Pub Date : 2026-01-13DOI: 10.1016/j.ygeno.2026.111204
Piao Liu , Guandi He , Zicheng Guo , Yu Tang , Zhengqian Tan , Yulin Song , Tengbing He , Siew Ling Lee
Household fermentation tanks offer simple, low-cost solutions for fruit and vegetable waste utilization, yet staged metabolite formation during sugar-mediated fermentation remains understudied. Using metagenomic and metabolomic approaches, we characterized microbial succession and metabolite dynamics over 28 days. Three phases emerged: substrate activation (1-7d) with Enterobacter/Escherichia dominance producing organic acids; metabolic transition (8-21d) with Lactiplantibacillus proliferation (312.5% increase) accumulating phytohormones 3-hydroxycinnamic acid (2.84-fold) and adenine (1.38-fold); functional stability (21-28d) establishing Lactiplantibacillus-Acetobacter synergy enriching antioxidants and antimicrobial peptides. Multi-omics analysis revealed strong correlations between amino acid metabolism and functional metabolites (r = 0.78, p < 0.01). Fermentation broth (1:500 dilution) enhanced lettuce germination to 92.22% (p < 0.05).Although the potential of household agriculture is demonstrated through staged microbial community development and the formation of bioactive products, functional characteristics still need to be verified in the soil-plant system beyond seed germination assays.
家用发酵罐为果蔬废弃物的利用提供了简单、低成本的解决方案，但糖介导的发酵过程中代谢物的分期形成仍有待研究。利用宏基因组学和代谢组学方法，我们对28天内的微生物演替和代谢物动态进行了表征。出现了三个阶段：底物激活（1-7d），肠杆菌/埃希氏菌优势产生有机酸；代谢转变（8-21d）与乳酸杆菌增殖（增加312.5%）积累植物激素3-羟基肉桂酸（2.84倍）和腺嘌呤（1.38倍）；功能稳定（21-28d）建立乳酸杆菌-醋酸杆菌协同作用，丰富抗氧化剂和抗菌肽。多组学分析显示，氨基酸代谢与功能代谢物之间存在很强的相关性（r = 0.78, p < 0.01）。发酵液（1:500稀释）使生菜发芽率提高到92.22% （p < 0.05）。虽然家庭农业的潜力是通过分阶段的微生物群落发展和生物活性产品的形成来证明的，但除了种子发芽试验之外，还需要在土壤-植物系统中验证功能特征。
{"title":"Characteristics of microbial community succession and functional metabolite accumulation during microaerobic fermentation of high-sugar-load fruit and vegetable residues: Potential implications for guiding home production of environmental-friendly bioactive fertilizer","authors":"Piao Liu , Guandi He , Zicheng Guo , Yu Tang , Zhengqian Tan , Yulin Song , Tengbing He , Siew Ling Lee","doi":"10.1016/j.ygeno.2026.111204","DOIUrl":"10.1016/j.ygeno.2026.111204","url":null,"abstract":"<div><div>Household fermentation tanks offer simple, low-cost solutions for fruit and vegetable waste utilization, yet staged metabolite formation during sugar-mediated fermentation remains understudied. Using metagenomic and metabolomic approaches, we characterized microbial succession and metabolite dynamics over 28 days. Three phases emerged: substrate activation (1-7d) with <em>Enterobacter</em>/<em>Escherichia</em> dominance producing organic acids; metabolic transition (8-21d) with <em>Lactiplantibacillus</em> proliferation (312.5% increase) accumulating phytohormones 3-hydroxycinnamic acid (2.84-fold) and adenine (1.38-fold); functional stability (21-28d) establishing <em>Lactiplantibacillus-Acetobacter</em> synergy enriching antioxidants and antimicrobial peptides. Multi-omics analysis revealed strong correlations between amino acid metabolism and functional metabolites (<em>r</em> = 0.78, <em>p</em> < 0.01). Fermentation broth (1:500 dilution) enhanced lettuce germination to 92.22% (<em>p</em> < 0.05).Although the potential of household agriculture is demonstrated through staged microbial community development and the formation of bioactive products, functional characteristics still need to be verified in the soil-plant system beyond seed germination assays.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"118 2","pages":"Article 111204"},"PeriodicalIF":3.0,"publicationDate":"2026-01-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145975340","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 : 2026-01-11DOI: 10.1016/j.ygeno.2026.111203
Yu Zhou , Yuxi Tong , Yonggang Wang , Xiaoqin Fu , Chen Zhang , Genlou Sun , Qifei Wang , Sisi Huang , Xifeng Ren
Understanding how barley domestication affects deleterious mutations is crucial for breeding and germplasm conservation. This study analyzed seven single-copy nuclear genes (Alcohol dehydrogenase 2 (ADH2), Alcohol dehydrogenase 3 (ADH3), Dehydrin9 (DHN9), Glyceraldehyde-3-phosphate dehydrogenase (GAPDH), Phosphoenolpyruvate carboxylase (PEPC), Photoperiod response gene (PPD-H1), and Granule-bound starch synthase (WAXY)) in 179 wild, 185 domesticated, and 21 de-domesticated barley accessions. Results showed that wild barley has the highest genetic diversity and the most private haplotypes. Deleterious SNPs were identified, with fewer in domesticated and de-domesticated groups compared to wild. Deleterious mutation load decreased from wild to domesticated barley as nucleotide diversity decreased (R = 0.78; p < 0.05), suggesting that domestication bottlenecks may purge these mutations. In wild barley, Nonsynonymous-to-synonymous substitution rate (dN/dS) ratios were ∼ 1 or > 1, indicating neutral or weak positive selection. These findings highlight how domestication shapes deleterious mutation patterns and provide insights for breeding and germplasm management.
{"title":"Dynamics of deleterious mutation and selection at seven nuclear genes during barley domestication and de-domestication","authors":"Yu Zhou , Yuxi Tong , Yonggang Wang , Xiaoqin Fu , Chen Zhang , Genlou Sun , Qifei Wang , Sisi Huang , Xifeng Ren","doi":"10.1016/j.ygeno.2026.111203","DOIUrl":"10.1016/j.ygeno.2026.111203","url":null,"abstract":"<div><div>Understanding how barley domestication affects deleterious mutations is crucial for breeding and germplasm conservation. This study analyzed seven single-copy nuclear genes (<em>Alcohol dehydrogenase 2</em> (<em>ADH2</em>), <em>Alcohol dehydrogenase 3</em> (<em>ADH3</em>), <em>Dehydrin9</em> (<em>DHN9</em>), <em>Glyceraldehyde-3-phosphate dehydrogenase</em> (<em>GAPDH</em>), <em>Phosphoenolpyruvate carboxylase</em> (<em>PEPC</em>), <em>Photoperiod response gene</em> (<em>PPD-H1</em>), and <em>Granule-bound starch synthase</em> (<em>WAXY</em>)) in 179 wild, 185 domesticated, and 21 de-domesticated barley accessions. Results showed that wild barley has the highest genetic diversity and the most private haplotypes. Deleterious SNPs were identified, with fewer in domesticated and de-domesticated groups compared to wild. Deleterious mutation load decreased from wild to domesticated barley as nucleotide diversity decreased (<em>R</em> = 0.78; <em>p</em> < 0.05), suggesting that domestication bottlenecks may purge these mutations. In wild barley, Nonsynonymous-to-synonymous substitution rate (dN/dS) ratios were ∼ 1 or > 1, indicating neutral or weak positive selection. These findings highlight how domestication shapes deleterious mutation patterns and provide insights for breeding and germplasm management.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"118 2","pages":"Article 111203"},"PeriodicalIF":3.0,"publicationDate":"2026-01-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145965882","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 : 2026-01-10DOI: 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":"2026-01-10","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 : 2026-01-09DOI: 10.1016/j.ygeno.2026.111199
Dan Xiong , Chao Zhang , Jian Xia
A growing body of research suggests that circular RNAs (circRNAs) and 5-methylcytosine (m5C) play crucial roles in the onset and progression of stroke. This includes their potential regulation of neuronal damage and repair under cerebral ischemic conditions. However, the specific features of m5C modification in circRNAs associated with stroke remain unclear. In this study, we established a mouse model of cerebral ischemia (MCAO) and utilized methylated RNA immunoprecipitation sequencing (MeRIP-Seq) to identify m5C peaks. In comparison to the control group, MCAO exhibited significant changes in 1982 m5C peaks, with 1096 peaks upregulated and 886 peaks downregulated. Differentially expressed genes in m5C were identified to have significant involvement in the MAPK signaling pathway, GABAergic synapse, and foxO signaling pathway. Additionally, through integrated analysis of MeRIP-Seq and RNA-Seq data, we identified 24 circRNAs that underwent significant changes in both methylation and expression. This suggests a potential association between stroke and circRNA m5C modification, providing insights into the prognosis of stroke patients and the identification of novel intervention targets.
{"title":"Comprehensive epigenetic analysis on 5-methylcytosine modification of circRNAs in the mouse cerebral ischemia model","authors":"Dan Xiong , Chao Zhang , Jian Xia","doi":"10.1016/j.ygeno.2026.111199","DOIUrl":"10.1016/j.ygeno.2026.111199","url":null,"abstract":"<div><div>A growing body of research suggests that circular RNAs (circRNAs) and 5-methylcytosine (m<sup>5</sup>C) play crucial roles in the onset and progression of stroke. This includes their potential regulation of neuronal damage and repair under cerebral ischemic conditions. However, the specific features of m<sup>5</sup>C modification in circRNAs associated with stroke remain unclear. In this study, we established a mouse model of cerebral ischemia (MCAO) and utilized methylated RNA immunoprecipitation sequencing (MeRIP-Seq) to identify m<sup>5</sup>C peaks. In comparison to the control group, MCAO exhibited significant changes in 1982 m5C peaks, with 1096 peaks upregulated and 886 peaks downregulated. Differentially expressed genes in m5C were identified to have significant involvement in the MAPK signaling pathway, GABAergic synapse, and foxO signaling pathway. Additionally, through integrated analysis of MeRIP-Seq and RNA-Seq data, we identified 24 circRNAs that underwent significant changes in both methylation and expression. This suggests a potential association between stroke and circRNA m<sup>5</sup>C modification, providing insights into the prognosis of stroke patients and the identification of novel intervention targets.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"118 2","pages":"Article 111199"},"PeriodicalIF":3.0,"publicationDate":"2026-01-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145951219","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 : 2026-01-08DOI: 10.1016/j.ygeno.2026.111198
Jinxing Su , Shangquan Jiang , Min Chu , Xiang Dong , Caiyun Zhang , Xiaoxing Li , Kan He
Background
Chronic overconsumption of high-fat diets contributes to obesity, with hyperlipidemia being a common comorbidity. The cardiovascular system is strongly influenced by diurnal rhythms, which regulate key functions such as endothelial activity, thrombosis, and blood pressure. Diurnal rhythms are central regulators of metabolic and physiological processes, and dietary pattern shifts can disrupt the synchronization of the internal clock within metabolic systems.
Results
Using a hyperlipidemic mouse model, we investigated diurnal rhythm-related effects on the liver and intestine through transcriptomic, metagenomic, and metabolomic profiling. We identified several key genes—including CD36, Hmgcs1, Ehhadh, Cyp4a12b, Ifi27l2b, Ugt2b1, Ces2a, Cyp3a11, Selenbp2, and Gal3st1—that are regulated by the hepatic circadian clock and modulate metabolites via the gut–liver axis. The gut microbiota exhibited diurnal rhythmicity that coordinates intestinal digestion and metabolism, forming a synergistic circadian metabolic network. Hyperlipidemia disrupted normal circadian regulation in the liver and intestine, affecting lipid synthesis, transport, accumulation, and catabolism.
Discussion
Our hepatic transcriptomic analysis revealed that a high-fat diet induces aberrant expression of lipid metabolism genes during the night. This diet also perturbs the diurnal rhythm of the gut microbiota, leading to intestinal metabolic dysregulation. Metabolites entering the portal circulation act as signaling molecules that bind to hepatic receptors and directly regulate the transcription of lipid metabolism genes. The loss of rhythmic metabolite secretion consequently disrupts circadian gene expression, contributing to hepatic lipid dysregulation via the gut–liver axis—a key mechanism in hyperlipidemia pathogenesis.
Conclusions
This study identifies critical temporal windows and core microbial taxa involved in microbiota–metabolite–gene crosstalk via the gut–liver axis, offering a theoretical foundation for diurnal rhythm-targeted interventions in metabolic diseases.
{"title":"Time-course with multi-omics reveals hyperlipidemia dysregulates diurnal rhythms in gut-liver axis","authors":"Jinxing Su , Shangquan Jiang , Min Chu , Xiang Dong , Caiyun Zhang , Xiaoxing Li , Kan He","doi":"10.1016/j.ygeno.2026.111198","DOIUrl":"10.1016/j.ygeno.2026.111198","url":null,"abstract":"<div><h3>Background</h3><div>Chronic overconsumption of high-fat diets contributes to obesity, with hyperlipidemia being a common comorbidity. The cardiovascular system is strongly influenced by diurnal rhythms, which regulate key functions such as endothelial activity, thrombosis, and blood pressure. Diurnal rhythms are central regulators of metabolic and physiological processes, and dietary pattern shifts can disrupt the synchronization of the internal clock within metabolic systems.</div></div><div><h3>Results</h3><div>Using a hyperlipidemic mouse model, we investigated diurnal rhythm-related effects on the liver and intestine through transcriptomic, metagenomic, and metabolomic profiling. We identified several key genes—including CD36, Hmgcs1, Ehhadh, Cyp4a12b, Ifi27l2b, Ugt2b1, Ces2a, Cyp3a11, Selenbp2, and Gal3st1—that are regulated by the hepatic circadian clock and modulate metabolites via the gut–liver axis. The gut microbiota exhibited diurnal rhythmicity that coordinates intestinal digestion and metabolism, forming a synergistic circadian metabolic network. Hyperlipidemia disrupted normal circadian regulation in the liver and intestine, affecting lipid synthesis, transport, accumulation, and catabolism.</div></div><div><h3>Discussion</h3><div>Our hepatic transcriptomic analysis revealed that a high-fat diet induces aberrant expression of lipid metabolism genes during the night. This diet also perturbs the diurnal rhythm of the gut microbiota, leading to intestinal metabolic dysregulation. Metabolites entering the portal circulation act as signaling molecules that bind to hepatic receptors and directly regulate the transcription of lipid metabolism genes. The loss of rhythmic metabolite secretion consequently disrupts circadian gene expression, contributing to hepatic lipid dysregulation via the gut–liver axis—a key mechanism in hyperlipidemia pathogenesis.</div></div><div><h3>Conclusions</h3><div>This study identifies critical temporal windows and core microbial taxa involved in microbiota–metabolite–gene crosstalk via the gut–liver axis, offering a theoretical foundation for diurnal rhythm-targeted interventions in metabolic diseases.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"118 2","pages":"Article 111198"},"PeriodicalIF":3.0,"publicationDate":"2026-01-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145948720","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 : 2026-01-08DOI: 10.1016/j.ygeno.2026.111200
Siqi Jin , Xinxing Dong , Chunlu Zhou , Jinyu Chu , Xinpeng Li , Wangjiao Li , Wenjun Dong , Yunlong Ma , Dawei Yan
In Diqing Prefecture, we identified two Tibetan pig groups that exhibit a significant difference in body size at six months of age, with the large-bodied pigs weighing 55.00 kg and the small-bodied pigs weighing 28.00 kg. To elucidate the genetic distance and relatedness between these two groups, we employed whole-genome resequencing and constructed a genomic dataset containing 247 pigs, including 60 newly sequenced individuals and 187 publicly available samples. We first assessed their phylogenetic relationships through population genetic differentiation analyses, and further explored their genome-wide differences using methods such as nucleotide diversity (θπ), integrated haplotype score (iHS), allele frequency difference (ΔAF), and genome-wide association analysis (GWAS). The results showed that both groups belong to the Diqing Tibetan pig population, and they can be classified as large-bodied and small-bodied Diqing Tibetan pigs, respectively. Combined analyses of selective sweep signals and GWAS revealed that the genomic regions with significant divergence between the two groups mainly contain genes involved in skeletal development, muscle growth, energy metabolism, and endocrine regulation. This study is the first to demonstrate, at the genomic level, that the Diqing Tibetan pig population contains distinct large- and small-bodied types. Although both belong to the same breed, their marked difference in body size leads to substantial variation in meat production capacity. Future studies may employ multi-omics approaches—including transcriptomics, proteomics, and metabolomics—using the two types as comparative models under the same genetic background to systematically identify key genes, proteins, and metabolites that influence meat production performance. The findings of this study not only provide valuable material for further elucidating the mechanisms underlying skeletal and muscle development, but also establish a foundation for breeding Diqing Tibetan pigs with improved meat production traits.
{"title":"Genetic insights into large and small body size variation in Diqing Tibetan pigs: A comparative genomic analysis","authors":"Siqi Jin , Xinxing Dong , Chunlu Zhou , Jinyu Chu , Xinpeng Li , Wangjiao Li , Wenjun Dong , Yunlong Ma , Dawei Yan","doi":"10.1016/j.ygeno.2026.111200","DOIUrl":"10.1016/j.ygeno.2026.111200","url":null,"abstract":"<div><div>In Diqing Prefecture, we identified two Tibetan pig groups that exhibit a significant difference in body size at six months of age, with the large-bodied pigs weighing 55.00 kg and the small-bodied pigs weighing 28.00 kg. To elucidate the genetic distance and relatedness between these two groups, we employed whole-genome resequencing and constructed a genomic dataset containing 247 pigs, including 60 newly sequenced individuals and 187 publicly available samples. We first assessed their phylogenetic relationships through population genetic differentiation analyses, and further explored their genome-wide differences using methods such as nucleotide diversity (θπ), integrated haplotype score (iHS), allele frequency difference (ΔAF), and genome-wide association analysis (GWAS). The results showed that both groups belong to the Diqing Tibetan pig population, and they can be classified as large-bodied and small-bodied Diqing Tibetan pigs, respectively. Combined analyses of selective sweep signals and GWAS revealed that the genomic regions with significant divergence between the two groups mainly contain genes involved in skeletal development, muscle growth, energy metabolism, and endocrine regulation. This study is the first to demonstrate, at the genomic level, that the Diqing Tibetan pig population contains distinct large- and small-bodied types. Although both belong to the same breed, their marked difference in body size leads to substantial variation in meat production capacity. Future studies may employ multi-omics approaches—including transcriptomics, proteomics, and metabolomics—using the two types as comparative models under the same genetic background to systematically identify key genes, proteins, and metabolites that influence meat production performance. The findings of this study not only provide valuable material for further elucidating the mechanisms underlying skeletal and muscle development, but also establish a foundation for breeding Diqing Tibetan pigs with improved meat production traits.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"118 2","pages":"Article 111200"},"PeriodicalIF":3.0,"publicationDate":"2026-01-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145948751","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 : 2026-01-08DOI: 10.1016/j.ygeno.2026.111196
Qi Guo, Yue Zhang, Xin Gui, Lijuan Zhong, Rong Zhong, Yan Jiang, Hongbo Qi
Background: Copy number variations (CNVs) are significant contributors to genetic disorders, making their accurate detection crucial for prenatal diagnosis. While clinical whole exome sequencing (cWES) is increasingly used to identify sequence variants in prenatal samples, the feasibility of using the same cWES data to detect CNVs remains underexplored, particularly in amniotic fluid samples.
Methods: We systematically evaluated seven CNV detection tools (CANOES, CODEX2, CLAMMS, ExomeDepth, XHMM, CNVkit, and GATK/gCNV) across various experimental conditions. Using 132 amniotic fluid (AF) samples, we assessed the impact of control sample type (AF and PB), CNV characteristics (including exon coverage and length), and tool integration strategies on detection accuracy. Performance was evaluated against CNV-seq results as the gold standard, with special focus on detecting pathogenic CNVs.
Results: The choice of control sample substantially influenced detection performance, with PB generally yielding better results than AF. CNV characteristics, particularly exon coverage, clearly affected detection rates, with multi-exon CNVs being more reliably detected than single-exon variants. Individual tools demonstrated varying capabilities, with CANOES achieving the highest recall rate for pathogenic CNVs (70.3%) but all tools showing limited precision (highest 3.4%). Integration of multiple tools appeared to improve overall detection capability for pathogenic variations. This study suggests that effective optimization of WES-based CNV detection should consider control-sample selection, CNV characteristics, and multi-tool integration. While the current precision limitations indicate that WES-based CNV detection cannot yet replace dedicated CNV-seq testing, the findings may inform strategies to streamline prenatal diagnostic workflows by using WES data as an initial CNV screening step, potentially helping to reduce unnecessary additional testing in selected cases.
Conclusion: These findings contribute to developing more effective and efficient genetic testing strategies in prenatal clinical settings, offering a foundation for future improvements in WES-based CNV detection methods.
{"title":"Evaluation of CNV detection tools for prenatal diagnosis using amniotic fluid clinical whole-exome sequencing data.","authors":"Qi Guo, Yue Zhang, Xin Gui, Lijuan Zhong, Rong Zhong, Yan Jiang, Hongbo Qi","doi":"10.1016/j.ygeno.2026.111196","DOIUrl":"https://doi.org/10.1016/j.ygeno.2026.111196","url":null,"abstract":"<p><strong>Background: </strong>Copy number variations (CNVs) are significant contributors to genetic disorders, making their accurate detection crucial for prenatal diagnosis. While clinical whole exome sequencing (cWES) is increasingly used to identify sequence variants in prenatal samples, the feasibility of using the same cWES data to detect CNVs remains underexplored, particularly in amniotic fluid samples.</p><p><strong>Methods: </strong>We systematically evaluated seven CNV detection tools (CANOES, CODEX2, CLAMMS, ExomeDepth, XHMM, CNVkit, and GATK/gCNV) across various experimental conditions. Using 132 amniotic fluid (AF) samples, we assessed the impact of control sample type (AF and PB), CNV characteristics (including exon coverage and length), and tool integration strategies on detection accuracy. Performance was evaluated against CNV-seq results as the gold standard, with special focus on detecting pathogenic CNVs.</p><p><strong>Results: </strong>The choice of control sample substantially influenced detection performance, with PB generally yielding better results than AF. CNV characteristics, particularly exon coverage, clearly affected detection rates, with multi-exon CNVs being more reliably detected than single-exon variants. Individual tools demonstrated varying capabilities, with CANOES achieving the highest recall rate for pathogenic CNVs (70.3%) but all tools showing limited precision (highest 3.4%). Integration of multiple tools appeared to improve overall detection capability for pathogenic variations. This study suggests that effective optimization of WES-based CNV detection should consider control-sample selection, CNV characteristics, and multi-tool integration. While the current precision limitations indicate that WES-based CNV detection cannot yet replace dedicated CNV-seq testing, the findings may inform strategies to streamline prenatal diagnostic workflows by using WES data as an initial CNV screening step, potentially helping to reduce unnecessary additional testing in selected cases.</p><p><strong>Conclusion: </strong>These findings contribute to developing more effective and efficient genetic testing strategies in prenatal clinical settings, offering a foundation for future improvements in WES-based CNV detection methods.</p>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":" ","pages":"111196"},"PeriodicalIF":3.0,"publicationDate":"2026-01-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145948731","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":"2026-01-07","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 : 2026-01-07DOI: 10.1016/j.ygeno.2026.111197
Yihan Li , Jiangwei Liu , Qian Wang , Yin Li , Xianzhong Wang , Jiaojiao Zhang
Adenosine triphosphate (ATP) is essential for sperm motility. We previously found that optimized non-thermal dielectric barrier discharge (DBD) plasma treatment enhanced boar sperm quality by increasing ATP levels. However, the molecular mechanisms underlying this process, particularly the role of competing endogenous RNA (ceRNA) networks, remain unclear. In this study, a total of 266 mRNAs, 163 miRNAs, and 37 circRNAs were identified as differentially expressed in boar spermatozoa treated with optimized DBD plasma. Functional enrichment analysis revealed that ATP-related pathways, including AMPK, mTOR, and cAMP signaling, were significantly enriched. A circRNA–miRNA–mRNA regulatory network was constructed, and two key ceRNA axes, circRNA7761–miR-7-3p–TECRL/CYP24A1/LOC100515741 and circRNA7508–miR-202-5p–CYP2A19/HHIP/WNT2, were identified in the network. These axes are predicted to enhance ATP production by regulating mitochondrial function and energy homeostasis, thereby improving sperm quality. This study provides novel mechanistic insights into the modulation of sperm energy metabolism by DBD plasma through ceRNA networks, thereby offering new theoretical foundations and potential molecular targets for improving male fertility and treating male infertility.
三磷酸腺苷（ATP）对精子的活力至关重要。我们之前发现，优化的非热介质阻挡放电（DBD）等离子体处理通过提高ATP水平来提高猪精子质量。然而，这一过程的分子机制，特别是内源性RNA （ceRNA）网络的竞争作用仍不清楚。在本研究中，共鉴定出266个mrna、163个mirna和37个circrna在经过优化的DBD血浆处理的猪精子中差异表达。功能富集分析显示，包括AMPK、mTOR和cAMP信号在内的atp相关通路显著富集。构建了一个circRNA-miRNA-mRNA调控网络，并在该网络中鉴定出两个关键的ceRNA轴circrna7761 - mir -7- 3d - tecrl /CYP24A1/LOC100515741和circRNA7508-miR-202-5p-CYP2A19/ hip /WNT2。预计这些轴通过调节线粒体功能和能量稳态来提高ATP的产生，从而提高精子质量。本研究为DBD血浆通过ceRNA网络调控精子能量代谢提供了新的机制见解，从而为提高男性生育能力和治疗男性不育症提供了新的理论基础和潜在的分子靶点。
{"title":"Identification and functional prediction of ceRNA networks regulating ATP levels in boar spermatozoa treated with non-thermal plasma","authors":"Yihan Li , Jiangwei Liu , Qian Wang , Yin Li , Xianzhong Wang , Jiaojiao Zhang","doi":"10.1016/j.ygeno.2026.111197","DOIUrl":"10.1016/j.ygeno.2026.111197","url":null,"abstract":"<div><div>Adenosine triphosphate (ATP) is essential for sperm motility. We previously found that optimized non-thermal dielectric barrier discharge (DBD) plasma treatment enhanced boar sperm quality by increasing ATP levels. However, the molecular mechanisms underlying this process, particularly the role of competing endogenous RNA (ceRNA) networks, remain unclear. In this study, a total of 266 mRNAs, 163 miRNAs, and 37 circRNAs were identified as differentially expressed in boar spermatozoa treated with optimized DBD plasma. Functional enrichment analysis revealed that ATP-related pathways, including AMPK, mTOR, and cAMP signaling, were significantly enriched. A circRNA–miRNA–mRNA regulatory network was constructed, and two key ceRNA axes, circRNA7761–miR-7-3p–TECRL/CYP24A1/LOC100515741 and circRNA7508–miR-202-5p–CYP2A19/HHIP/WNT2, were identified in the network. These axes are predicted to enhance ATP production by regulating mitochondrial function and energy homeostasis, thereby improving sperm quality. This study provides novel mechanistic insights into the modulation of sperm energy metabolism by DBD plasma through ceRNA networks, thereby offering new theoretical foundations and potential molecular targets for improving male fertility and treating male infertility.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"118 2","pages":"Article 111197"},"PeriodicalIF":3.0,"publicationDate":"2026-01-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145943202","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 : 2026-01-05DOI: 10.1016/j.ygeno.2026.111194
Qianqian Pan, Mengyu Lou, Jing Jing, Tianwei Liu, Yan Huang, Shuang Li, Lu Zhu, Yong Liu, Sihuan Zhang, Yinghui Ling
Skeletal muscle development is crucial for goat meat production. While most research focuses on transcriptional regulation, translational control is often overlooked. This study integrated transcriptomic data to analyze the translational landscape during myogenic differentiation of goat skeletal muscle satellite cells (SMSCs). We found that differentiation pathways were activated at both levels, with enhancement at translation. Furthermore, we identified 25 novel lncORFs and 36 circORFs with coding potential. Among these, LncORF32653 and LncORF98488 encoded micropeptides promoting SMSCs proliferation and differentiation. We also identified circUSP25, encoding circUSP25-177aa, which inhibited proliferation but promoted differentiation. Thus, lncORF32653-53aa, lncORF98488-98aa, and circUSP25-177aa are key regulators of myogenesis, revealing the potential of RNAs annotated as non-coding to encode functional micropeptides.
{"title":"The translation landscape revealed the novel micropeptides involved in myogenic differentiation of goat skeletal muscle satellite cells.","authors":"Qianqian Pan, Mengyu Lou, Jing Jing, Tianwei Liu, Yan Huang, Shuang Li, Lu Zhu, Yong Liu, Sihuan Zhang, Yinghui Ling","doi":"10.1016/j.ygeno.2026.111194","DOIUrl":"https://doi.org/10.1016/j.ygeno.2026.111194","url":null,"abstract":"<p><p>Skeletal muscle development is crucial for goat meat production. While most research focuses on transcriptional regulation, translational control is often overlooked. This study integrated transcriptomic data to analyze the translational landscape during myogenic differentiation of goat skeletal muscle satellite cells (SMSCs). We found that differentiation pathways were activated at both levels, with enhancement at translation. Furthermore, we identified 25 novel lncORFs and 36 circORFs with coding potential. Among these, LncORF32653 and LncORF98488 encoded micropeptides promoting SMSCs proliferation and differentiation. We also identified circUSP25, encoding circUSP25-177aa, which inhibited proliferation but promoted differentiation. Thus, lncORF32653-53aa, lncORF98488-98aa, and circUSP25-177aa are key regulators of myogenesis, revealing the potential of RNAs annotated as non-coding to encode functional micropeptides.</p>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":" ","pages":"111194"},"PeriodicalIF":3.0,"publicationDate":"2026-01-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145916794","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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