin in Actinopterygii.","authors":"Zhuoxin Lai, Hamad Khan, Lujun Chen, Jiahao Luo, Ming Li, Yusong Guo, Zhongduo Wang","doi":"10.1016/j.cbd.2025.101599","DOIUrl":"10.1016/j.cbd.2025.101599","url":null,"abstract":"<p><p>Ghrelin functions to stimulate appetite, promote the release of growth hormone, and regulate energy balance. Currently, research on the ghrelin is primarily focused on a single species, and there have been no systematic studies on the evolution of the ghrelin in fish. Therefore, this thesis conducts a comprehensive analysis of the ghrelin gene in 151 species of ray-finned bony fishes to reveal the universality and specificity of the ghrelin gene in the evolutionary history of fish, supplementing and perfecting the information on the ghrelin gene in Actinopterygii. The gene identification results show that the number of ghrelin genes varies among different fish species, 41 fish have lost the ghrelin gene, 98 fish having one ghrelin gene, and 12 fish having two ghrelin genes. Among the 110 fish species with the ghrelin gene, a total of 182 ghrelin gene sequences were identified, with transcript variant numbers ranging from 1 to 6, encoding 1 to 3 types of isoform proteins, and their mature peptides show a certain degree of similarity across different species. Phylogenetic analysis revealed that teleost ghrelin proteins segregate into three major evolutionary clades, with Salmoniformes orthologs comprising a distinct monophyletic cluster. The Cladistic and Chondrostei are clustered separately and then grouped with the more ancient Cypriniformes and Siluriformes species from the Neopterygii into a large group, while the other fish species from the Neopterygii form another large group. The Synteny analysis results indicate that the upstream gene of the ghrelin is CCDC174, and the downstream gene is TATDN2. The selection pressure analysis results show that there are no positive selection sites in the ghrelin gene, indicating that the ghrelin has been under strong functional constraint during the evolutionary process of fish. This study systematically investigates the evolutionary history of fish ghrelin, providing a theoretical basis for understanding the function and status of ghrelin in the feeding regulation system of fish, and deepening the recognition of its structural and functional evolution in the process of energy metabolism evolution.</p>","PeriodicalId":93949,"journal":{"name":"Comparative biochemistry and physiology. Part D, Genomics & proteomics","volume":"56 ","pages":"101599"},"PeriodicalIF":2.4,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144818622","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Transcriptomic analysis provides insights into gonad development and sex reversal of cultured largefin longbarbel catfish (Hemibagrus macropterus).","authors":"Huamei Yue, Ling Huang, Rui Ruan, Le Yu, Yong Xie, Chuangju Li, Huan Ye","doi":"10.1016/j.cbd.2025.101653","DOIUrl":"10.1016/j.cbd.2025.101653","url":null,"abstract":"<p><p>The largefin longbarbel catfish (Hemibagrus macropterus) is an important commercially cultured fish in southwestern China, whose regulatory mechanism of gonad development remains unknown. In this study, the first gonadal transcriptome sequencing of immature male, female, and intersexual individuals were performed. A total of 28,543 genes was annotated, of which 12,028, 6283 and 8019 differentially expressed genes (DEGs) were detected by pairwise comparisons of ovary versus (vs.) testis, ovary vs. intersex, and testis vs. intersex. Besides, 26 male-biased, 24 female-biased, and 7 intersex-biased DEGs were screened. Representative pathways related to gonadal development and sex reversal were further enriched. Interestingly, apart from the reproduction-related genes and pathways, apoptosis-related DEGs (bcl2, myc, caspase3 and tp53) and pathways such as JAK-STAT signaling pathway and P53 signaling pathway, were suggested to be involved in the sexual reversal process. The intersexual gonad might be developed by the sex change from ovary to testis, with transcriptions of female-biased genes reduced and male-biased genes increased. Relative real time PCR results of 14 DEGs verified the reliability of transcriptome data. These results will benefit our understanding of gonad development regulations, and further be useful for the achievement of improved artificial propagation of largefin longbarbel catfish.</p>","PeriodicalId":93949,"journal":{"name":"Comparative biochemistry and physiology. Part D, Genomics & proteomics","volume":"56 ","pages":"101653"},"PeriodicalIF":2.4,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145305039","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Molecular mechanisms of kidney-mediated salinity adaptation in Takifugu obscurus, T. rubripes and their hybrid offspring.","authors":"Xinyan Liang, Dongkui Gao, Chenqi Wang, Yushun Tian, Qi Liu, Hongwei Yan, Rui Gao, Liu Wang, Meiyuan Li, Ruonan Zhang, Jinfeng Chen, Chen Jiang, Xiuli Wang","doi":"10.1016/j.cbd.2025.101659","DOIUrl":"10.1016/j.cbd.2025.101659","url":null,"abstract":"<p><p>Salinity changes significantly impact fish physiology, requiring efficient osmoregulation for survival. The kidney is vital for maintaining ion and water balance, crucial for internal stability in varying salinity. This study used transcriptomic analysis to examine molecular responses in the kidneys of Takifugu obscurus, T. rubripes, and their hybrids (Tor1 and Tor2) in freshwater (0 ppt) and seawater (32 ppt). Following the transfer from seawater to freshwater, all four fish groups showed consistent expression trends of three genes in their kidneys-one downregulated gene (ca7) and two upregulated genes (MAP1B and MUC4)-indicating their pivotal roles in renal osmoregulation. Additionally, RNA sequencing unveiled distinct transcriptional profiles specific to each species T. obscurus displayed a limited number of DEGs (14 upregulated and 4 downregulated) in freshwater, suggesting streamlined regulatory mechanisms consistent with its broad salinity tolerance. In contrast, T. rubripes exhibited more extensive transcriptional adjustments (449 upregulated and 139 downregulated), involving ion transport genes and metabolic pathways. Moreover, we observed significant changes in the expression of immune-related genes, indicating that variations in ambient salinity affect the immune responses of the four fish species. Genetic correlation analysis indicated that Tor1 clustered with T. rubripes, while Tor2 grouped with T. obscurus, implying that hybrid offspring inherit adaptive strategies from both parental lineages. These findings shed light on the molecular mechanisms governing kidney function in euryhaline fish and provide a theoretical foundation for breeding aquaculture species with enhanced stress tolerance.</p>","PeriodicalId":93949,"journal":{"name":"Comparative biochemistry and physiology. Part D, Genomics & proteomics","volume":"56 ","pages":"101659"},"PeriodicalIF":2.4,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145350424","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Gonadal transcriptome analysis of Cirrhina molitorella reveals sex-associated genes.","authors":"Weijian Chen, Guojun Cai, Weiqian Liang, Shengyue Lin, Weibin Li, Sixun Li, Binhua Deng, Mengmeng Wu, Chong Han, Qiang Li","doi":"10.1016/j.cbd.2025.101652","DOIUrl":"10.1016/j.cbd.2025.101652","url":null,"abstract":"<p><p>Cirrhina molitorella is an important economic fish species in southern China, and it holds a significant position among the highest-yielding fish species in this region. However, studies on the identification of sex-related genes and gonadal development in C. molitorella remain scarce, which has severely hindered the development of its aquaculture industry. In the present study, transcriptome sequencing data from the female and male gonads of C. molitorella were analyzed and compared for the first time, leading to the successful assembly of 64,954 unigenes. Through comparative transcriptomic analysis, a total of 20,310 differentially expressed genes were identified, among which 16,003 were significantly upregulated in testis and 4307 were highly expressed in ovaries. Furthermore, real-time quantitative PCR was also employed to validate the differential expression profiles of some genes, and the results were in agreement with the transcriptome data. These findings of this study can provide fundamental data for in-depth investigations into the functions of genes and signaling pathways associated with gender determination and gonadal formation in C. molitorella.</p>","PeriodicalId":93949,"journal":{"name":"Comparative biochemistry and physiology. Part D, Genomics & proteomics","volume":"56 ","pages":"101652"},"PeriodicalIF":2.4,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145254065","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Comprehensive analysis of small non-coding RNAs in the liver of Onychostoma macrolepis during overwintering and non-overwintering periods provides insights into the metabolic mechanisms of fish overwintering.","authors":"Chao Zhu, Guofan Peng, Qimin Liu, Xiaolin Wang, Changqing Sun, Hanghang Zhu, Yibin Ding, Shili Liu, Fangxia Yang, Zhilong Chen, Wuzi Dong","doi":"10.1016/j.cbd.2025.101644","DOIUrl":"10.1016/j.cbd.2025.101644","url":null,"abstract":"<p><p>Fish in aquaculture face dual overwintering stressors: low temperature and food scarcity. However, the role of sncRNAs in this process remains unclear. Integrated histopathology, high-throughput sequencing, and bioinformatics analyses was employed to compare hepatic differences in Onychostoma macrolepis (O. macrolepis) liver between overwintering (January, March, and October) and non-overwintering (June). Significant changes were observed in liver morphology (progressive loss of hepatic cord-like organization and nuclear condensation in January and March), sncRNA expression, and tRNA-derived small RNA (tsRNA) splicing patterns between overwintering and non-overwintering periods, with a pronounced bias in tsRNA expression during non-overwintering. Upregulated sncRNAs during overwintering (miR-30-1, tiRNA5-Asp-GTC-1) could be involved in inhibiting mitochondrial and ribosome biogenesis, as well as ATPase and pyruvate kinase activity. In contrast, Upregulated sncRNAs in non-overwintering (let-7-1, tiRNA5-Lys-CTT-1) may activate cell growth/metabolic pathways and promote liver growth, potentially preparing the fish for feeding and reproduction. Functional experiments using fertilized eggs demonstrated that inhibitors of let-7-1 and tiRNA5-Lys-CTT-1 significantly suppressed embryonic development, further demonstrating confirming the accuracy of functional predictions. These results indicate that O. macrolepis can actively regulate relevant sncRNAs in the liver to reduce its own energy metabolism and growth, thereby entering a low-energy metabolic state during overwintering. In conclusion, these findings significantly advance our understanding of the roles of miRNAs and tsRNAs in enabling O. macrolepis to adapt to winter food scarcity and low-temperature stress.</p>","PeriodicalId":93949,"journal":{"name":"Comparative biochemistry and physiology. Part D, Genomics & proteomics","volume":"56 ","pages":"101644"},"PeriodicalIF":2.4,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145310319","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}