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

{"title":"Genomic runs of homozygosity and structural variation reveal muscle development-related genes in Qinghai-Tibetan Plateau yaks","authors":"Jianghao Chang ,&nbsp;Rong Huang ,&nbsp;Wei Peng ,&nbsp;Yibing Yue ,&nbsp;Huawei Su ,&nbsp;Yang He ,&nbsp;Weiru Song ,&nbsp;Chuzhao Lei ,&nbsp;Rende Song ,&nbsp;Jun Zhang ,&nbsp;Yongzhen Huang","doi":"10.1016/j.cbd.2025.101664","DOIUrl":"10.1016/j.cbd.2025.101664","url":null,"abstract":"<div><div>This study investigated genomic structural variations and their association with muscle development in Qinghai-Tibetan Plateau yaks to elucidate their genetic diversity and adaptive mechanisms. Whole-genome resequencing was performed on 145 Qinghai-Tibetan Plateau yaks, supplemented with sequence data from 12 wild yaks obtained from the National Center for Biotechnology Information (NCBI) database. Analyses characterized runs of homozygosity (ROH), copy number variations (CNV), and structural variations (SV). A genome-wide copy number variation map for Qinghai Plateau yaks was constructed. Qinghai-Tibetan Plateau yaks exhibited numerous ROHs (totaling 61,074 segments, covering 19,947.56 Mb), showing relatively high levels of genomic homozygosity compared to wild yaks (3255 segments, 1056.66 total length), and 1175 CNV regions and 59,694 SVs, primarily located in non-coding regions, were identified. Publicly available transcriptome data were integrated to identify candidate genes related to muscle development, followed by statistical validation of key candidates. Integrating genomic and transcriptomic data revealed 84 overlapping genes potentially involved in muscle development. Subsequent bioinformatic prioritization identified PTPN6, ATP2A1, LCP1, GNA15, ALOX5AP, FLT3, SLC34A3, and BCL11A as high-priority candidate genes potentially influencing this trait. These findings demonstrate that genomic variations significantly impact muscle development in Qinghai-Tibetan Plateau yaks, providing a valuable molecular basis for future yak breeding programs and adaptation research.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"57 ","pages":"Article 101664"},"PeriodicalIF":2.2,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145411055","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 and exploration of immune key genes of hepatopancreas after Poly(I:C) stimulation in Amphioctopus fangsiao","authors":"Xiaolan Huang ,&nbsp;Jingjing Gu ,&nbsp;Zhen Huang ,&nbsp;Xuebo Cui ,&nbsp;Daowen Qiu ,&nbsp;Zan Li ,&nbsp;Yanwei Feng ,&nbsp;Xiaohui Xu ,&nbsp;Jianmin Yang","doi":"10.1016/j.cbd.2025.101665","DOIUrl":"10.1016/j.cbd.2025.101665","url":null,"abstract":"<div><div><em>Amphioctopus fangsiao</em> is a commercially valuable cephalopod species prized for its distinctive flavor and nutritional profile. However, its large-scale aquaculture is hampered by significant challenges, particularly outbreaks of infectious diseases. Viral pathogens, which can be co-transmitted among marine species, pose a severe threat to sustainable population development. To elucidate the antiviral defense mechanisms in <em>A</em>. <em>fangsiao</em>, we conducted transcriptomic profiling of hepatopancreatic tissue following stimulation with polyinosinic-polycytidylic acid (Poly(I:C)), a well-established viral mimic known to activate innate immune pathways. Comparative transcriptomic profiling of the hepatopancreas—a key immune organ—at 6 h and 24 h post-stimulation identified 1406 and 904 differentially expressed genes (DEGs), respectively. Functional enrichment analysis revealed that these DEGs were significantly involved in critical immune-related pathways, including apoptosis, ECM-receptor interaction, and the MAPK and Hippo signaling pathways. Furthermore, by integrating protein-protein interaction (PPI) network analysis with KEGG pathway data, we identified 18 hub genes—such as <em>TNFSF10, JUN, EGFR</em>, and <em>CTSB</em>—that were potential key regulators of the antiviral response. The expression patterns of the aforementioned hub genes were successfully validated by means of quantitative reverse transcription polymerase chain reaction (qRT-PCR). This study comprehensively revealed the transcriptome characteristics of antiviral immune response of <em>A. fangsiao</em> for the first time. Our findings not only advance the understanding of innate immunity in cephalopods but also offer valuable genetic resources and potential molecular targets for developing strategies against viral diseases in octopus aquaculture.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"57 ","pages":"Article 101665"},"PeriodicalIF":2.2,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145411095","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":"The metabolome of humpback whales (Megaptera novaeangliae) reveals clues as to their extreme fasting capabilities","authors":"Erika Oteri ,&nbsp;Ido Bar ,&nbsp;Steven D. Melvin ,&nbsp;Eleanor Raffan ,&nbsp;Susan Bengtson Nash","doi":"10.1016/j.cbd.2025.101670","DOIUrl":"10.1016/j.cbd.2025.101670","url":null,"abstract":"<div><div>Southern Hemisphere humpback whales are capital breeders, relying on energy reserves accumulated through summer feeding in the Southern Ocean to fuel reproduction and migration. Understanding the fasting physiology of these populations, which lose up to 50 % of their post-summer feeding body mass during seasonal migration, is of great importance, particularly in the context of a rapidly changing Antarctic sea-ice ecosystem. Additionally, fluctuations in lipid reserves are known to mobilise lipophilic contaminants, potentially rendering seasonal fasting a time of elevated toxicological risk. This study analysed blubber biopsies from humpback whales migrating along the east coast of Australia. Biopsies were collected at two timepoints on the migration, corresponding to ∼3 and 6 months fasted, respectively. Nuclear Magnetic Resonance spectroscopy identified 32 polar metabolites in blubber, mainly involved in fatty acid and amino acid metabolism. Eleven of these metabolites showed significant differences between the two fasting stages, indicating changes in fatty acid oxidation, body condition, protein catabolism and glucose conservation. This is the first study to investigate the polar metabolomic alterations associated with migration in humpback whales, providing insights into biochemical pathways related to their fasting physiology. Metabolomic analysis holds the potential to identify metabolite patterns linked to nutritional and environmental stress, critical for ongoing biomonitoring of the Antarctic ecosystem.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"57 ","pages":"Article 101670"},"PeriodicalIF":2.2,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145475380","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":"Transcriptomic analysis of the hepatopancreas response to low-pH stress in kuruma shrimp (Marsupenaeus japonicus)","authors":"Yongkang Hou ,&nbsp;Caifeng Liang ,&nbsp;Dekhkonova Dilorakhon Rasuljon Kizi ,&nbsp;Jianyong Liu","doi":"10.1016/j.cbd.2025.101667","DOIUrl":"10.1016/j.cbd.2025.101667","url":null,"abstract":"<div><div>Ocean acidification has emerged as a globally recognized environmental issue, posing a serious threat to marine ecosystems. To elucidate the adaptive mechanisms of <em>Marsupenaeus japonicus</em> under acidified conditions, both biochemical and transcriptomic analyses were performed following low-pH exposure. Biochemical assays revealed that low pH stress significantly SOD and CAT activities while markedly elevating MDA levels, indicating oxidative damage. T-AOC exhibited a transient rise followed by a sharp decline at later stages, suggesting initial activation and subsequent exhaustion of antioxidant defense. Transcriptomic profiling identified 2705 DEGs that were primarily enriched in pathways related to immune regulation, redox balance, apoptosis, and energy metabolism, including the lysosome, Toll-like receptor, and PPAR signaling pathways. Protein interaction analysis identified 9 hub genes, including <em>NADH-GOGAT</em> and <em>MDHM</em>, which may play key roles in antioxidant defense and metabolic regulation. The integration of enzyme activity and transcriptomic data indicates that acid stress initially induces oxidative imbalance, followed by compensatory activation of antioxidant and immune systems to restore cellular homeostasis. These findings provide comprehensive insights into the oxidative stress adaptation of <em>M. japonicus</em> and offer a genetic and physiological foundation for breeding acid-tolerant shrimp strains.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"57 ","pages":"Article 101667"},"PeriodicalIF":2.2,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145475454","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 analysis of FOX genes in fish: Evolution, structure, and functional roles in environmental stress tolerance and growth regulation in Mugil cephalus","authors":"Urwah Ishaque ,&nbsp;Saima Naz ,&nbsp;Jhan Zeb ,&nbsp;Ahmad Manan Mustafa Chatha ,&nbsp;Ghazi Alatawi ,&nbsp;Saba Iqbal ,&nbsp;Bushra Irfan","doi":"10.1016/j.cbd.2025.101685","DOIUrl":"10.1016/j.cbd.2025.101685","url":null,"abstract":"<div><div>The forkhead box (FOX) gene family encodes transcription factors that control growth, development, stress response, and metabolism across vertebrates. While FOX genes have been widely explored in a few model fish species, their roles in <em>Mugil cephalus</em>, a commercially and ecologically important euryhaline species, are still not well described. Current study, explored the first ever genomic and structural analysis of FOX genes in <em>M. cephalus</em>. In this study, 42 FOX genes were identified in the genome of <em>M. cephalus</em> and the presence of conserved forkhead domains was confirmed. The study showed that there are significant differences in the physicochemical traits of studied proteins and the phylogenetic analysis grouped these proteins into 18 clades. Duplication history pointed toward a number of genome-wide duplication events, with all of them shaped mainly by purifying selection. The synteny analysis suggested that chromosomal arrangements were mostly conserved with humans, indicating a deep evolutionary link. The organization of Motif and domains pointed toward functional diversification, while structure modeling (2D and 3D) revealed noticeable variation in folding patterns of amino acids. Moreover, mutation predictions reported various destabilizing substitutions that could weaken the stability of proteins. In conclusion, this study gives the first integrated overview of FOX genes in <em>M. cephalus</em>, opening new perspectives on their evolution and possible functions in vertebrate species. Experimental studies are aimed in future to confirm the role of FOX genes for improved aquaculture practices, stress tolerance, and bio-conservation of <em>M. cephalus</em>.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"57 ","pages":"Article 101685"},"PeriodicalIF":2.2,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145524761","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":"Identification and expression analysis of long noncoding RNAs in response to infection with VHSV in rainbow trout","authors":"Mahmood Tavakoli-Alamouti ,&nbsp;Ghodrat Rahimi-Mianji ,&nbsp;Ardeshir Nejati-Javaremi ,&nbsp;Ayoub Farhadi ,&nbsp;Elham Younesi-Melerdi","doi":"10.1016/j.cbd.2025.101673","DOIUrl":"10.1016/j.cbd.2025.101673","url":null,"abstract":"<div><div>Viral infections in the aquaculture industry present a significant challenge that requires further investigation. Emerging evidence suggests that long noncoding RNAs (lncRNAs) play a crucial role in regulating various biological processes, including immune responses. However, most studies have focused on model organisms, leaving a gap in knowledge about non-coding RNAs in response to viral hemorrhagic septicemia (VHS) in rainbow trout. In this study, we investigated the profile of non-coding RNAs (ncRNAs) and their targeting-related subjects in the spleen of rainbow trout challenged with the VHS virus. We explored their potential roles in immune defense responses through transcriptomic analysis of both virus-treated and control groups. Our analysis identified 4207 lncRNAs from 7753 transcripts, with many categorized as potentially novel isoforms (code = j) and intergenic lncRNAs (code = u). The expression analysis demonstrated the impact of viral infection on the expression levels of lncRNAs and their target genes. The results showed 182 lncRNAs and 1326 mRNAs with differential expression. We identified pairs of DElncRNA-DEmRNA interactions, such as “TP63-MSTRG.62, IL10-MSTRG.9783, IL10-MSTRG.9784, TK1-MSTRG.22826, and GLI1-MSTRG.17881” as cis interactions, while DOCK10-MSTRG.30015, MSTRG.36357-LOC101268921, and MSTRG.34190-ENPP2 exhibited trans interactions. Additionally, key signaling pathways, including the PPAR signaling pathway, Toll-like receptor signaling pathway, and p53 pathway, were revealed as critical responders to viral infection linked to lncRNAs. We also introduced quantitative trait loci (QTLs) associated with these lncRNAs, underscoring their potential regulatory roles in viral stress responses. Overall, our findings provide novel insights into the molecular mechanisms underlying viral infections and lncRNA-mediated host immune responses.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"57 ","pages":"Article 101673"},"PeriodicalIF":2.2,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145552353","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":"Transcriptomic analysis reveals stage-specific cholesterol metabolism and steroidogenic in theca layer cells during follicular development in chickens","authors":"Yuechen Liao ,&nbsp;Ashi Li ,&nbsp;Yangqiwen Luo ,&nbsp;Runbang Zhu ,&nbsp;Cangning Zhang ,&nbsp;Meng Ma ,&nbsp;Yongfeng Li ,&nbsp;Liumei Sun ,&nbsp;Manman Shen ,&nbsp;Liang Qu","doi":"10.1016/j.cbd.2025.101682","DOIUrl":"10.1016/j.cbd.2025.101682","url":null,"abstract":"<div><div>Ovarian follicle development is a critical factor affecting laying performance in poultry. Follicles are mainly composed of the granulosa layer cells and theca layer cells (TLs). However, the regulatory role of TLs remains inadequately understood. This study explored the abundance of differentially expressed genes (DEGs) in chicken TLs across small yellow follicles (SYFT), the smallest hierarchical follicle (F6T), and the largest hierarchical follicle (F1T) through transcriptome analysis. Results revealed that the top abundance DEGs were linked to cholesterol metabolism (<em>MSMO1, NPC</em>1) and steroid hormone synthesis (<em>STAR, CYP11A1, CYP19A1, POR, NR0B1</em>). Notably, genes involved in steroid hormone synthesis (<em>STAR, CYP11A1</em>, and <em>CYP19A1</em>) were highly expressed at the F6T stage. Up-regulated DEGs in F6T were primarily enriched in metabolism pathways, including one carbon pool by folate and citrate cycle, which contribute to elevated cholesterol synthesis (<em>MSMO1</em>) at this stage. While cholesterol metabolism (<em>NPC1, NR0B1</em>, and <em>POR</em>) were prominent at the SYFT stage, where up-regulated DEGs were linked to cell differentiation such as Wnt and mTOR signaling pathways. Key genes including <em>CYP19A1, CYP17A1, POR, NPC1, VLDLR,</em> and <em>NR0B1</em> were predominantly found in profiles 3 and 1, which represented significant trends identified through trend analysis. The main KEGG pathways included cell cycle, homologous recombination, metabolism and transport. This study highlights that TLs shift their transcriptional program from cholesterol transport in small yellow follicles to cholesterol synthesis and steroidogenesis in hierarchical follicles, revealing a key transcriptional program governing follicle development in chickens.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"57 ","pages":"Article 101682"},"PeriodicalIF":2.2,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145497867","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 analysis of transcriptomics and gut microbiome in grass carp under alkalinity stress","authors":"Jianlin Guo ,&nbsp;Yi Xu ,&nbsp;Qi Chen ,&nbsp;Haiqi Zhang","doi":"10.1016/j.cbd.2025.101698","DOIUrl":"10.1016/j.cbd.2025.101698","url":null,"abstract":"<div><div>Alkalinity, a key environmental stressor in saline-alkali ecosystems, adversely affects the growth and survival of aquatic organisms. Genetic improvement of alkali-tolerant fish strains offers a promising strategy for utilizing saline-alkaline water resources; however, the molecular mechanisms underlying the response to alkalinity stress remain inadequately understood. This study aimed to identify novel molecular signatures of alkaline exposure in grass carp by integrating gut microbiome profiling with host transcriptome data. Histological analysis revealed significant alterations in the height of intestinal folds, muscle layer thickness, and fold width in response to NaHCO₃ exposure, along with an increased number of goblet cells under alkalinity stress. Differential gene expression (DEGs) analysis identified 1620, 6564, and 3190 genes with significant expression changes at 24, 48, and 72 h of NaHCO₃ treatment, respectively, compared to controls. Several known alkalinity-responsive genes, such as aquaporin 1a (<em>aqp1a</em>), carbonic anhydrase 6 (<em>ca6</em>), heat shock protein 30 (<em>hsp30</em>), prostaglandin-endoperoxide synthase 2b (<em>ptgs2b</em>), caspase 23 (<em>casp23</em>), solute carrier family 7a (<em>slc7a</em>), toll-like receptor 5 (<em>tlr5</em>), and toll-like receptor 13 (<em>tlr13</em>), were identified and validated through real-time quantitative PCR. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses revealed that immune- and disease-related signaling pathways played critical roles in mitigating acute alkaline stress. Furthermore, a total of 1,521,323 quality-filtered sequences with an average of 416 bp in length were generated through 16S rRNA sequencing. Bioinformatics analysis indicated that NaHCO₃ exposure reduced microbial diversity and altered the gut microbiota composition in grass carp. Notably, Fusobacteriota abundance significantly increased, while Firmicutes and Proteobacteria decreased substantially at 48 h post-alkalinity stress. Integrative analysis further highlighted strong correlations between specific bacterial taxa and alkalinity-responsive differentially expressed genes (DEGs). These findings provided valuable insights into the molecular mechanisms underlying alkalinity stress and identified potential targets for molecular breeding to enhance alkaline tolerance in grass carp.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"57 ","pages":"Article 101698"},"PeriodicalIF":2.2,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145662899","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":"Hydrolyzed Debaryomyces hansenii yeasts as paraprobiotics in fish: Omics-based characterization of Atlantic salmon gut during a natural pathogen outbreak in seawater stage","authors":"Byron Morales-Lange ,&nbsp;Sérgio D.C. Rocha ,&nbsp;Arturo Vera-Ponce de León ,&nbsp;Matthias Hötzinger ,&nbsp;Liv Torunn Mydland ,&nbsp;Brankica Djordjevic ,&nbsp;Phillip B. Pope ,&nbsp;Margareth Øverland","doi":"10.1016/j.cbd.2025.101671","DOIUrl":"10.1016/j.cbd.2025.101671","url":null,"abstract":"<div><div>Feed additives are an alternative to improve fish performance and health (without compromising growth) during farming conditions. To determine the physiological effects of two hydrolyzed <em>Debaryomyces hansenii</em> yeasts (LAN4 and LAN6 from Lallemand SAS) on the gut of post-smolts Atlantic salmon (<em>Salmo salar</em>), an <em>in vivo</em> experiment was conducted (7 weeks in freshwater and 6 weeks in seawater) using 0.1 % LAN4 or LAN6 in diets for vaccinated fish. Coincidentally, a natural outbreak of <em>Moritella viscosa</em> (a bacterial fish pathogen) was reported at week 5 in seawater. Thus, the current study focus incorporated the disease-inflicted modulation of intestinal proteome and microbiota composition, which was estimated through metaproteomics and 16S rRNA sequencing, respectively. Results showed a detection of 1170 amplicon sequence variants (ASVs) belonging to 52 genera (modulated among dietary groups). Moreover, a positive correlation between LAN4 and control group (Ctr) was detected based on ASVs analysis. Regarding metaproteomics data and enrichment analysis (using KEGG or GO databases), LAN4 group showed a higher abundance of proteins linked to 48 functional terms such as amino acid biosynthesis and metabolism, immune homeostasis and cellular response to oxidative stress. On contrary, the proteins detected in LAN6 were linked with 14 terms (e.g., ferroptosis, arachidonic acid metabolism and regulation of cell projection assembly) that can be related to the inflammatory process. These results suggest the potential of <em>D. hansenii</em> yeasts as a paraprobiotics for the intestinal proteome and microbiota structure of Atlantic salmon. Therefore, <em>D. hansenii</em> is a promising feed additive for aquaculture-related species during the production cycle.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"57 ","pages":"Article 101671"},"PeriodicalIF":2.2,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145460906","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, characterization, molecular evolution and expression profiling analysis of COMMD gene family in black rockfish (Sebastes schlegelii)","authors":"Xuechen Li ,&nbsp;Zhentao Chen ,&nbsp;Jingrun Pu,&nbsp;Xuangang Wang,&nbsp;Ze Tao,&nbsp;Zhixiang Duan,&nbsp;Gan Yu,&nbsp;Ping Han,&nbsp;Fan Zhang,&nbsp;Haiyang Yu","doi":"10.1016/j.cbd.2025.101694","DOIUrl":"10.1016/j.cbd.2025.101694","url":null,"abstract":"<div><div>The Copper Metabolism gene MURR1 Domain (<em>COMMD</em>) gene family is recognized as a highly conserved gene family in diverse species and involved in various important biological processes, including copper metabolism, NF-κB signaling and membrane transport. However, current research regarding the systematic identification of the <em>COMMD</em> gene family in teleosts and its role in the innate immunity of <em>Sebastes schlegelii</em> (<em>S. schlegelii</em>) remains limited. In this study, we identified and annotated 9 <em>COMMD</em> genes in <em>S. schlegelii</em>. Through phylogenetic analysis, analysis of gene structure, motif compositions, and molecular evolutionary patterns of the <em>COMMD</em> gene family, we found that <em>COMMD</em> gene maintains a highly conserved state in evolutionary process, and bears similar importance in metabolism of different species. Moreover, we analyzed the expression patterns of <em>COMMD</em> genes in macrophage and immune-relevant tissues of healthy <em>S. schlegelii</em> and those infected with <em>Acinetobacter johnsonii</em> by using qRT-PCR. The results revealed distinct tissue-specific expression profiles for <em>COMMD</em> genes, and their expression was significantly altered after <em>A. johnsonii</em> infection. We confirmed that <em>SsCOMMD1</em> could up-regulate the activity of NF-κB pathway. This study elaborates <em>COMMD</em> genes of <em>S. schlegelii</em>, providing a valuable reference for future research on understanding of the functions of <em>COMMD</em> gene family in the innate immune response of teleosts.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"57 ","pages":"Article 101694"},"PeriodicalIF":2.2,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145566639","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}