Genomics最新文献

{"title":"Identification of key genes and relevant genetic variants regulating muscle color in chicken using a multi-omics approach","authors":"Lilin Men ,&nbsp;Yang Yu ,&nbsp;Richun Cai ,&nbsp;Xiaojing Liu ,&nbsp;Yongli Wang ,&nbsp;Zhiwu Chen ,&nbsp;Guiping Zhao ,&nbsp;Jie Wen ,&nbsp;Hegang Li ,&nbsp;Huanxian Cui","doi":"10.1016/j.ygeno.2025.111105","DOIUrl":"10.1016/j.ygeno.2025.111105","url":null,"abstract":"<div><div>Meat color is an important economic trait of chicken that influences the willingness of consumers to buy it. Elucidating the genetic mechanisms regulating chicken color is essential to optimize poultry breeding strategies and improve meat quality. However, the genes and genetic variants involved remain unknown. In this study, the regulatory mechanism of the Jingxing yellow chicken color was revealed by a multi-omics approach, including transcriptomics/RNA sequencing (RNA-seq) analysis, comprehensive metabolomics analysis and carotenoid measurement. Our results showed that a significant region on chromosome 11 (15.36–15.47 Mb) was associated with the breast muscle meat color yellowness (b*), and <em>BCO1</em> was mapped to this region as a candidate gene. In addition, the detection of the higher expression level of <em>BCO1</em> mRNA in the group with the high-b* by RNA-seq analysis further supports that <em>BCO1</em> is a key candidate gene associated with the breast muscle meat color b*. Also, the relevant single-nucleotide polymorphism (SNP) rs315311588 identified among the SNPs present in the 10 introns of <em>BCO1</em>, was found to reduce the expression level of <em>BCO1</em> and increase the breast muscle meat color b*. Moreover, the multi-omics results reveal that decreased expression level of <em>BCO1</em> leads to reduced conversion of lycopene to retinol, but significantly increases the content of lutein, which gives the yellow color to the breast muscle meat. Additionally, we also found that increase in yellow pigment production may promote fat deposition in breast muscle meat.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 6","pages":"Article 111105"},"PeriodicalIF":3.0,"publicationDate":"2025-09-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145137161","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":"Exploration of novel biomarkers of obese asthma using RNA sequencing in high-fat-fed asthmatic model mice","authors":"Zhenzhen Pan ,&nbsp;Cengceng He ,&nbsp;Xuena Xu ,&nbsp;Yuting Jin ,&nbsp;Mingyi Xu ,&nbsp;Suwan Xiong ,&nbsp;Ling Li ,&nbsp;Chuangli Hao","doi":"10.1016/j.ygeno.2025.111115","DOIUrl":"10.1016/j.ygeno.2025.111115","url":null,"abstract":"<div><h3>Background</h3><div>Obese asthma is a specific phenotype of childhood asthma characterized by increased severity, decreased quality of life, and reduced treatment response. Herein, we applied transcriptomics to investigate biomarkers of obese asthma.</div></div><div><h3>Methods</h3><div>Mouse models of obesity and asthma were induced through high-fat diet (HFD) feeding and ovalbumin inhalation, respectively. RNA was extracted from lung samples from HFD-fed asthma, HFD-fed control, normal-fat diet (NFD)-fed asthma, and NFD-fed control mice. Transcriptome sequencing data were analyzed for quality control (QC), and differentially expressed genes (DEGs) were identified. From this list, candidate genes were obtained through intersections, followed by the construction of protein-protein interaction (PPI) networks to identify key genes. Subsequently, immune cell infiltration was analyzed across the different subgroups. Key genes were validated using Quantitative Polymerase Chain Reaction (PCR).</div></div><div><h3>Results</h3><div>Overall, 86 candidate genes were identified from the intersection of different DEG sets. PPI networks were constructed using three algorithms, revealing nine key genes (ITGM, Slc11a1, Nos2, PirB, IL1RN, LCN2, CD33, MSR1, and CXCL2). Immune infiltration analysis revealed distinct responses in immune cells, including naïve B cells and plasma cells. Following verification by qPCR, ITGAM, Nos2, LCN2, CD33, MSR1, and CXCL2 were confirmed to be significantly higher in the HFD-fed asthma group than in the NFD-fed asthma group. Slc11a1 was significantly downregulated, while PirB and IL1RN showed no significant differences. The expression levels of ITGAM, Nos2, and LCN2 demonstrated a consistent trend in human peripheral blood samples. However, to further substantiate their roles in obesity-associated asthma, an expanded sample size is required for confirmation.</div></div><div><h3>Conclusion</h3><div>This study systematically investigated the molecular mechanisms underlying the associated obesity and metabolic disorders, identified biomarkers, and provided new directions for future therapeutic and clinical studies on obese asthma.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 6","pages":"Article 111115"},"PeriodicalIF":3.0,"publicationDate":"2025-09-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145130571","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":"Organelle genomes of progeny of Tripidium arundinaceum × Saccharum spontaneum and sugarcane cultivar revealed their inheritance and characterization after hybridization","authors":"Sicheng Li ,&nbsp;Shan Zhou ,&nbsp;Fengzhen Wu ,&nbsp;Yuxin Huang ,&nbsp;Yang Zhao ,&nbsp;Baoqing Zhang ,&nbsp;Gemin Zhang ,&nbsp;Weixing Duan ,&nbsp;Xiping Yang","doi":"10.1016/j.ygeno.2025.111107","DOIUrl":"10.1016/j.ygeno.2025.111107","url":null,"abstract":"<div><div>Sugarcane (<em>Saccharum</em> spp.) breeding often involves hybridization with distantly related wild species (such as <em>Tripidium arundinaceum</em>) to improve stress resistance, but mitochondrial and chloroplast inheritance across multiple backcross generations remains poorly understood. In this study, we employed PacBio and Illumina sequencing to assemble and compare the mitochondrial genomes (mitogenomes) and chloroplast genome of four genotypes: an distant hybrid F₁ GXAS 07–6-1 (<em>Tripidium arundinaceum</em> × <em>Saccharum spontaneum</em>), a subsequent hybrid F₁ GXASF₁ 08–2-28, a first-generation backcross GXASBC₁ 12-A6–3, and a second-generation backcross GXASBC₂ 15–114. Maternal inheritance preserves key co-linear gene clusters, whereas MTPT content varies, indicating post-hybridization structural adjustments. Our study confirms strict maternal inheritance of mitochondrial and chloroplast genomes across hybrid and backcross generations and validates mitochondrial transmission using organelle-specific markers, providing insights into organellar inheritance and references for sugarcane breeding.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 6","pages":"Article 111107"},"PeriodicalIF":3.0,"publicationDate":"2025-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145091662","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":"Analysis of the potential mechanism of stem cells in the treatment of diabetic nephropathy based on 16S, metabolome and transcriptome","authors":"Xing-na Liao ,&nbsp;Li-lan Huang ,&nbsp;Ji Yang,&nbsp;Yue-yuan Hou,&nbsp;Yi-xiao Quan,&nbsp;Yi-hua Bai","doi":"10.1016/j.ygeno.2025.111113","DOIUrl":"10.1016/j.ygeno.2025.111113","url":null,"abstract":"<div><h3>Background</h3><div>Diabetic nephropathy (DN) has become a major cause of end-stage renal failure. The therapeutic mechanism of mesenchymal stem cells (MSCs) in DN is not fully understood.</div><div>In this study, we used transcriptome sequencing, 16S rRNA sequencing, and metabolomics sequencing to perform a combined multi-omics analysis to investigate the potential mechanisms of MSCs for DN.</div></div><div><h3>Methods</h3><div>First, DN mouse model was established. Kidneys, feces, and blood were collected from 6 control, 6 model, and 6 intervention (MSCs) groups for transcriptome sequencing, 16S RNA sequencing, and metabolome sequencing, respectively. Then, candidate genes between the 3 groups were identified and enriched using transcriptomic analysis. Next, with the help of metabolomics analysis, differential metabolites were screened by OPLS-DA analysis for control and model groups, as well as model and MSCs groups, respectively. Similarly, differential microorganisms and candidate microorganisms were selected by 16S rRNA gene sequencing data. Subsequently, the correlations between candidate genes and candidate metabolites, candidate genes and candidate microorganisms, as well as candidate metabolites and candidate microorganisms were explored by Spearman correlation analysis, respectively. Finally, a microbe-metabolite-gene network was constructed to identify key genes, key metabolites and key microbes, and their expression levels were analyzed.</div></div><div><h3>Results</h3><div>There were differences in genes, microorganisms, and metabolites among the samples in the control, model, and MSCs groups. Candidate genes enriched in the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways included adhesion molecules and 2-oxocarboxylic acid metabolism. GDP-mannose biosynthesis and purine ribonucleoside degradation were significantly enriched by different microorganisms. The KEGG pathways mainly enriched for differential metabolites were PPAR signaling pathway, arachidonic acid metabolism, and Rap1 signaling pathway. A microorganisms-metabolite-gene network containing 25 nodes and 53 edges was constructed with interactions including <em>Sorangium</em>-neg-M501T271 and Tmem238l-pos-M373T270, among others. In addition, 10 key genes, 5 key microorganisms and 10 key metabolites were significantly expressed in both the MSCs group and the control group.</div></div><div><h3>Conclusion</h3><div>This study identified 10 key genes, 10 key metabolites and 5 key microorganisms and a correlation network diagram was constructed. It provided a theoretical reference for exploring the molecular mechanisms of MSCs for DN treatment.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 6","pages":"Article 111113"},"PeriodicalIF":3.0,"publicationDate":"2025-09-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145085734","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":"Combination of circular RNA-miRNA-mRNA expression profiles and bioinformatic analysis in ovarian endometriosis","authors":"Xiaoli Li ,&nbsp;Ding Cui ,&nbsp;Yang Liu","doi":"10.1016/j.ygeno.2025.111112","DOIUrl":"10.1016/j.ygeno.2025.111112","url":null,"abstract":"<div><div>Endometriosis is a mysterious disease that affects 5 %–10 % of the women of reproductive age. Circular RNAs (circRNAs), a type of noncoding RNA, are involved in its progression, yet their regulatory mechanisms via integrated circRNA–miRNA–mRNA networks remain poorly studied. We profiled circRNAs, miRNAs, and mRNAs expression in paired eutopic and ectopic endometrium from patients with ovarian endometriosis. Differential expression analysis revealed 325 circRNAs, 295 miRNAs, and 4605 mRNAs. Using bioinformatic predictions and negative correlation analysis, we constructed a ceRNA network comprising 134 circRNAs, 72 miRNAs, and 107 mRNAs. Moreover, we identified hsa_circ_0005918/miR-504-5p/<em>PDLIM2</em> and hsa_circ_0005918/miR-105-5p/<em>OBSL1</em> as crucial regulatory axes in endometriosis. Functional experiments confirmed that hsa_circ_0005918 promotes cells migration and invasion by sponging miR-504-5p and miR-105-5p, upregulating <em>PDLIM2</em> and <em>OBSL1,</em> which may consequently contribute to the progression of endometriotic lesions. Our constructed network presents robust credibility, facilitating the exploration of complex mechanisms of circRNAs in endometriosis.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 6","pages":"Article 111112"},"PeriodicalIF":3.0,"publicationDate":"2025-09-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145080375","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":"Comparative transcriptome analysis revealed the molecular response mechanism of sugar beet (Beta vulgaris L.) against Cercospora Leaf Spot disease","authors":"Hongyong Lou ,&nbsp;Guangzhou Ding ,&nbsp;Fangpu Cai ,&nbsp;Chunlei Zhao ,&nbsp;Yanli Li","doi":"10.1016/j.ygeno.2025.111109","DOIUrl":"10.1016/j.ygeno.2025.111109","url":null,"abstract":"<div><div><em>Cercospora leaf spot</em> (CLS), caused by the hemibiotrophic fungus <em>Cercospora beticola</em> (<em>C. beticola</em>), critically threatens global sugar beet production through defoliation and chlorosis, reducing root yields by ≤50 % and impairing sucrose crystallization. As fungicide resistance escalates in <em>C. beticola</em> populations, developing genetically resistant sugar beet becomes imperative. We dissected CLS resistance mechanisms via comparative transcriptomics of resistant (81GM241) and susceptible (KWS6661) genotypes across four infection stages (0–30 dpi). Resistant plants deployed a triphasic defense strategy: During early infection (10 dpi), rapid activation of phenylpropanoid biosynthesis, fatty acid elongation, and glutathione metabolism established dual barriers of lignin-mediated cell wall fortification and ROS scavenging. By mid-infection (20 dpi), pathogen recognition receptors triggered MAPK-WRKY cascades that amplified jasmonate-mediated defenses while mobilizing flavonoid antimicrobials. In late infection (30 dpi), systemic downregulation of photosynthetic antenna proteins redirected resources to tryptophan-derived phytoalexins, sustaining defense without growth penalties. Crucially, resistant plants proactively anticipated stress through coordinated calcium signaling (CDPK), pectin methylesterase-driven cell wall remodeling, and antioxidant activation before pathogen proliferation. In contrast, susceptible plants exhibited delayed ROS detoxification and impaired signal transduction. This phased defense architecture—initiating with pathogen recognition and transient oxidative bursts, progressing through sustained immune activation, and culminating in metabolic optimization—provides a molecular framework for breeding resistant varieties by stacking phase-specific defense regulators.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 6","pages":"Article 111109"},"PeriodicalIF":3.0,"publicationDate":"2025-09-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145045580","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":"Chromosome-level assembly of the genome of the Aythya nyroca provides insights into diving adaptations","authors":"Jianqun Ding ,&nbsp;Tian Xia ,&nbsp;Shuhong Li ,&nbsp;Xiaodong Gao ,&nbsp;Zhicheng Yao ,&nbsp;Shengyang Zhou ,&nbsp;Lei Zhang ,&nbsp;Zhihao Zhang ,&nbsp;Shunting Chen ,&nbsp;Mingke Han ,&nbsp;Honghai Zhang","doi":"10.1016/j.ygeno.2025.111103","DOIUrl":"10.1016/j.ygeno.2025.111103","url":null,"abstract":"<div><h3>Background</h3><div><em>Aythya nyroca</em> (Ferruginous Duck), a small to medium-sized chestnut-colored diving duck, is mainly distributed in central, western, and southern Asia, southern Europe, and central Africa. We employed Oxford Nanopore sequencing and Hi-C technique to assemble the first chromosome-level genome of <em>A. nyroca</em>. The assembled genome had a scaffold N50 of 86,001,877 bp, with 35 pseudochromosomes mounted. Repeat sequences accounted for approximately 14.84 % of the genome.</div></div><div><h3>Results</h3><div>To uncover the molecular mechanisms of diving adaptations in <em>A. nyroca</em>, we conducted separate enrichment analyses on species-unique genes, expanded and contracted gene families, and positively selected genes. The results indicated the enrichment of pathways related to blood oxygen concentration regulation and energy metabolism. The enrichment of related pathways and the positive selection of related genes may reveal the adaptive evolutionary mechanism of <em>A. nyroca</em> in the diving environment.</div></div><div><h3>Conclusions</h3><div>This high-quality genome provides a valuable resource for studying the evolution of the diving adaptation mechanism in birds. Whole-genome assemblies are crucial for comprehensively understanding various aspects of <em>A. nyroca</em> biology, including morphology, ecology, and physiology, and thus play an essential role in its conservation.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 6","pages":"Article 111103"},"PeriodicalIF":3.0,"publicationDate":"2025-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145058598","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":"A chromosome-level genome assembly of Termitomyces fuliginosus using Oxford Nanopore and Hi-C sequencing","authors":"Wei-ying Chen,&nbsp;Yang-sen Qin,&nbsp;Ting-fu Zhang,&nbsp;Jian Zou,&nbsp;Jun Yang,&nbsp;Zhen-yong Chen","doi":"10.1016/j.ygeno.2025.111110","DOIUrl":"10.1016/j.ygeno.2025.111110","url":null,"abstract":"<div><div><em>Termitomyces fuliginosus</em> is a tasty edible mushroom with both nutritional and medicinal values, consumed by native people throughout Asia. However, studies about this mushroom are limited due to lack of fine genomic information, such as the molecular mechanisms underlying development, symbiosis with termites, and plant biomass degradation. In this study, we reported a chromosome-level reference genome of <em>T. fuliginosus</em> assembled using Oxford Nanopore technologies (ONT) and Hi-C technologies. In total, the clean data obtained from ONT and Hi-C sequencing amounted to 10.42 Gb and 21.75 Gb, respectively. The assembled genome consisted of 13 chromosomes with a total length of 65.66 Mb. Completeness evaluations showed that this assembled genome had high quality, with a complete BUSCO score of 91.6 %. In total, 10,319 protein-coding genes were identified, and each gene received at least one functional annotation hit across the queried databases. Based on single-copy orthologous genes, phylogenetic analysis revealed that <em>T. fuliginosus</em> shared a close evolutionary relationship with <em>Termitomyces cryptogamus</em>, <em>Arthromyces matolae</em>, <em>Tricholoma furcatifolium</em>, <em>Tephrocybe rancida</em>, <em>Lyophyllum atratum</em>, and <em>Tricholoma matsutake</em>. A total of 303 carbohydrate-active enzymes (CAZyme) genes were identified in the <em>T. fuliginosus</em> genome, enabling a better understanding of the carbohydrate degradation capabilities for <em>T. fuliginosus</em>. This chromosome-level genome of <em>T. fuliginosus</em> provides valuable reference data for utilizing the medicinal and nutritional value of this mushroom, such as accurate genomic sequences without gaps, genomic analysis of functional genes, and visualization of chromosomal structural variations.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 6","pages":"Article 111110"},"PeriodicalIF":3.0,"publicationDate":"2025-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145058576","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":"Unmapped reads from whole-genome sequencing data reveal pathogen diversity in European and African cattle breeds","authors":"Daniil Ruvinskiy ,&nbsp;Kisun Pokharel ,&nbsp;Rodney Okwasiimire ,&nbsp;Rayner Gonzalez-Prendes ,&nbsp;Catarina Ginja ,&nbsp;Nasser Ghanem ,&nbsp;Donald R. Kugonza ,&nbsp;Mahlako L. Makgahlela ,&nbsp;Heli Lindeberg ,&nbsp;Melak Weldenegodguad ,&nbsp;Juha Kantanen ,&nbsp;Martijn Derks ,&nbsp;Richard P.M.A. Crooijmans","doi":"10.1016/j.ygeno.2025.111108","DOIUrl":"10.1016/j.ygeno.2025.111108","url":null,"abstract":"<div><div>Climate change is impacting the global spread of infectious diseases, altering pathogen distribution and transmission, and threatening human and animal health. This study investigates the presence of potential pathogens in blood within unmapped reads obtained from whole-genome sequencing (WGS) data of various cattle breeds across geographically diverse regions, including South Africa, Uganda, Egypt, Portugal, The Netherlands, and Finland. Unmapped reads were extracted, assembled into contigs, and subjected to taxonomic analysis based on an extensive literature search. The analysis revealed significant geographic variation in pathogen composition, with breeds in the Southern Hemisphere (Uganda, Egypt, and South Africa) showing higher pathogen alignment counts while Northern breeds (particularly from Finland) exhibited lower diversity and counts. Portugal, representing a transition zone, exhibited a higher burden of parasites and tick-borne related pathogens than their Northern counterparts, which were also prevalent in Southern Hemisphere breeds such as <em>Theileria parva</em>, <em>Anaplasma platys</em>, <em>Theileria orientalis</em>, and <em>Babesia bigemina,</em> which is in line with the known capacity of these breeds to cope with local pathogens. Dutch breeds were found to harbor <em>Escherichia coli O157</em>, a known public health concern. The study provided key insights into emerging disease risks influenced by climate change and livestock management practices, but also on the need to investigate possible adaptive responses underlying disease resistance in some breeds. This study highlights the potential for climate-driven variations in disease ecology and transmission, emphasizing the need for integrating genomic and environmental data, and is currently the most comprehensive study to date investigating the microbial diversity present in unmapped reads obtained from WGS data of cattle populations.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 6","pages":"Article 111108"},"PeriodicalIF":3.0,"publicationDate":"2025-09-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145052701","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 of cross-talk pathways and PANoptosis-related genes in periodontitis and atherosclerosis by bioinformatics analysis and machine learning","authors":"Nan Yang ,&nbsp;Shiqun Sun ,&nbsp;Xiantao Chen ,&nbsp;Tongtong Yan ,&nbsp;Nan Gu ,&nbsp;Zhihui Liu","doi":"10.1016/j.ygeno.2025.111106","DOIUrl":"10.1016/j.ygeno.2025.111106","url":null,"abstract":"<div><h3>Background and objectives</h3><div>Periodontitis(PD) is a chronic inflammatory disease that poses a serious threat to oral health and is one of the risk factors for atherosclerosis(AS). A growing body of evidence suggests that the two diseases are closely related. However, current studies have yet to fully understand the common genes and common mechanisms between PD and AS. This study aimed to screen the tandem genes of PD and AS and the potential relationship between the tandem genes and pan-apoptosis-related genes. By analyzing the relationship between the core genes and immune cells, it will provide new targets for clinical treatment.</div></div><div><h3>Materials and methods</h3><div>The PD and AS datasets were downloaded from the GEO database and differential expression analysis was performed to obtain DEGs. AS-related genes were downloaded from the GeneCards database, and PANoptosis-related genes were obtained through literature review. AS-related genes were merged into AS DEGs, and overlapping DEGs were cross-talk genes for PD and AS. Protein-protein interaction (PPI) network was constructed using the STRING database and Cytoscape software. Pearson coefficients were used to calculate the correlation between cross-talk genes and PANoptosis-related genes in the PD and AS datasets. The intersection of cross-talk genes and PANoptosis-related genes was defined as cross-talk-PANoptosis genes. Core genes were screened using ROC analysis and XGBoost. PPI sub-network, gene-biological processes and gene-pathway networks were constructed based on the core genes. In addition, immune infiltration on the PD and AS datasets was analyzed using the CIBERSORT algorithm.</div></div><div><h3>Results</h3><div>285 cross-talk genes overlapped between PD DEGs and AS DEGs. The intersection of cross-talk genes with 109 PANoptosis-related genes was defined as cross-talk-PAoptosis genes. ROC and XGBoost showed that MLKL, ZBP1, CD14, and IL6 were more accurate than the other cross-talk-PAoptosis genes in predicting the diseases, and were better in terms of the overall characteristics. GO and KEGG analyses showed that these four core genes were involved in the immune and inflammatory response of the organism. The results of immune infiltration showed that Monocytes and Mast cells resting were altered to a greater extent in PD and AS patients. Finally, 24 drugs related to the core genes were retrieved from the DGIDB database.</div></div><div><h3>Conclusions</h3><div>This study reveals the joint mechanism between PD and AS associated with PANoptosis. Analyzing the four core genes and immune cells may provide new therapeutic directions for the pathogenesis of PD combined with AS.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 6","pages":"Article 111106"},"PeriodicalIF":3.0,"publicationDate":"2025-09-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145045581","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}