Pub Date : 2026-01-27DOI: 10.1016/j.ygeno.2026.111210
Qing Liu, Dongli Cui, Yaqi Tian, Yehan Wang, Mathieu Rouard, John Seymour Heslop-Harrison, Trude Schwarzacher, Ziwei Wang
Musella lasiocarpa (MLA, 2n = 18, Musaceae) is an endangered species native to south-western China. We assembled its haplotype-resolved, telomere-to-telomere genomes with a genome size of 503.6 Mb consisting of 52.8% repetitive DNA. A 134 bp tandem repeat, Mlcen, was identified at all centromeres, and telomere sequences were present at 30 of 36 assembled pseudo-chromosome ends. The distal gene-rich regions display high synteny, whereas retrotransposon polymorphisms between haplotypes occurred throughout chromosomes, contributing to diversity. Phylogenetic analysis shows MLA diverged from Ensete 42 million years ago, and together they share a common ancestor with Musa. Among 35,312 protein-coding genes, 14 up-regulated and 34 down-regulated transcription factors were identified under cold treatment. This high-quality genomic resource advances our understanding of MLA chromosomal evolution characterized by structural variations, repetitive DNA dynamics, and cold-responsive genes at both haplotype and species levels; and enables genome-assisted improvement of more resilient crops such as bananas and Ensete.
{"title":"Haplotype-resolved genome assembly of Musella lasiocarpa reveals the critical role of structural variations in chromosomal and genome evolution.","authors":"Qing Liu, Dongli Cui, Yaqi Tian, Yehan Wang, Mathieu Rouard, John Seymour Heslop-Harrison, Trude Schwarzacher, Ziwei Wang","doi":"10.1016/j.ygeno.2026.111210","DOIUrl":"10.1016/j.ygeno.2026.111210","url":null,"abstract":"<p><p>Musella lasiocarpa (MLA, 2n = 18, Musaceae) is an endangered species native to south-western China. We assembled its haplotype-resolved, telomere-to-telomere genomes with a genome size of 503.6 Mb consisting of 52.8% repetitive DNA. A 134 bp tandem repeat, Mlcen, was identified at all centromeres, and telomere sequences were present at 30 of 36 assembled pseudo-chromosome ends. The distal gene-rich regions display high synteny, whereas retrotransposon polymorphisms between haplotypes occurred throughout chromosomes, contributing to diversity. Phylogenetic analysis shows MLA diverged from Ensete 42 million years ago, and together they share a common ancestor with Musa. Among 35,312 protein-coding genes, 14 up-regulated and 34 down-regulated transcription factors were identified under cold treatment. This high-quality genomic resource advances our understanding of MLA chromosomal evolution characterized by structural variations, repetitive DNA dynamics, and cold-responsive genes at both haplotype and species levels; and enables genome-assisted improvement of more resilient crops such as bananas and Ensete.</p>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":" ","pages":"111210"},"PeriodicalIF":3.0,"publicationDate":"2026-01-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146085369","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":"2026-01-26","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}
Pub Date : 2026-01-25DOI: 10.1016/j.ygeno.2026.111208
Peter Muchina , Johnson Kinyua , Fathiya Khamis , Chrysantus M. Tanga , Rawlynce Bett , Geoffrey Ssepuuya , Dorothy Nakimbugwe , Mikkel-Holger S. Sinding , Grum Gebreyesus , Goutam Sahana , Zexi Cai
Human activities, either intentional or unintentional, have significantly influenced the global distribution and genetic composition of many species. The black soldier fly (Hermetia illucens; BSF) is a species native to North America that has rapidly gained commercial importance due to its bioconversion efficiency, upcycling organic waste into higher-value products. Through human-mediated dispersal associated with trade and insect farming, BSF has been introduced widely across the Old World, including Africa, where both wild and captive populations are now established. Despite its expanding global distribution, the demographic history and genomic consequences of these introductions remain poorly understood, particularly in Africa. This work integrates whole-genome sequencing of newly sampled East African wild and captive populations with publicly available global datasets to characterize patterns of genetic diversity, population structure, and historical spread. Wild populations displayed high genetic diversity and clear geographic structuring, whereas many captive populations showed markedly reduced diversity, elevated inbreeding, and extensive runs of homozygosity. Our results reveal that a substantial fraction of global captive lines can be traced to a narrow lineage of North American origin, while additional captive colonies reflect more recent, independent derivations from local wild populations. These genomic patterns are consistent with demographic processes such as founder effects, genetic drift, and small effective population sizes, rather than coordinated or directional domestication. By resolving the origins and demographic trajectories of African and global BSF populations, this work clarifies the genetic consequences of unstructured breeding and provides a foundation for managing genetic resources in this rapidly expanding insect-farming industry.
{"title":"Human-mediated dispersal and breeding reshape global genomic patterns in black soldier flies","authors":"Peter Muchina , Johnson Kinyua , Fathiya Khamis , Chrysantus M. Tanga , Rawlynce Bett , Geoffrey Ssepuuya , Dorothy Nakimbugwe , Mikkel-Holger S. Sinding , Grum Gebreyesus , Goutam Sahana , Zexi Cai","doi":"10.1016/j.ygeno.2026.111208","DOIUrl":"10.1016/j.ygeno.2026.111208","url":null,"abstract":"<div><div>Human activities, either intentional or unintentional, have significantly influenced the global distribution and genetic composition of many species. The black soldier fly (<em>Hermetia illucens</em>; BSF) is a species native to North America that has rapidly gained commercial importance due to its bioconversion efficiency, upcycling organic waste into higher-value products. Through human-mediated dispersal associated with trade and insect farming, BSF has been introduced widely across the Old World, including Africa, where both wild and captive populations are now established. Despite its expanding global distribution, the demographic history and genomic consequences of these introductions remain poorly understood, particularly in Africa. This work integrates whole-genome sequencing of newly sampled East African wild and captive populations with publicly available global datasets to characterize patterns of genetic diversity, population structure, and historical spread. Wild populations displayed high genetic diversity and clear geographic structuring, whereas many captive populations showed markedly reduced diversity, elevated inbreeding, and extensive runs of homozygosity. Our results reveal that a substantial fraction of global captive lines can be traced to a narrow lineage of North American origin, while additional captive colonies reflect more recent, independent derivations from local wild populations. These genomic patterns are consistent with demographic processes such as founder effects, genetic drift, and small effective population sizes, rather than coordinated or directional domestication. By resolving the origins and demographic trajectories of African and global BSF populations, this work clarifies the genetic consequences of unstructured breeding and provides a foundation for managing genetic resources in this rapidly expanding insect-farming industry.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"118 2","pages":"Article 111208"},"PeriodicalIF":3.0,"publicationDate":"2026-01-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146061792","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":"2026-01-22","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 : 2026-01-20DOI: 10.1016/j.ygeno.2026.111206
Peter Muchina , Johnson Kinyua , Fathiya Khamis , Chrysantus M. Tanga , Maria Altaf Satti , Grum Gebreyesus , Goutam Sahana , Zexi Cai
Low-coverage whole genome sequencing (lcWGS) combined with genotype imputation provides a cost-efficient alternative to high-coverage sequencing for large-scale genotyping. Although widely implemented in human and livestock genomics, this strategy has not yet been systematically optimized for insects of industrial importance. The black soldier fly (BSF, Hermetia illucens) is increasingly used in global waste bioconversion and sustainable protein production, but genomic resources remain limited. Here, we develop the first BSF haplotype reference panel, containing ∼29.8 million high-quality SNPs from 168 high-coverage genomes, and benchmark imputation performance using a validation experiment in which 33 high-coverage individuals were down-sampled to low coverage and imputed against a reference panel of 135 individuals. We evaluated the performance of three imputation tools, QUILT v1.0.5, GLIMPSE2, and STITCH v1.7.2, across multiple sequencing depths (0.5 × −3×) and allele frequency bins. Based on this validation, QUILT v1.0.5 achieved the highest accuracy overall, particularly for rare variants (MAF < 0.05), whereas GLIMPSE2 delivered comparable accuracy for common variants with approximately twofold faster runtimes. STITCH enabled reference-free imputation but exhibited reduced accuracy relative to reference-based approaches. We then applied the optimized framework to 180 low-coverage (∼1×) BSF genomes, demonstrating the practical utility of the reference panel for large-scale genotyping when true genotypes are unavailable. Together, the reference panel, benchmarking results, and accompanying lcWGS pipeline establish a validated framework for cost-effective BSF genotyping, enabling downstream applications in population monitoring, diversity assessment, and selective breeding.
{"title":"A haplotype reference panel and genotype imputation framework for the black soldier fly (Hermetia illucens)","authors":"Peter Muchina , Johnson Kinyua , Fathiya Khamis , Chrysantus M. Tanga , Maria Altaf Satti , Grum Gebreyesus , Goutam Sahana , Zexi Cai","doi":"10.1016/j.ygeno.2026.111206","DOIUrl":"10.1016/j.ygeno.2026.111206","url":null,"abstract":"<div><div>Low-coverage whole genome sequencing (lcWGS) combined with genotype imputation provides a cost-efficient alternative to high-coverage sequencing for large-scale genotyping. Although widely implemented in human and livestock genomics, this strategy has not yet been systematically optimized for insects of industrial importance. The black soldier fly (BSF, <em>Hermetia illucens</em>) is increasingly used in global waste bioconversion and sustainable protein production, but genomic resources remain limited. Here, we develop the first BSF haplotype reference panel, containing ∼29.8 million high-quality SNPs from 168 high-coverage genomes, and benchmark imputation performance using a validation experiment in which 33 high-coverage individuals were down-sampled to low coverage and imputed against a reference panel of 135 individuals. We evaluated the performance of three imputation tools, QUILT v1.0.5, GLIMPSE2, and STITCH v1.7.2, across multiple sequencing depths (0.5 × −3×) and allele frequency bins. Based on this validation, QUILT v1.0.5 achieved the highest accuracy overall, particularly for rare variants (MAF < 0.05), whereas GLIMPSE2 delivered comparable accuracy for common variants with approximately twofold faster runtimes. STITCH enabled reference-free imputation but exhibited reduced accuracy relative to reference-based approaches. We then applied the optimized framework to 180 low-coverage (∼1×) BSF genomes, demonstrating the practical utility of the reference panel for large-scale genotyping when true genotypes are unavailable. Together, the reference panel, benchmarking results, and accompanying lcWGS pipeline establish a validated framework for cost-effective BSF genotyping, enabling downstream applications in population monitoring, diversity assessment, and selective breeding.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"118 2","pages":"Article 111206"},"PeriodicalIF":3.0,"publicationDate":"2026-01-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146018040","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 : 2026-01-14DOI: 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":"2026-01-14","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}
Pub Date : 2026-01-14DOI: 10.1016/j.ygeno.2026.111205
Xuhui Liu , Junxia Zhang , Yanmei Niu , Yanbin Bai , Xue Jia , Siyi Cai , Yicheng Wang , Xiaolan Zhang , Bingang Shi , Jiang Hu , Chengfu Zhang , Zhidong Zhao
Rumen microbiota and their metabolites in ruminants across reproductive stages benefit the animals' growth, health and offspring's development. However, the impact of rumen fermentation profiles, microbial composition, and metabolite dynamics between non-pregnant and gestating Ashidan yaks remains poorly understood. This study analyzed the rumen fermentation, metagenome and metabolome of five 2–3-year-old Ashidan yaks during the non-pregnant period (NP; 11–30 days pre-mating) and the gestational period (GP; 112–148 days post-conception). Research has found that gestation had higher acetic acid and ammonia nitrogen (NH3−N) (P < 0.05), increased Ascomycota, Apicomplexa, Rhodococcus, Acinetobacter, Methanosphaera (P < 0.05); differential metabolites enriched in valine, leucine, isoleucine biosynthesis and histidine metabolism (P < 0.05), with L-threonine and urocanic acid as major ones. Additionally, microorganisms, metabolites and fermentation parameters correlated. The study shows Ashidan yaks adapt to reproductive stages via regulating rumen microbiota and metabolism, providing a basis for feeding management.
{"title":"Dynamic changes in rumen fermentation, microbial communities, and metabolite profiles of non-pregnant and gestational Ashidan yaks","authors":"Xuhui Liu , Junxia Zhang , Yanmei Niu , Yanbin Bai , Xue Jia , Siyi Cai , Yicheng Wang , Xiaolan Zhang , Bingang Shi , Jiang Hu , Chengfu Zhang , Zhidong Zhao","doi":"10.1016/j.ygeno.2026.111205","DOIUrl":"10.1016/j.ygeno.2026.111205","url":null,"abstract":"<div><div>Rumen microbiota and their metabolites in ruminants across reproductive stages benefit the animals' growth, health and offspring's development. However, the impact of rumen fermentation profiles, microbial composition, and metabolite dynamics between non-pregnant and gestating Ashidan yaks remains poorly understood. This study analyzed the rumen fermentation, metagenome and metabolome of five 2–3-year-old Ashidan yaks during the non-pregnant period (NP; 11–30 days pre-mating) and the gestational period (GP; 112–148 days post-conception). Research has found that gestation had higher acetic acid and ammonia nitrogen (NH<sub>3</sub>−N) (<em>P</em> < 0.05), increased Ascomycota, Apicomplexa, <em>Rhodococcus</em>, <em>Acinetobacter</em>, <em>Methanosphaera</em> (<em>P</em> < 0.05); differential metabolites enriched in valine, leucine, isoleucine biosynthesis and histidine metabolism (<em>P</em> < 0.05), with L-threonine and urocanic acid as major ones. Additionally, microorganisms, metabolites and fermentation parameters correlated. The study shows Ashidan yaks adapt to reproductive stages via regulating rumen microbiota and metabolism, providing a basis for feeding management.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"118 2","pages":"Article 111205"},"PeriodicalIF":3.0,"publicationDate":"2026-01-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145988936","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 : 2026-01-13DOI: 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}
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