Genomics最新文献

{"title":"Genetic structure, KASP markers, and core germplasm resources of rice landraces from the Taihu Lake Basin","authors":"Zijie Shen ,&nbsp;Naiwei Li ,&nbsp;Zhengbin Zhu ,&nbsp;Xin Zou ,&nbsp;Xiaoqin Sun ,&nbsp;Jia Liu ,&nbsp;Ruisen Lu","doi":"10.1016/j.ygeno.2025.111069","DOIUrl":"10.1016/j.ygeno.2025.111069","url":null,"abstract":"<div><div>Rice (<em>Oryza sativa</em> L.), a global staple crop, is crucial to food security, particularly in Asia. The Taihu Lake Basin, located in the middle and lower reaches of the Yangtze River, is a secondary origin center for rice, with a cultivation history dating back over 8000 years. However, the genetic diversity of traditional rice landraces in this region faces significant threats due to the widespread adoption of high-yielding cultivars. This study aimed to characterize the genetic structure of rice landraces from the Taihu Lake Basin, develop KASP markers for precise identification, and establish a core germplasm collection, using high-throughput resequencing technologies. A total of 114 rice landrace accessions from the Taihu Lake Basin were sampled and analyzed. Population genetic structure analysis revealed seven distinct genetic groups. Utilizing this dataset, a set of 27 kompetitive allele specific PCR (KASP) markers were developed, enabling accurate genotyping and efficient landrace identification. Furthermore, a core germplasm collection was established, representing 99 % of the genetic diversity of the original collection. Overall, this study provides a valuable resource for the conservation and sustainable utilization of rice landraces in the Taihu Lake Basin, supporting future rice breeding programs and ensuring the preservation of genetic resources crucial for crop improvement.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 4","pages":"Article 111069"},"PeriodicalIF":3.4,"publicationDate":"2025-06-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144263093","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":"Morphological, physiological, and transcriptomic insights into response the of Lycium barbarum L. (‘Ningqi No.1’) seedlings to low-nitrogen stress","authors":"Ru Wan ,&nbsp;Hezhen Wang ,&nbsp;Tian Hui ,&nbsp;Libing Yang ,&nbsp;Xiao Wang ,&nbsp;Youlong Cao ,&nbsp;Wei An ,&nbsp;Xiyan Zhang ,&nbsp;Jianhua Zhao ,&nbsp;Yajun Wang ,&nbsp;Yuekun Li ,&nbsp;Zhigang Shi","doi":"10.1016/j.ygeno.2025.111065","DOIUrl":"10.1016/j.ygeno.2025.111065","url":null,"abstract":"<div><div>Nitrogen is one of the essential elements for plant growth and development. In this study, we assessed the effects of low-nitrogen (LN) on <em>Lycium barbarum</em> L. seedlings, finding that LN stress caused a notable decrease in plant height, fresh and dry weights, and leaf nitrate nitrogen levels. LN stress also altered the activities of the antioxidant defense system, key enzymes involved in nitrogen assimilation, and phytohormone levels. Transcriptomic analysis identified 3015, 2032, and 3382 differentially expressed genes (DEGs) in roots, stems, and leaves, respectively. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis further highlighted the significant impact of LN stress on nitrogen metabolism, phenylpropanoid biosynthesis, flavonoid biosynthesis, and ascorbate and aldarate metabolism. These findings enhance our understanding of the molecular mechanisms governing the response of <em>Lycium barbarum</em> L. to LN stress and provide a theoretical basis for the targeted breeding of nitrogen-efficient wolfberry varieties.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 4","pages":"Article 111065"},"PeriodicalIF":3.4,"publicationDate":"2025-06-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144240195","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":"Uncovering novel exosome-specific miRNA markers and potential molecular mechanisms in autoimmune pancreatitis","authors":"Yamin Lai ,&nbsp;Mengmeng Shang ,&nbsp;Hong Yang ,&nbsp;Hong Lv ,&nbsp;Panpan Zhang ,&nbsp;Tao Guo ,&nbsp;Wen Zhang ,&nbsp;Aiming Yang ,&nbsp;Jia Yu ,&nbsp;Jiaming Qian ,&nbsp;Dong Wu","doi":"10.1016/j.ygeno.2025.111068","DOIUrl":"10.1016/j.ygeno.2025.111068","url":null,"abstract":"<div><h3>Background</h3><div>Autoimmune pancreatitis (AIP) is a rare disease and sometimes difficult to make a diagnosis. This study aimed to identify exosomal miRNAs that could serve as novel biomarkers of type 1 AIP.</div></div><div><h3>Methods</h3><div>We extracted miRNAs from the exosomes of patients with AIP, chronic pancreatitis (CP), pancreatic cancer, and healthy control individuals. To identify differentially expressed miRNAs (DEmiRNAs) associated with AIP, second-generation sequencing and differential expression analysis were performed. Target gene prediction, immune correlation analysis, functional annotation, and construction of lncRNA-miRNA-mRNA and transcription factor (TF)-miRNA-mRNA networks were then performed. Finally, qPCR analysis and ROC evaluation were performed for hub DEmiRNA.</div></div><div><h3>Results</h3><div>Exosomal miRNAs exhibited specific expression profiles in patients with type 1 AIP. The differentially expressed target genes PLXNA2 and PGM3, and the differentially expressed lncRNA MALAT1 associated with hsa-miR-30b-5p were identified. KEGG analysis showed that PLXNA2 was enriched in the axon guidance. Pearson's correlation analysis showed that PLXNA2 and PGM3 were significantly negatively correlated with activated CD4 T cells, type 1 T helper cells and other immune cells. The TF-miRNA-mRNA regulatory network showed that FOXA1 was a TF for PLXNA2 and PGM3, and RUNX2 was a TF for PLXNA2. Moreover, FOXA1 and RUNX2 were also the target genes of hsa-miR-30b-5p.</div></div><div><h3>Conclusion</h3><div>Hsa-miR-30b-5p identified from exosomes may be a miRNA marker specific to type 1 AIP and therefore has the potential to serve as a novel biomarker.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 4","pages":"Article 111068"},"PeriodicalIF":3.4,"publicationDate":"2025-06-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144247342","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":"MiR-100-5p as a biomarker in hand-arm vibration disease: Mediating pathogenesis through angiogenesis suppression","authors":"Hanjun Zheng ,&nbsp;Li Lang ,&nbsp;Wankang Li ,&nbsp;Qia Wang ,&nbsp;Bin Xiao ,&nbsp;Yanxia Jia ,&nbsp;Siyu Pan ,&nbsp;Maosheng Yan","doi":"10.1016/j.ygeno.2025.111067","DOIUrl":"10.1016/j.ygeno.2025.111067","url":null,"abstract":"<div><div>Hand-arm vibration disease (HAVD), also known as occupational Raynaud's disease, is an occupational disease that can cause injuries to the microcirculation in the fingertips, might leading to severe vascular and neurological damage. While HAVD has been defined as a peripheral vascular injury disorders, its comprehensive disease mechanisms—spanning molecular drivers, pathophysiological cascades, and clinically actionable biomarkers remain substantially unelucidated. Our study has used miRNA sequencing (miRNA-seq) to investigate the differential expression of miRNAs in HAVD patients compared to workers exposed to hand-transmitted vibration. In vitro, human umbilical vein endothelial cells (HUVECs) have been utilized to explore the role of miR-100-5p in endothelial cell dysfunction. Our results reveal that 36 miRNAs were upregulated and 2 miRNAs were downregulated in HAVD patients. Notably, miR-100-5p and miR-4735-5p exhibited the most significant differential expression.The area under the curve (AUC) for miR-100-5p in distinguishing hand-transmitted vibration-exposed workers from healthy individuals was 0.9906, while its AUC for identifying HAVD was 0.9922. The combination of those two miRNAs as the diagnostic marker of HAVD showed great potential has higher AUC, with high sensitivity, and specificity. Furthermore, miR-100-5p might mediate the pathology of HAVD by inhibiting vascular cell angiogenesis via VEGFA/VEGFR pathway, which could be regulated by decreased <em>TRIB2</em> expression and inhibition of the p38 MAPK signaling pathway.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 4","pages":"Article 111067"},"PeriodicalIF":3.4,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144215536","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":"Unraveling the genetic mechanisms of UV radiation resistance in Bacillus through biofilm formation, sporulation, and carotenoid production","authors":"Prasansah Shrestha ,&nbsp;Byeollee Kim ,&nbsp;So-Ra Han ,&nbsp;Hyun Lee ,&nbsp;Tae-Jin Oh","doi":"10.1016/j.ygeno.2025.111066","DOIUrl":"10.1016/j.ygeno.2025.111066","url":null,"abstract":"<div><div><em>Bacillus</em> species are Gram-positive bacteria that are rod-shaped, endospore-forming, and aerobic or facultatively anaerobic. With over 300 recognized species, <em>Bacillus subtilis</em> stands out as a well-studied model organism. The genus's various species exhibit a wide range of physiological capabilities, allowing them to thrive in diverse environmental conditions. Each cell produces a single endospore, which is highly resistant to heat, cold, radiation, desiccation, and disinfectants. Among <em>Bacillus</em> strains, those capable of producing spores, biofilms, and carotenoids demonstrate significant resilience to UV light. This review examines the genes involved in spore formation, biofilm development, and carotenoid synthesis, emphasizing their roles in UV radiation survival. We explore the interconnections between these processes and their combined contribution to UV resistance, focusing on the underlying genetic mechanisms. These insights will benefit researchers studying the genetic basis of UV radiation resistance in <em>Bacillus</em> species.</div></div><div><h3>Importance</h3><div>Bacteria employ adaptive strategies in extreme environments through rapid changes in gene expression, altering their phenotype for survival. <em>Bacillus</em> species, for example, defend against UV radiation by making spores, creating biofilms, and producing pigments<em>.</em> During sporulation, sigma factors (σ^F, σ^E, σ^G, and σ^K) regulate gene expression to adapt to environmental shifts. It has been found that the spores of some species may contain pigments that strongly absorb UV radiation, playing a crucial role in spore UV resistance. UV light penetrates biofilm matrices minimally, mainly affecting surface cells, which produce compounds like mycosporine-like amino acids and carotenoids to shield against UV damage.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 4","pages":"Article 111066"},"PeriodicalIF":3.4,"publicationDate":"2025-05-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144204134","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":"Genomic insights into the potency and functional roles of Lactobacillus species in term and preterm births","authors":"Daizee Talukdar ,&nbsp;Yodhaanjali Jinnenahalli Raju ,&nbsp;Pradipta Jana ,&nbsp;Komal Sharma ,&nbsp;Prabhakar Babele ,&nbsp;Akansha Kothidar ,&nbsp;Taruna Ahrodia ,&nbsp;Lekshmi Narendrakumar ,&nbsp;K. Ramani Shyam ,&nbsp;Upma Singh ,&nbsp;Subhash Tanwar ,&nbsp;Sachin Harle ,&nbsp;Susmita Chaudhuri ,&nbsp;Sreevatsan Raghavan ,&nbsp;Nitya Wadhwa ,&nbsp;Souvik Mukherjee ,&nbsp;Shinjini Bhatnagar ,&nbsp;Bhabatosh Das","doi":"10.1016/j.ygeno.2025.111063","DOIUrl":"10.1016/j.ygeno.2025.111063","url":null,"abstract":"<div><div>The vaginal microbiome, typically dominated by <em>Lactobacillus</em> species, plays a key role in reducing the risk of preterm birth (PTB) by protecting against infections. In this study, we sequenced 133 <em>Lactobacillus</em> genomes isolated from the reproductive tracts of pregnant Indian women. Genomic analysis identified genes linked to pathogen resistance and anti-inflammatory functions. Further proteome analysis of cell-free supernatant revealed antimicrobial properties, including lysin and bacteriocin, while antibacterial tests confirmed their ability to inhibit reproductive tract pathogens. These findings suggest that <em>Lactobacillus</em> strains protect against harmful microbes, potentially reducing infection risks and PTB. This <em>Lactobacillus</em> consortium holds promise for developing biotherapeutics aimed at improving maternal health.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 4","pages":"Article 111063"},"PeriodicalIF":3.4,"publicationDate":"2025-05-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144208258","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":"Draft genome sequence of Kodamaea ohmeri, an emerging human pathogen","authors":"Liping Liu ,&nbsp;Qiuping Wang ,&nbsp;Hui Wang ,&nbsp;Shufen Quan ,&nbsp;Mian Wang ,&nbsp;Dechun Xie ,&nbsp;Yu'e Hao","doi":"10.1016/j.ygeno.2025.111062","DOIUrl":"10.1016/j.ygeno.2025.111062","url":null,"abstract":"<div><div><em>Kodamaea ohmeri</em> is recognized as an emerging human pathogen responsible for severe infections. However, the lack of genome sequence for this pathogenic fungus hampers molecular and genetic investigations of its pathogenic mechanism. In this study, we reported the draft genome of <em>K. ohmeri</em> 3873 isolated from clinical samples. The genome has a size of 13.86 Mb, including 3734 putative genes with 54.22 % of dispersed and tandem repeat sequences. Further bioinformatics analysis found 159 carbohydrate-active enzymes, 19 CYP genes and 44 secondary metabolite genes in <em>K. ohmeri</em> genome. A total of 657 pathogenicity related genes (including multidrug resistance genes) and 216 fungal virulence factors (172 genes associated with human diseases) were identified, which were more than those of other seven strains, suggesting the potential of <em>K. ohmeri</em> as an emerging human pathogen. This study provides a foundation for future works on the biology, molecular pathogenesis, and virulence of <em>K. ohmeri</em>.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 4","pages":"Article 111062"},"PeriodicalIF":3.4,"publicationDate":"2025-05-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144208257","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":"Deciphering common bean (Phaseolus Vulgaris L.) microbiome assemblages reveal mechanistic insights into host-pathogen-microbiome interactions","authors":"Aggrey Keya Osogo ,&nbsp;Francis Muyekho ,&nbsp;Hassan Were ,&nbsp;Patrick Okoth","doi":"10.1016/j.ygeno.2025.111064","DOIUrl":"10.1016/j.ygeno.2025.111064","url":null,"abstract":"<div><div>Common bean (<em>Phaseolus vulgaris L</em>.) is the primary source of proteins and nutrients in most households in sub-Saharan Africa. However, production of this crop is constrained by several biotic factors. While research on common bean plant-pathogen interactions has predominantly focused on binary relationships, the diversity of microbes naturally inhabiting plant tissues and their interactions has often been overlooked. Recent findings, however, show that these resident microbes actively contribute to plant defense mechanisms, rather than merely acting as passive bystanders. This study aimed to document and explore potential interactions within the common bean microbiome assemblages through field investigations in selected locations across the western regions of Kenya. Common bean leaf samples were collected from farmer's fields along motorable roads 3–5 km apart. Shotgun metagenomic analysis identified a diverse range of microorganisms, including bacteria, fungi, yeast, phytoplasmas, viruses, and bacteriophages, across multiple taxonomic levels—spanning 4 Kingdoms, 136 Phyla, 168 Classes, 360 Orders, 792 Families, 2039 Genera, and 6130 Species—both epiphytic and endophytic, and pathogenic or non-pathogenic. Pseudomonadota consistently showed the highest taxonomic annotation for antimicrobial-resistant organisms, highlighting its central role in resistance across the studied area. The sequences obtained were mapped to the EggNOG, CAZy, and KEGG databases to explore, assign, and predict gene functions. The EggNOG database emphasized the importance of “Replication, recombination, and repair” processes in maintaining genomic stability, along with amino acid transport, energy production, and metabolism. CAZy analysis revealed a significant presence of glycosyltransferases, particularly from GT1 and GT32 families, and noted the role of enzymes like Glycoside Hydrolases in plant defense against pathogens. KEGG pathway analysis underscored the central role of metabolic processes such as energy metabolism, translation, and carbohydrate metabolism. Key pathways linked to plant defense and resilience, including 2-oxocarboxylic acid metabolism, amino acid biosynthesis, and secondary metabolite biosynthesis, were identified. These findings underscore the role of metabolic and enzymatic processes in strengthening plant defenses and stress tolerance while laying the groundwork for multidisciplinary research to advance sustainable agriculture and food safety.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 4","pages":"Article 111064"},"PeriodicalIF":3.4,"publicationDate":"2025-05-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144198808","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":"Ancient genomes reveal complex population interactions in the middle Yellow River basin during the Late Neolithic period","authors":"Zishuai Huang ,&nbsp;Jiaqi Gao ,&nbsp;Mingzhi Ma ,&nbsp;Wengao Hu ,&nbsp;Xin Xiao ,&nbsp;Hui Li","doi":"10.1016/j.ygeno.2025.111061","DOIUrl":"10.1016/j.ygeno.2025.111061","url":null,"abstract":"<div><div>The middle reaches of the Yellow River in the Late Neolithic period were the frontier of cultural communication between the Central Plains and the northern steppe. The remarkable sites that emerged during this period, such as Taosi, Shimao, and Lushanmao, played important roles in the formation of early Chinese civilization. Here we report ancient genomic data from 8 individuals from the three sites. Population genetics analysis revealed that the ancestries of these individuals were mainly related to the Yangshao culture populations from the Central Plains, supplemented by Northeast Asian ancestry. We also found an individual who was a genetic outlier at the Lushanmao site who carried excess Northeast Asian ancestry and harbored a genetic background similar to that of the Hongshan culture population. These findings provide a more detailed picture of genetic interactions and population migrations in northern China of Late Neolithic period and suggest potential cross-regional population interactions.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 4","pages":"Article 111061"},"PeriodicalIF":3.4,"publicationDate":"2025-05-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144185407","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":"Integrating multi-omics analysis unveils the key mechanisms of PQS-enhanced Algicidal activity in Enterobacter hormaechei F2","authors":"Bin Zhang,&nbsp;Meiqi Yang,&nbsp;Wei Liu","doi":"10.1016/j.ygeno.2025.111060","DOIUrl":"10.1016/j.ygeno.2025.111060","url":null,"abstract":"<div><div>Quorum sensing, as a pivotal bacterial signaling pathway, exhibits substantial potential for regulating algicidal activity. This study pioneers the integration of multi-omics analyses (transcriptomics, proteomics, metabolomics) with phenotypic profiling to systematically unravel the molecular mechanisms underlying Pseudomonas Quinolone Signal (2-heptyl-3-hydroxy-4(1H)-quinolinone, PQS)-enhanced algicidal activity in <em>Enterobacter hormaechei</em> F2. Co-cultivation with PQS triggered marked reductions in algal biomass and chlorophyll-a levels, outperforming traditional approaches. Fourier-transform infrared spectroscopy (FTIR) revealed PQS-induced metabolic disruption and membrane degradation in algal cells. Transcriptomic profiling identified novel regulatory hubs, including upregulated glycolysis (<em>tktA</em>, transketolase), fatty acid degradation (<em>fadE</em>, acyl-CoA dehydrogenase), and chemotaxis (<em>malE</em>, maltose-binding protein) pathways. Proteomics confirmed PQS-driven enrichment of terpenoid precursors, notably DXS synthase (1-deoxy-D-xylulose-5-phosphate synthase), and quorum sensing effectors. Metabolomics highlighted amino acid derivatives (e.g., L-glutamate) and heterocyclic antibiotics as dominant algicidal metabolites. Crucially, multi-omics integration delineated a core network of 46 key nodes (e.g., ribose transporter <em>rbsB</em>, L-glutamate) coordinating energy metabolism, motility, and algicide synthesis. Fatty acid degradation enzymes (e.g., FadE) and flagellar assembly regulators (e.g., FlgK) emerged as previously unrecognized targets, with PQS significantly enhancing bacterial swarming motility (<em>p &lt;</em> 0.01) and biofilm formation. These findings establish the first mechanistic framework linking PQS signaling to algicidal process, demonstrating its role in synchronizing metabolic flux toward terpenoid synthesis while optimizing bacterial-algal interactions. Key pathways—including chemotaxis (<em>malE</em>) and terpenoid biosynthesis (DXS synthase)—provide actionable targets for engineering bioaugmented consortia or precision algicidal formulations. This work advances quorum sensing-driven strategies for sustainable harmful algal bloom (HAB) mitigation, offering scalable solutions for aquaculture and eutrophic water remediation with minimal ecological disruption. By bridging molecular mechanisms to field applications, the study underscores the translational potential of this approach in global water security initiatives.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 4","pages":"Article 111060"},"PeriodicalIF":3.4,"publicationDate":"2025-05-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144180123","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}