Genomics最新文献

{"title":"Corrigendum to “Heterogeneity of fibroblasts from different anatomical sites in healthy human knee ligaments revealed by single-cell RNA sequencing” [Genomics 117 (2025), 111040]","authors":"Haibo Zhao, Yizhi Yao, Fan Jiang, Xuesai Zhu, Tengbo Yu, Xiao Xiao","doi":"10.1016/j.ygeno.2026.111297","DOIUrl":"10.1016/j.ygeno.2026.111297","url":null,"abstract":"","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"118 5","pages":"Article 111297"},"PeriodicalIF":3.6,"publicationDate":"2026-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148619270","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Exploring differences across pangenome-graph representations using Escherichia coli O157:H7 as a model","authors":"Peilin Liu,&nbsp;Kaixin Hu,&nbsp;Lapo Mughini-Gras,&nbsp;Aldert L. Zomer,&nbsp;Michael S.M. Brouwer,&nbsp;Timothy J. Dallman,&nbsp;Julian A. Paganini","doi":"10.1016/j.ygeno.2026.111309","DOIUrl":"10.1016/j.ygeno.2026.111309","url":null,"abstract":"<div><div>Pangenome graphs are increasingly used to represent population-scale bacterial diversity, yet construction methods span fundamentally different representation paradigms whose outputs and sensitivities to assembly quality remain poorly quantified. We systematically reviewed microbial pangenome graph tools and benchmarked seven representative methods spanning gene-cluster, compacted coloured de Bruijn graph, one hybrid approach and one multiple sequence alignment method. Using a repeat-rich <em>Escherichia coli</em> O157:H7 dataset with complete genomes and matched short-read data, we constructed graphs from identical inputs and observed orders-of-magnitude differences in graph size and fragmentation, indicating that global topology is driven by representation strategy. Varying completeness composition revealed that assembly fragmentation is a first-order determinant of graph structure: gene-cluster graphs contracted as draft assemblies replaced complete genomes, whereas compacted coloured de Bruijn graphs expanded, with distinct degree–prevalence fingerprints across tools. In contrast, the multiple sequence alignment method could not be evaluated across fragmented inputs because it did not run reliably on draft-assembly datasets. Computational cost mirrored these shifts and depended strongly on completeness composition, including a pronounced runtime penalty for one compacted coloured de Bruijn graph implementation on all-draft inputs. Finally, analysis of Shiga toxin loci showed that pangenome-level reconciliation by gene-cluster-based tools does not reliably correct assembly artefacts at challenging multi-copy genes and that performance varies by locus. Together, these findings show that pangenome graphs are representation-dependent models of bacterial diversity, and that, in this repeat-rich O157:H7 benchmark dataset, assembly completeness is a primary determinant of their topology, scalability, and locus-level accuracy.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"118 5","pages":"Article 111309"},"PeriodicalIF":3.6,"publicationDate":"2026-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148808468","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Comparative metabolomic and transcriptomic profiling of flavonoid diversity and antioxidant capacity in three Isatis species","authors":"Rong Chen,&nbsp;Yan Qing,&nbsp;Xiaoshan Geng,&nbsp;Qiaoyun Cai,&nbsp;Dayong Han,&nbsp;Huijun Cheng,&nbsp;Chunfeng Tang,&nbsp;Yude Peng,&nbsp;Huaxi Huang,&nbsp;Qin Liu","doi":"10.1016/j.ygeno.2026.111314","DOIUrl":"10.1016/j.ygeno.2026.111314","url":null,"abstract":"<div><div>Flavonoids are key bioactive compounds in plants with significant health benefits. This study employs an integrated multi-omics approach to investigate flavonoid diversity and antioxidant capacity across three <em>Isatis</em> species: <em>I. oblongata</em>, <em>I. tinctoria</em>, and <em>I. indigotica</em>. Metabolomic profiling identified 200 flavonoids, with glycosides being the most abundant class. <em>I. tinctoria</em> exhibited the highest total flavonoid content and antioxidant activity, strongly correlated with the accumulation of 53 core differential flavonoid metabolites, most of which were glycosylated derivatives. Transcriptomic analysis revealed coordinated upregulation of phenylpropanoid pathway genes and specific UDP-glycosyltransferases (<em>UGTs</em>) in <em>I. tinctoria</em>, providing a genetic basis for its enhanced glycoside production. The study establishes a clear genotype–metabolite–phenotype linkage, highlighting glycosylation as a key mechanism underlying flavonoid-driven antioxidant superiority in <em>Isatis</em>. Although the current evidence is primarily correlative, the consistent and strong associations across independent transcriptomic, metabolomic, and antioxidant datasets provide a robust foundation for this conclusion. These findings offer new insights into the metabolic evolution and regulatory networks of flavonoids, with implications for breeding and metabolic engineering of high-value medicinal plants.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"118 5","pages":"Article 111314"},"PeriodicalIF":3.6,"publicationDate":"2026-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148873731","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Comprehensive analysis of metabolomics and transcriptomics of radiation-induced rectal injury","authors":"Huajun Cai,&nbsp;Donglai Guo,&nbsp;Yanwei Lai,&nbsp;Bingwang Zhu,&nbsp;Yong Wu,&nbsp;Xing Liu,&nbsp;Jinfu Zhuang,&nbsp;Guoxian Guan","doi":"10.1016/j.ygeno.2026.111313","DOIUrl":"10.1016/j.ygeno.2026.111313","url":null,"abstract":"<div><div>Radiation-induced rectal injury (RRI) significantly affects the quality of life in patients with locally advanced rectal cancer (LARC) undergoing neoadjuvant chemoradiotherapy (NCRT). Non-targeted liquid chromatography-mass spectrometry metabolomics analysis and transcriptomic analysis were conducted to explore RRI characteristics. Hematoxylin-eosin and Masson staining confirmed radiation-induced injury in rectal tissue within the radiotherapy target region. Orthogonal partial least squares discriminant analysis identified 823 differentially expressed metabolites (DEMs). Transcriptomic analysis revealed 400 differentially expressed genes (DEGs). Enrichment analysis revealed that DEMs and DEGs were primarily involved in metabolic, immune, and signal transduction pathways. Integrated analysis demonstrated significant enrichment of DEMs and DEGs in the arachidonic acid metabolism pathway. Pearson's correlation and canonical correlation analyses were used to assess the association between DEMs and DEGs within this pathway. In conclusion, this study identified key biological regulatory pathways involved in RRI through a multi-omics approach, offering potential targets for its diagnosis and treatment.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"118 5","pages":"Article 111313"},"PeriodicalIF":3.6,"publicationDate":"2026-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148879811","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Mechanistic insights into sheep pulmonary adenomatosis based on whole transcriptome sequencing","authors":"Lina Zhu,&nbsp;Qiao Li,&nbsp;Kaiyan Xiao,&nbsp;Shujun Shi,&nbsp;Zhenghan Chen,&nbsp;Yumei Wang,&nbsp;Rui Zhang,&nbsp;Xuejiao An,&nbsp;Yaojing Yue","doi":"10.1016/j.ygeno.2026.111273","DOIUrl":"10.1016/j.ygeno.2026.111273","url":null,"abstract":"<div><h3>Objective</h3><div>Sheep pulmonary adenocarcinoma (SPA), a chronic contagious lung neoplasm induced by jaagsiekte sheep retrovirus (JSRV), represents a unique animal model for studying virus-driven lung carcinogenesis. This study aimed to systematically dissect host transcriptional reprogramming in naturally infected lung tissues using whole-transcriptome sequencing and to identify core regulatory factors associated with SPA pathogenesis.</div></div><div><h3>Methods</h3><div>Lung tumor tissues from naturally SPA-infected sheep and matched healthy lung tissues were collected as experimental samples. High-throughput whole-transcriptome sequencing was performed to profile coding and non-coding RNA expression. Differentially expressed mRNAs (DE-mRNAs), long non-coding RNAs (DE-lncRNAs), microRNAs (DE-miRNAs), and circular RNAs (DE-circRNAs) were identified through bioinformatic analyses. Functional enrichment analyses (Gene Ontology, GO) and Kyoto Encyclopedia of Genes and Genomes,KEGG) were conducted to elucidate the biological roles of these differentially expressed molecules. An integrative multi-omics approach was employed to construct a host endogenous competing endogenous RNA (ceRNA) regulatory network. Key differentially expressed molecules were further validated by RT-qPCR.</div></div><div><h3>Results</h3><div>A total of 2067 DE-mRNAs, 72 DE-lncRNAs, 210 DE-miRNAs, and 477 DE-circRNAs were identified. Functional enrichment analyses revealed significant involvement of these molecules in key oncogenic signaling pathways, including MAPK, PI3K–Akt, mTOR, and Hippo. Integrative analysis enabled the construction of an SPA-specific ceRNA network, highlighting several critical regulatory axes: Novel_circ_008415–oar-miR-16b–ALDH1A2, MSTRG.36927.2–oar-miR-16b–CD22, and MSTRG.36932.1–oar-miR-16b–BCL2/CCND1. RT-qPCR validation confirmed that the expression trends of these key molecules were highly consistent with the sequencing data.</div></div><div><h3>Conclusion</h3><div>This study provides a comprehensive whole-transcriptome landscape of lung tissues from sheep naturally infected with SPA, uncovering the potential roles of non-coding RNAs—mediated via ceRNA mechanisms—in regulating tumor cell apoptosis, immune evasion, and malignant proliferation. Our findings offer novel molecular insights into JSRV-induced oncogenesis, identify candidate biomarkers for early diagnosis, and lay a theoretical foundation for the development of targeted therapeutic strategies against SPA.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"118 4","pages":"Article 111273"},"PeriodicalIF":3.6,"publicationDate":"2026-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148217057","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Single-nucleus RNA sequencing reveals molecular determinants of functional and physiological differences between extraocular and quadriceps muscles in Macaca fascicularis","authors":"Peipei Jiang,&nbsp;Moxin Chen,&nbsp;Qiming Wang,&nbsp;Jinbao Qin,&nbsp;Qian Bian,&nbsp;Lin Li","doi":"10.1016/j.ygeno.2026.111283","DOIUrl":"10.1016/j.ygeno.2026.111283","url":null,"abstract":"<div><div>Extraocular muscles (EOM) display distinct physiological and pathological characteristics compared with limb skeletal muscles. To define the molecular basis of these differences, we performed single-nucleus RNA sequencing on EOM and quadriceps femoris muscle (QFM) from <em>Macaca fascicularis</em>. Transcriptomic profiling revealed distinct cell type compositions, with EOM enriched in fast-twitch fibers (2 A/2×), fibro-adipogenic progenitors, and neural-associated cells. EOM myonuclei expressed genes involved in synaptic transmission and axon development, whereas QFM myofibers were enriched for oxidative phosphorylation and glycolysis pathways. EOM uniquely expressed diverse myosin isoforms, including MYH13 and MYH4, supporting specialized contractile function. Disease-associated genes showed differential expression between the two muscle types, suggesting distinct susceptibilities. Intercellular communication analysis further revealed neuromuscular and regenerative signaling dominance in EOM, contrasting with immune and metabolic signaling in QFM. Together, these findings provide a comprehensive molecular framework for understanding EOM specialization and disease vulnerability.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"118 4","pages":"Article 111283"},"PeriodicalIF":3.6,"publicationDate":"2026-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148301559","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Impact of genotype on histopathology and clinical characters in a Chinese cohort with obstructive hypertrophic cardiomyopathy","authors":"Kunlun Yin,&nbsp;Yang Sun,&nbsp;Huazheng Zhao,&nbsp;Hang Yang,&nbsp;Yanhai Meng,&nbsp;Tianjiao Li,&nbsp;Wenke Li,&nbsp;Bianmei Han,&nbsp;Xuewen Liu,&nbsp;Shuiyun Wang,&nbsp;Zhou Zhou","doi":"10.1016/j.ygeno.2026.111286","DOIUrl":"10.1016/j.ygeno.2026.111286","url":null,"abstract":"<div><h3>Background</h3><div>While genotype has been related to specific clinical phenotype in hypertrophic cardiomyopathy (HCM), the critical intervening role of histopathological damage remains unclear. Specifically, how graded variant pathogenicity drives the spectrum of myocardial tissue alterations, which in turn mediate the severity and precocity of clinical features is poorly defined.</div></div><div><h3>Methods</h3><div>A 93-cardiomyopathy-related-gene panel was used to screen 193 Chinese Obstructive Hypertrophic Cardiomyopathy (HOCM) patients. In this study, “genetic variants” were classified into four categories: Pathogenic(P), Likely Pathogenic (LP), and variants of unknown significance (VUS), an additional tier of VUS-LP. The histopathological alterations were evaluated using 172 septal tissue sections with HE and Masson trichromatic staining. Through comprehensive case review and longitudinal follow-up, we investigated the genotype-phenotype correlations, focusing on the mediating role of myocardial histology in shaping clinical presentation and outcomes.</div></div><div><h3>Results</h3><div>The median age at operation was 40.2 years, and 111 (57.5%) were men. Compared with the patients with VUS and no variants, those with LP/P and VUS-LP variants exhibited relatively severe phenotypes including earlier diagnosis age and greater asymmetric hypertrophy, and significantly worse histopathological alterations. The existence of the variant, regardless of the number, was also related to similar severe effects. Pathogenic variants and more severe histological changes were associated with an aggravated clinical phenotype, including prolonged QRS duration and elevated NT-proBNP revealing a genotype-histology-phenotype interplay in HOCM. Among patients with a family history of sudden death, the LP/P variant detection rate was 71.4% (10/14).</div></div><div><h3>Conclusions</h3><div>Core gene panel sequencing represents an efficacious approach for genetic testing in individuals with hypertrophic cardiomyopathy (HCM). Among those at elevated risk for sudden cardiac death, there is a higher prevalence of pathogenic variants. Patients harboring higher-grade pathogenic variants demonstrate more severe pathological changes and exhibit more pronounced alterations in cardiac rhythm and clinical parameters. The consistent “fibrosis-dominant” remodeling observed in patients with variants of uncertain significance likely pathogenic (VUS-LP) indicates that histopathological severity may serve as an auxiliary phenotypic metric for the future re-evaluation of such variants. Consequently, the integration of genetic testing results with a multidisciplinary assessment of phenotypes—including clinical, pathological, and laboratory findings—is essential for guiding disease management in HCM.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"118 4","pages":"Article 111286"},"PeriodicalIF":3.6,"publicationDate":"2026-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148316743","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Evolocumab protects mice from radiation-induced damage by affecting hematopoietic cell lineage","authors":"Yuhan Gan,&nbsp;Jiawei Zhou,&nbsp;Bendong Li,&nbsp;Daqian Huang,&nbsp;Yuejun Ma,&nbsp;Lu Pei,&nbsp;Kaiwen Sheng,&nbsp;Liao Zhang,&nbsp;Ying Cheng,&nbsp;Jicong Du,&nbsp;Shengyun Cai,&nbsp;Cong Liu","doi":"10.1016/j.ygeno.2026.111277","DOIUrl":"10.1016/j.ygeno.2026.111277","url":null,"abstract":"<div><h3>Background</h3><div>The hematopoietic system is extremely sensitive to ionizing radiation(IR) and is easily damaged after exposure. Recent studies [1, 2] have shown that hematopoietic lineage differentiation may play a key role in Ionizing radiation -induced acute injury.</div></div><div><h3>Methods</h3><div>C57BL/6 mice matched for age, sex and weight were randomly grouped and intraperitoneal injected with PBS, Evolocumab (80.0 mg/kg) or MMP9-IN (20.0 mg/kg). Survival time, body weight, pathology, hematopoietic cell differentiation changes and organoids of the mice after IR (10.0 Gy) were compared, and the mechanism of action in tissues was verified by transcriptome sequencing.</div></div><div><h3>Results</h3><div>Ionizing radiation can inhibit hematopoietic cell lineage differentiation and affect cholesterol metabolism. The expression of the <em>Pcsk9</em> gene was significantly upregulated after IR. Treatment with a <em>Pcsk9</em> monoclonal antibody (Evolocumab) exerted significant radioprotective effects, including improving the survival rate of irradiated mice, reducing body weight loss, preserving the integrity of the bone marrow cavity, and promoting cellular proliferation. Flow cytometric analysis showed that Evolocumab significantly increased hematopoietic precursor cells and hematopoietic stem cells and promoted their differentiation into ST-LSKs and MPPs. In addition, the proportions of CMPs and GMPs were increased, whereas the proportion of MEPs was decreased. RNA sequencing results suggested that the IR-induced downregulation of <em>Cd3e</em> within the hematopoietic cell lineage pathway could be rescued by Evolocumab, which was further validated at the cellular level. CD3e is a T-cell-associated marker, and Evolocumab treatment was associated with an increased proportion of CD3e⁺ T cells. Analysis of previously reported hematopoiesis-related factors [3–5] indicated that Evolocumab markedly upregulated <em>Mmp9</em> expression. Correlation analysis revealed that <em>Pcsk9</em> was negatively correlated with <em>Cd3e</em>, whereas <em>Cd3e</em> was positively correlated with <em>Mmp9</em>. Following ionizing radiation, <em>Mmp9</em> knockout (<em>Mmp9</em> KO) mice exhibited reduced survival compared with wild-type mice. Moreover, in wild-type mice, administration of an MMP9 inhibitor (MMP9-IN) attenuated the radioprotective effects of Evolocumab, indicating that <em>Mmp9</em> contributes to Evolocumab-mediated radioprotection.</div></div><div><h3>Conclusion</h3><div>Evolocumab exerts a positive effect on promoting the proliferation and differentiation of hematopoietic stem cells against IR-induced hematopoietic system injury, with its protective mechanism likely involving the activation of hematopoietic cell lineages to upregulate CD3e⁺ T cells and Mmp9 expression.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"118 4","pages":"Article 111277"},"PeriodicalIF":3.6,"publicationDate":"2026-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148239100","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A single-nucleus transcriptomic atlas of early marine shrimp embryogenesis reveals cell-type specification and eye pigment transport mechanisms","authors":"Hao Zhong,&nbsp;Zulaikha Mat Deris,&nbsp;Panpan Wang,&nbsp;Panpan Niu,&nbsp;Yu Wang,&nbsp;Shanshan Jiang,&nbsp;Jing Xu,&nbsp;Jie Kong,&nbsp;Sheng Luan,&nbsp;Yik Sung Yeong,&nbsp;Li Lian Wong,&nbsp;Huan Gao","doi":"10.1016/j.ygeno.2026.111280","DOIUrl":"10.1016/j.ygeno.2026.111280","url":null,"abstract":"<div><div>Early embryogenesis and their underlying regulatory mechanisms in crustaceans remains unclear at the cellular level. Here, we mapped the early developmental stages of marine shrimp <em>Palaemon carinicauda</em> using single nucleus RNA sequencing (snRNA-seq), spanning the transitional stages of blastula to protozoea. Profiling over 60,000 nuclei, we identify six distinct embryonic cell types, including the multiple neuronal subtypes, extracellular matrix- producing cells, cuticle-forming cells, and an eye-related cells that emerged during protozoea development. Cell-type identities were validated using selected marker genes expression and spatial expression patterns via fluorescent in situ hybridization (FISH). <em>PcWhite</em> and <em>PcScarlet</em> contain a highly conserved nucleotide-binding domain (NBD) motif, including Walker A, ABC signature sequence and Walker B domain and a conserved six transmembrane domain (TMD). RNA interference (RNAi) analysis targeting the ABC transporter genes White (W) and Scarlet (St) demonstrated that these genes are essential for eye pigment precursor transport, morphogenesis, and embryonic viability. Collectively, this integrative approach demonstrates the robustness of snRNA-seq for dissecting early embryogenesis in non-model species, linking cell-type-specific gene expression to key developmental processes that enables comparative evolutionary genomics across crustaceans.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"118 4","pages":"Article 111280"},"PeriodicalIF":3.6,"publicationDate":"2026-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148283426","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Shifting genomes, rising threats: Adaptive evolution and antimicrobial resistance of E. coli ST10 across African ecologies","authors":"Refiloe Malesa,&nbsp;Rian Pierneef,&nbsp;Kudakwashe Magwedere,&nbsp;Thendo Mafuna,&nbsp;Itumeleng Matle","doi":"10.1016/j.ygeno.2026.111278","DOIUrl":"10.1016/j.ygeno.2026.111278","url":null,"abstract":"<div><div><em>Escherichia coli</em> sequence type 10 (ST10) is an emerging zoonotic lineage with global distribution and a high antimicrobial resistance (AMR) burden, yet its population dynamics across Africa remain poorly understood. Here, we analysed 159 <em>E. coli</em> ST10 genomes including four newly sequenced isolates and 155 publicly available genomes from 19 African countries spanning human, animal, food, and environmental sources. Whole genome sequencing revealed high species-level similarity (mean average nucleotide identity: 99.44%), but single nucleotide polymorphism (SNP)-based phylogenetics delineated 122 distinct clusters, indicating substantial intra-lineage diversity. Over 71% of isolates were multidrug-resistant, with 29% carrying the extended-spectrum β-lactamase gene <em>bla_CTX-M-15</em>. Plasmid replicon analysis highlighted the widespread presence of IncFIB and ColRNAI plasmids, strongly linked to AMR gene carriage. Human-derived isolates predominated both phylogenetic clusters and resistance profiles. SNP-based comparisons revealed evidence of both localized evolution and long-distance dissemination across countries. These interconnected pathways underscore the bacterium's ecological ubiquity and the limitations of siloed surveillance strategies. The predominance of human-derived isolates and evidence of both local and cross-border transmission highlight humans as key reservoirs and underscore the need for coordinated surveillance. These findings underscore the urgent need for integrated continent-wide One Health approach strategies to monitor and combat antimicrobial resistance, economic impact on trade restrictions and health security threats.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"118 4","pages":"Article 111278"},"PeriodicalIF":3.6,"publicationDate":"2026-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148264080","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}