Pub Date : 2025-11-26DOI: 10.1016/j.ygeno.2025.111160
Endashaw Jebessa , Yanhua He , Hao Qu , Lin Chuxiao , Zhifeng Zhao , Haile Berihulay , Peng Chen , Xian Zou , Jian Ji , Dingming Shu , Chenglong Luo
Despite the integrative function of miRNAs and genes in chicken embryonic gonadal sex differentiation, their roles remain poorly understood. Here, we used RNA-seq to analyze 12 gonadal samples from embryonic days 5 (E5) and 9 (E9). Our analysis of miRNA and mRNA expression during this key developmental stage revealed five DEmiRNAs and 235 DEmRNAs consistently associated with left-right asymmetry in female gonads in both F5L vs F5R and F9L vs F9R comparisons. The interaction between DEmiRNAs and target DEmRNAs in the left-right asymmetry of embryonic gonadal development at E5 and E9 in chickens, along with the KEGG pathway enrichment analysis, revealed the involvement of several significant pathways. These include the complement and coagulation cascades, tight junctions, and synthesis and secretion of aldosterone. Differentially expressed miRNAs and target genes at embryonic days 5 and 9 reveal key molecular mechanisms driving gonadal sex differentiation in chickens.
{"title":"Transcriptome profile analysis of miRNA and mRNA in chicken embryo gonad sex differentiation","authors":"Endashaw Jebessa , Yanhua He , Hao Qu , Lin Chuxiao , Zhifeng Zhao , Haile Berihulay , Peng Chen , Xian Zou , Jian Ji , Dingming Shu , Chenglong Luo","doi":"10.1016/j.ygeno.2025.111160","DOIUrl":"10.1016/j.ygeno.2025.111160","url":null,"abstract":"<div><div>Despite the integrative function of miRNAs and genes in chicken embryonic gonadal sex differentiation, their roles remain poorly understood. Here, we used RNA-seq to analyze 12 gonadal samples from embryonic days 5 (E5) and 9 (E9). Our analysis of miRNA and mRNA expression during this key developmental stage revealed five DEmiRNAs and 235 DEmRNAs consistently associated with left-right asymmetry in female gonads in both F5L vs F5R and F9L vs F9R comparisons. The interaction between DEmiRNAs and target DEmRNAs in the left-right asymmetry of embryonic gonadal development at E5 and E9 in chickens, along with the KEGG pathway enrichment analysis, revealed the involvement of several significant pathways. These include the complement and coagulation cascades, tight junctions, and synthesis and secretion of aldosterone. Differentially expressed miRNAs and target genes at embryonic days 5 and 9 reveal key molecular mechanisms driving gonadal sex differentiation in chickens.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"118 1","pages":"Article 111160"},"PeriodicalIF":3.0,"publicationDate":"2025-11-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145631388","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 : 2025-11-25DOI: 10.1016/j.ygeno.2025.111158
Fanny Mollandin , Hervé Acloque , Maria Ballester , Marco Bink , Mario Calus , Daniel Crespo-Piazuelo , Pascal Croiseau , Sarah Djebali , Sylvain Foissac , Hélène Gilbert , Elisabetta Giuffra , Cervin Guyomar , Ole Madsen , Marie-José Mercat , Bruno da Costa Perez , Jani de Vos , Andrea Rau
Gene expression is a dynamic phenotype influenced by tissue-specific regulatory mechanisms, which can modulate expression directly or indirectly through cis or trans factors. Identifying genetic variants in these regulatory regions can improve both expression quantitative trait locus (eQTL) mapping and gene expression prediction. Whole genome sequences offer the possibility for enhanced eQTL mapping accuracy, but detecting causal variants remains challenging. Here, we evaluate the potential added-value of integrating tissue-specific epigenetic annotations, such as chromatin accessibility and methylation status, into within-breed genomic predictions of expression for three pig breeds. Functional annotations from early developmental stages improved eQTL mapping interpretability as shown by the enrichment of trait-relevant QTLs. However, despite the use of functional annotations, predictions across breeds remain challenging due to differences in genetic architectures. Our work contributes to the understanding of gene expression regulation in livestock and highlights the value of functional annotations, despite continued challenges for predictions across breeds.
{"title":"Guiding eQTL mapping and genomic prediction of gene expression in three pig breeds with tissue-specific epigenetic annotations from early development","authors":"Fanny Mollandin , Hervé Acloque , Maria Ballester , Marco Bink , Mario Calus , Daniel Crespo-Piazuelo , Pascal Croiseau , Sarah Djebali , Sylvain Foissac , Hélène Gilbert , Elisabetta Giuffra , Cervin Guyomar , Ole Madsen , Marie-José Mercat , Bruno da Costa Perez , Jani de Vos , Andrea Rau","doi":"10.1016/j.ygeno.2025.111158","DOIUrl":"10.1016/j.ygeno.2025.111158","url":null,"abstract":"<div><div>Gene expression is a dynamic phenotype influenced by tissue-specific regulatory mechanisms, which can modulate expression directly or indirectly through <em>cis</em> or <em>trans</em> factors. Identifying genetic variants in these regulatory regions can improve both expression quantitative trait locus (eQTL) mapping and gene expression prediction. Whole genome sequences offer the possibility for enhanced eQTL mapping accuracy, but detecting causal variants remains challenging. Here, we evaluate the potential added-value of integrating tissue-specific epigenetic annotations, such as chromatin accessibility and methylation status, into within-breed genomic predictions of expression for three pig breeds. Functional annotations from early developmental stages improved eQTL mapping interpretability as shown by the enrichment of trait-relevant QTLs. However, despite the use of functional annotations, predictions across breeds remain challenging due to differences in genetic architectures. Our work contributes to the understanding of gene expression regulation in livestock and highlights the value of functional annotations, despite continued challenges for predictions across breeds.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"118 1","pages":"Article 111158"},"PeriodicalIF":3.0,"publicationDate":"2025-11-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145617608","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 : 2025-11-24DOI: 10.1016/j.ygeno.2025.111154
Yan Wang , Jiahao Zhou , Mingqi Yang , Youhua Yao , Yongmei Cui , Xin Li , Baojun Ding , Xiaohua Yao , Kunlun Wu
Grain size critically determines both yield and quality in crops. This study systematically investigated two distinct qingke varieties with contrasting grain sizes through integrated dynamic phenotyping, transcriptomics, and weighted gene co-expression network analysis (WGCNA). Key observations indicated that statistically significant differences in grain length and width between the two qingke varieties became apparent from 13 DAF. Transcriptome sequencing (RNA-seq) analysis revealed a peak in the number of differentially expressed genes (DEGs) at 13 days after flowering, indicating that gene expression patterns during this stage might regulate the establishment of grain length and width morphology. These DEGs were likely key regulators of grain dimensions. WGCNA analysis identified a highly correlated brown module enriched with MAPK pathway genes, which showed significant associations with grain size (length, width, thickness) and weight. Functional analysis of the MAPK pathway candidate gene HvPR1 demonstrated that its over-expression in barley significantly increased thousand-grain weight (TGW) while reducing grain hardness (GH), thereby uncovering a previously uncharacterized regulatory role in grain development. The observed reduction in grain hardness in over-expression lines was primarily attributed to decreased lignin and cellulose content. These results provide critical genetic resources and novel mechanistic insights to support precision breeding strategies for qingke and other cereal crops.
{"title":"HvPR1: A dual-role architect in balancing grain weight and hardness in barley","authors":"Yan Wang , Jiahao Zhou , Mingqi Yang , Youhua Yao , Yongmei Cui , Xin Li , Baojun Ding , Xiaohua Yao , Kunlun Wu","doi":"10.1016/j.ygeno.2025.111154","DOIUrl":"10.1016/j.ygeno.2025.111154","url":null,"abstract":"<div><div>Grain size critically determines both yield and quality in crops. This study systematically investigated two distinct qingke varieties with contrasting grain sizes through integrated dynamic phenotyping, transcriptomics, and weighted gene co-expression network analysis (WGCNA). Key observations indicated that statistically significant differences in grain length and width between the two qingke varieties became apparent from 13 DAF. Transcriptome sequencing (RNA-seq) analysis revealed a peak in the number of differentially expressed genes (DEGs) at 13 days after flowering, indicating that gene expression patterns during this stage might regulate the establishment of grain length and width morphology. These DEGs were likely key regulators of grain dimensions. WGCNA analysis identified a highly correlated brown module enriched with MAPK pathway genes, which showed significant associations with grain size (length, width, thickness) and weight. Functional analysis of the MAPK pathway candidate gene <em>HvPR1</em> demonstrated that its over-expression in barley significantly increased thousand-grain weight (TGW) while reducing grain hardness (GH), thereby uncovering a previously uncharacterized regulatory role in grain development. The observed reduction in grain hardness in over-expression lines was primarily attributed to decreased lignin and cellulose content. These results provide critical genetic resources and novel mechanistic insights to support precision breeding strategies for qingke and other cereal crops.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"118 1","pages":"Article 111154"},"PeriodicalIF":3.0,"publicationDate":"2025-11-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145632259","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 : 2025-11-01DOI: 10.1016/j.ygeno.2025.111153
Miao Yang , Xiuming Mei , Xiaofeng Yu , Jing Wu , Yuwei Qiang , Xiaoxiao Wu , Hanxu Ji , Yufeng Li , Diyao Jiang , Jingjing Xu , Chi Zhang
Tilletia laevis is a fungal pathogen that causes the severe wheat disease known as common bunt, which is widespread in wheat-growing areas worldwide. Nevertheless, insufficient genome data hinders research at the molecular level. In this study, we reported a high-quality whole genome assembly of T. laevis isolated from China utilizing the integration of Illumina and PacBio sequencing technologies. The genome assembly consisted of 40 contigs with a total length of 38.09 Mb, a contig N50 of 1.50 Mb, and a maximum contig length of 2.61 Mb. The genome encoded 10,682 genes, with a notable enrichment of metabolism-related genes identified by functional annotations. The comparative genomic analysis was conducted between this assembly and closely related Tilletia strains, revealing its evolutionary trajectory. Overall, the genome assembly is currently the most continuous genome for T. laevis, facilitating future research on the pathogenic mechanism and control of this pathogen.
{"title":"Whole genome sequencing of Tilletia laevis, the fungal pathogen causing common bunt","authors":"Miao Yang , Xiuming Mei , Xiaofeng Yu , Jing Wu , Yuwei Qiang , Xiaoxiao Wu , Hanxu Ji , Yufeng Li , Diyao Jiang , Jingjing Xu , Chi Zhang","doi":"10.1016/j.ygeno.2025.111153","DOIUrl":"10.1016/j.ygeno.2025.111153","url":null,"abstract":"<div><div><em>Tilletia laevis</em> is a fungal pathogen that causes the severe wheat disease known as common bunt, which is widespread in wheat-growing areas worldwide. Nevertheless, insufficient genome data hinders research at the molecular level. In this study, we reported a high-quality whole genome assembly of <em>T. laevis</em> isolated from China utilizing the integration of Illumina and PacBio sequencing technologies. The genome assembly consisted of 40 contigs with a total length of 38.09 Mb, a contig N50 of 1.50 Mb, and a maximum contig length of 2.61 Mb. The genome encoded 10,682 genes, with a notable enrichment of metabolism-related genes identified by functional annotations. The comparative genomic analysis was conducted between this assembly and closely related <em>Tilletia</em> strains, revealing its evolutionary trajectory. Overall, the genome assembly is currently the most continuous genome for <em>T. laevis</em>, facilitating future research on the pathogenic mechanism and control of this pathogen.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 6","pages":"Article 111153"},"PeriodicalIF":3.0,"publicationDate":"2025-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145548977","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}
Idiopathic congenital nystagmus (ICN) is characterized by involuntary horizontal eye oscillations and is frequently associated with X-linked FRMD7 mutations. Despite over 150 FRMD7 variants have been reported, their pathogenic mechanisms remain poorly understood. In this study, we identified a novel FRMD7 deletion (c.742-211_1050+59del p.Leu249_Val351del) in an ICN-affected family. Minigenes analysis demonstrated that this FRMD7 mutation caused skipping of exon 9– 11. RT-qPCR and western blotting revealed unchanged FRMD7 mRNA levels but a significantly upregulated in protein expression. Structural modeling indicated the loss of a crucial amino acid segment in the mutated FRMD7 protein (FRMD7-m1). These findings suggest that this FRMD7 deletion disrupts protein translation and stability, contributing to ICN pathogenesis, and expand our understanding of FRMD7-related molecular mechanisms.
{"title":"Functional analysis of a novel segment deletion in the FRMD7 gene causing X-linked idiopathic congenital nystagmus","authors":"Xiaoli Zhao , Xinyang Li , Jian Yuan, Xiaolei Wang, Qinxue Meng, Xinwen Zhang","doi":"10.1016/j.ygeno.2025.111138","DOIUrl":"10.1016/j.ygeno.2025.111138","url":null,"abstract":"<div><div>Idiopathic congenital nystagmus (ICN) is characterized by involuntary horizontal eye oscillations and is frequently associated with X-linked <em>FRMD7</em> mutations. Despite over 150 <em>FRMD7</em> variants have been reported, their pathogenic mechanisms remain poorly understood. In this study, we identified a novel <em>FRMD7</em> deletion (c.742-211_1050+59del p.Leu249_Val351del) in an ICN-affected family. Minigenes analysis demonstrated that this <em>FRMD7</em> mutation caused skipping of exon 9– 11. RT-qPCR and western blotting revealed unchanged <em>FRMD7</em> mRNA levels but a significantly upregulated in protein expression. Structural modeling indicated the loss of a crucial amino acid segment in the mutated FRMD7 protein (<em>FRMD7</em>-m1). These findings suggest that this <em>FRMD7</em> deletion disrupts protein translation and stability, contributing to ICN pathogenesis, and expand our understanding of <em>FRMD7</em>-related molecular mechanisms.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 6","pages":"Article 111138"},"PeriodicalIF":3.0,"publicationDate":"2025-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145354375","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 : 2025-11-01DOI: 10.1016/j.ygeno.2025.111156
Jun Xiang , Jingyi Cheng , Yidan Fan , Jiawen Wu , Zhaoyuan Lyu , Jiayu Gu , Jianjiang Xu , Ning Lyu
Purpose
Pterygium was a common progressive ocular disease with unclear pathogenesis. The aim of this study was to identify biomarkers associated with the integrated stress response (ISR) in pterygia and explore the underlying molecular mechanisms.
Methods
Differentially expressed genes (DEGs) were identified using transcriptome sequencing. ISR-related genes (IRGs) and DEGs were integrated to identify candidate genes, and biomarkers were identified by machine learning. A nomogram was generated using these biomarkers. Enrichment analysis, immune infiltration analysis, correlation analysis, construction of transcription-factor (TF)-mRNA-miRNA regulatory networks, drug prediction, and molecular docking were performed to assess the functional mechanisms underlying these biomarkers.
Results
EGLN3, HSPA8, and NDRG1 were identified as ISR-related biomarkers. EGLN3, HSPA8, and NDRG1 were associated with oxidative phosphorylation, cellular response to hypoxia, and decreased oxygen levels according to enrichment analysis. EGLN3 and NDRG1 were significantly and negatively correlated with immune cells, including immature B cells, but not HSPA8. ARNTL-EGLN3-hsa-miR-520a-3p, ARNTL-HSPA8-hsa-miR-520a-3p, and SNAPC4-NDRG1-hsa-miR-518a-5p played regulatory roles in pterygium development. Drug prediction and molecular docking analyses suggested Metribolone and Valproic Acid as potential therapeutic targets for pterygium. According to qRT-PCR, the expressions of EGLN3, HSPA8, and NDRG1 significantly differed between control and pterygium tissues.
Conclusions
EGLN3, HSPA8, and NDRG1 were identified as biomarkers associated with ISR in pterygium. The regulatory networks composed of differed expressions of ISR-related genes, miRNA-mRNA-TF regulatory axes, and immune response played crucial roles in the development of pterygium.
{"title":"Unveiling the role of integrated stress response in pterygium: EGLN3, HSPA8, and NDRG1 as novel biomarkers and therapeutic targets","authors":"Jun Xiang , Jingyi Cheng , Yidan Fan , Jiawen Wu , Zhaoyuan Lyu , Jiayu Gu , Jianjiang Xu , Ning Lyu","doi":"10.1016/j.ygeno.2025.111156","DOIUrl":"10.1016/j.ygeno.2025.111156","url":null,"abstract":"<div><h3>Purpose</h3><div>Pterygium was a common progressive ocular disease with unclear pathogenesis. The aim of this study was to identify biomarkers associated with the integrated stress response (ISR) in pterygia and explore the underlying molecular mechanisms.</div></div><div><h3>Methods</h3><div>Differentially expressed genes (DEGs) were identified using transcriptome sequencing. ISR-related genes (IRGs) and DEGs were integrated to identify candidate genes, and biomarkers were identified by machine learning. A nomogram was generated using these biomarkers. Enrichment analysis, immune infiltration analysis, correlation analysis, construction of transcription-factor (TF)-mRNA-miRNA regulatory networks, drug prediction, and molecular docking were performed to assess the functional mechanisms underlying these biomarkers.</div></div><div><h3>Results</h3><div><em>EGLN3</em>, <em>HSPA8</em>, and <em>NDRG1</em> were identified as ISR-related biomarkers. <em>EGLN3</em>, <em>HSPA8</em>, and <em>NDRG1</em> were associated with oxidative phosphorylation, cellular response to hypoxia, and decreased oxygen levels according to enrichment analysis. <em>EGLN3</em> and <em>NDRG1</em> were significantly and negatively correlated with immune cells, including immature B cells, but not <em>HSPA8</em>. ARNTL-EGLN3-hsa-miR-520a-3p, ARNTL-HSPA8-hsa-miR-520a-3p, and SNAPC4-NDRG1-hsa-miR-518a-5p played regulatory roles in pterygium development. Drug prediction and molecular docking analyses suggested Metribolone and Valproic Acid as potential therapeutic targets for pterygium. According to qRT-PCR, the expressions of <em>EGLN3</em>, <em>HSPA8</em>, and <em>NDRG1</em> significantly differed between control and pterygium tissues.</div></div><div><h3>Conclusions</h3><div><em>EGLN3, HSPA8,</em> and <em>NDRG1</em> were identified as biomarkers associated with ISR in pterygium. The regulatory networks composed of differed expressions of ISR-related genes, miRNA-mRNA-TF regulatory axes, and immune response played crucial roles in the development of pterygium.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 6","pages":"Article 111156"},"PeriodicalIF":3.0,"publicationDate":"2025-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145596392","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 : 2025-11-01DOI: 10.1016/j.ygeno.2025.111136
Guangyi Chen , Junhui Zhang , Jiayi Wang , Wenxiu Chen , Haoran Li , Haoran Su , Shaoyi Dai , Yumei Tao , Yunxia Cao , Qiang Hong , Fenfen Xie
Liver lipid disorders are common in polycystic ovary syndrome (PCOS) patients. A DHEA-induced PCOS mouse model exhibited elevated liver triglyceride (TG) and total cholesterol (TC), reinforcing this association between liver lipids and PCOS. Liver transcriptomic sequencing revealed that 168 differentially expressed genes and 285 alternative splicing (AS) event genes, significantly enriching retinol metabolism. Further combined analyses showed the Cyp4a32 and Hsd17b6 genes were abnormally expressed in the livers of PCOS mice. AS analysis revealed that Cyp4a32 had upregulated exon skipping (SE), including SE and mutually exclusive exons (MXE), while among the modes of SE, MXE, and alternative 3′ splice site (A3SS), Hsd17b6 showed downregulated MXE. These findings suggest that Cyp4a32 and Hsd17b6 may change the retinol metabolism by modulating AS patterns, which then dysregulate hepatic lipid metabolism in PCOS. This study highlights potential therapeutic targets for PCOS-associated liver lipid disorders.
{"title":"Regulation of alternative splicing of retinol metabolism in lipid abnormality of PCOS liver by Cyp4a32 and Hsd17b6","authors":"Guangyi Chen , Junhui Zhang , Jiayi Wang , Wenxiu Chen , Haoran Li , Haoran Su , Shaoyi Dai , Yumei Tao , Yunxia Cao , Qiang Hong , Fenfen Xie","doi":"10.1016/j.ygeno.2025.111136","DOIUrl":"10.1016/j.ygeno.2025.111136","url":null,"abstract":"<div><div>Liver lipid disorders are common in polycystic ovary syndrome (PCOS) patients. A DHEA-induced PCOS mouse model exhibited elevated liver triglyceride (TG) and total cholesterol (TC), reinforcing this association between liver lipids and PCOS. Liver transcriptomic sequencing revealed that 168 differentially expressed genes and 285 alternative splicing (AS) event genes, significantly enriching retinol metabolism. Further combined analyses showed the Cyp4a32 and Hsd17b6 genes were abnormally expressed in the livers of PCOS mice. AS analysis revealed that Cyp4a32 had upregulated exon skipping (SE), including SE and mutually exclusive exons (MXE), while among the modes of SE, MXE, and alternative 3′ splice site (A3SS), Hsd17b6 showed downregulated MXE. These findings suggest that Cyp4a32 and Hsd17b6 may change the retinol metabolism by modulating AS patterns, which then dysregulate hepatic lipid metabolism in PCOS. This study highlights potential therapeutic targets for PCOS-associated liver lipid disorders.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 6","pages":"Article 111136"},"PeriodicalIF":3.0,"publicationDate":"2025-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145285962","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 : 2025-11-01DOI: 10.1016/j.ygeno.2025.111151
Kai-Wen Cai , Ying-Ying Xie , Zi-Yan Deng , Zong-Chao Yu , Hong-Wei Wu , Zhuang-Feng Weng , Zhen-Chuan Lin , Bin Xia , Xiao-Hua Wang , Zhi-Hua Zheng , Chun Tang , Ting Zhu , Yong-Ping Lu
Background
Obesity-related glomerulopathy (ORG) is a kidney disorder associated with obesity, where dysbiosis of the gut microbiota and disturbances in lipid metabolism play crucial roles in its development. However, the exact mechanisms by which imbalances in gut microbiota influence lipid metabolism and contribute to the pathogenesis of ORG are still not fully understood.
Methods
A high-fat diet (HFD)-induced ORG model was established using 6-week-old male C57BL/6 J mice to investigate the role of gut microbiota and gut-derived metabolites in ORG progression. 16S rRNA sequencing was employed to profile the gut microbiota, while liquid chromatography-tandem mass spectrometry (LC-MS/MS) was applied for metabolite analysis in fecal, serum, and kidney samples.
Results
Compared to age-matched normal diet (ND) mice, ORG mice exhibited significant increases in triglycerides (TG), cholesterol (CHO), and urinary albumin-to-creatinine ratio (UACR), alongside enhanced lipid droplet accumulation in renal tubules and glomerular hypertrophy. Metabolomic analysis revealed altered metabolic profiles in ORG mice, particularly the reprogramming of glycerophospholipid metabolism. Additionally, 16S rRNA sequencing demonstrated reduced gut microbiota diversity in ORG mice relative to the ND group. Further investigation revealed that the shift in renal glycerophospholipid metabolism and elevated blood lipid levels in ORG mice were closely linked to gut microbiota dysbiosis, specifically increased abundance of Lachnospiraceae and decreased abundance of Muribaculaceae.
Conclusion
The dysbiosis of gut microbiota induced by a HFD leads to glycerophospholipid metabolic reprogramming, promoting lipid droplet deposition in the kidneys and contributing to ORG progression. Our study highlights the contribution of gut microbial metabolism to the development of ORG, offering new perspectives for potential therapeutic strategies targeting the gut in ORG treatment.
{"title":"High-fat diet promotes kidney lipid droplet deposition contributing to the pathogenesis of obesity-related glomerulopathy in mice through gut microbial metabolism","authors":"Kai-Wen Cai , Ying-Ying Xie , Zi-Yan Deng , Zong-Chao Yu , Hong-Wei Wu , Zhuang-Feng Weng , Zhen-Chuan Lin , Bin Xia , Xiao-Hua Wang , Zhi-Hua Zheng , Chun Tang , Ting Zhu , Yong-Ping Lu","doi":"10.1016/j.ygeno.2025.111151","DOIUrl":"10.1016/j.ygeno.2025.111151","url":null,"abstract":"<div><h3>Background</h3><div>Obesity-related glomerulopathy (ORG) is a kidney disorder associated with obesity, where dysbiosis of the gut microbiota and disturbances in lipid metabolism play crucial roles in its development. However, the exact mechanisms by which imbalances in gut microbiota influence lipid metabolism and contribute to the pathogenesis of ORG are still not fully understood.</div></div><div><h3>Methods</h3><div>A high-fat diet (HFD)-induced ORG model was established using 6-week-old male C57BL/6 J mice to investigate the role of gut microbiota and gut-derived metabolites in ORG progression. 16S rRNA sequencing was employed to profile the gut microbiota, while liquid chromatography-tandem mass spectrometry (LC-MS/MS) was applied for metabolite analysis in fecal, serum, and kidney samples.</div></div><div><h3>Results</h3><div>Compared to age-matched normal diet (ND) mice, ORG mice exhibited significant increases in triglycerides (TG), cholesterol (CHO), and urinary albumin-to-creatinine ratio (UACR), alongside enhanced lipid droplet accumulation in renal tubules and glomerular hypertrophy. Metabolomic analysis revealed altered metabolic profiles in ORG mice, particularly the reprogramming of glycerophospholipid metabolism. Additionally, 16S rRNA sequencing demonstrated reduced gut microbiota diversity in ORG mice relative to the ND group. Further investigation revealed that the shift in renal glycerophospholipid metabolism and elevated blood lipid levels in ORG mice were closely linked to gut microbiota dysbiosis, specifically increased abundance of <em>Lachnospiraceae</em> and decreased abundance of <em>Muribaculaceae</em>.</div></div><div><h3>Conclusion</h3><div>The dysbiosis of gut microbiota induced by a HFD leads to glycerophospholipid metabolic reprogramming, promoting lipid droplet deposition in the kidneys and contributing to ORG progression. Our study highlights the contribution of gut microbial metabolism to the development of ORG, offering new perspectives for potential therapeutic strategies targeting the gut in ORG treatment.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 6","pages":"Article 111151"},"PeriodicalIF":3.0,"publicationDate":"2025-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145451456","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 : 2025-11-01DOI: 10.1016/j.ygeno.2025.111157
Fenfei Liang , Zhiru Yang , Wei Liu , Faling Zhang , Xia Liang , Cheng Zhao , Guosong Zhang
The Chinese longsnout catfish (Leiocassis longirostris) is an important freshwater aquaculture species, and the selective breeding of fast-growth and hypoxia tolerance population will have a positive impact on its industry. In order to promote the breeding process of Chinese longsnout catfish, construction of the genetic linkage map and identification of molecular markers associated with fast-growth and hypoxia tolerance is critical for the marker-assisted selection (MAS) of Chinese longsnout catfish. In the present study, whole-genome resequencing was used to construct a high-density genetic linkage map of the Chinese longsnout catfish. The map containing 2946 bin markers was distributed over 26 linkage groups (LGs) with a total genetic coverage of 1980.76 cM and an average density of 0.67 cM. Based on the genetic map, quantitative trait locus (QTL) mapping results suggested that 17 QTLs associated with growth traits and 1 QTL associated with hypoxia tolerance were identified in eight LGs with the phenotypic variability explained (PVE) ranged from 5.1 % to 9.3 %. Four SNP loci from these QTLs were associated with the phenotypic traits validated by Kompetitive Allele Specific PCR or Sanger sequencing. In addition, the expression of three candidate genes for growth traits and five candidate genes for hypoxia tolerance was examined in different growth speed populations and the process of hypoxia exposure and reoxygenation, respectively. The high-density genetic linkage map and QTLs for growth traits and hypoxia tolerance obtained in the present study could further provide the basis for genetic breeding and molecular marker-assisted breeding of Chinese longsnout catfish.
{"title":"Construction of a genome-wide linkage map and QTL mapping for growth and hypoxia tolerance traits in Chinese longsnout catfish (Leiocassis longirostris)","authors":"Fenfei Liang , Zhiru Yang , Wei Liu , Faling Zhang , Xia Liang , Cheng Zhao , Guosong Zhang","doi":"10.1016/j.ygeno.2025.111157","DOIUrl":"10.1016/j.ygeno.2025.111157","url":null,"abstract":"<div><div>The Chinese longsnout catfish (<em>Leiocassis longirostris</em>) is an important freshwater aquaculture species, and the selective breeding of fast-growth and hypoxia tolerance population will have a positive impact on its industry. In order to promote the breeding process of Chinese longsnout catfish, construction of the genetic linkage map and identification of molecular markers associated with fast-growth and hypoxia tolerance is critical for the marker-assisted selection (MAS) of Chinese longsnout catfish. In the present study, whole-genome resequencing was used to construct a high-density genetic linkage map of the Chinese longsnout catfish. The map containing 2946 bin markers was distributed over 26 linkage groups (LGs) with a total genetic coverage of 1980.76 cM and an average density of 0.67 cM. Based on the genetic map, quantitative trait locus (QTL) mapping results suggested that 17 QTLs associated with growth traits and 1 QTL associated with hypoxia tolerance were identified in eight LGs with the phenotypic variability explained (PVE) ranged from 5.1 % to 9.3 %. Four SNP loci from these QTLs were associated with the phenotypic traits validated by Kompetitive Allele Specific PCR or Sanger sequencing. In addition, the expression of three candidate genes for growth traits and five candidate genes for hypoxia tolerance was examined in different growth speed populations and the process of hypoxia exposure and reoxygenation, respectively. The high-density genetic linkage map and QTLs for growth traits and hypoxia tolerance obtained in the present study could further provide the basis for genetic breeding and molecular marker-assisted breeding of Chinese longsnout catfish.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 6","pages":"Article 111157"},"PeriodicalIF":3.0,"publicationDate":"2025-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145568304","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 : 2025-11-01DOI: 10.1016/j.ygeno.2025.111139
Manuel J. Arnold , Matthias A. Ehrmann , Yohanes N. Kurniawan , Koji Suzuki , Wolfgang Liebl
Beer spoiling bacteria represent a major concern for the brewing industry. Anaerobic spoilers of the genus Megasphaera are especially dreadful. Until now, the genome analysis of Megasphaera spp. was limited to mammal-associated species, yet beer borne Megasphaera species and their abilities to tolerate the multiple high stress factors in their niche were broadly overlooked. This study is the first to carry out an in silico genome comparison of ten strains from three different beer spoiling Megasphaera species (M. cerevisiae, M. paucivorans and M. sueciensis). We experimentally show a hitherto unseen resilience of beer spoiling Megasphaera strains, which can grow in lager beer with an isoα-acids content of up to 120 IBU, an ethanol concentration of up to 7.0 % (v/v) and at pH 4.0. The genomes revealed genes appearing to aid survival in the harsh brewing environment mainly comprised of hop, ethanol and acid stress.
啤酒腐坏细菌是酿酒行业关注的主要问题。Megasphaera属的厌氧破坏者尤其可怕。到目前为止，人们对巨斑蛛的基因组分析仅限于哺乳动物的亲缘种，而啤酒源的巨斑蛛及其对生态位中多种高应激因素的耐受能力却被广泛忽视。本研究首次对三种不同的啤酒腐坏Megasphaera物种（M. cerevisiae， M. paucivorans和M. sueciensis）的10株菌株进行了计算机基因组比较。我们通过实验显示了迄今为止未见的啤酒变质Megasphaera菌株的恢复能力，它可以在异α-酸含量高达120 IBU、乙醇浓度高达7.0 % （v/v）和pH 4.0的啤酒中生长。基因组揭示了在恶劣的酿造环境中帮助生存的基因，主要包括啤酒花、乙醇和酸胁迫。
{"title":"Genomic and physiological characterization of beer spoiling Megasphaera spp.","authors":"Manuel J. Arnold , Matthias A. Ehrmann , Yohanes N. Kurniawan , Koji Suzuki , Wolfgang Liebl","doi":"10.1016/j.ygeno.2025.111139","DOIUrl":"10.1016/j.ygeno.2025.111139","url":null,"abstract":"<div><div>Beer spoiling bacteria represent a major concern for the brewing industry. Anaerobic spoilers of the genus Megasphaera are especially dreadful. Until now, the genome analysis of Megasphaera spp. was limited to mammal-associated species, yet beer borne Megasphaera species and their abilities to tolerate the multiple high stress factors in their niche were broadly overlooked. This study is the first to carry out an in silico genome comparison of ten strains from three different beer spoiling Megasphaera species (<em>M. cerevisiae</em>, <em>M. paucivorans</em> and <em>M. sueciensis</em>). We experimentally show a hitherto unseen resilience of beer spoiling Megasphaera strains, which can grow in lager beer with an isoα-acids content of up to 120 IBU, an ethanol concentration of up to 7.0 % (<em>v</em>/v) and at pH 4.0. The genomes revealed genes appearing to aid survival in the harsh brewing environment mainly comprised of hop, ethanol and acid stress.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 6","pages":"Article 111139"},"PeriodicalIF":3.0,"publicationDate":"2025-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145400499","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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