Frontiers in Genetics最新文献

{"title":"Moss-pathogen interactions: a review of the current status and future opportunities.","authors":"Huan Zhang, Qilin Yang, Leyi Wang, Huawei Liu, Daoyuan Zhang, Cheng-Guo Duan, Xiaoshuang Li","doi":"10.3389/fgene.2025.1539311","DOIUrl":"10.3389/fgene.2025.1539311","url":null,"abstract":"<p><p>In complex and diverse environments, plants face constant challenges from various pathogens, including fungi, bacteria, and viruses, which can severely impact their growth, development, and survival. Mosses, representing early divergent lineages of land plants, lack traditional vascular systems yet demonstrate remarkable adaptability across diverse habitats. While sharing the fundamental innate immune systems common to all land plants, mosses have evolved distinct chemical and physical defense mechanisms. Notably, they exhibit resistance to many pathogens that typically affect vascular plants. Their evolutionary significance, relatively simple morphology, and well-conserved defense mechanisms make mosses excellent model organisms for studying plant-pathogen interactions. This article reviews current research on moss-pathogen interactions, examining host-pathogen specificity, characterizing infection phenotypes and physiological responses, and comparing pathogen susceptibility and defense mechanisms between mosses and angiosperms. Through this analysis, we aim to deepen our understanding of plant immune system evolution and potentially inform innovative approaches to enhancing crop disease resistance.</p>","PeriodicalId":12750,"journal":{"name":"Frontiers in Genetics","volume":"16 ","pages":"1539311"},"PeriodicalIF":2.8,"publicationDate":"2025-02-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11850516/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143500594","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Dual graph-embedded fusion network for predicting potential microbe-disease associations with sequence learning.","authors":"Junlong Wu, Liqi Xiao, Liu Fan, Lei Wang, Xianyou Zhu","doi":"10.3389/fgene.2025.1511521","DOIUrl":"10.3389/fgene.2025.1511521","url":null,"abstract":"<p><p>Recent studies indicate that microorganisms are crucial for maintaining human health. Dysbiosis, or an imbalance in these microbial communities, is strongly linked to a variety of human diseases. Therefore, understanding the impact of microbes on disease is essential. The DuGEL model leverages the strengths of graph convolutional neural network (GCN) and graph attention network (GAT), ensuring that both local and global relationships within the microbe-disease association network are captured. The integration of the Long Short-Term Memory Network (LSTM) further enhances the model's ability to understand sequential dependencies in the feature representations. This comprehensive approach allows DuGEL to achieve a high level of accuracy in predicting potential microbe-disease associations, making it a valuable tool for biomedical research and the discovery of new therapeutic targets. By combining advanced graph-based and sequence-based learning techniques, DuGEL addresses the limitations of existing methods and provides a robust framework for the prediction of microbe-disease associations. To evaluate the performance of DuGEL, we conducted comprehensive comparative experiments and case studies based on two databases, HMDAD, and Disbiome to demonstrate that DuGEL can effectively predict potential microbe-disease associations.</p>","PeriodicalId":12750,"journal":{"name":"Frontiers in Genetics","volume":"16 ","pages":"1511521"},"PeriodicalIF":2.8,"publicationDate":"2025-02-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11850361/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143500593","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"ADAM-multi: software to simulate complex breeding programs for animals and plants with different ploidy levels and generalized genotypic effect models to account for multiple alleles.","authors":"Thinh Tuan Chu, Just Jensen","doi":"10.3389/fgene.2025.1513615","DOIUrl":"10.3389/fgene.2025.1513615","url":null,"abstract":"<p><p>Stochastic simulation software, ADAM, has been developed for the purpose of breeding optimization in animals and plants, and for validation of statistical models used in genetic evaluations. Just like other common simulation programs, ADAM assumed the bi-allelic state of quantitative trait locus (QTL). While the bi-allelic state of marker loci is due to the common choice of genotyping technology of single nucleotide polymorphism (SNP) chip, the assumption may not hold for the linked QTL. In the version of ADAM-Multi, we employ a novel simulation model capable of simulating additive, dominance, and epistatic genotypic effects for species with different levels of ploidy, providing with a more realistic assumption of multiple allelism for QTL variants. When assuming bi-allelic QTL, our proposed model becomes identical to the model assumption in common simulation programs, and in genetic textbooks. Along with the description of the updated simulation model in ADAM-Multi, this paper shows two small-scale studies that investigate the effects of multi-allelic versus bi-allelic assumptions in simulation and the use of different prediction models in a single-population breeding program for potatoes. We found that genomic models using dense bi-allelic markers could effectively predicted breeding values of individuals in a well-structure population despite the presence of multi-allelic QTL. Additionally, the small-scale study indicated that including non-additive genetic effects in the prediction model for selection did not lead to an improvement in the rate of genetic gains of the breeding program.</p>","PeriodicalId":12750,"journal":{"name":"Frontiers in Genetics","volume":"16 ","pages":"1513615"},"PeriodicalIF":2.8,"publicationDate":"2025-02-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11847855/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143491639","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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 the taxonomical and functional profiles of marine microorganisms in Submarine Groundwater Discharge vent water from Mabini, Batangas, Philippines through metagenome-assembled genomes.","authors":"Joshua T Veluz, Laurence Anthony N Mallari, Paul Christian T Gloria, Maria Auxilia T Siringan","doi":"10.3389/fgene.2025.1522253","DOIUrl":"https://doi.org/10.3389/fgene.2025.1522253","url":null,"abstract":"","PeriodicalId":12750,"journal":{"name":"Frontiers in Genetics","volume":"16 ","pages":"1522253"},"PeriodicalIF":2.8,"publicationDate":"2025-02-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11868764/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143541074","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Editorial: The non-coding RNA world in animals and plants.","authors":"Lingling Wang, Bin Hu, Min-Jin Han, Q-Z Zhou","doi":"10.3389/fgene.2025.1558406","DOIUrl":"10.3389/fgene.2025.1558406","url":null,"abstract":"","PeriodicalId":12750,"journal":{"name":"Frontiers in Genetics","volume":"16 ","pages":"1558406"},"PeriodicalIF":2.8,"publicationDate":"2025-02-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11842322/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143482971","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Sequencing whole genomes of the West Javanese population in Indonesia reveals novel variants and improves imputation accuracy.","authors":"Edwin Ardiansyah, Anca-Lelia Riza, Sofiati Dian, Ahmad Rizal Ganiem, Bachti Alisjahbana, Todia P Setiabudiawan, Arjan van Laarhoven, Reinout van Crevel, Vinod Kumar","doi":"10.3389/fgene.2024.1492602","DOIUrl":"10.3389/fgene.2024.1492602","url":null,"abstract":"<p><p>Existing genotype imputation reference panels are mainly derived from European populations, limiting their accuracy in non-European populations. To improve imputation accuracy for Indonesians, the world's fourth most populous country, we combined Whole Genome Sequencing (WGS) data from 227 West Javanese individuals with East Asian data from the 1,000 Genomes Project. This created three reference panels: EAS 1KGP3 (EASp), Indonesian (INDp), and a combined panel (EASp + INDp). We also used ten West-Javanese samples with WGS and SNP-typing data for benchmarking. We identified 1.8 million novel single nucleotide variants (SNVs) in the West Javanese population, which, while similar to the East Asians, are distinct from the Central Indonesian Flores population. Adding INDp to the EASp reference panel improved imputation accuracy (R2) from 0.85 to 0.90, and concordance from 87.88% to 91.13%. These findings underscore the importance of including West-Javanese genetic data in reference panels, advocating for broader WGS of diverse Indonesian populations to enhance genomic studies.</p>","PeriodicalId":12750,"journal":{"name":"Frontiers in Genetics","volume":"15 ","pages":"1492602"},"PeriodicalIF":2.8,"publicationDate":"2025-02-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11843580/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143482970","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Noncoding RNA profiling in omentum adipose tissue from obese patients and the identification of novel metabolic biomarkers.","authors":"Yongjiao Zhang, Ao Chen, Sumei Lu, Dong Liu, Xiaolei Xuan, Xiaofei Lei, Mingwei Zhong, Fei Gao","doi":"10.3389/fgene.2025.1533637","DOIUrl":"10.3389/fgene.2025.1533637","url":null,"abstract":"<p><strong>Background: </strong>Obesity, a prevalent metabolic disorder, is linked to perturbations in the balance of gene expression regulation. Noncoding RNAs (ncRNAs), including long noncoding RNAs (lncRNAs), circular RNAs (circRNAs), and microRNAs (miRNAs), play pivotal roles in regulating gene expression. The aim of this study was to identify additional ncRNA candidates that are implicated in obesity, elucidating their potential as key regulators of the pathogenesis of obesity.</p><p><strong>Methods: </strong>We identified distinct ncRNA expression profiles in omental adipose tissue in obese and healthy subjects through comprehensive whole-transcriptome sequencing. Subsequent analyses included functional annotation with GO and KEGG pathway mapping, validation via real-time quantitative polymerase chain reaction (qRT‒PCR), the exploration of protein‒protein interactions (PPIs), and the identification of key regulatory genes through network analysis.</p><p><strong>Results: </strong>The results indicated that, compared with those in healthy individuals, various lncRNAs, circRNAs, and miRNAs were significantly differentially expressed in obese subjects. Further verifications of top changed gene expressions proved the most genes' consistence with RNA-sequencing including 11 lncRNAs and 4 circRNAs. Gene network analysis highlighted the most significant features associated with metabolic pathways, specifically ENST00000605862, ENST00000558885, and ENST00000686149. Collectively, our findings suggest potential ncRNA therapeutic targets for obesity, including ENST00000605862, ENST00000558885, and ENST00000686149.</p>","PeriodicalId":12750,"journal":{"name":"Frontiers in Genetics","volume":"16 ","pages":"1533637"},"PeriodicalIF":2.8,"publicationDate":"2025-02-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11839770/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143467831","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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 the relationship between sepsis and Golgi apparatus dysfunction: bioinformatics insights and diagnostic marker discovery.","authors":"Wanli Ma, Xinyi Liu, Ran Yu, Jiannan Song, Lina Hou, Ying Guo, Hongwei Wu, Dandan Feng, Qi Zhou, Haibo Li","doi":"10.3389/fgene.2025.1483493","DOIUrl":"10.3389/fgene.2025.1483493","url":null,"abstract":"<p><strong>Background: </strong>Sepsis, a critical infectious disease, is intricately linked to the dysfunction of the intracellular Golgi apparatus. This study aims to explore the relationship between sepsis and the Golgi apparatus using bioinformatics, offering fresh insights into its diagnosis and treatment.</p><p><strong>Methods: </strong>To explore the role of Golgi-related genes in sepsis, we analyzed mRNA expression profiles from the NCBI GEO database. We identified differentially expressed genes (DEGs). These DEGs, Golgi-associated genes obtained from the MSigDB database, and key modules identified through WGCNA were intersected to determine Golgi-associated differentially expressed genes (GARGs) linked to sepsis. Subsequently, functional enrichment analyses, including GO, KEGG, and GSEA, were performed to explore the biological significance of the GARGs.A PPI network was constructed to identify core genes, and immune infiltration analysis was performed using the ssGSEA algorithm. To further evaluate immune microenvironmental features, unsupervised clustering was applied to identify immunological subgroups. A diagnostic model was developed using logistic regression, and its performance was validated using ROC curve analysis. Finally, key diagnostic biomarkers were identified and validated across multiple datasets to confirm their diagnostic accuracy.</p><p><strong>Results: </strong>By intersecting DEGs, WGCNA modules, and Golgi-related gene sets, 53 overlapping GARGs were identified. Functional enrichment analysis indicated that these GARGs were predominantly involved in protein glycosylation and Golgi membrane-related processes. PPI analysis further identified eight hub genes: B3GNT5, FUT11, MFNG, ST3GAL5, MAN1C1, ST6GAL1, C1GALT1C1, and GALNT14. Immune infiltration analysis revealed significant differences in immune cell populations, mainly activated dendritic cells, and effector memory CD8⁺ T cells, between sepsis patients and healthy controls. A diagnostic model constructed using five pivotal genes (B3GNT5, FUT11, MAN1C1, ST6GAL1, and C1GALT1C1) exhibited predictive accuracy, with AUC values exceeding 0.96 for all genes. Validation with an independent dataset confirmed the differential expression patterns of B3GNT5, C1GALT1C1, and GALNT14, reinforcing their potential as robust diagnostic biomarkers for sepsis.</p><p><strong>Conclusion: </strong>This study elucidates the link between sepsis and the Golgi apparatus, introduces novel biomarkers for sepsis diagnosis, and offers valuable insights for future research on its pathogenesis and treatment strategies.</p>","PeriodicalId":12750,"journal":{"name":"Frontiers in Genetics","volume":"16 ","pages":"1483493"},"PeriodicalIF":2.8,"publicationDate":"2025-02-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11839613/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143467828","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Negative frequency-dependent selection through variations in seedling fitness due to genetic differentiation of parents' pair in a tropical rainforest tree, <i>Rubroshorea curtisii</i> (Dipterocarpaceae).","authors":"Naoki Tani, Chin Hong Ng, Soon Leong Lee, Chai Ting Lee, Norwati Muhammad, Toshiaki Kondo, Yoshihiko Tsumura, Saori Sugiyama, Kaoru Niiyama, Azizi Ripin, Abdul Rahman Kassim, Samsudin Musa","doi":"10.3389/fgene.2025.1552024","DOIUrl":"10.3389/fgene.2025.1552024","url":null,"abstract":"<p><strong>Introduction: </strong>The role of syngameons in adaption to microgeographical environmental heterogeneity is important and could be one of the sources of rich species diversity in tropical forests. In addition, negative frequency- or density-dependent selection is one of the major processes contributing to the maintenance of genetic diversity.</p><p><strong>Methods: </strong>To assess genetic factors that affect the fitness of seedlings of <i>Rubroshorea curtisii</i>, a dominant canopy tree species in hill dipterocarp forests, the inter- and intra-population genetic structure of individuals from natural populations and individuals at two permanent plots in a hill dipterocarp forest with reproductive stage was studied. Further, a total of 460 seedlings derived from six mother trees in the plot were raised in a nursery, and their pollen donors were identified using genetic marker based paternity assignment. Seed weight, bi-parental genetic relatedness, and bi-parental genetic heterogeneity based on the clustering analysis were used to analyze their effects on seedling fitness.</p><p><strong>Results: </strong>A Bayesian based clustering analysis revealed that three genetically distinct clusters were observed in almost all populations throughout the distributional range of the species in Malay Peninsula and provided the optimum explanation for the genetic structure of 182 mature individuals in the plots. The two clusters showed larger genetic differentiation from the ancestral admixture population, but the other one was not differentiated. The bi-parental larger genetic heterogeneity was associated with a significantly higher probability of seedling survivorship, and likewise, higher performance of vertical growth of the seedlings; but the seed weight and genetic relatedness did not significantly affect those.</p><p><strong>Discussion: </strong>This evidence suggests that fitter seedlings derived from mating between parents with different genetic clusters contribute to maintaining genetic diversity through negative frequency-dependent selection and may have an important role in adaptation in the tropical forest plant community.</p>","PeriodicalId":12750,"journal":{"name":"Frontiers in Genetics","volume":"16 ","pages":"1552024"},"PeriodicalIF":2.8,"publicationDate":"2025-02-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11839620/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143467830","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Editorial: Towards the embedding of artificial intelligence into synthetic organisms: engineering intelligence in microorganisms.","authors":"Martín Eduardo Gutiérrez, Rafael Lahoz-Beltrá, Alberto J Donayre-Torres","doi":"10.3389/fgene.2025.1562092","DOIUrl":"https://doi.org/10.3389/fgene.2025.1562092","url":null,"abstract":"","PeriodicalId":12750,"journal":{"name":"Frontiers in Genetics","volume":"16 ","pages":"1562092"},"PeriodicalIF":2.8,"publicationDate":"2025-02-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11835967/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143457659","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}