Genomics最新文献

{"title":"Genetic insights into large and small body size variation in Diqing Tibetan pigs: A comparative genomic analysis","authors":"Siqi Jin ,&nbsp;Xinxing Dong ,&nbsp;Chunlu Zhou ,&nbsp;Jinyu Chu ,&nbsp;Xinpeng Li ,&nbsp;Wangjiao Li ,&nbsp;Wenjun Dong ,&nbsp;Yunlong Ma ,&nbsp;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}

{"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 ,&nbsp;Yangyang Chen ,&nbsp;Lisha Luo ,&nbsp;Yuanyuan Jia ,&nbsp;Kaijie Qi ,&nbsp;Zhihua Xie ,&nbsp;Hao Yin ,&nbsp;Shaoling Zhang ,&nbsp;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}

{"title":"Identification and functional prediction of ceRNA networks regulating ATP levels in boar spermatozoa treated with non-thermal plasma","authors":"Yihan Li ,&nbsp;Jiangwei Liu ,&nbsp;Qian Wang ,&nbsp;Yin Li ,&nbsp;Xianzhong Wang ,&nbsp;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}

{"title":"The translation landscape revealed the novel micropeptides involved in myogenic differentiation of goat skeletal muscle satellite cells","authors":"Qianqian Pan ,&nbsp;Mengyu Lou ,&nbsp;Jing Jing ,&nbsp;Tianwei Liu ,&nbsp;Yan Huang ,&nbsp;Shuang Li ,&nbsp;Lu Zhu ,&nbsp;Yong Liu ,&nbsp;Sihuan Zhang ,&nbsp;Yinghui Ling","doi":"10.1016/j.ygeno.2026.111194","DOIUrl":"10.1016/j.ygeno.2026.111194","url":null,"abstract":"<div><div>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.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"118 2","pages":"Article 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}

{"title":"Single cell transcriptomic atlas reveals distinct immune signatures following transfusion of COVID-19 convalescent plasma in severe COVID-19","authors":"Chengqi Gao ,&nbsp;Wei Xiao ,&nbsp;Chao Zhu ,&nbsp;Mengwei Liu ,&nbsp;Zhenguo Zeng ,&nbsp;Kun Xiao ,&nbsp;Kuai Yu","doi":"10.1016/j.ygeno.2025.111191","DOIUrl":"10.1016/j.ygeno.2025.111191","url":null,"abstract":"<div><div>The inflammatory responses of severe patients before and after Convalescent COVID-19 plasma (CCP) transfusion are poorly understood. To clarify the immune response and potential pro-inflammatory factors in severe patients after CCP transfusion, we performed single-cell RNA sequencing on peripheral blood mononuclear cells (PBMCs) from severe COVID-19 patients before and 24 h after CCP transfusion. At 24 h after CCP transfusion, T and B cell proportions increased modestly without significant changes in TCR/BCR diversity. Importantly, concurrent upregulation of S100A8 in both CD4 memory T cells and B cells suggests that CCP transfusion may promote an inflammatory response in these cell subsets. Cell communication analysis revealed that CCP transfusion induced selective disruption of NK cell communication with TCR-negative T cells and BCR-positive B cells. Our data suggest CCP transfusion promoted the inflammatory response and interrupt the communication between adaptive immune cells and innate immune cells in severe COVID-19.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"118 2","pages":"Article 111191"},"PeriodicalIF":3.0,"publicationDate":"2026-01-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145916817","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Co-regulatory crosstalk between m5C, m7G, and o8G RNA modifications via QKI/YBX1 axis in myocardial ischemia-reperfusion injury","authors":"Ziqiang Yang ,&nbsp;Suyun Chen ,&nbsp;Siman Shen ,&nbsp;Wanglong Liu ,&nbsp;Kun Ding ,&nbsp;Fangni Cao ,&nbsp;Simeng Li ,&nbsp;Minjuan Zeng ,&nbsp;Jianning Chen ,&nbsp;Li Xu ,&nbsp;Liangqing Zhang","doi":"10.1016/j.ygeno.2026.111193","DOIUrl":"10.1016/j.ygeno.2026.111193","url":null,"abstract":"<div><h3>Background</h3><div>Ischemia–reperfusion (I/R) injury in the heart triggers oxidative stress and alters post-transcriptional gene regulation. Reactive oxygen species (ROS) generated during oxidative stress induce RNA modifications such as 8-oxo-guanosine (o8G). Other modifications including 5-methylcytosine (m5C) and 7-methylguanosine (m7G) may also contribute to cardiac dysfunction. While the roles of individual RNA modifications in I/R injury are increasingly recognized, the global dynamics and crosstalk among these modifications under oxidative stress remain largely unexplored.</div></div><div><h3>Methods</h3><div>We performed high-throughput sequencing specific to each modification, integrated with mRNA transcriptome profiling of an IR injury mouse model. Differentially modified transcripts were subjected to GO and KEGG enrichment analyses to elucidate their functional relevance. Mechanistically, we demonstrated that RNA modification regulators with distinct functional roles can physically interact with each other, as shown by co-immunoprecipitation and immunofluorescence assays. Global changes in RNA modification levels under the model conditions were assessed using dot blot analysis. Furthermore, the regulatory effects of these enzymes on target mRNA stability were evaluated via Actinomycin D transcriptional inhibition assays.</div></div><div><h3>Results</h3><div>We found that the levels of all three modifications, m5C, m7G, and o8G were increased in IR by dot blot and observed a significant upregulation of three modification peaks under I/R by MeRIP-seq. Both m5C and o8G were predominantly enriched in CDS, while m7G displayed a dynamic redistribution. Our study focuses on the co-regulation crosstalk among three modifications. Functionally, singly or combinatorially modified transcripts were enriched in actin cytoskeleton regulation. Mechanistically, the transcripts of the regulators can be modified by each other and QKI can modulate the global modification level of o8G. QKI and YBX1 interact with each other to cooperatively stabilize ACTN4 mRNA, thereby maintaining cytoskeletal integrity.</div></div><div><h3>Conclusion</h3><div>Our results establish that QKI and YBX1 modulate the actin cytoskeleton via a coordinated network of m5C, m7G, and o8G in I/R injury.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"118 2","pages":"Article 111193"},"PeriodicalIF":3.0,"publicationDate":"2026-01-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145911189","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Mechanism of lead resistance in Wickerhamomyces anomalus: Insights from whole genome sequencing","authors":"Lijie Li,&nbsp;Ganqiqige Cha,&nbsp;Fengsheng Zhang","doi":"10.1016/j.ygeno.2025.111192","DOIUrl":"10.1016/j.ygeno.2025.111192","url":null,"abstract":"<div><div>Lead contamination in air, water, and soil has infiltrated foods and feeds, posing severe health risks to humans and animals and remaining a tough challenge. Yeast is a safe and efficient biosorbent for lead removal. This study explored <em>W. anomalus QF-11</em> lead resistance via whole-genome sequencing, finding it tolerates up to 7000 mg/L Pb²⁺. Under 4000 mg/L Pb²⁺ stress, it enhances resistance by scavenging ROS, increasing soluble protein, boosting SOD, POD and CAT activities, and elevating glutathione and trehalose levels. Its genome annotates 63 ABC transporters and antioxidant genes involved in lead adsorption, transportation and compartmentalization, with SODC, SODM, VAN1, TSL1 and others significantly upregulated. This study provides a theoretical basis for <em>W. anomalus QF-11</em> application as a Pb²⁺ biosorbent and data support for novel heavy metal adsorbent development.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"118 2","pages":"Article 111192"},"PeriodicalIF":3.0,"publicationDate":"2026-01-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145905906","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Comprehensive analysis of multiple species identifies novel molecular signatures and pathways involved in aging","authors":"Weijuan Cai ,&nbsp;Kunying Chong ,&nbsp;Bo Zhou ,&nbsp;Yanni Zhao ,&nbsp;Binchang Lao ,&nbsp;Liang Yin","doi":"10.1016/j.ygeno.2025.111161","DOIUrl":"10.1016/j.ygeno.2025.111161","url":null,"abstract":"<div><div>Aging is an important pathological basis of age-related diseases. However, the similarities and differences among different types of senescent cells of different species and their role in normal homeostasis are poorly understood. Herein, in order to comprehensively map age-related transcriptome changes in multiple tissues of vertebrates during the ageing process, we analyzed 581 samples from 54 aging transcriptome datasets spanning 4 species including Homo sapiens, Mus musculus, Rattus norvegicus and Danio rerio, and identified the novel age-related differentially expressed genes, and obtained specific enriched expression of age-related pathways. Protein-protein interactions of differentially expressed genes in different species with the PTPRC or CD45 as the core were predicted. Through this study, we screened the key biomarkers and signaling pathways that regulate the aging process of tissues and organs in multiple species, which is of great significance for improving age-related tissues and organs by identifying senescent cells.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"118 1","pages":"Article 111161"},"PeriodicalIF":3.0,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145648190","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"TOGAR: Token-gated generative refinement for high-fidelity spatial transcriptomics and robust spatial domain clustering","authors":"Dachen Liu ,&nbsp;Hua Shi ,&nbsp;Yihang Lin ,&nbsp;Zhen Chen ,&nbsp;Quan Zou","doi":"10.1016/j.ygeno.2025.111179","DOIUrl":"10.1016/j.ygeno.2025.111179","url":null,"abstract":"<div><div>Spatial transcriptomics maps gene expression across tissues, yet data sparsity and noise challenge long-range dependency modeling, limiting accurate spatial domain delineation. In this study, we present TOGAR, a token-gated generative refinement model that unifies denoising, spatial enhancement, and clustering for spatial transcriptomics. Firstly, the model combines a graph convolutional network loss with a loss based on the zero-inflated negative binomial distribution to reduce noise and enhance signal clarity in sparse count data. It then employs a UGate-based diffusion backbone, which integrates token gating, gated linear attention, and rotary positional embedding for generative spatial refinement. Finally, similarity-guided averaging along diffusion trajectories provides stable spot-level estimates, and clustering of the refined representations produces spatial domains with sharp boundaries suitable for downstream analyses. We evaluate TOGAR across three spatial transcriptomics platforms. In benchmarks on twelve slices against seven popular methods, TOGAR consistently achieves or exceeds clustering accuracy, demonstrating superior stability. TOGAR effectively recovers coherent cortical layer organization, delineates fine-grained tumor subdomains associated with immune activity and extracellular matrix remodeling, and generates clearer, biologically interpretable domain boundaries. Notably, TOGAR excels in detecting extremely small and rare spatial structures, successfully identifying biologically important regions that other methods completely miss, while maintaining boundary integrity in complex multi-cluster structures and avoiding issues of over-connectivity or incomplete detection.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"118 1","pages":"Article 111179"},"PeriodicalIF":3.0,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145803967","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Comprehensive small non-coding RNA profiling reveals novel diagnostic biomarkers for primary open-angle glaucoma","authors":"Juntao Zhang ,&nbsp;Hengqian He ,&nbsp;Fang Wang ,&nbsp;Huilei Yu ,&nbsp;Bowen Liu ,&nbsp;Jingwen Yang ,&nbsp;Qinkang Lu","doi":"10.1016/j.ygeno.2025.111187","DOIUrl":"10.1016/j.ygeno.2025.111187","url":null,"abstract":"<div><div>Primary open-angle glaucoma (POAG) is the most prevalent type of glaucoma, and early-stage optic neuropathy may cause visual field defects. As these early defects have minimal effects on vision, they are often overlooked, resulting in the loss of optimal treatment timing. Urgent identification of novel early diagnostic biomarkers is needed. In this study, blood samples from 30 POAG patients and 30 healthy controls were analyzed for Small Non-Coding RNAs (sncRNAs) transcriptomics and validated. We performed PANDORA-seq to profile quantitative sncRNAs signature, and a total of 169 differentially expressed sncRNAs were identified, including 147 PIWI-interacting RNAs, 10 microRNAs, and 12 transfer RNA-derived small RNAs. Functional enrichment analysis of sncRNAs target genes revealed significant involvement in key pathological processes, including apoptosis, inflammation, and intraocular pressure homeostasis. Regulatory network analysis demonstrated substantial functional overlap among different sncRNAs groups, suggesting potential cooperative roles in POAG pathogenesis. The expressions of 6 candidate sncRNAs were validated by quantitative real-time polymerase chain reaction, confirming the downregulation of tsRNA-5009b-ValCAC (<em>p</em> &lt; 0.05), piR-hsa-767,596 (<em>p</em> &lt; 0.05), piR-hsa-731,834 (<em>p</em> &lt; 0.01) and hsa-miR-451a (p &lt; 0.05) in POAG patients. Besides, receiver operating characteristic (ROC) curve analysis demonstrated that individual sncRNAs exhibited moderate diagnostic performance, with hsa-miR-451a showing good performance (AUC = 0.83).Our study provides novel insights into the role of sncRNAs in POAG and highlights their potential as diagnostic biomarkers for early disease detection and monitoring.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"118 1","pages":"Article 111187"},"PeriodicalIF":3.0,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145846464","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}