G3: Genes|Genomes|Genetics最新文献_第9页

The genetic basis of chloride exclusion in grapevines. 葡萄植物排除氯化物的遗传基础。

IF 2.2 3区生物学

G3: Genes|Genomes|Genetics Pub Date : 2025-09-03 DOI: 10.1093/g3journal/jkaf149

Sadikshya Sharma, Noe Cochetel, Jose R Munoz, Hollywood Banayad, Yaniv Lupo, Veronica Nunez, Ana Gaspar, Christopher Chen, Krishna Bhattarai, Brandon S Gaut, Dario Cantu, Luis Diaz-Garcia

{"title":"The genetic basis of chloride exclusion in grapevines.","authors":"Sadikshya Sharma, Noe Cochetel, Jose R Munoz, Hollywood Banayad, Yaniv Lupo, Veronica Nunez, Ana Gaspar, Christopher Chen, Krishna Bhattarai, Brandon S Gaut, Dario Cantu, Luis Diaz-Garcia","doi":"10.1093/g3journal/jkaf149","DOIUrl":"10.1093/g3journal/jkaf149","url":null,"abstract":"Mediterranean regions are among the most important areas for global grape production, characterized by dry climates and frequent challenges associated with soil salinity. In these environments, chloride toxicity is a major factor limiting vine growth and fruit quality. Despite the critical role of chloride exclusion in salinity tolerance, the genetic mechanisms underlying this trait remain poorly understood. In this study, we analyzed natural variation in chloride exclusion using a diverse panel of 335 accessions representing 18 wild and cultivated Vitis species. This panel, comprising accessions from the southwestern United States and Mexico, captures a broad range of evolutionary adaptations to abiotic stress and provides a valuable genetic resource for breeding efforts aimed at introducing novel traits. Using genome-wide association and quantitative trait loci (QTL) mapping, we identified a major QTL on chromosome 8, now designated qClEx8.1, containing candidate genes encoding cation/H⁺ exchangers (CHXs), which are involved in ion transport and homeostasis. To validate these findings, we analyzed a mapping population derived from Vitis acerifolia longii 9018 and the commercial rootstock GRN3, confirming the chromosome 8 locus as a major determinant of chloride exclusion. Structural variant analysis revealed nonsynonymous substitutions within CHX genes that may influence protein function and salinity tolerance. Additionally, we discovered a novel QTL on chromosome 19 enriched with G-type lectin S-receptor-like serine/threonine-protein kinases, known regulators of stress signaling. By integrating phenotypic and genomic data across a diverse Vitis collection, this study advances our understanding of the genetic architecture underlying chloride exclusion and highlights candidate genes for breeding salt-tolerant rootstocks.","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":" ","pages":""},"PeriodicalIF":2.2,"publicationDate":"2025-09-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12405893/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144527147","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}

引用次数: 0

Distinct satellite DNA composition between core and germline restricted chromosomes in Bradysia (Sciara) coprophila. coprophila的核心染色体和种系限制性染色体之间不同的卫星DNA组成。

IF 2.2 3区生物学

G3: Genes|Genomes|Genetics Pub Date : 2025-09-03 DOI: 10.1093/g3journal/jkaf155

Anne Kerrebrock, Jullien M Flynn, Robert B Baird, Christina N Hodson, Laura Ross, Yukiko M Yamashita

{"title":"Distinct satellite DNA composition between core and germline restricted chromosomes in Bradysia (Sciara) coprophila.","authors":"Anne Kerrebrock, Jullien M Flynn, Robert B Baird, Christina N Hodson, Laura Ross, Yukiko M Yamashita","doi":"10.1093/g3journal/jkaf155","DOIUrl":"10.1093/g3journal/jkaf155","url":null,"abstract":"Programmed DNA elimination, a phenomenon wherein cells eliminate a subset of genetic material during certain stages of development, is observed in a broad range of organisms. The fungus gnat Bradysia (formerly Sciara) coprophila undergoes a series of programmed DNA elimination events during their development, including elimination of germline-restricted chromosomes (called L chromosomes) in the soma and elimination of paternal chromosomes during male meiosis. However, a lack of understanding surrounding the nature of eliminated chromosomes poses a barrier to studying programmed DNA elimination in this system. Highly repetitive satellite DNA, which often shows chromosome-specific distribution, is a possible candidate for sequences involved in programmed DNA elimination. In this study, we utilized recent genomic data and genome assemblies to identify new satellite DNA sequences of B. coprophila, and characterized their distribution on chromosomes. The results imply that the X and autosomes do not share centromeric satellite DNA sequence (BcopSat-155) with the L chromosomes. We further provide cytological evidence that confirms a recent finding based on the genome assembly that there are 2 distinct L chromosomes that were not previously distinguished cytologically. Together, our work lays a foundation for future studies to explore the possible connection between satellite DNA and the mechanism of programmed DNA elimination in B. coprophila.","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":" ","pages":""},"PeriodicalIF":2.2,"publicationDate":"2025-09-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12405879/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144559716","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}

引用次数: 0

Mainly high phenotypic stability of black spruce clones for growth and wood traits in contrasted environments within the current breeding zones and multitrait selection in Québec's seed and breeding zones. 主要是黑云杉无性系在现有育种区对比环境下的生长和木材性状的高表型稳定性，以及在曲氏种子区和育种区多性状选择的高表型稳定性。

IF 2.2 3区生物学

G3: Genes|Genomes|Genetics Pub Date : 2025-09-03 DOI: 10.1093/g3journal/jkaf120

Mireille Desponts, Josianne DeBlois, Guillaume Otis-Prud'homme, Martin Perron

{"title":"Mainly high phenotypic stability of black spruce clones for growth and wood traits in contrasted environments within the current breeding zones and multitrait selection in Québec's seed and breeding zones.","authors":"Mireille Desponts, Josianne DeBlois, Guillaume Otis-Prud'homme, Martin Perron","doi":"10.1093/g3journal/jkaf120","DOIUrl":"10.1093/g3journal/jkaf120","url":null,"abstract":"Selected trees from various progeny trials cannot be directly compared. As parents of clonal seed orchards and components of the next breeding cycle, it is crucial to verify their stability in different soil and climatic conditions and to rank them for multiple traits. A subset of the best trees selected for height at 10 or 15 years was cloned to establish 2 clone trials per population for 4 breeding populations, covering different bioclimatic domains of Québec. Between 80 and 119 clones per population were compared for height, diameter at breast height, indirect measure of wood density (Pilodyn 6J Forest device) and acoustic velocity (Fiber-gen Hitman ST300). Linear mixed models were used to estimate various genetic parameters, including genotypic values, using the Best Linear Unbiased Prediction (BLUP) method. With the genotypic values at 15 or 16 years for acoustic velocity and height, a selection index was calculated for ranking the clones. Clonal variances are significant for all growth and wood traits. Clonal heritabilities are low for growth traits with 1 exception (0.11-0.30) and range mainly from moderate to high for wood traits (0.29-0.70). Genotype × environment (G × E) interactions for growth traits are low for 2 populations (0.87-1) and mainly moderate for the 2 others (0.53-0.92). For wood traits, G × E interactions are low to almost nil and are mostly moderate for 1 population (0.69-1). In general, clones exhibit high stability (2 BLUP-based stability indexes) for growth and wood traits in contrasting soil and climatic conditions, except for the growth traits of 2 populations.","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":" ","pages":""},"PeriodicalIF":2.2,"publicationDate":"2025-09-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12405895/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144179888","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}

引用次数: 0

Genetic linkage mapping in Megathyrsus maximus (Jacq.) with multiple dosage markers. 基于多剂量标记的巨巨猴遗传连锁定位。

IF 2.2 3区生物学

G3: Genes|Genomes|Genetics Pub Date : 2025-09-03 DOI: 10.1093/g3journal/jkaf126

Gabriel de Siqueira Gesteira, Getulio Caixeta Ferreira, Marcelo Mollinari, Mateus Figueiredo Santos, Liana Jank, Mariane de Mendonça Vilela, Andrea Raposo, Lucimara Chiari, Zhao-Bang Zeng, Antonio Augusto Franco Garcia

{"title":"Genetic linkage mapping in Megathyrsus maximus (Jacq.) with multiple dosage markers.","authors":"Gabriel de Siqueira Gesteira, Getulio Caixeta Ferreira, Marcelo Mollinari, Mateus Figueiredo Santos, Liana Jank, Mariane de Mendonça Vilela, Andrea Raposo, Lucimara Chiari, Zhao-Bang Zeng, Antonio Augusto Franco Garcia","doi":"10.1093/g3journal/jkaf126","DOIUrl":"10.1093/g3journal/jkaf126","url":null,"abstract":"Megathyrsus maximus (Jacq.), commonly known as guinea grass, is a forage crop widely used to form pastures and feed livestock. The species stands out for presenting high yield and nutritional quality in the leaves and its ability to be clonally propagated by seeds. In this work, we construct a dense and informative genetic linkage map for M. maximus using multiple dosage markers. We sequenced DNA from leaf samples of 224 individuals from a biparental cross between two tetraploid genotypes, then analyzed the raw sequencing data to find variants and call dosage-based genotypes using four related reference genomes. With the multiple dosage genotypes for both parents and all individuals, we constructed a highly informative genetic linkage map using state-of-the-art methods coupled with the multipoint Hidden Markov Model approach. We present the densest and most informative genetic linkage map to date for the species, with 7,095 markers distributed across eight homology groups, spanning 1573.31 cM of the genome. Both parents and all individuals in the mapping population were phased according to the species' ploidy level. There was no evidence of double-reduction or preferential pairing in the studied population. The linkage analysis provided in this work can help unravel the evolutionary pathway of the species, understand the genetic behavior of quantitative traits, assist in the assembly of reference genomes, and support the adoption of genomics-assisted selection strategies in M. maximus breeding programs.","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":" ","pages":""},"PeriodicalIF":2.2,"publicationDate":"2025-09-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12405877/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144642200","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}

引用次数: 0

Comprehensive analysis of 1,771 transcriptomes from 7 tissues enhance genetic and biological interpretations of maize complex traits. 对来自7个组织的1771个转录组的综合分析增强了对玉米复合性状的遗传和生物学解释。

IF 2.2 3区生物学

G3: Genes|Genomes|Genetics Pub Date : 2025-09-03 DOI: 10.1093/g3journal/jkaf140

Mengyu Lei, Huan Si, Mingjia Zhu, Yu Han, Wei Liu, Yifei Dai, Yan Ji, Zhengwen Liu, Fan Hao, Ran Hao, Jiarui Zhao, Guoyou Ye, Yanjun Zan

{"title":"Comprehensive analysis of 1,771 transcriptomes from 7 tissues enhance genetic and biological interpretations of maize complex traits.","authors":"Mengyu Lei, Huan Si, Mingjia Zhu, Yu Han, Wei Liu, Yifei Dai, Yan Ji, Zhengwen Liu, Fan Hao, Ran Hao, Jiarui Zhao, Guoyou Ye, Yanjun Zan","doi":"10.1093/g3journal/jkaf140","DOIUrl":"10.1093/g3journal/jkaf140","url":null,"abstract":"By reanalyzing 1,771 RNA-seq datasets from 7 tissues in a maize diversity panel, we explored the landscape of multi-tissue transcriptome variation, evolution patterns of tissue-specific genes, and built a comprehensive multi-tissue gene regulation atlas to understand the genetic regulation of maize complex traits. Through an integrative analysis of tissue-specific gene regulatory variation with genome-wide association studies, we detected relevant tissue types and several candidate genes for a number of agronomic traits, including leaf during the day for the anthesis-silking interval, leaf during the day for kernel Zeinoxanthin level, and root for ear height, highlighting the potential contribution of tissue-specific gene expression to variation in agronomic traits. Using transcriptome-wide association and colocalization analysis, we associated tissue-specific expression variation of 74 genes to agronomic traits variation. Our findings provide novel insights into the genetic and biological mechanisms underlying maize complex traits, and the multi-tissue regulatory atlas serves as a primary source for biological interpretation, functional validation, and genomic improvement of maize.","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":" ","pages":""},"PeriodicalIF":2.2,"publicationDate":"2025-09-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12405892/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144682314","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}

引用次数: 0

Genome Report: First whole genome assembly of Python regius (ball python), a model of extreme physiological and metabolic plasticity. 基因组报告：第一个全基因组组装的蟒蛇regius（球蟒），一个极端的生理和代谢可塑性模型。

IF 2.2 3区生物学

G3: Genes|Genomes|Genetics Pub Date : 2025-09-02 DOI: 10.1093/g3journal/jkaf197

Dakota R Hunt, Holly Allen, Thomas G Martin, Sophia N Feghali, Edward B Chuong, Leslie A Leinwand

{"title":"Genome Report: First whole genome assembly of Python regius (ball python), a model of extreme physiological and metabolic plasticity.","authors":"Dakota R Hunt, Holly Allen, Thomas G Martin, Sophia N Feghali, Edward B Chuong, Leslie A Leinwand","doi":"10.1093/g3journal/jkaf197","DOIUrl":"10.1093/g3journal/jkaf197","url":null,"abstract":"The study of nontraditional model organisms, particularly those exhibiting extreme phenotypes, offers unique insights into adaptive mechanisms of stress response and survival. Snakes, with their remarkable physiological, metabolic, and morphological adaptations, serve as powerful models for investigating these processes. Burmese pythons (Python bivittatus) have been used as a model for studying the plasticity of extreme physiological systems. The low contiguity of the Python bivittatus genome and rising challenges in obtaining Burmese pythons for study prompted us to sequence, assemble, and annotate the genome of the closely related ball python (Python regius). Using a hybrid sequencing approach, we generated a 1.45 Gb genome assembly with a scaffold N50 greater than 61 Mb and a BUSCO score of 98%, representing one of the highest quality genomes to date for a member of the Pythonidae family. This assembly provides a valuable resource for studying snake-specific traits and evolutionary biology. Furthermore, it enables exploration of the molecular mechanisms underlying the remarkable cardiac and muscular adaptations in pythons, such as their ability to rapidly remodel their heart following feeding and resist muscular atrophy during prolonged fasting. These insights have potential applications in human health, particularly in the development of therapies targeting cardiac hypertrophy and muscular atrophy.","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":" ","pages":""},"PeriodicalIF":2.2,"publicationDate":"2025-09-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144949159","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

From Fragmentation to Resolution: High-Fidelity Genome Assembly of Zancudomyces culisetae through Comparative Insights from PacBio, Nanopore, and Illumina Sequencing. 从碎片化到分辨率：通过PacBio， Nanopore和Illumina测序的比较见解对culisetae赞库菌的高保真基因组组装。

IF 2.2 3区生物学

G3: Genes|Genomes|Genetics Pub Date : 2025-09-01 DOI: 10.1093/g3journal/jkaf204

Huimei Yang, Yan Wang

{"title":"From Fragmentation to Resolution: High-Fidelity Genome Assembly of Zancudomyces culisetae through Comparative Insights from PacBio, Nanopore, and Illumina Sequencing.","authors":"Huimei Yang, Yan Wang","doi":"10.1093/g3journal/jkaf204","DOIUrl":"https://doi.org/10.1093/g3journal/jkaf204","url":null,"abstract":"Zancudomyces culisetae is an obligate symbiotic fungus inhabiting the digestive tracts of aquatic insect larvae, including black flies, midges, and mosquitoes. With a global distribution and high prevalence in disease-transmitting insects, Z. culisetae serves as a model for studying insect gut fungi. A previous draft genome assembly using Illumina short reads provided insights into its genome composition, such as a low GC ratio and evidence of horizontal gene transfer. However, its fragmented nature has limited deeper exploration of the evolutionary mechanisms shaping these gut symbionts. To address this gap, we generated a wealth of genomic resources for Z. culisetae using multiple sequencing platforms, including Illumina, Oxford Nanopore, PacBio-CLR (Complete Long Reads), and PacBio-HiFi (High Fidelity). This also provides an opportunity to compare these popular sequencing methods to suggest the optimal approach for fungal genome assembly. Our results suggest that PacBio-HiFi produced the most complete assembly, yielding a 27.8 Mb genome size with 26 contigs, representing the highest-quality genome of insect gut fungi to date. Additionally, we generated transcriptomic data to support genome annotation, identifying 8,484 protein-coding genes. Despite the improved genome quality, Z. culisetae lacks approximately 20% of Benchmarking Universal Single-Copy Orthologue (BUSCO) commonly found in fungi, reflecting adaptations to its obligate symbiotic lifestyle. This study not only provides valuable genomic resources for insect gut fungal research but also evaluates the strengths and limitations of current genome sequencing and assembly approaches, offering best practices for fungal genome analysis and genetic research.","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":" ","pages":""},"PeriodicalIF":2.2,"publicationDate":"2025-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144949156","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Variation in inbreeding depression within and among Caenorhabditis species. 杆状线虫种内和种间近交抑制的变异。

IF 2.2 3区生物学

G3: Genes|Genomes|Genetics Pub Date : 2025-08-29 DOI: 10.1093/g3journal/jkaf200

Matthew V Rockman, Max R Bernstein, Derin Çağlar, M Victoria Cattani, Audrey S Chang, Taniya Kaur, Luke M Noble, Annalise B Paaby

{"title":"Variation in inbreeding depression within and among Caenorhabditis species.","authors":"Matthew V Rockman, Max R Bernstein, Derin Çağlar, M Victoria Cattani, Audrey S Chang, Taniya Kaur, Luke M Noble, Annalise B Paaby","doi":"10.1093/g3journal/jkaf200","DOIUrl":"10.1093/g3journal/jkaf200","url":null,"abstract":"Outbreeding populations harbor large numbers of recessive deleterious alleles that reduce the fitness of inbred individuals, and this inbreeding depression potentially shapes the evolution of mating systems, acting as a counterweight to the inherent selective advantage of self-fertilization. The population biological factors that influence inbreeding depression are numerous and often difficult to disentangle. We investigated the utility of obligately-outcrossing Caenorhabditis nematodes as models for inbreeding depression. By systematically inbreeding lines from ten populations and tracking line extinction, we found that inbreeding depression is universal but highly variable among species and populations. Inbreeding depression was detected across the life cycle, from mating to embryo production to embryonic viability and larval growth, and reciprocal crosses implicated female-biased effects. In most cases, the surviving inbred lines have dramatically reduced fitness, but the variance among inbred lines is substantial and compatible with the idea that inbreeding depression need not be an obstacle to the evolution of selfing in these worms. Populations of some species, including Caenorhabditis becei, exhibited modest inbreeding depression and could be tractable laboratory models for obligately outcrossing Caenorhabditis.","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":" ","pages":""},"PeriodicalIF":2.2,"publicationDate":"2025-08-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144949172","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Genomic Correlates of Tailocin Sensitivity in Pseudomonas syringae. 丁香假单胞菌对Tailocin敏感性的基因组相关性研究。

IF 2.2 3区生物学

G3: Genes|Genomes|Genetics Pub Date : 2025-08-29 DOI: 10.1093/g3journal/jkaf203

David A Baltrus, Savannah Weaver, Laura Krings, Anh Evy Nguyen

{"title":"Genomic Correlates of Tailocin Sensitivity in Pseudomonas syringae.","authors":"David A Baltrus, Savannah Weaver, Laura Krings, Anh Evy Nguyen","doi":"10.1093/g3journal/jkaf203","DOIUrl":"https://doi.org/10.1093/g3journal/jkaf203","url":null,"abstract":"Phage-derived bacteriocins, also referred to as tailocins, are structures encoded by bacterial genomes and deployed into the extracellular environment to kill sensitive cells. Tailocins display great potential as agricultural antimicrobials due to their durability, efficiency, and specificity of killing with prophylactic application demonstrated to prevent infection by multiple phytopathogens. Previous reports suggest that tailocins of Pseudomonas syringae interact with sugar moieties in the lipopolysaccharide (LPS) to target sensitive cells, but it remains unclear how genetic and genomic variation at loci encoding LPS biosynthesis influences tailocin resistance and/or sensitivity across the species. We therefore carried out a genome-wide association study investigating tailocin sensitivity across a diverse set of P. syringae genomes. Our results demonstrate that genes strongly correlated with tailocin sensitivity are localized to one contiguous region on the chromosome encoding LPS structures similar to the Common Polysaccharide Antigen of P. aeruginosa. We further find that enzymes involved in the biosynthesis and transport of D-rhamnose and L-rhamnose are associated with tailocin sensitivity classes A and B, respectively, with large-scale recombination of the O-antigen biosynthesis region likely underlying rapid and fundamental changes in LPS structure between strains. Building on these results, we identify rfbD as a genomic indicator to predict tailocin sensitivity and use this information to test tailocin interactions with unscreened strains, including some in which LPS chains have been previously characterized. Overall, our results strongly support that tailocin sensitivity for P. syringae is broadly determined by recombination events across strains that lead to differential production of either D or L-rhamnose moieties in the main O-antigen chain.","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":" ","pages":""},"PeriodicalIF":2.2,"publicationDate":"2025-08-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144949169","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

An examination of the quinic acid utilization genes in Aspergillus niger reveals the involvement of two pH-dependent permeases. 对黑曲霉中奎宁酸利用基因的研究揭示了两种ph依赖性渗透物的参与。

IF 2.2 3区生物学

G3: Genes|Genomes|Genetics Pub Date : 2025-08-25 DOI: 10.1093/g3journal/jkaf199

Michael Sgro, Ian D Reid, Mark Arentshorst, Arthur F J Ram, Adrian Tsang

{"title":"An examination of the quinic acid utilization genes in Aspergillus niger reveals the involvement of two pH-dependent permeases.","authors":"Michael Sgro, Ian D Reid, Mark Arentshorst, Arthur F J Ram, Adrian Tsang","doi":"10.1093/g3journal/jkaf199","DOIUrl":"https://doi.org/10.1093/g3journal/jkaf199","url":null,"abstract":"Many microorganisms are able to use plant-derived aromatic and cyclic compounds like the common plant secondary metabolite quinic acid as carbon and energy sources. In fungi, three enzymatic steps convert quinic acid into the common intermediate protocatechuic acid, which is then further converted into TCA cycle intermediates. The genes encoding these three enzymes are known to be part of a gene cluster in Neurospora crassa along with a permease, a gene of unknown function, and an activator-repressor module controlling expression of the cluster. This gene cluster is conserved in fungi and has also been studied in Aspergillus nidulans, where an additional gene of unknown function is included. Here, we studied these genes in the filamentous fungus Aspergillus niger, where the availability of high-quality, well-annotated genomes and efficient tools for genome-editing and global gene expression analysis could provide new insights into quinic acid utilization in fungi. Using homology and whole transcriptome sequencing, we identified the genes involved in quinic acid utilization. Knockout mutants of these genes were then created to observe the growth phenotype on quinic acid media. We showed that not all the genes involved in quinic acid utilization in A. niger are linked. In addition to the in-cluster permease gene, we identified a second, previously unknown off-cluster permease gene which was upregulated in the presence of quinic acid. These two permeases were determined to function optimally at different pH levels, with the in-cluster permease being more effective at pH 6.5 and the off-cluster permease more effective at pH 3.5.","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":" ","pages":""},"PeriodicalIF":2.2,"publicationDate":"2025-08-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144949174","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0