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

{"title":"Metagenomic insights into the alterations of gut microbial community in Bufo gargarizans tadpoles following lead exposure","authors":"Yanjiao Song ,&nbsp;Lod Fabuleux Tresor Baniakina ,&nbsp;Ling Jiang ,&nbsp;Lihong Chai","doi":"10.1016/j.cbd.2025.101522","DOIUrl":"10.1016/j.cbd.2025.101522","url":null,"abstract":"<div><div>Lead (Pb), a prevalent heavy metal contaminant in aquatic environments, has complex effects on the gut microbiome function of aquatic animals. In this study, metagenomic analysis of <em>Bufo gargarizans</em> tadpoles was carried out following Pb exposure. Moreover, histological analysis was performed on the intestines. The results showed that Pb exposure induced histological damage to the intestinal epithelium. Significant differences in microbial abundance and function were detected in the 200 μg/L Pb group compared to the control group. Specifically, an increase in <em>Bosea</em> and <em>Klebsiella</em> was noted at 200 μg/L Pb, which potentially could induce inflammation in tadpoles. Notably, the decrease in the abundance of glycoside hydrolases subsequent to exposure to 200 μg/L Pb is likely to attenuate carbohydrate metabolism. Furthermore, increased fluoroquinolone-related antibiotic resistance genes (ARGs), phenolic-related ARGs, and iron uptake systems following 200 μg/L Pb exposure might heighten the disease risk for tadpoles. These discoveries augment our comprehension of the influences of Pb on the intestinal well-being of amphibians and offer valuable insights for further assessment of the ecological risks that Pb poses to amphibians.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"55 ","pages":"Article 101522"},"PeriodicalIF":2.2,"publicationDate":"2025-04-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143876902","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":"Lipid droplets play versatile roles in ovarian development of the razor clam Sinonovacula constricta: Insights from proteomic and lipidomic analyses","authors":"Xuxu Tian ,&nbsp;Zhaoshou Ran ,&nbsp;Bowen Yan ,&nbsp;Jiaxin Zhu ,&nbsp;Qiang Zhou ,&nbsp;Fei Kong ,&nbsp;Xiaojun Yan ,&nbsp;Jilin Xu","doi":"10.1016/j.cbd.2025.101519","DOIUrl":"10.1016/j.cbd.2025.101519","url":null,"abstract":"<div><div>Lipid droplet (LD) deposition is a common phenomenon during ovarian development across marine mollusks; however, studies on the protein and lipid composition of their ovarian LDs remain limited. Here, we purified LDs from the ovaries of <em>Sinonovacula constricta</em> and isolated proteins and lipids from these purified LDs for proteomic and lipidomic analyses. Our proteomic analysis identified 3243 proteins, with PLIN2 being the most abundant (37.03 ± 13.56 %). We subsequently conducted a functional analysis of the top 500 most abundant LD-associated proteins, categorizing them into 15 groups, including those involved in lipid metabolism, sterol biosynthesis, tricarboxylic acid cycle, carbohydrate metabolism, G protein superfamily, protein chaperones, transport proteins, nucleotide-catabolic process, protein processing and degradation, cytoskeletal proteins, oxidative stress and immunity, and ribosome-associated proteins. In our lipidomic analysis, we identified 1158 molecules across 52 lipid classes, with phosphatidylcholine (PC) exhibiting the greatest diversity at 209 varieties, followed by EtherPC with 177 varieties and triglyceride (TG) with 149 varieties. The fatty acid (FA) analysis of LDs revealed that 16:0 was the most abundant (30.01 ± 0.42 %). Additionally, LDs were found rich in long-chain polyunsaturated FAs (35.63 ± 4.36 %), particularly EPA and DHA. Moreover, we analyzed the FA composition of TGs, PCs, and EtherPCs derived from ovarian LDs. In PCs and TGs, the predominant FAs were 16:0, 16:1, and 18:3, while 16:0, 22:6, and 18:4 constituted the major FA species in EtherPCs. Together, our results suggest that ovarian LDs in <em>S. constricta</em> not only participate in lipid metabolism but also interact with other organelles and metabolic processes, thereby facilitating ovarian development.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"55 ","pages":"Article 101519"},"PeriodicalIF":2.2,"publicationDate":"2025-04-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143877003","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":"Transforming growth factor-beta gene family in Labeo rohita: Genome-wide molecular characterization and phylogenetic relationship with other vertebrates","authors":"Saima Naz ,&nbsp;Ahmad Manan Mustafa Chatha","doi":"10.1016/j.cbd.2025.101511","DOIUrl":"10.1016/j.cbd.2025.101511","url":null,"abstract":"<div><div>Recent advancements in animal genetics, biotechnology, and bioinformatics can potentially contribute to the required improvement in fish production and quality. Current study explored for the first-time, various genes from Transforming growth factor-beta (TGF-β) gene family which could play vital role in growth and development of <em>Labeo rohita</em>, an economically important freshwater fish. A number of tools and analysis like characterizing the selected genes, multiple alignment and clade-wise phylogeny, dual Synteny analysis and chromosomal distribution, characterization of proteins, secondary structure and 3D models of proteins, PROSITE scan analysis, and transcription factor binding sites (TFBSs) of selected genes were performed to explore the relationship between selected genes from <em>Labeo rohita</em> and referenced species (<em>Homo sapiens</em>, <em>Danio rerio</em>, <em>Oreochromis niloticus</em>, <em>Chelonia mydas</em>, and <em>Parus major</em>). The study evaluated 27 genes from TGF-β gene family. The results suggested that physicochemical characteristics of studied genes exhibit a basic nature with the few exceptions. Two main clades (BPM like and GDF like) were obtained by the phylogenetic analysis across six vertebrate species. Homogeneity was observed in the gene structure for all selected genes of TGF-β gene superfamily. TGF-β family and TGF-β propeptide family were dominant in domain regions of studied genes. Gene structure comparisons suggested that the TGF-β gene superfamily has arisen by gene duplications events. The study identified five pairs of duplicated gene (segmental duplications) with the Ka/Ks &lt; 1, indicating the negative selection pressure of these genes. The length of selected TFBSs (GATA, HOXD, STAT, HNF-1A, and YY1) ranged from 5 to 9 bp, with the HOXD having maximum bp. This study explored the molecular characterization for TGF-β gene family and related proteins in L. <em>rohita</em> and will potentially serve as basis of development of novel strategies in improvement of fish culture.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"55 ","pages":"Article 101511"},"PeriodicalIF":2.2,"publicationDate":"2025-04-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143860696","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 of TRAF family genes in Urechis unicinctus (Annelida, Echiura) and their responses in resistance to high temperature stress","authors":"Dawei Lin ,&nbsp;Wenwen Jiang ,&nbsp;Yuxin Feng ,&nbsp;Long Zhang ,&nbsp;Wengqing Zhang ,&nbsp;Zhifeng Zhang","doi":"10.1016/j.cbd.2025.101516","DOIUrl":"10.1016/j.cbd.2025.101516","url":null,"abstract":"<div><div>TRAFs (Tumor necrosis factor receptor-associated factors), serving as important signaling mediators, are essential for organismal immunity and biological responses to environmental stress. Temperature is an important environmental factor for the survival of organisms, but so far, the studies on sequence characteristics of the TRAF family genes and their responses to high temperature stress in marine animals are very limited. In this study, we conducted a genome-wide analysis of the TRAF family genes and revealed their characteristics of responding to high temperature stress in <em>Urechis unicinctus</em>, an economic coastal burrowing Echuran worm. Nine TRAF sequences were identified based on <em>U. unicinctus</em> genome database, which belonged to 5 TRAF members by phylogenetic analysis, namely <em>Uu</em>TRAF2, <em>Uu</em>TRAF3a, <em>Uu</em>TRAF3b, <em>Uu</em>TRAF3c, <em>Uu</em>TRAF4a, <em>Uu</em>TRAF4b, <em>Uu</em>TRAF4c, <em>Uu</em>TRAF6 and <em>Uu</em>TRAF7. Especially, the copy number of <em>TRAF3</em> and <em>TRAF4</em> was higher, while the length and number of introns in <em>TRAF2</em> and <em>TRAF3</em> were significantly shorter and fewer in <em>U. unicinctus</em> compared to other invertebrates. Furthermore, the expression of the TRAF family genes showed obvious spatio-temporal specificity in the embryos, larvae, and adult tissues of <em>U. unicinctus</em>, with more TRAF family genes expressed in larvae, body wall, and hind-gut. When <em>U. unicinctus</em> adults were stressed by high temperature (29 °C), all the <em>UuTRAFs</em> were significantly up-regulated, especially <em>UuTRAF2</em> and <em>UuTRAF3a</em>, which were kept at high levels during the experimental phase, indicating their importance in responding to the high temperature stress. Our findings will facilitate a greater comprehension of the sequence characteristics of TRAF family genes in annelids, and provide essential data for future exploring the genetic mechanism and breeding of high temperature tolerance of <em>U. unicinctus</em>.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"55 ","pages":"Article 101516"},"PeriodicalIF":2.2,"publicationDate":"2025-04-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143860695","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":"Biochemical indices, histological observations and transcriptome sequencing reveal the response mechanism of largemouth bass (Micropterus salmoides) to transport stress","authors":"Xue Jun Duan ,&nbsp;Yi Fan Tao ,&nbsp;Jixiang Hua ,&nbsp;Qing Chun Wang ,&nbsp;Jun Qiang","doi":"10.1016/j.cbd.2025.101514","DOIUrl":"10.1016/j.cbd.2025.101514","url":null,"abstract":"<div><div>In this study, transport conditions were simulated to investigate changes in intestinal tissue structure, oxidative stress, apoptosis and transcriptome levels during transport stress of largemouth bass (<em>Micropterus salmoides</em>). The results showed that the serum cortisol and lactic acid levels in largemouth bass significantly increased with increasing transport time, and the glucose content peaked after 8 h of transport. After 8 h and 12 h, the Reactive oxygen species, superoxide dismutase, malondialdehyde, and lipid peroxide contents in the intestine were significantly higher than those in the control group and the stressed group at 4 h. Additionally, more of the mucous membrane of intestinal tissue was exfoliated, resulting in edema, and the intestinal villi height and density significantly decreased. The differentially expressed genes were further analyzed after 0 h, 8 h, and 12 h of transport stress. There were significant differences in genes associated with the p53 signaling pathway (<em>igfbp1a</em>, <em>ccnb1</em>, <em>cdk1</em>, and <em>igfbp6b</em>) and apoptosis (<em>bcl2l11</em>, <em>parp3</em>, <em>pik3r1</em>, <em>fadd</em>, <em>aifm1</em>, and <em>lmnb1</em>). Combined with the increasing amount of apoptotic cells after stress, these results indicated that transport stress had a substantial effect on intestinal cell apoptosis. The intestinal antioxidant activity and tissue structure of the stressed groups recovered to the pre-stress level after 7 d of recovery from 8 h of transport; however, these parameters did not return to pre-stress levels after 7 d of recovery from 12 h of transport. This finding further demonstrated that long-term transport stress induced apoptosis and tissue damage in the largemouth bass intestine through p53 signaling.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"55 ","pages":"Article 101514"},"PeriodicalIF":2.2,"publicationDate":"2025-04-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143855768","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":"Changes in histone abundance and post-translational modifications in Rana [Lithobates] catesbeiana tissues during temperature-mediated thyroid hormone-induced metamorphosis","authors":"Haley N. Kuecks-Winger,&nbsp;Anita A. Thambirajah,&nbsp;Lorissa M. Corrie,&nbsp;Caren C. Helbing","doi":"10.1016/j.cbd.2025.101513","DOIUrl":"10.1016/j.cbd.2025.101513","url":null,"abstract":"<div><div>Amphibian metamorphosis involves thyroid hormone (TH)-dependent postembryonic remodeling of differentiated tissues as a tadpole transforms into a frog. <em>Rana [Lithobates] catesbeiana</em> (American bullfrog) metamorphosis can be precociously induced in premetamorphic tadpoles by treatment with exogenous TH. However, metamorphosis is temperature-dependent and does not occur at 5 °C, even with TH treatment. Remarkably, exposure to TH at 5 °C establishes a molecular memory that primes the tadpole for an accelerated metamorphosis when shifted to a permissive temperature (24 °C). Previous research suggests that histone post-translational modifications (PTMs) and the incorporation of histone variants are altered upon cold temperature exposure in the presence and absence of TH. Herein, we use mass spectrometry to analyze the histone composition of premetamorphic <em>R. catesbeiana</em> blood, liver, and tailfin following TH injection at a permissive temperature (24 °C), a non-permissive temperature (5 °C), and a shifted condition (5 → 24 °C). Using stringent selection criteria, we identified tissue- and temperature-specific changes in the abundance and putative PTMs of chromatin-binding proteins, including histones. Linker histone variant H1.0 abundance increased in all three tissues following TH treatment under permissive temperatures only. TH-dependent changes in the abundance of methyl-CpG binding protein 2 (MeCP2) and high mobility group (HMG) proteins were temperature- and tissue-specific. PTMs, including variations in H3K27 and H3K36 methylations in the liver, were differentially abundant following TH treatment under the different temperature conditions. We also identified newly discovered HMGB2 methylation marks that exhibited temperature-specific changes in abundance following TH treatment. These observations suggest that epigenetic variations may contribute to early TH signaling events and to molecular memory.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"55 ","pages":"Article 101513"},"PeriodicalIF":2.2,"publicationDate":"2025-04-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143855767","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":"Intestinal mucosal transcriptomic responses of Asian seabass (Lates calcarifer) vaccinated with an oral hydrogel-encapsulated multivalent Vibrio antigen following Vibrio spp. infection","authors":"Benchawan Kumwan ,&nbsp;Pakapon Meachasompop ,&nbsp;Kim D. Thompson ,&nbsp;Pattanapong Thangsunan ,&nbsp;Wararut Buncharoen ,&nbsp;Patcharapong Thangsunan ,&nbsp;Prapansak Srisapoome ,&nbsp;Anurak Uchuwittayakul","doi":"10.1016/j.cbd.2025.101512","DOIUrl":"10.1016/j.cbd.2025.101512","url":null,"abstract":"<div><div>This study examined the intestinal mucosal immune responses elicited by an oral hydrogel-encapsulated multivalent <em>Vibrio</em> vaccine in Asian seabass (<em>Lates calcarifer</em>) to protect against vibriosis caused by <em>Vibrio harveyi</em>, <em>V. vulnificus</em>, and <em>Photobacterium damselae (formerly Vibrio damsela)</em>. Both 7-day and 14-day oral vaccination regimens effectively enhanced innate and adaptive immune responses while supporting gut recovery post-infection. Transcriptomic analyses of intestines from fish that received consecutive 7- and 14-day vaccination regimens, followed by co-infection with multistrain <em>Vibrio</em> spp., revealed significant upregulation of innate and specific immune markers at week 8 post-vaccination. These responses were further bolstered by a strong adaptive immune activation, characterized by T-cell and B-cell receptor signaling as well as antibody production. In addition, the vaccine also demonstrated cross-protective immunomodulatory effects, evidenced by elevated interferon-related pathways (e.g., IFNAR2 and IFN-induced proteins), suggesting its potential to protect against co-infecting pathogens, a critical advantage in aquaculture systems facing diverse pathogen pressures. Beyond immune activation, the involvement proteins of TGF-β family members, including BMP3 and BMP4, highlights the vaccine's role in tissue repair and remodeling. These responses likely mitigate epithelial damage and preserve gut barrier integrity post-infection, showcasing the dual benefits of immunoprotection and post-infection recovery. The findings highlight the oral hydrogel-encapsulated multivalent <em>Vibrio</em> vaccine's ability to enhance immunity against specific bacterial pathogens while offering broader immunomodulatory and tissue-repair benefits. Its cross-protective and recovery-supporting properties make it a promising solution for sustainable aquaculture practices, effectively addressing pathogen control and boosting host resilience.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"55 ","pages":"Article 101512"},"PeriodicalIF":2.2,"publicationDate":"2025-04-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143843289","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":"Corrigendum to “Comparative transcriptome sequencing of two shell colour variants of Haliotis discus hannai identifying genes involved in shell formation and photosensitivity” [Comp. Biochem. Physiol. Part D: Genomics Proteomics, Volume: 55 (2025) 101461]","authors":"Mengqiang Yuan,&nbsp;Kun Liu,&nbsp;Tianshuo Liu,&nbsp;Qianqian Li,&nbsp;Wenjian Guo,&nbsp;Meiwei Zhang,&nbsp;Xiaona Wang,&nbsp;Xuekai Zhang,&nbsp;Xiaotong Wang","doi":"10.1016/j.cbd.2025.101508","DOIUrl":"10.1016/j.cbd.2025.101508","url":null,"abstract":"","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"55 ","pages":"Article 101508"},"PeriodicalIF":2.2,"publicationDate":"2025-04-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143820950","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":"Impact of exogenous glutamine on growth-related gene expression and metabolic pathways in Trachinotus blochii","authors":"Shukui Sun ,&nbsp;Lei Wang ,&nbsp;Huapeng Chen ,&nbsp;Da Zheng ,&nbsp;Xinxin Wang ,&nbsp;Haoran Yu ,&nbsp;Yesong Liang ,&nbsp;Junlong Sun ,&nbsp;Jian Luo ,&nbsp;Feibiao Song","doi":"10.1016/j.cbd.2025.101507","DOIUrl":"10.1016/j.cbd.2025.101507","url":null,"abstract":"<div><div>In recent years, the scale of <em>Trachinotus blochii</em> aquaculture has been expanding. Our previous research identified glutamine metabolism related genes as key regulators of <em>T. blochii</em> growth. Recently, fish essential amino acids have been developed as nutritional additives in aquaculture feed. To explore the effects of glutamine on growth related genes in <em>T. blochii</em>, we formulated <em>T. blochii</em> feed and conducted a feeding trial. No exogenous glutamine was added to the control group, alongside four experimental groups supplemented with 0.3 %, 0.6 %, 0.9 %, and 1.2 % exogenous glutamine, respectively. After eight weeks feeding, liver enzyme activity analysis indicated that adding 0.3 % and 0.6 % exogenous glutamine reduced MDA levels. Similarly, T-AOC and T-SOD activities were higher in the livers of <em>T. blochii</em> supplemented with 0.3 % glutamine. Liver samples were also collected for transcriptome sequencing. The results showed that the oxidative phosphorylation pathway was activated, and the fat digestion system pathway was significantly enriched following the addition of exogenous glutamine. Co-mRNA network analysis showed enrichment in a large number of genes related to the ubiquinone oxidoreductase family. However, significant differences were observed in disease related genes when glutamine was added at 0.9 % and 1.2 %. In summary, supplementing 0.3 % to 0.6 % glutamine in <em>T. blochii</em> feed can enhance amino acid metabolism and fat utilization. It can also activate pathways related to oxidative phosphorylation and fat digestion and absorption, thereby making more energy available to influence other physiological factors. These results provide an important reference for the optimization of the feed formula for <em>T. blochii</em>.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"55 ","pages":"Article 101507"},"PeriodicalIF":2.2,"publicationDate":"2025-04-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143799867","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":"Epigenetic regulation of physiological resilience to ammonia nitrogen stress in the Pacific whiteleg shrimp Penaeus vannamei: Evidence from genome-wide DNA methylation dynamics","authors":"Yiguo Lei ,&nbsp;Hanliang Lin ,&nbsp;Yunhua Chen ,&nbsp;Boquan Wan ,&nbsp;Chunmei Ao ,&nbsp;Jianyong Liu ,&nbsp;Wei Wang","doi":"10.1016/j.cbd.2025.101510","DOIUrl":"10.1016/j.cbd.2025.101510","url":null,"abstract":"<div><div>Although DNA methylation has emerged as an essential epigenetic mechanism modulating organismal responses to abiotic stresses, its involvement in the physiological resilience of marine invertebrates like shrimp to ammonia nitrogen toxicity remains enigmatic. Here, we performed the first comprehensive dissection of genome-wide DNA methylation dynamics in the Pacific whiteleg shrimp <em>Penaeus vannamei</em> exposed to ammonia nitrogen, based on whole-genome bisulfite sequencing and transcriptome analyses. In the genome of <em>P. vannamei</em>, three DNA methyltransferases (DNMT1, DNMT2 and DNMT3a), one DNA demethylase (TET2) and four methyl-CpG binding proteins (MBD2, MBD4, Kaiso, and UHRF1) were present. About 1.68–1.87 % of cytosine nucleotides were methylated, and higher percentages of cytosines in the CpG context (5.23 %–6.34 %) was methylated compared with the CHG and CHH contexts. Methylated cytosines were mostly enriched in the coding DNA sequence, and methylation peaks occurred near the transcription end sites. Following ammonia exposure, 4203 differentially expressed genes (DEGs) and 1100 differentially methylated genes (DMGs) were identified. The DMGs accounted for 4.4 % of the total gene reservoir in <em>P. vannamei</em> genome, and 212 shared genes were found between the DEGs and DMGs. Genes exhibiting significant methylation and expression changes were enriched in various pathways including the FoxO signaling pathway, autophagy and endocytosis. Among them was a group of genes related to energy metabolism, antioxidation response and detoxification metabolism, highlighting involvement of DNA methylation in fine-tuning these crucial physiological processes. These findings provide new insights into the regulatory roles of DNA methylation in the physiological resilience of marine invertebrates to aquatic stressors.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"55 ","pages":"Article 101510"},"PeriodicalIF":2.2,"publicationDate":"2025-04-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143820949","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}