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

{"title":"Integrated gut microbiota and multi-omics analysis revealed the growth differences of female giant freshwater prawn (Macrobrachium rosenbergii)","authors":"Xiuxin Zhao ,&nbsp;Peimin Liu ,&nbsp;Zhenglong Xia ,&nbsp;Miuying Cai ,&nbsp;Qiongying Tang ,&nbsp;Guoliang Yang ,&nbsp;Quanxin Gao ,&nbsp;Shaokui Yi","doi":"10.1016/j.cbd.2025.101432","DOIUrl":"10.1016/j.cbd.2025.101432","url":null,"abstract":"<div><div><em>Macrobrachium rosenbergii</em> (giant freshwater prawn; GFP) holds considerable importance in aquaculture due to its high market demand and economic significance. Female GFP growth varies significantly, however, the processes responsible for these growth disparities remain unknown. In this study, intestinal and hemolymph samples of large (FL), medium (FM), and small (FS) female GFPs were collected to investigate the molecular mechanism of female GFP growth. Through the utilization of 16S rRNA sequencing and liquid chromatography-mass spectrometry metabolomics, significant intestinal flora and metabolites linked to the growth performance of female GFPs were identified. The dominant phyla of the three groups were the same, namely Firmicutes and Proteobacteria. Among groups, small females exhibited the lowest abundance of Proteobacteria (27.26 %) and the highest abundance of Firmicutes (70.10 %). The most abundant genus in each group was <em>Lactococcus</em>. Liquid chromatography-mass spectrometry identified 115 annotated differential metabolites, and essential metabolites related to female GFP growth performance were screened. The concentration of serum metabolites in the larger females exhibited a statistically significant variance compared to that of the smaller females. Through association analysis, we identified key genes, metabolites, and gut microbiota that influence the growth of female GFPs. Likewise, we used multi-omics techniques to establish two relationship models (“gut microbiota-GFP phenotype-metabolite”, “gut microbiota-GFP phenotype-transcript”), and three important network association models (“DN5520_c0_g1-CW1-Bacteroides”, “DN537746_c0_g1-BW-<em>Roseburia</em>” and “Picolinic acid-phenotype-<em>Roseburia</em>”) were further developed. The present study provides novel insights into the mechanisms underlying the variability in individual growth among female GFPs. Our findings offer valuable information for future investigations exploring the correlation between gut flora and host organisms in aquatic environments.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"54 ","pages":"Article 101432"},"PeriodicalIF":2.2,"publicationDate":"2025-01-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143076671","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, evolution, and expression analysis of the bone morphogenetic protein gene family in Myxocyprinus asiaticus","authors":"Yizheng Zhang ,&nbsp;Meng Zhang ,&nbsp;Jinhui Yu ,&nbsp;Zhigang Ma ,&nbsp;Xin Chen ,&nbsp;Yongtao Tang ,&nbsp;Chuanjiang Zhou ,&nbsp;Qiang Li","doi":"10.1016/j.cbd.2025.101431","DOIUrl":"10.1016/j.cbd.2025.101431","url":null,"abstract":"<div><div>Bone morphogenetic proteins (BMPs) are important growth factors belonging to the TGF-β superfamily. These factors not only play a vital role in skeleton formation in young fish but also regulate the morphological development of <em>M. asiaticus</em>, with Group II genes regulating morphology mainly during the juvenile stage. This study investigated how BMP genes regulate <em>Myxocyprinus asiaticus</em> development and function and explored the role of the BMP family in fish morphological development. In this study, 43 BMPs were identified and classified into five groups: BMP1/3/11/15 (Group I), BMP12/13/14 (Group II), BMP2/4/16 (Group III), BMP9/10 (Group IV), and BMP5/6/7/8 (Group V). Analyses of the gene structures and conserved motifs revealed the conservation of the BMP gene family in <em>M. asiaticus</em>. In <em>M. asiaticus</em>, gene fragmentation, duplication, and 4R whole-genome duplication events contributed to BMP gene family expansion. Furthermore, expression pattern analysis and qRT-PCR revealed that changes in <em>M. asiaticus</em> BMP gene expression during different developmental stages were due to body size alterations, highlighting the major impact of the BMP gene on body size variation in this species. Our study provides fundamental data for investigating the morphological development of <em>M. asiaticus</em> and lays the framework for understanding the genetic mechanisms of body size variation in scleractinian fishes, with potential applications in the artificial breeding and conservation of <em>M. asiaticus</em>.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"54 ","pages":"Article 101431"},"PeriodicalIF":2.2,"publicationDate":"2025-01-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143082611","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 immune response analysis to vibrio for heme peroxidase in the blood clam Anadara granosa","authors":"Yazhuo Hu ,&nbsp;Chengtian Zhang ,&nbsp;Zongming Wu ,&nbsp;Sufang Wang ,&nbsp;Yongbo Bao","doi":"10.1016/j.cbd.2025.101430","DOIUrl":"10.1016/j.cbd.2025.101430","url":null,"abstract":"<div><div>Heme peroxidases (HPs), an essential class of oxidoreductases that may have an important role in molluscan immune defense, remain inadequately studied in mollusks. In this study, HPs in <em>Anadara granosa</em> (AgHPs) were comprehensively analyzed on a genome-wide scale and their immune responses under stress from three species of Vibrio were investigated. A total of 18 AgHPs were identified in the genome of <em>A. granosa</em>, unequally distributed in four subfamilies, peroxinectin (Pxt), prostaglandin G/H synthase (PGHS), dual oxidases (DuOx) and peroxidasin (Pxd). AgHPs were mainly expressed in gills and mantle, with AgHP6 being the only member expressed in hemocytes. The immune response of <em>A. granosa</em> to Vibrio stress demonstrated dynamic alterations in gene expression, characterized by prominent upregulation of <em>AgHP3</em> and <em>AgHP4</em> in both gills and mantle, alongside significant downregulation of several other genes; these expression changes likely underpin antimicrobial immunity in <em>A. granosa</em> and suggest distinct regulatory mechanisms and functional roles. Further analyses suggest that <em>AgHP11</em> (Pxt) may enhance cell adhesion when invaded by exogenous bacteria, and <em>AgHP3</em> (PGHS) and <em>AgHP4</em> (PGHS) contribute to the immunity by synthesizing various prostaglandins. <em>AgHP6</em> (DuOx) and <em>AgHP7</em> (DuOx) may activate epithelial immunity by reducing expression levels. Additionally, during the anti-Vibrio process, hemoglobin may substitute for ROS-producing HPs to provide antimicrobial defense in <em>A. granosa</em>. This study represents the first genome-wide identification and immune response analysis of HPs in <em>A. granosa</em>, laying a foundation for future research into the immune functions of HPs in mollusks.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"54 ","pages":"Article 101430"},"PeriodicalIF":2.2,"publicationDate":"2025-01-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143349621","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":"High-throughput screening of thermal tolerant candidate genes in the ivory shell (Babylonia areolata) based on the yeast strain INVSc1","authors":"Yanyun Zhu ,&nbsp;Deng Fu ,&nbsp;Haonan Cai ,&nbsp;Jie Qin ,&nbsp;Yingyin Wu ,&nbsp;Meng Zhang ,&nbsp;Yu Zou ,&nbsp;Hebert Ely Vasquez ,&nbsp;Xing Zheng ,&nbsp;Chunsheng Liu ,&nbsp;Aimin Wang ,&nbsp;Caihuan Ke ,&nbsp;Feng Yu ,&nbsp;Zhifeng Gu","doi":"10.1016/j.cbd.2025.101428","DOIUrl":"10.1016/j.cbd.2025.101428","url":null,"abstract":"<div><div>Global climate warming and frequent heatwaves present significant threats to the growth and survival of marine organisms. The ivory shell, <em>Babylonia areolata</em>, plays a crucial role in marine aquaculture as a widely distributed mollusk in tropical and subtropical seas. However, limited research has been conducted on its molecular mechanisms in response to heat stress. This study aims to explore thermal-tolerant related genes and regulatory pathways by constructing a cDNA library under heat stress and using a yeast-based high-throughput screening method. Following exposure of three populations to acute heat stress, a heat stress cDNA library was constructed with a capacity of 1.104 × 10⁸, containing 2.208 × 10⁸ clones. Subsequently, the library was transformed into yeast INVSc1 and underwent high-temperature screening at 39 °C. All positive clones were then subjected to next-generation sequencing (NGS) for rapid identification of 1148 candidate genes associated with thermal tolerance. Enrichment analysis revealed that these genes were significantly enriched in seven KEGG pathways, including Protein processing in endoplasmic reticulum, Ribosome and Ubiquitin mediated proteolysis. Additionally, through first-generation sequencing of 96 randomly selected positive clones at 39 °C, we identified 51 unique sequences associated with heat stress which included previously reported genes like <em>EEF2</em>, <em>HSPB1</em>, <em>UBC</em> and <em>HSPA4</em>. Subsequent yeast heat tolerance experiments further validated the essential role played by these 51 genes in response to thermal stress conditions. Finally, RNA-seq data provided evidence for upregulated expression levels of these genes during exposure to elevated temperatures. This study successfully constructed the first cDNA library for <em>B. areolata</em> under heat stress conditions, identified key pathways and candidate genes associated with thermal tolerance, and demonstrated the applicability of yeast high-throughput screening methods in investigating stress resistance traits in invertebrates. These findings contribute to a deeper understanding of the strategies employed by <em>B. areolata</em> to respond to heat stress, and provide technical support for studying the molecular mechanisms underlying abiotic stress responses in aquatic organisms.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"54 ","pages":"Article 101428"},"PeriodicalIF":2.2,"publicationDate":"2025-01-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143076666","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":"Effects of fasting and inflammatory challenges on the swine hepatic metabolome","authors":"Andrea N. Gomez ,&nbsp;Bruce R. Southey ,&nbsp;Maria B. Villamil ,&nbsp;Sandra L. Rodriguez-Zas","doi":"10.1016/j.cbd.2025.101429","DOIUrl":"10.1016/j.cbd.2025.101429","url":null,"abstract":"<div><div>The liver is simultaneously impacted by environmental challenges and modulates the response to these insults. Efforts to understand the effects of stressors on the activity of the liver typically consider one type of challenge (e.g., nutrition, toxin, disease), profile targeted molecules, or study the hepatic disruptions in one sex. The present study characterized hepatic changes in the metabolome of females and males exposed to the nutritional challenge of fasting and inflammatory signals elicited by the viral mimetic Poly(I:C). The hepatic metabolome of pigs was profiled using untargeted liquid chromatography-mass spectrometry analysis enabling the quantification of metabolites. The analysis of pathways enriched among metabolites showing sex-by-distress interactions revealed molecular processes affected by fasting and immune stresses in a sex-specific manner, including SLC-mediated transmembrane transport, the urea cycle, and G-protein coupled receptor signaling. Metabolites differentially abundant across sex-distress groups in the previous pathways included creatine, taurine, and glycine derivatives. Pathways over-represented among metabolites significantly affected by distress included glucose homeostasis, the Krebs cycle, and the metabolism of water-soluble vitamins, with key metabolites including S-adenosylmethionine, histidine, glycerophosphocholine, and lactic acid. These results indicate that 24-h fasting, and low-grade systemic inflammation modulate the liver metabolism. The detection of metabolic disruption that varies with sex enforces the need to develop therapies that can restore hepatic homeostasis in females and males.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"54 ","pages":"Article 101429"},"PeriodicalIF":2.2,"publicationDate":"2025-01-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143076513","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Transcriptome analysis reveals molecular mechanism of Dosinia corrugata in response to acute heat stress","authors":"Changsheng Gao,&nbsp;Hongtao Nie","doi":"10.1016/j.cbd.2025.101426","DOIUrl":"10.1016/j.cbd.2025.101426","url":null,"abstract":"<div><div>This study seeks to explore the molecular regulatory mechanism within <em>Dosinia corrugata</em> in response to extreme high-temperature conditions, aiming to enhance the sustainable development of the <em>D. corrugata</em> aquaculture industry. To identify heat-responsive genes and elucidate adaptive mechanisms, we conducted transcriptional profiling of <em>D. corrugata</em> gills after 12 h and 24 h of acute heat stress. At 12 h and 24 h under acute heat stress, we detected 6842 and 1112 differentially expressed genes (DEGs), respectively. KEGG (Kyoto Encyclopedia of Genes and Genomes) enrichment analysis revealed that co-enriched pathways at both time points included Apoptosis-multiple species, Ubiquitin-mediated proteolysis, Tumor Necrosis Factor (TNF) signaling pathway, and Retinoic acid-inducible Gene I (RIG-I)-like receptor signaling pathway in response to acute heat stress. It is noteworthy that at 12 h of acute heat stress, metabolic pathways were significantly enriched, while at 24 h, immune-related pathways showed significant enrichment. Based on the co-enrichment pathways identified at both time points during acute heat stress (12 h and 24 h), we constructed a potential regulatory network for differentially expressed genes under heat stress. This study offers valuable insights into comprehending the potential molecular regulatory mechanisms that underlie <em>D. corrugata</em>'s response to elevated temperatures.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"54 ","pages":"Article 101426"},"PeriodicalIF":2.2,"publicationDate":"2025-01-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143070180","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":"Proteomic analysis reveals immune-related proteins of coelomic fluid in Urechis unicinctus","authors":"Sijie Wang ,&nbsp;Yuxin Wu ,&nbsp;Baiyu Li ,&nbsp;Chenxiao Xi ,&nbsp;Xiangjun Deng ,&nbsp;Guanran Ye ,&nbsp;Xinghong Xu","doi":"10.1016/j.cbd.2025.101427","DOIUrl":"10.1016/j.cbd.2025.101427","url":null,"abstract":"<div><div><em>Urechis unicinctus</em> is a marine benthic invertebrate that relies primarily on humoral immunity within the nonspecific immune system for body defense. In order to elucidate the protein components of the coelomic fluid and investigate its immune response mechanism, proteomic analysis and antimicrobial characterization of the coelomic fluid of <em>U. unicinctus</em> were carried out. A total of 2194 proteins were identified, with 427 showing differential expression in coelomocytes compared to those in the coelomic fluid supernatant. Of these proteins, 346 were upregulated and 81 were downregulated. Next, these identified proteins were analyzed for biological information, including GO, COG, and KEGG pathway analysis. The results from the GO analysis revealed that cytoplasm and ATP-binding were the two prominent categories of proteins found in the coelomocytes as well as the coelomic fluid supernatant of <em>U. unicinctus</em>. From the COG analysis, it was evident that the categories of proteins identified in the coelomocytes were essentially the same as those identified in the coelomic fluid supernatant, with only the number of proteins differing. The KEGG pathway analysis indicated that 45 pathways from the coelomic fluid supernatant and 42 from the coelomocytes were profiled, with carbon metabolism and ribosome being the two most prominent pathways. The Pfam database displayed that the immune-related proteins in <em>U. unicinctus</em> were neurofascin, cell adhesion molecule 4, receptor-type tyrosine-protein phosphatase F, limbic system-associated membrane protein, four and a half LIM domains protein 2, neuroglian, fasciclin-2, and neural cell adhesion molecule. Furthermore, the active substances from the coelomic fluid underwent isolation, purification, and antimicrobial characterization. The process yielded two purified components (b₁ and b₂), that were found to significantly inhibit the growth of <em>Vibrio anguillarum</em>, <em>Aeromonas veronii</em>, <em>Micrococcus lysodeik</em>, and <em>Staphylococcus aureus</em>. Based on the nano LC-MS/MS and homology analysis, it was concluded the two purified proteins from b₁ and b₂ might have been histones with a molecular weight of 11,367 Da. Our study is the first to provide proteomic information on <em>U. unicinctus</em>, which can extend our understanding on the roles of functional proteins in the defense mechanism of <em>U. unicinctus</em> and contribute to the advancement of related drug development in <em>U. unicinctus</em> farming.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"54 ","pages":"Article 101427"},"PeriodicalIF":2.2,"publicationDate":"2025-01-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143141325","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 expression analysis of the SIRT gene family in Nile tilapia (Oreochromis niloticus)","authors":"Jiabao Peng ,&nbsp;Jiaqi Zou ,&nbsp;Jinliang Zhao ,&nbsp;Aqin Chen","doi":"10.1016/j.cbd.2025.101425","DOIUrl":"10.1016/j.cbd.2025.101425","url":null,"abstract":"<div><div>The sirtuin (SIRT) family is a nicotine adenine dinucleotide (NAD⁺)-dependent class III histone deacetylase, which is widely involved in numerous physiological processes of organisms, such as metabolism, reproduction, and immunity. Here, based on the genomics database, comprehensive analysis of the SIRT gene in Nile tilapia (<em>Oreochromis niloticus</em>) was analyzed using bioinformatics methods and quantitative real-time PCR. The nine <em>SIRT</em> genes of <em>O. niloticus</em> (<em>OnSIRT</em>) were distributed on eight chromosomes. The <em>OnSIRTs</em> contain distinct sequences from 3 exons in <em>OnSIRT4</em> to 16 exons in <em>OnSIRT2</em>, however, they share conserved domains and protein motifs. Phylogenetic analysis shows that the OnSIRTs belong to four subfamilies and are highly conserved in teleosts, and evolution is characterized primarily by purification selection. The <em>OnSIRT</em> genes showed diversified expression patterns in fourteen tissues of <em>O. niloticus</em>. <em>OnSIRT2</em>, <em>OnSIRT3</em>, <em>OnSIRT3.2</em>, <em>OnSIRT6</em>, and <em>OnSIRT7</em> are mainly expressed in the gonads, especially in the ovary. <em>OnSIRT1</em> and <em>OnSIRT4</em> are mainly expressed in the kidney. <em>OnSIRT5a</em> is mainly expressed in the stomach, however, <em>OnSIRT5b</em> is mainly expressed in the liver and spleen. The results of this study provide a basis information for further exploration of the function and molecular mechanism of the SIRT gene family in teleosts.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"54 ","pages":"Article 101425"},"PeriodicalIF":2.2,"publicationDate":"2025-01-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143076654","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, evolution and expression of pax gene family members in mandarin fish (Siniperca chuatsi)","authors":"Chong Han ,&nbsp;Shiyan Liu ,&nbsp;Shuzheng Ye ,&nbsp;Kaichun Chen ,&nbsp;Dingxian Chen ,&nbsp;Kaifeng Wang ,&nbsp;Weiqian Liang ,&nbsp;Simin Zhong ,&nbsp;Lanyuan Liu ,&nbsp;Sipeng Li ,&nbsp;Weijian Chen ,&nbsp;Qiang Li","doi":"10.1016/j.cbd.2025.101423","DOIUrl":"10.1016/j.cbd.2025.101423","url":null,"abstract":"<div><div>The <em>pax</em> gene family is involved in the development process through its extensive effects on cell proliferation, differentiation, and apoptosis. Herein, the whole <em>pax</em> gene family members of mandarin fish (<em>Siniperca chuatsi</em>) were first identified and characterized. By comparing <em>pax</em> gene family members from another 13 representative animals, an expansion of <em>pax</em> gene family members was observed in teleosts. In mandarin fish, a total of 15 potential <em>pax</em> gene family members, distributed on 13 chromosomes, were found, which shared conserved synteny with other teleosts. The expression profiles revealed that members of <em>pax</em> gene family showed time-specific expression profiles during embryonic and gonad development in mandarin fish, which indicated they might play a specific role in organogenesis during embryonic development and the process of gonad development and differentiation. Our research will lay a good foundation for further functional investigation of <em>pax</em> gene family during fish embryonic and gonad development.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"54 ","pages":"Article 101423"},"PeriodicalIF":2.2,"publicationDate":"2025-01-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143026064","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":"Integrative multi-omics analysis reveals liver-gut axis adaptation in high-altitude goats","authors":"Haiyan Li ,&nbsp;Xin Zhang ,&nbsp;Yangzong Zhaxi ,&nbsp;Cheng Pan ,&nbsp;Zhenzhen Zhang ,&nbsp;Junru Pan ,&nbsp;Khuram Shahzad ,&nbsp;Fengbo Sun ,&nbsp;Yang Zhen ,&nbsp;Jiacuo Jinmei ,&nbsp;Wangsheng Zhao ,&nbsp;Tianzeng Song","doi":"10.1016/j.cbd.2025.101422","DOIUrl":"10.1016/j.cbd.2025.101422","url":null,"abstract":"<div><div>The liver-gut axis is an important regulatory axis for the host's metabolic functions. The study of liver gene expression, changes in metabolic products and the regulation of gut microbial communities in plateau animals under harsh environments can reveal the mechanisms by which Tibetan goats adapt to the plateau environment. This study employs transcriptome, metabolome and metagenomic analyses to reveal the differences in genes, metabolism, and gut microbiota between Jianzhou big-eared goats (JBG) and Xizang cashmere goats (TCG), which is of significant importance for improving survival models of high-altitude ruminants. The results showed that there were 553 DEGs in the liver of JBG and TCG. Hepatic metabolomic analysis revealed significant differences in metabolic activity between the JBG and TCG groups, with notable increases in glycerophospholipid and retinol metabolic pathways. The gut microbiota, including <em>Andreesenia</em>, <em>Dielma</em>, <em>Oscillibacter</em>, <em>Agrobacterium</em>, <em>Hyella</em> and <em>Th</em>ermosinus, interact with liver metabolites and can regulate the high-altitude adaptability of goats. This study reveals that TCG enhance immune regulation and energy utilization efficiency by regulating liver gene expression, modulating metabolic pathways, and improving gut microbiota, thereby helping TCG maintain healthy survival capabilities in hypoxic and high-radiation environments.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"54 ","pages":"Article 101422"},"PeriodicalIF":2.2,"publicationDate":"2025-01-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143026069","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}