Pub Date : 2026-03-01Epub Date: 2026-01-03DOI: 10.1016/j.ygeno.2025.111192
Lijie Li, Ganqiqige Cha, Fengsheng Zhang
Lead contamination in air, water, and soil has infiltrated foods and feeds, posing severe health risks to humans and animals and remaining a tough challenge. Yeast is a safe and efficient biosorbent for lead removal. This study explored W. anomalus QF-11 lead resistance via whole-genome sequencing, finding it tolerates up to 7000 mg/L Pb2+. Under 4000 mg/L Pb2+ stress, it enhances resistance by scavenging ROS, increasing soluble protein, boosting SOD, POD and CAT activities, and elevating glutathione and trehalose levels. Its genome annotates 63 ABC transporters and antioxidant genes involved in lead adsorption, transportation and compartmentalization, with SODC, SODM, VAN1, TSL1 and others significantly upregulated. This study provides a theoretical basis for W. anomalus QF-11 application as a Pb2+ biosorbent and data support for novel heavy metal adsorbent development.
{"title":"Mechanism of lead resistance in Wickerhamomyces anomalus: Insights from whole genome sequencing","authors":"Lijie Li, Ganqiqige Cha, Fengsheng Zhang","doi":"10.1016/j.ygeno.2025.111192","DOIUrl":"10.1016/j.ygeno.2025.111192","url":null,"abstract":"<div><div>Lead contamination in air, water, and soil has infiltrated foods and feeds, posing severe health risks to humans and animals and remaining a tough challenge. Yeast is a safe and efficient biosorbent for lead removal. This study explored <em>W. anomalus QF-11</em> lead resistance via whole-genome sequencing, finding it tolerates up to 7000 mg/L Pb<sup>2+</sup>. Under 4000 mg/L Pb<sup>2+</sup> stress, it enhances resistance by scavenging ROS, increasing soluble protein, boosting SOD, POD and CAT activities, and elevating glutathione and trehalose levels. Its genome annotates 63 ABC transporters and antioxidant genes involved in lead adsorption, transportation and compartmentalization, with SODC, SODM, VAN1, TSL1 and others significantly upregulated. This study provides a theoretical basis for <em>W. anomalus QF-11</em> application as a Pb<sup>2+</sup> biosorbent and data support for novel heavy metal adsorbent development.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"118 2","pages":"Article 111192"},"PeriodicalIF":3.0,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145905906","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}
Methyl jasmonate (MeJA) regulates plant development and reproductive processes and significantly influences metabolism. Pears are important economic fruits, but there is still limited research on the changes in primary metabolites in pears after MeJA treatment, and their molecular mechanisms are not yet clear.
Results
This study employed GC–TOF–MS to analyze primary metabolite changes in the peel and flesh of ‘Nanguo’ pears after MeJA treatment. The results showed that 174 and 156 metabolites were detected in the peel and flesh respectively, from which 7 and 2 differentially altered metabolites were subsequently screened out. We analysed the combined whole-transcriptome data and constructed relevant competitive endogenous RNA (ceRNA) and miRNA–target transcription factor regulatory networks for each differentially expressed compound.
Conclusions
Our results provide an informative insight to the molecular regulatory network by which MeJA treatment changes the primary metabolism in pears, providing a theoretical basis for improving fruit quality during storage.
{"title":"GC–TOF–MS-based metabolomic and whole-transcriptomic analyses reveal the molecular mechanism of primary metabolite changes in pear fruit after methyl jasmonate treatment","authors":"Yubo Yuan , Yangyang Chen , Lisha Luo , Yuanyuan Jia , Kaijie Qi , Zhihua Xie , Hao Yin , Shaoling Zhang , Xiao Wu","doi":"10.1016/j.ygeno.2026.111195","DOIUrl":"10.1016/j.ygeno.2026.111195","url":null,"abstract":"<div><h3>Background</h3><div>Methyl jasmonate (MeJA) regulates plant development and reproductive processes and significantly influences metabolism. Pears are important economic fruits, but there is still limited research on the changes in primary metabolites in pears after MeJA treatment, and their molecular mechanisms are not yet clear.</div></div><div><h3>Results</h3><div>This study employed GC–TOF–MS to analyze primary metabolite changes in the peel and flesh of ‘Nanguo’ pears after MeJA treatment. The results showed that 174 and 156 metabolites were detected in the peel and flesh respectively, from which 7 and 2 differentially altered metabolites were subsequently screened out. We analysed the combined whole-transcriptome data and constructed relevant competitive endogenous RNA (ceRNA) and miRNA–target transcription factor regulatory networks for each differentially expressed compound.</div></div><div><h3>Conclusions</h3><div>Our results provide an informative insight to the molecular regulatory network by which MeJA treatment changes the primary metabolism in pears, providing a theoretical basis for improving fruit quality during storage.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"118 2","pages":"Article 111195"},"PeriodicalIF":3.0,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145943237","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}
Pub Date : 2026-03-01Epub Date: 2026-02-03DOI: 10.1016/j.ygeno.2026.111211
Gaëlle Lefort , Aurélien Brionne , Benoît Piégu , Frédéric Terrier , Antoine Pigeon , Linda Beauclair , Jérôme Roy , Lucie Marandel , Stéphane Panserat , Delphine Lallias , Vincent Coustham
Interindividual epigenetic variability, particularly in DNA methylation, is now recognized as a significant contributor to phenotypic diversity in mammals including humans. These epivariable regions, which make up a small fraction of the genome, are strongly influenced by genetic factors and environmental factors, especially during early development. In this context, epigenetic variability of DNA methylation has been proposed as an adaptive force involved in various environmental responses. In fish and other vertebrates, environmental factors are known to influence the health, performance and welfare, likely through the alteration of the epigenetic landscape. However, whether interindividual epigenetic variability may contribute to the phenotypic plasticity of fishes is unknown. Here we provide a first description of the rainbow trout methylome interindividual variability using a whole-genome bisulfite sequencing approach in an isogenic line to minimize genetic variation. Variable methylation regions were identified in both liver and hypothalamus tissues of 12 replicate fishes and were found enriched at gene regulatory elements, such as promoters and first introns. Gene Ontology analysis revealed functional clusters related to cellular development, neural communication, metabolic balance, and immune response. Interestingly, some variably methylated regions are found at the same genomic loci in both tissues and showed a strong intraindividual correlation in methylation levels, suggesting establishment during early embryogenesis. Overall, our work demonstrates the existence of interindividual epigenetic variability in rainbow trout and provides valuable insights into the regulatory function of DNA methylation variation that is likely involved in developmental and physiological processes.
{"title":"Characterization of interindividual DNA methylation variability in rainbow trout (Oncorhynchus mykiss)","authors":"Gaëlle Lefort , Aurélien Brionne , Benoît Piégu , Frédéric Terrier , Antoine Pigeon , Linda Beauclair , Jérôme Roy , Lucie Marandel , Stéphane Panserat , Delphine Lallias , Vincent Coustham","doi":"10.1016/j.ygeno.2026.111211","DOIUrl":"10.1016/j.ygeno.2026.111211","url":null,"abstract":"<div><div>Interindividual epigenetic variability, particularly in DNA methylation, is now recognized as a significant contributor to phenotypic diversity in mammals including humans. These epivariable regions, which make up a small fraction of the genome, are strongly influenced by genetic factors and environmental factors, especially during early development. In this context, epigenetic variability of DNA methylation has been proposed as an adaptive force involved in various environmental responses. In fish and other vertebrates, environmental factors are known to influence the health, performance and welfare, likely through the alteration of the epigenetic landscape. However, whether interindividual epigenetic variability may contribute to the phenotypic plasticity of fishes is unknown. Here we provide a first description of the rainbow trout methylome interindividual variability using a whole-genome bisulfite sequencing approach in an isogenic line to minimize genetic variation. Variable methylation regions were identified in both liver and hypothalamus tissues of 12 replicate fishes and were found enriched at gene regulatory elements, such as promoters and first introns. Gene Ontology analysis revealed functional clusters related to cellular development, neural communication, metabolic balance, and immune response. Interestingly, some variably methylated regions are found at the same genomic loci in both tissues and showed a strong intraindividual correlation in methylation levels, suggesting establishment during early embryogenesis. Overall, our work demonstrates the existence of interindividual epigenetic variability in rainbow trout and provides valuable insights into the regulatory function of DNA methylation variation that is likely involved in developmental and physiological processes.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"118 2","pages":"Article 111211"},"PeriodicalIF":3.0,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146124515","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}
Pub Date : 2026-03-01Epub Date: 2026-01-04DOI: 10.1016/j.ygeno.2026.111193
Ziqiang Yang , Suyun Chen , Siman Shen , Wanglong Liu , Kun Ding , Fangni Cao , Simeng Li , Minjuan Zeng , Jianning Chen , Li Xu , Liangqing Zhang
Background
Ischemia–reperfusion (I/R) injury in the heart triggers oxidative stress and alters post-transcriptional gene regulation. Reactive oxygen species (ROS) generated during oxidative stress induce RNA modifications such as 8-oxo-guanosine (o8G). Other modifications including 5-methylcytosine (m5C) and 7-methylguanosine (m7G) may also contribute to cardiac dysfunction. While the roles of individual RNA modifications in I/R injury are increasingly recognized, the global dynamics and crosstalk among these modifications under oxidative stress remain largely unexplored.
Methods
We performed high-throughput sequencing specific to each modification, integrated with mRNA transcriptome profiling of an IR injury mouse model. Differentially modified transcripts were subjected to GO and KEGG enrichment analyses to elucidate their functional relevance. Mechanistically, we demonstrated that RNA modification regulators with distinct functional roles can physically interact with each other, as shown by co-immunoprecipitation and immunofluorescence assays. Global changes in RNA modification levels under the model conditions were assessed using dot blot analysis. Furthermore, the regulatory effects of these enzymes on target mRNA stability were evaluated via Actinomycin D transcriptional inhibition assays.
Results
We found that the levels of all three modifications, m5C, m7G, and o8G were increased in IR by dot blot and observed a significant upregulation of three modification peaks under I/R by MeRIP-seq. Both m5C and o8G were predominantly enriched in CDS, while m7G displayed a dynamic redistribution. Our study focuses on the co-regulation crosstalk among three modifications. Functionally, singly or combinatorially modified transcripts were enriched in actin cytoskeleton regulation. Mechanistically, the transcripts of the regulators can be modified by each other and QKI can modulate the global modification level of o8G. QKI and YBX1 interact with each other to cooperatively stabilize ACTN4 mRNA, thereby maintaining cytoskeletal integrity.
Conclusion
Our results establish that QKI and YBX1 modulate the actin cytoskeleton via a coordinated network of m5C, m7G, and o8G in I/R injury.
{"title":"Co-regulatory crosstalk between m5C, m7G, and o8G RNA modifications via QKI/YBX1 axis in myocardial ischemia-reperfusion injury","authors":"Ziqiang Yang , Suyun Chen , Siman Shen , Wanglong Liu , Kun Ding , Fangni Cao , Simeng Li , Minjuan Zeng , Jianning Chen , Li Xu , Liangqing Zhang","doi":"10.1016/j.ygeno.2026.111193","DOIUrl":"10.1016/j.ygeno.2026.111193","url":null,"abstract":"<div><h3>Background</h3><div>Ischemia–reperfusion (I/R) injury in the heart triggers oxidative stress and alters post-transcriptional gene regulation. Reactive oxygen species (ROS) generated during oxidative stress induce RNA modifications such as 8-oxo-guanosine (o8G). Other modifications including 5-methylcytosine (m5C) and 7-methylguanosine (m7G) may also contribute to cardiac dysfunction. While the roles of individual RNA modifications in I/R injury are increasingly recognized, the global dynamics and crosstalk among these modifications under oxidative stress remain largely unexplored.</div></div><div><h3>Methods</h3><div>We performed high-throughput sequencing specific to each modification, integrated with mRNA transcriptome profiling of an IR injury mouse model. Differentially modified transcripts were subjected to GO and KEGG enrichment analyses to elucidate their functional relevance. Mechanistically, we demonstrated that RNA modification regulators with distinct functional roles can physically interact with each other, as shown by co-immunoprecipitation and immunofluorescence assays. Global changes in RNA modification levels under the model conditions were assessed using dot blot analysis. Furthermore, the regulatory effects of these enzymes on target mRNA stability were evaluated via Actinomycin D transcriptional inhibition assays.</div></div><div><h3>Results</h3><div>We found that the levels of all three modifications, m5C, m7G, and o8G were increased in IR by dot blot and observed a significant upregulation of three modification peaks under I/R by MeRIP-seq. Both m5C and o8G were predominantly enriched in CDS, while m7G displayed a dynamic redistribution. Our study focuses on the co-regulation crosstalk among three modifications. Functionally, singly or combinatorially modified transcripts were enriched in actin cytoskeleton regulation. Mechanistically, the transcripts of the regulators can be modified by each other and QKI can modulate the global modification level of o8G. QKI and YBX1 interact with each other to cooperatively stabilize ACTN4 mRNA, thereby maintaining cytoskeletal integrity.</div></div><div><h3>Conclusion</h3><div>Our results establish that QKI and YBX1 modulate the actin cytoskeleton via a coordinated network of m5C, m7G, and o8G in I/R injury.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"118 2","pages":"Article 111193"},"PeriodicalIF":3.0,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145911189","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}
Pub Date : 2026-03-01Epub Date: 2026-01-14DOI: 10.1016/j.ygeno.2026.111201
Huan Liu , Faxu Guo , Longyu Huang , Jian Wang , Guomin Zhou , Jianhua Zhang
Cis-regulatory elements (CREs) are key determinants of gene expression underlying complex agronomic traits. However, accurately identifying CREs in crops with large and highly repetitive genomes (such as upland cotton) remains extremely challenging. To address this, we developed Dbert2_LR, a novel hybrid deep-learning framework that integrates the pretrained genomic foundation model DNABERT-2 with parallel bidirectional RNN and LSTM networks. This architecture efficiently captures both deep contextual dependencies and local sequence patterns in DNA, enabling high-accuracy classification of promoters, enhancers, and non-regulatory sequences. Systematic evaluations on Arabidopsis thaliana and upland cotton show that Dbert2_LR outperforms multiple benchmark models, achieving macro-averaged F1 scores of 0.890 and 0.637, respectively. More importantly, in-silico saturation mutagenesis (ISM) analysis confirmed that the model's decisions strongly depend on known transcription factor binding motifs such as TATA-box, DOF, and E-box, revealing its biological interpretability and helping overcome the “black-box” nature of deep learning. To facilitate broader use, we also developed user-friendly A_cre and C_cre prediction systems. This study provides a powerful new tool for functional annotation of complex crop genomes and lays the foundation for CRE-based molecular breeding design.
{"title":"Dbert2_LR: A deep learning-based model for predicting cis-regulatory elements in crops","authors":"Huan Liu , Faxu Guo , Longyu Huang , Jian Wang , Guomin Zhou , Jianhua Zhang","doi":"10.1016/j.ygeno.2026.111201","DOIUrl":"10.1016/j.ygeno.2026.111201","url":null,"abstract":"<div><div>Cis-regulatory elements (CREs) are key determinants of gene expression underlying complex agronomic traits. However, accurately identifying CREs in crops with large and highly repetitive genomes (such as upland cotton) remains extremely challenging. To address this, we developed Dbert2_LR, a novel hybrid deep-learning framework that integrates the pretrained genomic foundation model DNABERT-2 with parallel bidirectional RNN and LSTM networks. This architecture efficiently captures both deep contextual dependencies and local sequence patterns in DNA, enabling high-accuracy classification of promoters, enhancers, and non-regulatory sequences. Systematic evaluations on Arabidopsis <em>thaliana</em> and upland cotton show that Dbert2_LR outperforms multiple benchmark models, achieving macro-averaged F1 scores of 0.890 and 0.637, respectively. More importantly, in-silico saturation mutagenesis (ISM) analysis confirmed that the model's decisions strongly depend on known transcription factor binding motifs such as TATA-box, DOF, and E-box, revealing its biological interpretability and helping overcome the “black-box” nature of deep learning. To facilitate broader use, we also developed user-friendly A_cre and C_cre prediction systems. This study provides a powerful new tool for functional annotation of complex crop genomes and lays the foundation for CRE-based molecular breeding design.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"118 2","pages":"Article 111201"},"PeriodicalIF":3.0,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145988944","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}
The health problems of the elderly, especially the elderly women, are increasingly concerned. The prevalence of abnormal liver lipid metabolism in women after menopause is increasing, which is highly related to estrogen and follicle stimulating hormone. However, hormone replacement therapy is highly controversial, and will bring risks such as breast cancer and coronary heart disease. Therefore, this study aims to build an effective and convenient in vitro disease model and perform functional verification to analyze the molecular mechanism of candidate lncRNAs participating in FSH-induced liver lipid metabolism.
Result
The results indicated the successful preliminary establishment of an in vitro model for FSH-induced lipid metabolism abnormalities. High-throughput sequencing and bioinformatics analysis revealed a total of 174 differentially expressed lncRNAs. Utilizing a comprehensive database, we screened five candidate lncRNAs and conducted interference tests specifically on the upregulated lncRNA ENSMUST00000244884. The findings demonstrated that knocking down this lncRNA led to an increase in the expression of the LXR and ACOX1 genes, which are crucial for lipid metabolism. Consequently, the lipid metabolism abnormality phenotype was alleviated.
Conclusion
Based on the experimental results, we have determined that bile-derived liver organoids are well-suited for constructing an in vitro disease model of hormone-induced lipid metabolism abnormalities, enabling effective observation of lipid phenotypes. Furthermore, we have screened and identified lncRNAs involved in hormone-regulated lipid metabolism abnormalities at the non-coding regulatory level. These findings offer potential diagnostic markers and therapeutic targets for disorders related to lipid metabolism.
{"title":"Construction of an FSH induced liver organoid model for investigating lipid metabolism abnormalities and study of the regulatory role of key lncRNAs","authors":"Xue Yu, Congcong Shen, Pingping Huang, Bingwen Li, Bailing Zhou, Lijing Wang, Shuoxuan Wang, Yurui Xu, Meng Li, Jie Qu, Guodong Hu, Jihua Wang","doi":"10.1016/j.ygeno.2026.111209","DOIUrl":"10.1016/j.ygeno.2026.111209","url":null,"abstract":"<div><h3>Background</h3><div>The health problems of the elderly, especially the elderly women, are increasingly concerned. The prevalence of abnormal liver lipid metabolism in women after menopause is increasing, which is highly related to estrogen and follicle stimulating hormone. However, hormone replacement therapy is highly controversial, and will bring risks such as breast cancer and coronary heart disease. Therefore, this study aims to build an effective and convenient in vitro disease model and perform functional verification to analyze the molecular mechanism of candidate lncRNAs participating in FSH-induced liver lipid metabolism.</div></div><div><h3>Result</h3><div>The results indicated the successful preliminary establishment of an in vitro model for FSH-induced lipid metabolism abnormalities. High-throughput sequencing and bioinformatics analysis revealed a total of 174 differentially expressed lncRNAs. Utilizing a comprehensive database, we screened five candidate lncRNAs and conducted interference tests specifically on the upregulated lncRNA ENSMUST00000244884. The findings demonstrated that knocking down this lncRNA led to an increase in the expression of the LXR and ACOX1 genes, which are crucial for lipid metabolism. Consequently, the lipid metabolism abnormality phenotype was alleviated.</div></div><div><h3>Conclusion</h3><div>Based on the experimental results, we have determined that bile-derived liver organoids are well-suited for constructing an in vitro disease model of hormone-induced lipid metabolism abnormalities, enabling effective observation of lipid phenotypes. Furthermore, we have screened and identified lncRNAs involved in hormone-regulated lipid metabolism abnormalities at the non-coding regulatory level. These findings offer potential diagnostic markers and therapeutic targets for disorders related to lipid metabolism.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"118 2","pages":"Article 111209"},"PeriodicalIF":3.0,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146074491","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}
Residual feed intake (RFI) is an important indicator of feed efficiency influenced by social interactions. However, the molecular mechanisms underlying social genetic effects on RFI (RFI-SGE) remain unclear. This study employed multi-omics analysis to investigate RFI-SGE in pigs, analyzing liver, ileum, and cecum tissues from high and low RFI-SGE groups. Transcriptomic and proteomic analyses revealed significant differences in gene and protein expressions, with liver pathways enriched in oxidative phosphorylation and ileum pathways linked to amino acid metabolism. Metabolomic analysis identified gamma-aminobutyric acid (GABA) as consistently upregulated in high RFI-SGE pigs. Integrated analysis revealed strong associations between GABA and its biosynthetic genes and upstream precursors (MAOB, DAO, ASS1, and OAT). Enhanced GABA signaling may improve social adaptability, metabolic regulation, and feed efficiency in pigs. The identification of GABA as a potential key regulator of RFI-SGE provides valuable insights for improving feed efficiency and animal welfare through targeted breeding strategies.
{"title":"Integrated multi-omics analysis reveals gamma-aminobutyric acid as a key regulator of social genetic effects on residual feed intake in pigs","authors":"Patrick Kofi Makafui Tecku , Zhenjian Zhao , Dong Chen , Shengdi Cui , Junge Wang , Shixin Yu , Ziyang Chen , Yaoxi Zhou , Runjie Huang , Wenxuan Zhou , Jia Xue , Guoqing Tang","doi":"10.1016/j.ygeno.2026.111207","DOIUrl":"10.1016/j.ygeno.2026.111207","url":null,"abstract":"<div><div>Residual feed intake (RFI) is an important indicator of feed efficiency influenced by social interactions. However, the molecular mechanisms underlying social genetic effects on RFI (RFI-SGE) remain unclear. This study employed multi-omics analysis to investigate RFI-SGE in pigs, analyzing liver, ileum, and cecum tissues from high and low RFI-SGE groups. Transcriptomic and proteomic analyses revealed significant differences in gene and protein expressions, with liver pathways enriched in oxidative phosphorylation and ileum pathways linked to amino acid metabolism. Metabolomic analysis identified gamma-aminobutyric acid (GABA) as consistently upregulated in high RFI-SGE pigs. Integrated analysis revealed strong associations between GABA and its biosynthetic genes and upstream precursors (<em>MAOB</em>, <em>DAO</em>, <em>ASS1</em>, and <em>OAT</em>). Enhanced GABA signaling may improve social adaptability, metabolic regulation, and feed efficiency in pigs. The identification of GABA as a potential key regulator of RFI-SGE provides valuable insights for improving feed efficiency and animal welfare through targeted breeding strategies.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"118 2","pages":"Article 111207"},"PeriodicalIF":3.0,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146044015","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}
Pub Date : 2026-03-01Epub Date: 2026-01-10DOI: 10.1016/j.ygeno.2026.111202
Chao Cheng , Songhe Xu , Zhiguo Liu , Hui Zhang , Yuening Yang , Yiheng Zhang , Ermeng Ge , Jiaming Xu , Qingze Zhu , Xinru Li , Bo Yu , Mengqi Liu , Yan Guo
Ustilago, a pathogenic fungus, poses a serious threat to oat growth and yield. However, the species composition, abundance, and distribution of microbial communities in Ustilago-infected oats remain poorly characterized. In this study, we conducted 16S rRNA and internal transcribed spacer (ITS) amplicon sequencing and biochemical assays to compare microbial profiles and physiological traits between healthy (n = 60) and Ustilago-infected oats (n = 60). Our analyses revealed higher bacterial diversity in healthy oats, particularly in the spikes and stems. Significant shifts in microbial community structure were observed across all tissues in diseased plants. While the microbiome of healthy oats predominantly comprised beneficial bacteria, including Exiguobacterium indicum, infected plants were largely colonized by pathogens, including Ustilago hordei, Pyrenophora chaetomioides, and Curtobacterium flaccumfaciens pv. flaccumfaciens, suggesting the occurrence of disease-driven microbial restructuring. Functional predictions indicated that enriched pathways were primarily associated with metabolism, followed by genetic information processing and environmental signal transduction. Malondialdehyde content was significantly lower in most healthy oat tissues compared to Ustilago-infected oats, whereas the activities of the antioxidant enzymes superoxide dismutase and peroxidase were markedly higher. These results implied that Ustilago infection induced severe oxidative damage to membrane systems, likely compromising the plant's ability to scavenge superoxide ions and hydrogen peroxide, thereby reducing overall plant health.
{"title":"Microbial community differences between healthy and Ustilago-infected oats","authors":"Chao Cheng , Songhe Xu , Zhiguo Liu , Hui Zhang , Yuening Yang , Yiheng Zhang , Ermeng Ge , Jiaming Xu , Qingze Zhu , Xinru Li , Bo Yu , Mengqi Liu , Yan Guo","doi":"10.1016/j.ygeno.2026.111202","DOIUrl":"10.1016/j.ygeno.2026.111202","url":null,"abstract":"<div><div><em>Ustilago</em>, a pathogenic fungus, poses a serious threat to oat growth and yield. However, the species composition, abundance, and distribution of microbial communities in <em>Ustilago</em>-infected oats remain poorly characterized. In this study, we conducted 16S rRNA and internal transcribed spacer (ITS) amplicon sequencing and biochemical assays to compare microbial profiles and physiological traits between healthy (<em>n</em> = 60) and <em>Ustilago</em>-infected oats (n = 60). Our analyses revealed higher bacterial diversity in healthy oats, particularly in the spikes and stems. Significant shifts in microbial community structure were observed across all tissues in diseased plants. While the microbiome of healthy oats predominantly comprised beneficial bacteria, including <em>Exiguobacterium indicum</em>, infected plants were largely colonized by pathogens, including <em>Ustilago hordei</em>, <em>Pyrenophora chaetomioides</em>, and <em>Curtobacterium flaccumfaciens pv</em>. <em>flaccumfaciens</em>, suggesting the occurrence of disease-driven microbial restructuring. Functional predictions indicated that enriched pathways were primarily associated with metabolism, followed by genetic information processing and environmental signal transduction. Malondialdehyde content was significantly lower in most healthy oat tissues compared to <em>Ustilago</em>-infected oats, whereas the activities of the antioxidant enzymes superoxide dismutase and peroxidase were markedly higher. These results implied that <em>Ustilago</em> infection induced severe oxidative damage to membrane systems, likely compromising the plant's ability to scavenge superoxide ions and hydrogen peroxide, thereby reducing overall plant health.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"118 2","pages":"Article 111202"},"PeriodicalIF":3.0,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145959145","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}
Pub Date : 2026-03-01Epub Date: 2026-02-09DOI: 10.1016/j.ygeno.2026.111219
Zhenzhen Gu , Weiwei Duan , Chenxi Liu , Wenrong Li , Bin Han , Mingjun Liu
Skeletal muscle development is a complex biological process orchestrated by precisely regulated gene expression networks. Understanding the molecular mechanisms during fetal myogenesis is crucial for improving meat yield and quality in livestock. In this study, we performed RNA-seq analysis on skeletal muscle tissues from Chinese Merino sheep across 11 key developmental time points, from embryonic day 26 (D26) to near birth (D135). Using weighted gene co-expression network analysis (WGCNA), we identified nine distinct gene modules significantly associated with specific developmental stages. These modules revealed stage-specific biological processes, including myogenic progenitor cell (MPC) proliferation and differentiation, primary (PM) and secondary myofiber (SM) formation, energy metabolism, and muscle maturation. Key hub genes and signaling pathways-such as Wnt, TGF-β, MAPK, and PI3K-AKT-were further validated through functional enrichment and protein-protein interaction (PPI) networks. Notably, we identified critical developmental transition points at D29 (MPC differentiation initiation), D45 (embryonic-to-fetal transition), and D85 (myofiber maturation shift). Moreover, several novel hub genes, including CORIN, SMOC1/2, and ADAMTS family members, were identified. In summary, by identifying nine stage-specific co-expression modules, pinpointing three pivotal developmental transitions (D29, D45, D85), and uncovering novel hub genes of potential regulatory importance, this study provides a systems-level framework for understanding ovine fetal myogenesis and offers candidate targets for livestock genetic improvement.
{"title":"A spatiotemporal atlas of gene expression in ovine fetal muscle reveals critical transitions and modular networks driving myogenesis","authors":"Zhenzhen Gu , Weiwei Duan , Chenxi Liu , Wenrong Li , Bin Han , Mingjun Liu","doi":"10.1016/j.ygeno.2026.111219","DOIUrl":"10.1016/j.ygeno.2026.111219","url":null,"abstract":"<div><div>Skeletal muscle development is a complex biological process orchestrated by precisely regulated gene expression networks. Understanding the molecular mechanisms during fetal myogenesis is crucial for improving meat yield and quality in livestock. In this study, we performed RNA-seq analysis on skeletal muscle tissues from Chinese Merino sheep across 11 key developmental time points, from embryonic day 26 (D26) to near birth (D135). Using weighted gene co-expression network analysis (WGCNA), we identified nine distinct gene modules significantly associated with specific developmental stages. These modules revealed stage-specific biological processes, including myogenic progenitor cell (MPC) proliferation and differentiation, primary (PM) and secondary myofiber (SM) formation, energy metabolism, and muscle maturation. Key hub genes and signaling pathways-such as Wnt, TGF-β, MAPK, and PI3K-AKT-were further validated through functional enrichment and protein-protein interaction (PPI) networks. Notably, we identified critical developmental transition points at D29 (MPC differentiation initiation), D45 (embryonic-to-fetal transition), and D85 (myofiber maturation shift). Moreover, several novel hub genes, including CORIN, SMOC1/2, and ADAMTS family members, were identified. In summary, by identifying nine stage-specific co-expression modules, pinpointing three pivotal developmental transitions (D29, D45, D85), and uncovering novel hub genes of potential regulatory importance, this study provides a systems-level framework for understanding ovine fetal myogenesis and offers candidate targets for livestock genetic improvement.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"118 2","pages":"Article 111219"},"PeriodicalIF":3.0,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146165048","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}
Pub Date : 2026-03-01Epub Date: 2026-02-18DOI: 10.1016/j.ygeno.2026.111214
Hui Shen , Wen Liu , Lilian Zhao , Yanfang Guo , Yuanheng Li , Ting Wu , Shu Han
Garlic (Allium sativum) is an important crop with significant value in both agriculture and medicine, yet its mitochondrial genome remains uncharacterized. This gap has limited the understanding of organellar evolution and genomic diversity. The mitogenome was assembled with Illumina and PacBio revealed a complex, multipartite architecture spanning 548,160 bp with six contigs, a size that is within the common range for angiosperm mitochondrial genomes. The structure demonstrated considerable plasticity, and was characterized by abundant repetitive sequences. Annotation identified 25 protein-coding genes, 14 tRNAs, and three rRNAs, representing a conserved gene set. Extensive chloroplast-to-mitochondrion DNA transfer was observed, with 38 homologous fragments totaling 33.6 kb that included functionally intact genes. Codon usage analysis revealed a pronounced A/U-ending preference in synonymous codons. Additionally, 494C-to-U RNA editing sites were predicted, indicating significant concentrations in NADH dehydrogenase genes. Phylogenetic analysis based on 23 conserved mitochondrial genes robustly resolved A. sativum as sister to Allium fistulosum. This study presents the first complete mitochondrial genome of A. sativum, which reveals substantial structural complexity and dynamic evolution. This genome provides a foundational resource for further investigation into organellar genome evolution within the Allium genus.
{"title":"The complex and dynamic mitochondrial genome of garlic (Allium sativum): Insights from structural and evolutionary analysis","authors":"Hui Shen , Wen Liu , Lilian Zhao , Yanfang Guo , Yuanheng Li , Ting Wu , Shu Han","doi":"10.1016/j.ygeno.2026.111214","DOIUrl":"10.1016/j.ygeno.2026.111214","url":null,"abstract":"<div><div>Garlic (<em>Allium sativum</em>) is an important crop with significant value in both agriculture and medicine, yet its mitochondrial genome remains uncharacterized. This gap has limited the understanding of organellar evolution and genomic diversity. The mitogenome was assembled with Illumina and PacBio revealed a complex, multipartite architecture spanning 548,160 bp with six contigs, a size that is within the common range for angiosperm mitochondrial genomes. The structure demonstrated considerable plasticity, and was characterized by abundant repetitive sequences. Annotation identified 25 protein-coding genes, 14 tRNAs, and three rRNAs, representing a conserved gene set. Extensive chloroplast-to-mitochondrion DNA transfer was observed, with 38 homologous fragments totaling 33.6 kb that included functionally intact genes. Codon usage analysis revealed a pronounced A/U-ending preference in synonymous codons. Additionally, 494C-to-U RNA editing sites were predicted, indicating significant concentrations in NADH dehydrogenase genes. Phylogenetic analysis based on 23 conserved mitochondrial genes robustly resolved <em>A. sativum</em> as sister to <em>Allium fistulosum</em>. This study presents the first complete mitochondrial genome of <em>A. sativum</em>, which reveals substantial structural complexity and dynamic evolution. This genome provides a foundational resource for further investigation into organellar genome evolution within the <em>Allium</em> genus.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"118 2","pages":"Article 111214"},"PeriodicalIF":3.0,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146257858","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}
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