Pub Date : 2025-09-15DOI: 10.1016/j.ygeno.2025.111112
Xiaoli Li , Ding Cui , Yang Liu
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/PDLIM2 and hsa_circ_0005918/miR-105-5p/OBSL1 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 PDLIM2 and OBSL1, 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.
{"title":"Combination of circular RNA-miRNA-mRNA expression profiles and bioinformatic analysis in ovarian endometriosis","authors":"Xiaoli Li , Ding Cui , 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}
Pub Date : 2025-09-12DOI: 10.1016/j.ygeno.2025.111109
Hongyong Lou , Guangzhou Ding , Fangpu Cai , Chunlei Zhao , Yanli Li
Cercospora leaf spot (CLS), caused by the hemibiotrophic fungus Cercospora beticola (C. beticola), critically threatens global sugar beet production through defoliation and chlorosis, reducing root yields by ≤50 % and impairing sucrose crystallization. As fungicide resistance escalates in C. beticola 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.
{"title":"Comparative transcriptome analysis revealed the molecular response mechanism of sugar beet (Beta vulgaris L.) against Cercospora Leaf Spot disease","authors":"Hongyong Lou , Guangzhou Ding , Fangpu Cai , Chunlei Zhao , 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}
Pub Date : 2025-09-11DOI: 10.1016/j.ygeno.2025.111103
Jianqun Ding , Tian Xia , Shuhong Li , Xiaodong Gao , Zhicheng Yao , Shengyang Zhou , Lei Zhang , Zhihao Zhang , Shunting Chen , Mingke Han , Honghai Zhang
Background
Aythya nyroca (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 A. nyroca. 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.
Results
To uncover the molecular mechanisms of diving adaptations in A. nyroca, 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 A. nyroca in the diving environment.
Conclusions
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 A. nyroca biology, including morphology, ecology, and physiology, and thus play an essential role in its conservation.
{"title":"Chromosome-level assembly of the genome of the Aythya nyroca provides insights into diving adaptations","authors":"Jianqun Ding , Tian Xia , Shuhong Li , Xiaodong Gao , Zhicheng Yao , Shengyang Zhou , Lei Zhang , Zhihao Zhang , Shunting Chen , Mingke Han , 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}
Termitomyces fuliginosus 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 T. fuliginosus 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 T. fuliginosus shared a close evolutionary relationship with Termitomyces cryptogamus, Arthromyces matolae, Tricholoma furcatifolium, Tephrocybe rancida, Lyophyllum atratum, and Tricholoma matsutake. A total of 303 carbohydrate-active enzymes (CAZyme) genes were identified in the T. fuliginosus genome, enabling a better understanding of the carbohydrate degradation capabilities for T. fuliginosus. This chromosome-level genome of T. fuliginosus 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.
{"title":"A chromosome-level genome assembly of Termitomyces fuliginosus using Oxford Nanopore and Hi-C sequencing","authors":"Wei-ying Chen, Yang-sen Qin, Ting-fu Zhang, Jian Zou, Jun Yang, 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}
Pub Date : 2025-09-10DOI: 10.1016/j.ygeno.2025.111108
Daniil Ruvinskiy , Kisun Pokharel , Rodney Okwasiimire , Rayner Gonzalez-Prendes , Catarina Ginja , Nasser Ghanem , Donald R. Kugonza , Mahlako L. Makgahlela , Heli Lindeberg , Melak Weldenegodguad , Juha Kantanen , Martijn Derks , Richard P.M.A. Crooijmans
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 Theileria parva, Anaplasma platys, Theileria orientalis, and Babesia bigemina, which is in line with the known capacity of these breeds to cope with local pathogens. Dutch breeds were found to harbor Escherichia coli O157, 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.
{"title":"Unmapped reads from whole-genome sequencing data reveal pathogen diversity in European and African cattle breeds","authors":"Daniil Ruvinskiy , Kisun Pokharel , Rodney Okwasiimire , Rayner Gonzalez-Prendes , Catarina Ginja , Nasser Ghanem , Donald R. Kugonza , Mahlako L. Makgahlela , Heli Lindeberg , Melak Weldenegodguad , Juha Kantanen , Martijn Derks , 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}
Pub Date : 2025-09-10DOI: 10.1016/j.ygeno.2025.111106
Nan Yang , Shiqun Sun , Xiantao Chen , Tongtong Yan , Nan Gu , Zhihui Liu
Background and objectives
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.
Materials and methods
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.
Results
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.
Conclusions
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.
{"title":"Identification of cross-talk pathways and PANoptosis-related genes in periodontitis and atherosclerosis by bioinformatics analysis and machine learning","authors":"Nan Yang , Shiqun Sun , Xiantao Chen , Tongtong Yan , Nan Gu , 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}
Pub Date : 2025-09-08DOI: 10.1016/j.ygeno.2025.111104
Anastasiia Zaremba, Małgorzata Marszałek-Zeńczak, Annasha Dutta, Anna Samelak-Czajka, Paulina Jackowiak
Despite advancements in genome annotation tools, challenges persist for non-classical model organisms with limited genomic resources, such as Schmidtea mediterranea. To address these challenges, we developed a flexible and scalable genome annotation pipeline that integrates short-read (Illumina) and long-read (PacBio) sequencing technologies. The pipeline combines reference-based and de novo assembly methods, effectively handling genomic variability and alternative splicing events. To improve splice site detection accuracy, DeepSplice deep learning predictions are used. Functional annotation is conducted to filter out low-confidence transcripts and ensure biological relevance. Applying this pipeline to the asexual strain of S. mediterranea revealed thousands of previously undescribed putative genes and transcripts, and improved the existing gene models, highlighting its utility in annotating complex, underexplored genomes. The modularity and comprehensiveness of our pipeline ensure its adaptability for genome annotation across diverse species, making it a valuable tool for annotating genomes of non-model organisms and supporting broader genomic research. The source code and implementation details are available at https://github.com/Norreanea/SmedAnno.
{"title":"A modular pipeline for evidence-integrated genome annotation across species: A case study on Schmidtea mediterranea","authors":"Anastasiia Zaremba, Małgorzata Marszałek-Zeńczak, Annasha Dutta, Anna Samelak-Czajka, Paulina Jackowiak","doi":"10.1016/j.ygeno.2025.111104","DOIUrl":"10.1016/j.ygeno.2025.111104","url":null,"abstract":"<div><div>Despite advancements in genome annotation tools, challenges persist for non-classical model organisms with limited genomic resources, such as <em>Schmidtea mediterranea</em>. To address these challenges, we developed a flexible and scalable genome annotation pipeline that integrates short-read (Illumina) and long-read (PacBio) sequencing technologies. The pipeline combines reference-based and <em>de novo</em> assembly methods, effectively handling genomic variability and alternative splicing events. To improve splice site detection accuracy, DeepSplice deep learning predictions are used. Functional annotation is conducted to filter out low-confidence transcripts and ensure biological relevance. Applying this pipeline to the asexual strain of <em>S. mediterranea</em> revealed thousands of previously undescribed putative genes and transcripts, and improved the existing gene models, highlighting its utility in annotating complex, underexplored genomes. The modularity and comprehensiveness of our pipeline ensure its adaptability for genome annotation across diverse species, making it a valuable tool for annotating genomes of non-model organisms and supporting broader genomic research. The source code and implementation details are available at <span><span>https://github.com/Norreanea/SmedAnno</span><svg><path></path></svg></span>.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 6","pages":"Article 111104"},"PeriodicalIF":3.0,"publicationDate":"2025-09-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145033061","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}
Predicting bacterial oxygen preference and identifying associated genes is critical in microbiology. This study developed a machine learning model using genomic features to predict bacterial oxygen preference and discover potential functional genes. Trained on a dataset of 1813 bacterial genomes, a Random Forest model achieved 90.62 % accuracy in predicting oxygen preference, outperforming prior methods. Feature analysis pinpointed key protein domains and candidate genes. Experimental overexpression of model-identified genes (encoding SOD, SAM radical enzyme, GCV-T, FDH domains) in Escherichia coli enhanced growth under aerobic conditions, validating their role in oxygen adaptation. Applying the model to rumen metagenomes revealed a predominantly anaerobic community. This work establishes machine learning as an effective strategy for bacterial oxygen preference prediction and functional gene identification, offering a novel strategy and tool for in-depth understanding of bacterial oxygen adaptation mechanisms, discovering key functional genes, and efficient exploration of uncultured microbial resources.
{"title":"Decoding oxygen preference: Machine learning discovers functional genes in Bacteria.","authors":"Siqi Wan, Haida Liu, Geyi Zhu, Yuanming Geng, Wenhao Li, Lijuan Chen, Yunhua Zhang, Guomin Han","doi":"10.1016/j.ygeno.2025.111095","DOIUrl":"10.1016/j.ygeno.2025.111095","url":null,"abstract":"<p><p>Predicting bacterial oxygen preference and identifying associated genes is critical in microbiology. This study developed a machine learning model using genomic features to predict bacterial oxygen preference and discover potential functional genes. Trained on a dataset of 1813 bacterial genomes, a Random Forest model achieved 90.62 % accuracy in predicting oxygen preference, outperforming prior methods. Feature analysis pinpointed key protein domains and candidate genes. Experimental overexpression of model-identified genes (encoding SOD, SAM radical enzyme, GCV-T, FDH domains) in Escherichia coli enhanced growth under aerobic conditions, validating their role in oxygen adaptation. Applying the model to rumen metagenomes revealed a predominantly anaerobic community. This work establishes machine learning as an effective strategy for bacterial oxygen preference prediction and functional gene identification, offering a novel strategy and tool for in-depth understanding of bacterial oxygen adaptation mechanisms, discovering key functional genes, and efficient exploration of uncultured microbial resources.</p>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":" ","pages":"111095"},"PeriodicalIF":3.0,"publicationDate":"2025-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144803940","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 : 2025-08-26DOI: 10.1016/j.ygeno.2025.111102
Terhi Iso-Touru , Daniel Fischer , Frank Panitz , Suvi Taponen , Zexi Cai , Goutam Sahana , Ilma Tapio , Johanna Vilkki
This study focuses on the initial cellular response to a causal pathogen in the mammary gland of dairy cows aiming to uncover genomic features associated with mastitis resistance. We analyzed transcriptomes from Escherichia coli -challenged primary bovine mammary epithelial cells derived from milk of cows with high or low genomic index value for udder health. The most striking difference was the markedly higher number of differentially expressed genes post-challenge in the low mastitis resistance group. Gene enrichment analysis indicates a slightly delayed adaptive immune response and early modification of primary metabolic processes in the low mastitis resistance group. Notably, there was no overlap between the DEGs or their potential cis-eQTL with the location of candidate SNPs from association studies of the same cow population. This implies that the genes and pathways involved in the early immune response in the mammary epithelium may not be central for phenotypic mastitis resistance.
{"title":"Response of primary mammary epithelial cells to pathogen challenge in dairy cows with divergent genomic breeding values for udder health","authors":"Terhi Iso-Touru , Daniel Fischer , Frank Panitz , Suvi Taponen , Zexi Cai , Goutam Sahana , Ilma Tapio , Johanna Vilkki","doi":"10.1016/j.ygeno.2025.111102","DOIUrl":"10.1016/j.ygeno.2025.111102","url":null,"abstract":"<div><div>This study focuses on the initial cellular response to a causal pathogen in the mammary gland of dairy cows aiming to uncover genomic features associated with mastitis resistance. We analyzed transcriptomes from <em>Escherichia coli</em> -challenged primary bovine mammary epithelial cells derived from milk of cows with high or low genomic index value for udder health. The most striking difference was the markedly higher number of differentially expressed genes post-challenge in the low mastitis resistance group. Gene enrichment analysis indicates a slightly delayed adaptive immune response and early modification of primary metabolic processes in the low mastitis resistance group. Notably, there was no overlap between the DEGs or their potential cis-eQTL with the location of candidate SNPs from association studies of the same cow population. This implies that the genes and pathways involved in the early immune response in the mammary epithelium may not be central for phenotypic mastitis resistance.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 5","pages":"Article 111102"},"PeriodicalIF":3.0,"publicationDate":"2025-08-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144913036","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 : 2025-08-24DOI: 10.1016/j.ygeno.2025.111101
Guobao Wang , Lei Nie , Huanxin Li
Bioluminescence in fireflies is dependent on luciferin metabolism in luminous organs. Our study applied RNA-seq to compare the transcriptome profiles between the luminous and non-luminous tissues from the larvae of the firely Pyrocoelia pectoralis. Genes that were differentially expressed between the two tissue samples were screened to identify candidate genes involved in luciferin metabolism. Among which, cystathionine gamma-lyase, 4-hydroxyphenylpyruvate dioxygenase, and β-glucosidase 2 were upregulated, whereas cysteine dioxygenase type 1 was downregulated in the luminous group compared to that in the non-luminous group, suggesting that these genes may participate in the synthesis of luciferin precursors including L-cysteine and 1, 4-benzoquinone. Several genes encoding 4-coumarate: CoA ligases were upregulated in the luminous organs compared to that in the non-luminous organs, indicating that they may be involved in the formation of 2-S-cysteinylhydroquinone, an intermediate in the luciferin biosynthesis pathway. A sterol carrier protein 2 (Scp2) gene (58 kDa) was speculated to play a role similar to that of ScpXs, which are involved in β-oxidation in peroxisomes of P. pectoralis. Moreover, the expression levels of genes encoding acyl-CoA thioesterases, alpha-methylacyl-CoA racemase, bifunctional 3′-phosphoadenosine 5′-phosphosulfate synthase 1, and luciferin sulfotransferase were higher in the luminous tissues than those in the non-luminous tissues, suggesting their possible roles in the biosynthesis and storage of D-luciferin. Overall, the results of this study may serve as a theoretical basis for further elucidation of the bioluminescence-related mechanisms in P. pectoralis.
萤火虫的生物发光依赖于发光器官的荧光素代谢。本研究应用RNA-seq技术比较了胸火蛾幼虫发光组织和非发光组织的转录组谱。筛选两个组织样本之间差异表达的基因，以确定参与荧光素代谢的候选基因。其中，半胱甘氨酸γ -裂解酶、4-羟基苯基丙酮酸双加氧酶和β-葡萄糖苷酶2在发光组中表达上调，而半胱氨酸双加氧酶1型在发光组中表达下调，提示这些基因可能参与了l -半胱氨酸和1,4 -苯醌等荧光素前体的合成。与非发光器官相比，发光器官中编码4-香豆酸辅酶a连接酶的几个基因表达上调，表明它们可能参与了2- s -半胱氨酸对苯二酚的形成，这是荧光素生物合成途径中的一种中间体。据推测，甾醇载体蛋白2 （Scp2）基因（58 kDa）与ScpXs的作用类似，参与胸胸肌过氧化物酶体的β-氧化。此外，编码酰基辅酶a硫酯酶、α -甲基酰基辅酶a消旋酶、双功能3′-磷酸腺苷5′-硫酸磷合成酶1和荧光素硫转移酶的基因在发光组织中的表达水平高于非发光组织，表明它们可能在d -荧光素的生物合成和储存中起作用。综上所述，本研究结果可为进一步阐明胸胸草生物发光相关机制提供理论依据。
{"title":"Comparative transcriptomic analysis reveals bioluminescence-related genes in firely Pyrocoelia pectoralis","authors":"Guobao Wang , Lei Nie , Huanxin Li","doi":"10.1016/j.ygeno.2025.111101","DOIUrl":"10.1016/j.ygeno.2025.111101","url":null,"abstract":"<div><div>Bioluminescence in fireflies is dependent on luciferin metabolism in luminous organs. Our study applied RNA-seq to compare the transcriptome profiles between the luminous and non-luminous tissues from the larvae of the firely <em>Pyrocoelia pectoralis</em>. Genes that were differentially expressed between the two tissue samples were screened to identify candidate genes involved in luciferin metabolism. Among which, cystathionine gamma-lyase, 4-hydroxyphenylpyruvate dioxygenase, and β-glucosidase 2 were upregulated, whereas cysteine dioxygenase type 1 was downregulated in the luminous group compared to that in the non-luminous group, suggesting that these genes may participate in the synthesis of luciferin precursors including L-cysteine and 1, 4-benzoquinone. Several genes encoding 4-coumarate: CoA ligases were upregulated in the luminous organs compared to that in the non-luminous organs, indicating that they may be involved in the formation of 2-<em>S</em>-cysteinylhydroquinone, an intermediate in the luciferin biosynthesis pathway. A sterol carrier protein 2 (<em>Scp2</em>) gene (58 kDa) was speculated to play a role similar to that of ScpXs, which are involved in β-oxidation in peroxisomes of <em>P. pectoralis</em>. Moreover, the expression levels of genes encoding acyl-CoA thioesterases, alpha-methylacyl-CoA racemase, bifunctional 3′-phosphoadenosine 5′-phosphosulfate synthase 1, and luciferin sulfotransferase were higher in the luminous tissues than those in the non-luminous tissues, suggesting their possible roles in the biosynthesis and storage of D-luciferin. Overall, the results of this study may serve as a theoretical basis for further elucidation of the bioluminescence-related mechanisms in <em>P. pectoralis</em>.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 5","pages":"Article 111101"},"PeriodicalIF":3.0,"publicationDate":"2025-08-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144895719","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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