Pub Date : 2025-05-02DOI: 10.1016/j.fgb.2025.103990
Vinicius Delgado da Rocha , Everton Geraldo Capote Ferreira , Fernanda Machado Castanho , Marcia Kamogae Kuwahara , Cláudia Vieira Godoy , Maurício Conrado Meyer , Kerry F. Pedley , Ralf T. Voegele , Anna Lipzen , Kerrie Barry , Igor V. Grigoriev , Marco Loehrer , Ulrich Schaffrath , Catherine Sirven , Sebastien Duplessis , Francismar Corrêa Marcelino-Guimarães
Phakopsora pachyrhizi, an obligate biotrophic rust fungus, is the causal agent of Asian Soybean Rust (ASR) disease. Here, we utilized whole-genome data to explore the evolutionary patterns and population structure across 45 P. pachyrhizi isolates collected from 1972 to 2017 from diverse geographic regions worldwide. We also characterized in-silico mating-type (MAT) genes of P. pachyrhizi, in the predicted proteome of three isolates, to investigate the sexual compatibility system. Our molecular phylogenetic analysis in P. pachyrhizi inferred two distinct evolutionary lineages structured on a temporal scale, with lineage Pp1 grouping isolates obtained from 1972 to 1994, while more recently collected isolates formed a second lineage, Pp2. We found higher levels of genetic diversity in lineage Pp1, whereas lineage Pp2 exhibited a strong clonal genetic structure, with a significant lower diversity. The widespread propagation of P. pachyrhizi clonal spores across soybean-growing regions likely explains the absence of a large-scale spatial genetic structure within each lineage. Two independent isolates (TW72–1 and AU79–1) showed moderate levels of genetic admixture, suggesting potential somatic hybridization between the two P. pachyrhizi lineages. We observed no clear congruence between virulence levels of P. pachyrhizi isolates and their phylogenetic patterns. Our findings support a probable tetrapolar mating system in P. pachyrhizi. Taken together, our study offers new insights into the evolutionary history of P. pachyrhizi and demonstrates that multiple MAT genes are highly expressed during the later stages of soybean infection, suggesting their potential role in the formation of urediniospores within the life cycle of P. pachyrhizi.
{"title":"Analysis of the genetic diversity of the soybean rust pathogen Phakopsora pachyrhizi reveals two major evolutionary lineages","authors":"Vinicius Delgado da Rocha , Everton Geraldo Capote Ferreira , Fernanda Machado Castanho , Marcia Kamogae Kuwahara , Cláudia Vieira Godoy , Maurício Conrado Meyer , Kerry F. Pedley , Ralf T. Voegele , Anna Lipzen , Kerrie Barry , Igor V. Grigoriev , Marco Loehrer , Ulrich Schaffrath , Catherine Sirven , Sebastien Duplessis , Francismar Corrêa Marcelino-Guimarães","doi":"10.1016/j.fgb.2025.103990","DOIUrl":"10.1016/j.fgb.2025.103990","url":null,"abstract":"<div><div><em>Phakopsora pachyrhizi</em>, an obligate biotrophic rust fungus, is the causal agent of Asian Soybean Rust (ASR) disease. Here, we utilized whole-genome data to explore the evolutionary patterns and population structure across 45 <em>P. pachyrhizi</em> isolates collected from 1972 to 2017 from diverse geographic regions worldwide. We also characterized <em>in-silico</em> mating-type (<em>MAT</em>) genes of <em>P. pachyrhizi</em>, in the predicted proteome of three isolates, to investigate the sexual compatibility system. Our molecular phylogenetic analysis in <em>P. pachyrhizi</em> inferred two distinct evolutionary lineages structured on a temporal scale, with lineage Pp1 grouping isolates obtained from 1972 to 1994, while more recently collected isolates formed a second lineage, Pp2. We found higher levels of genetic diversity in lineage Pp1, whereas lineage Pp2 exhibited a strong clonal genetic structure, with a significant lower diversity. The widespread propagation of <em>P. pachyrhizi</em> clonal spores across soybean-growing regions likely explains the absence of a large-scale spatial genetic structure within each lineage. Two independent isolates (TW72–1 and AU79–1) showed moderate levels of genetic admixture, suggesting potential somatic hybridization between the two <em>P. pachyrhizi</em> lineages. We observed no clear congruence between virulence levels of <em>P. pachyrhizi</em> isolates and their phylogenetic patterns. Our findings support a probable tetrapolar mating system in <em>P. pachyrhizi</em>. Taken together, our study offers new insights into the evolutionary history of <em>P. pachyrhizi</em> and demonstrates that multiple <em>MAT</em> genes are highly expressed during the later stages of soybean infection, suggesting their potential role in the formation of urediniospores within the life cycle of <em>P. pachyrhizi</em>.</div></div>","PeriodicalId":55135,"journal":{"name":"Fungal Genetics and Biology","volume":"179 ","pages":"Article 103990"},"PeriodicalIF":2.4,"publicationDate":"2025-05-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143918032","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}
Pub Date : 2025-04-29DOI: 10.1016/j.fgb.2025.103987
Erik P.W. Beijen, Marieke H. van Maanen, Esther S. van den Bergh, Rose Brouns, Ioana M. Marian, Thomas J. de Vries, Peter Jan Vonk, Robin A. Ohm
Mushroom-forming fungi encounter numerous competitors during their lifecycle and have developed strategies to defend themselves. However, the regulation of this fungal immune system is largely unknown. We studied the role of transcription factors Fst8, Ftr3 and Gat1 during the interaction between the mushroom-forming fungus Schizophyllum commune and the ascomycete mycoparasites Trichoderma harzianum and Trichoderma aggressivum. These proteins are conserved to varying degrees in basidiomycetes, with a high degree of conservation in Agaricales. We showed that the regulators Fst8 and Ftr3 play a role in regulating the immune system, similar to Gat1 which we previously identified. Deletion of the fst8 and ftr3 genes led to varying degrees of defensive impairment in S. commune. A Δgat1Δfst8 double knockout strain was most affected, indicating that these regulators are likely involved in different pathways. We identified putative (direct or indirect) targets of these transcription factors using a transcriptomics approach. These genes include small secreted proteins and transporters. Combining data from the single deletion strains, we identified a core group of 18 putative targets, including thaumatins, cell wall modifiers, and detoxifiers. Combined, we identified the regulatory network initiated by the regulators Fst8, Ftr3 and Gat1 during interaction with fungal competitors.
{"title":"Transcription factors Fst8, Ftr3 and Gat1 are regulators of the immune system of the mushroom Schizophyllum commune","authors":"Erik P.W. Beijen, Marieke H. van Maanen, Esther S. van den Bergh, Rose Brouns, Ioana M. Marian, Thomas J. de Vries, Peter Jan Vonk, Robin A. Ohm","doi":"10.1016/j.fgb.2025.103987","DOIUrl":"10.1016/j.fgb.2025.103987","url":null,"abstract":"<div><div>Mushroom-forming fungi encounter numerous competitors during their lifecycle and have developed strategies to defend themselves. However, the regulation of this fungal immune system is largely unknown. We studied the role of transcription factors Fst8, Ftr3 and Gat1 during the interaction between the mushroom-forming fungus <em>Schizophyllum commune</em> and the ascomycete mycoparasites <em>Trichoderma harzianum</em> and <em>Trichoderma aggressivum</em>. These proteins are conserved to varying degrees in basidiomycetes, with a high degree of conservation in Agaricales. We showed that the regulators Fst8 and Ftr3 play a role in regulating the immune system, similar to Gat1 which we previously identified. Deletion of the <em>fst8</em> and <em>ftr3</em> genes led to varying degrees of defensive impairment in <em>S. commune</em>. A Δ<em>gat1</em>Δ<em>fst8</em> double knockout strain was most affected, indicating that these regulators are likely involved in different pathways. We identified putative (direct or indirect) targets of these transcription factors using a transcriptomics approach. These genes include small secreted proteins and transporters. Combining data from the single deletion strains, we identified a core group of 18 putative targets, including thaumatins, cell wall modifiers, and detoxifiers. Combined, we identified the regulatory network initiated by the regulators Fst8, Ftr3 and Gat1 during interaction with fungal competitors.</div></div>","PeriodicalId":55135,"journal":{"name":"Fungal Genetics and Biology","volume":"179 ","pages":"Article 103987"},"PeriodicalIF":2.4,"publicationDate":"2025-04-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143891717","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}
The maturation of the fruiting body primordia in the Agaricomycete Coprinopsis cinerea is triggered by light exposure, followed by a required dark period to complete maturation. During this maturation phase, meiosis occurs within basidia arranged on the surface of the gills (lamellae) on the underside of the cap. However, the molecular events required during the dark period for fruiting body maturation remain elusive. We identified a developmental mutant that fails to mature fruiting bodies under light/dark conditions. The mutant fruiting bodies resembled those arrested by the wild-type strains cultured under continuous light. The gene responsible for this mutant phenotype encodes a chromodomain helicase DNA-binding protein 1 (Chd1) homolog, Cc.Chd1. RNA-seq revealed a low transcriptional region (LTcR) within the Cc.chd1 gene. This suggests that a short version of Cc.Chd1 (predicted 1125 aa, Cc.Chd1S) is translated from the vegetative mycelium stage until before karyogamy. In contrast, the full-length Cc.Chd1 (predicted 1441 aa, Cc.Chd1L) is translated during or after the dark period when karyogamy occurs in the basidia. Western blot analysis confirmed these types of Cc.Chd1 at the expected stages. Microscopic observations further revealed that meiotic chromosomes in basidia become arrested at prophase I in the Cc.chd1–1 mutant and wild-type strains cultured under continuous light. These findings suggest that Cc.Chd1L is required for progression from meiotic prophase I to metaphase I. Additionally, the Cc.chd1 mutant exhibits defects in light-induced secondary knot formation, suggesting a role for Cc.Chd1S in this process.
{"title":"Full-length Chd1 of Coprinopsis cinerea is expressed after the dark period required for fruiting body maturation and impacts meiotic progression","authors":"Haruki Abe, Satoshi Mimura, Kozue Hatanaka, Tetsuya Kakizaki, Hajime Muraguchi","doi":"10.1016/j.fgb.2025.103988","DOIUrl":"10.1016/j.fgb.2025.103988","url":null,"abstract":"<div><div>The maturation of the fruiting body primordia in the Agaricomycete <em>Coprinopsis cinerea</em> is triggered by light exposure, followed by a required dark period to complete maturation. During this maturation phase, meiosis occurs within basidia arranged on the surface of the gills (lamellae) on the underside of the cap. However, the molecular events required during the dark period for fruiting body maturation remain elusive. We identified a developmental mutant that fails to mature fruiting bodies under light/dark conditions. The mutant fruiting bodies resembled those arrested by the wild-type strains cultured under continuous light. The gene responsible for this mutant phenotype encodes a chromodomain helicase DNA-binding protein 1 (Chd1) homolog, Cc.Chd1. RNA-seq revealed a low transcriptional region (LTcR) within the <em>Cc.chd1</em> gene. This suggests that a short version of Cc.Chd1 (predicted 1125 aa, Cc.Chd1S) is translated from the vegetative mycelium stage until before karyogamy. In contrast, the full-length Cc.Chd1 (predicted 1441 aa, Cc.Chd1L) is translated during or after the dark period when karyogamy occurs in the basidia. Western blot analysis confirmed these types of Cc.Chd1 at the expected stages. Microscopic observations further revealed that meiotic chromosomes in basidia become arrested at prophase I in the <em>Cc.chd1–1</em> mutant and wild-type strains cultured under continuous light. These findings suggest that Cc.Chd1L is required for progression from meiotic prophase I to metaphase I. Additionally, the <em>Cc.chd1</em> mutant exhibits defects in light-induced secondary knot formation, suggesting a role for Cc.Chd1S in this process.</div></div>","PeriodicalId":55135,"journal":{"name":"Fungal Genetics and Biology","volume":"179 ","pages":"Article 103988"},"PeriodicalIF":2.4,"publicationDate":"2025-04-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143891768","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}
Aspergillus flavus is a saprophytic fungus that can infect economic crops and produce aflatoxins with high toxicity, carcinogenicity and mutagenicity, which is a serious threat to human and animal health. In order to find a more efficient biological control way to inhibit A. flavus and its production of aflatoxins, we isolated 7 fungal strains F1-F7 from Camellia sinensis. Only the strains F1 and F2, isolated from the flowers of C. sinensis and identified as Alternaria alstroemeriae and Alternaria burnsii, exhibited significant antagonistic activities against A. flavus. In addition, the contents of AFB1 and AFB2 significantly decreased when A. flavus was antagonized by Alternaria alstroemeriae F1. By the transcriptome and qRT-PCR analysis, some genes related to A. flavus growth and secondary metabolism were differentially expressed, and the expression levels of 14 genes in aflatoxins synthesis gene cluster that positively regulate aflatoxins synthesis all showed down-trends, and 2 genes (aflC and aflG) that negatively regulate aflatoxins synthesis showed up-trends. We hypothesize that the A. alstroemeriae F1 may secrete some secondary metabolites to inhibit the growth of A. flavus and decrease aflatoxins biosynthesis to a certain extent by regulating the expression levels of genes in aflatoxins biosynthesis gene cluster. In summary, this work lays a foundation for more effective biological controls against A. flavus growth and aflatoxins biosynthesis.
{"title":"Alternaria alstroemeriae F1 inhibits aspergillus flavus growth and weakens aflatoxins biosynthesis","authors":"Yingying Ye , Qiaoyun Wu , Yiran Liu, Yufan He, Xiufang Hu, Xiaodan Zhang, Guohong Zeng","doi":"10.1016/j.fgb.2025.103989","DOIUrl":"10.1016/j.fgb.2025.103989","url":null,"abstract":"<div><div><em>Aspergillus flavus</em> is a saprophytic fungus that can infect economic crops and produce aflatoxins with high toxicity, carcinogenicity and mutagenicity, which is a serious threat to human and animal health. In order to find a more efficient biological control way to inhibit <em>A. flavus</em> and its production of aflatoxins, we isolated 7 fungal strains F1-F7 from <em>Camellia sinensis</em>. Only the strains F1 and F2, isolated from the flowers of <em>C. sinensis</em> and identified as <em>Alternaria alstroemeriae</em> and <em>Alternaria burnsii</em>, exhibited significant antagonistic activities against <em>A. flavus</em>. In addition, the contents of AFB1 and AFB2 significantly decreased when <em>A. flavus</em> was antagonized by <em>Alternaria alstroemeriae</em> F1. By the transcriptome and qRT-PCR analysis, some genes related to <em>A. flavus</em> growth and secondary metabolism were differentially expressed, and the expression levels of 14 genes in aflatoxins synthesis gene cluster that positively regulate aflatoxins synthesis all showed down-trends, and 2 genes (<em>aflC</em> and <em>aflG</em>) that negatively regulate aflatoxins synthesis showed up-trends. We hypothesize that the <em>A. alstroemeriae</em> F1 may secrete some secondary metabolites to inhibit the growth of <em>A. flavus</em> and decrease aflatoxins biosynthesis to a certain extent by regulating the expression levels of genes in aflatoxins biosynthesis gene cluster. In summary, this work lays a foundation for more effective biological controls against <em>A. flavus</em> growth and aflatoxins biosynthesis.</div></div>","PeriodicalId":55135,"journal":{"name":"Fungal Genetics and Biology","volume":"179 ","pages":"Article 103989"},"PeriodicalIF":2.4,"publicationDate":"2025-04-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143948607","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}
Pub Date : 2025-04-25DOI: 10.1016/j.fgb.2025.103986
Jie Zeng , Yu Cao , Qingrui Xu , Yulu Ran , Yihan Guo , Pengrui Jiao , Xiaoqiang Lang , Dairong Qiao , Hui Xu , Yi Cao
Sugar transporters (STs) are critical biological macromolecules that involved in the regulation of fungal development and responses to abiotic stresses. While monosaccharide- and sucrose-specific transporters have been extensively characterized in yeast and plants, knowledge of STs in filamentous fungi remains limited. Here, through genome mining, we identified 173 STs in the salt-tolerant fungus Aspergillus sydowii H-1 and classified them into nine subgroups. Notably, 37 of these STs showed active responses to high-salt stress, with the glycerol transporter AsSTL exhibiting particularly strong induction. Protein–protein interaction analysis revealed that AsSTL is regulated by multiple mitogen-activated protein kinases, including Hog1, Ssk22, Ste11, Pbs2 and Fus3. Functional validation via Hog1 knockout experiments demonstrated that Hog1 positively regulates AsSTL. Localization studies revealed that AsSTL localizes to the plasma membrane, where it mediates glycerol absorption. The deletion of AsSTL significantly impaired glycerol uptake, conidial production, growth, and stress tolerance to NaCl and H₂O₂ stress, and purple pigment synthesis. These findings establish AsSTL as a key Hog1-reglulated protein, essential for glycerol homeostasis, salt stress adaptation, and secondary metabolite production in A. sydowii H-1. This study highlights the critical roles of ST proteins in fungal stress responses and provides insights into potential mechanisms for improving stress tolerance in fungi.
{"title":"The sugar transporter AsSTL is regulated by the kinase Hog1 and is involved in glycerol transport and the response to osmotic stress in the salt-tolerant ascomycete aspergillus sydowii H-1","authors":"Jie Zeng , Yu Cao , Qingrui Xu , Yulu Ran , Yihan Guo , Pengrui Jiao , Xiaoqiang Lang , Dairong Qiao , Hui Xu , Yi Cao","doi":"10.1016/j.fgb.2025.103986","DOIUrl":"10.1016/j.fgb.2025.103986","url":null,"abstract":"<div><div>Sugar transporters (STs) are critical biological macromolecules that involved in the regulation of fungal development and responses to abiotic stresses. While monosaccharide- and sucrose-specific transporters have been extensively characterized in yeast and plants, knowledge of STs in filamentous fungi remains limited. Here, through genome mining, we identified 173 STs in the salt-tolerant fungus Aspergillus sydowii H-1 and classified them into nine subgroups. Notably, 37 of these STs showed active responses to high-salt stress, with the glycerol transporter AsSTL exhibiting particularly strong induction. Protein–protein interaction analysis revealed that AsSTL is regulated by multiple mitogen-activated protein kinases, including Hog1, Ssk22, Ste11, Pbs2 and Fus3. Functional validation via Hog1 knockout experiments demonstrated that Hog1 positively regulates AsSTL. Localization studies revealed that AsSTL localizes to the plasma membrane, where it mediates glycerol absorption. The deletion of AsSTL significantly impaired glycerol uptake, conidial production, growth, and stress tolerance to NaCl and H₂O₂ stress, and purple pigment synthesis. These findings establish AsSTL as a key Hog1-reglulated protein, essential for glycerol homeostasis, salt stress adaptation, and secondary metabolite production in A. sydowii H-1. This study highlights the critical roles of ST proteins in fungal stress responses and provides insights into potential mechanisms for improving stress tolerance in fungi.</div></div>","PeriodicalId":55135,"journal":{"name":"Fungal Genetics and Biology","volume":"179 ","pages":"Article 103986"},"PeriodicalIF":2.4,"publicationDate":"2025-04-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143923752","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}
Early blight, caused by Alternaria alternata, poses a critical challenge to tomato (Solanum lycopersicum L.) production, causing significant yield losses worldwide. Despite advancements in plant disease detection, existing methods often lack the robustness, speed, and accuracy needed for real-time, field-level applications, particularly under variable environmental conditions. This study addresses these gaps by leveraging transfer learning with optimized MobileNet architectures to develop a highly efficient and generalizable detection system. A diverse dataset of 6451 tomato leaf images, encompassing healthy and varying disease severity levels (low, medium, high) under multiple lighting conditions, was curated to improve model performance across real-world scenarios. Four MobileNet variants—MobileNet, MobileNet V2, MobileNet V3 Small, and MobileNet V3 Large—were fine-tuned, with MobileNet V3 Large achieving the highest classification accuracy of 99.88 %, an F1 score of 0.996, and a rapid inference time of 67 milliseconds. These attributes make it ideal for real-time IoT applications, including smartphone-based disease monitoring, automated precision spraying, and smart agricultural systems. To further validate diseased samples, internal transcribed spacer (ITS) sequence analysis confirmed A. alternata with over 98 % similarity to known isolates in the NCBI database. This study bridges critical research gaps by providing a robust, non-destructive, and real-time solution for early blight severity assessment, enabling timely, targeted interventions to mitigate crop losses in precision agriculture.
{"title":"Optimized convolutional neural networks for real-time detection and severity assessment of early blight in tomato (Solanum lycopersicum L.)","authors":"Tushar Dhar , Roaf Ahmad Parray , Bishnu Maya Bashyal , Awani Kumar Singh , Parveen Dhanger , Tapan Kumar Khura , Rajeev Kumar , Murtaza Hasan , Md Yeasin","doi":"10.1016/j.fgb.2025.103984","DOIUrl":"10.1016/j.fgb.2025.103984","url":null,"abstract":"<div><div>Early blight, caused by <em>Alternaria alternata</em>, poses a critical challenge to tomato (<em>Solanum lycopersicum L.</em>) production, causing significant yield losses worldwide. Despite advancements in plant disease detection, existing methods often lack the robustness, speed, and accuracy needed for real-time, field-level applications, particularly under variable environmental conditions. This study addresses these gaps by leveraging transfer learning with optimized MobileNet architectures to develop a highly efficient and generalizable detection system. A diverse dataset of 6451 tomato leaf images, encompassing healthy and varying disease severity levels (low, medium, high) under multiple lighting conditions, was curated to improve model performance across real-world scenarios. Four MobileNet variants—MobileNet, MobileNet V2, MobileNet V3 Small, and MobileNet V3 Large—were fine-tuned, with MobileNet V3 Large achieving the highest classification accuracy of 99.88 %, an F1 score of 0.996, and a rapid inference time of 67 milliseconds. These attributes make it ideal for real-time IoT applications, including smartphone-based disease monitoring, automated precision spraying, and smart agricultural systems. To further validate diseased samples, internal transcribed spacer (ITS) sequence analysis confirmed <em>A. alternata</em> with over 98 % similarity to known isolates in the NCBI database. This study bridges critical research gaps by providing a robust, non-destructive, and real-time solution for early blight severity assessment, enabling timely, targeted interventions to mitigate crop losses in precision agriculture.</div></div>","PeriodicalId":55135,"journal":{"name":"Fungal Genetics and Biology","volume":"178 ","pages":"Article 103984"},"PeriodicalIF":2.4,"publicationDate":"2025-04-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143878589","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}
Pub Date : 2025-04-18DOI: 10.1016/j.fgb.2025.103985
Li Xu, Jamy Schulpen, Ronald P. de Vries, Mao Peng
RNA-sequencing (RNA-seq) is the dominant technology for genome-wide transcript quantification in various biological studies. The wide applications of RNA-seq have played an essential role in elucidating complex molecular mechanisms of fungal physiology, and have generated large volumes of related data that are valuable for further bioinformatic mining. In this study, we focus on identifying fungal reference genes from large available transcriptome datasets. In total, 44 candidate reference genes from Aspergillus niger were identified through strict statistical analysis of 332 transcriptomic samples. These candidates cover both newly identified genes and previously reported housekeeping genes and were enriched in several basic cellular pathways, such as genes encoding ubiquitin-conjugating enzyme, 26S proteasome regulatory subunits, vacuolar H+-ATPase subunits, mitochondrial import protein and Ras-related GTPase. Moreover, 26 of the newly identified reference genes with a single ortholog in four other fungi showed stable expression patterns across these fungi. Additionally, these new candidates showed more stable expression than the traditionally used reference genes in the tested datasets, such as gapdh, highlighting their potential to improve normalization of RT-qPCR and transcriptome data.
{"title":"Identification of putative fungal reference genes with stable expression from large RNA-seq datasets","authors":"Li Xu, Jamy Schulpen, Ronald P. de Vries, Mao Peng","doi":"10.1016/j.fgb.2025.103985","DOIUrl":"10.1016/j.fgb.2025.103985","url":null,"abstract":"<div><div>RNA-sequencing (RNA-seq) is the dominant technology for genome-wide transcript quantification in various biological studies. The wide applications of RNA-seq have played an essential role in elucidating complex molecular mechanisms of fungal physiology, and have generated large volumes of related data that are valuable for further bioinformatic mining. In this study, we focus on identifying fungal reference genes from large available transcriptome datasets. In total, 44 candidate reference genes from <em>Aspergillus niger</em> were identified through strict statistical analysis of 332 transcriptomic samples. These candidates cover both newly identified genes and previously reported housekeeping genes and were enriched in several basic cellular pathways, such as genes encoding ubiquitin-conjugating enzyme, 26S proteasome regulatory subunits, vacuolar H<sup>+</sup>-ATPase subunits, mitochondrial import protein and Ras-related GTPase. Moreover, 26 of the newly identified reference genes with a single ortholog in four other fungi showed stable expression patterns across these fungi. Additionally, these new candidates showed more stable expression than the traditionally used reference genes in the tested datasets, such as <em>gapdh</em>, highlighting their potential to improve normalization of RT-qPCR and transcriptome data.</div></div>","PeriodicalId":55135,"journal":{"name":"Fungal Genetics and Biology","volume":"178 ","pages":"Article 103985"},"PeriodicalIF":2.4,"publicationDate":"2025-04-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143869425","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}
Pub Date : 2025-04-03DOI: 10.1016/j.fgb.2025.103983
Marius Kriegler, Satur Herrero, Reinhard Fischer
Filamentous fungi grow as very elongated tubular cells that extend by membrane extension and cell-wall biosynthesis. Membrane and enzyme delivery depend on secretory vesicles that travel along microtubules, accumulate in a structure called the Spitzenkörper and then move along actin cables towards the apical membrane. Whereas vesicle fusion and membrane insertion are well studied, less is known about the mechanisms with which the zones of vesicle fusion and hence the growth zones are defined. One mechanism by which polarity is established and maintained is the polar localization of cell-end marker proteins (CEMPs). They form multi-protein complexes with formin as F-actin polymerase. CEMP delivery depends on microtubules, and hence CEMPs coordinate the microtubule with the actin cytoskeleton. Actin filaments capture microtubule ends, and this positive feedback loop quickly establishes active growth sites. However, CEMP complexes are self-limiting, because fusing vesicles disturb local growth zones and Ca2+ influx pulses lead to F-actin disassembly. This model emerged from studies in Schizosaccharomyces pombe and Aspergillus nidulans. Surprisingly, deletion of CEMP-coding genes is not lethal. S. pombe mutants form T-shaped cells and A. nidulans germlings grow less straight. In comparison, CEMP-mutants had a strong phenotype in Arthrobotrys flagrans, a nematode-trapping fungus, which produces ring-like trapping structures. CEMP-mutants fail to form adhesive rings and instead form sticks. CEMP overexpression caused a hyperbranching phenotype. Hence, CEMPs are involved in polarity maintenance and play critical roles during modulations of polarity. Here, we are going to discuss the functions of CEMPs and their connections to other polarity determinants.
{"title":"Where to grow and where to go","authors":"Marius Kriegler, Satur Herrero, Reinhard Fischer","doi":"10.1016/j.fgb.2025.103983","DOIUrl":"10.1016/j.fgb.2025.103983","url":null,"abstract":"<div><div>Filamentous fungi grow as very elongated tubular cells that extend by membrane extension and cell-wall biosynthesis. Membrane and enzyme delivery depend on secretory vesicles that travel along microtubules, accumulate in a structure called the <em>Spitzenkörper</em> and then move along actin cables towards the apical membrane. Whereas vesicle fusion and membrane insertion are well studied, less is known about the mechanisms with which the zones of vesicle fusion and hence the growth zones are defined. One mechanism by which polarity is established and maintained is the polar localization of <em><u>c</u>ell-<u>e</u>nd <u>m</u>arker <u>p</u>roteins</em> (CEMPs). They form multi-protein complexes with formin as F-actin polymerase. CEMP delivery depends on microtubules, and hence CEMPs coordinate the microtubule with the actin cytoskeleton. Actin filaments capture microtubule ends, and this positive feedback loop quickly establishes active growth sites. However, CEMP complexes are self-limiting, because fusing vesicles disturb local growth zones and Ca<sup>2+</sup> influx pulses lead to F-actin disassembly. This model emerged from studies in <em>Schizosaccharomyces pombe</em> and <em>Aspergillus nidulans</em>. Surprisingly, deletion of CEMP-coding genes is not lethal. <em>S. pombe</em> mutants form T-shaped cells and <em>A. nidulans</em> germlings grow less straight. In comparison, CEMP-mutants had a strong phenotype in <em>Arthrobotrys flagrans</em>, a nematode-trapping fungus, which produces ring-like trapping structures. CEMP-mutants fail to form adhesive rings and instead form sticks. CEMP overexpression caused a hyperbranching phenotype. Hence, CEMPs are involved in polarity maintenance and play critical roles during modulations of polarity. Here, we are going to discuss the functions of CEMPs and their connections to other polarity determinants.</div></div>","PeriodicalId":55135,"journal":{"name":"Fungal Genetics and Biology","volume":"178 ","pages":"Article 103983"},"PeriodicalIF":2.4,"publicationDate":"2025-04-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143789359","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}
Pub Date : 2025-03-26DOI: 10.1016/j.fgb.2025.103982
Barry Bowman
Filamentous fungi have been very useful organisms for the investigation of organelles in eukaryotic cells. The structure and function of fungal organelles is generally very similar to that observed in animal cells. However, the nature of a “cell” in many filamentous fungi is unusual, because in many of these organisms the filaments are structured as a large syncytium. In the Ascomycota hyphae are typically a very long tube divided into different compartments by an incomplete cell wall called the septum. The pore in the middle of the septum is large enough to allow virtually all organelles to move from one hyphal compartment to another. In this review, I will look at the dynamics of this movement of organelles and describe what we know about how the structure and distribution of organelles varies from one hyphal compartment to another.
{"title":"Distribution and dynamics of hyphal organelles","authors":"Barry Bowman","doi":"10.1016/j.fgb.2025.103982","DOIUrl":"10.1016/j.fgb.2025.103982","url":null,"abstract":"<div><div>Filamentous fungi have been very useful organisms for the investigation of organelles in eukaryotic cells. The structure and function of fungal organelles is generally very similar to that observed in animal cells. However, the nature of a “cell” in many filamentous fungi is unusual, because in many of these organisms the filaments are structured as a large syncytium. In the Ascomycota hyphae are typically a very long tube divided into different compartments by an incomplete cell wall called the septum. The pore in the middle of the septum is large enough to allow virtually all organelles to move from one hyphal compartment to another. In this review, I will look at the dynamics of this movement of organelles and describe what we know about how the structure and distribution of organelles varies from one hyphal compartment to another.</div></div>","PeriodicalId":55135,"journal":{"name":"Fungal Genetics and Biology","volume":"178 ","pages":"Article 103982"},"PeriodicalIF":2.4,"publicationDate":"2025-03-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143725237","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}
Pub Date : 2025-03-04DOI: 10.1016/j.fgb.2025.103974
J. Alberto Patiño-Medina , David Vargas-Tejeda , Nancy Y. Reyes-Mares , Viridiana Alejandre-Castañeda , Cesar J. Torres-Cortes , Carlos Pérez-Arques , Leon F. Ruiz-Herrera , Joel Ramírez-Emiliano , Sandeep Vellanki , Marco I. Valle-Maldonado , Karla Viridiana Castro-Cerritos , Martha I. Ramirez-Diaz , Soo Chan Lee , Victoriano Garre , Víctor Meza-Carmen
Previous work from our lab indicates that the heterotrimeric Gβ subunit 1 (Gpb1) enhances hyphal development and virulence in Mucor lusitanicus. In this study, three Gγ- and two additional Gβ-encoding genes were deleted to identify which ones might have a similar role as Gpb1. Deletion of gpg1 reduces hyphal growth, virulence, cyclic adenosine monophosphate (cAMP) levels, and protein kinase A (PKA) activity, similar to gpb1 deletion, suggesting that gpg1 participates in the same regulatory pathway as gpb1. The defects observed in Δgpg1 or Δgpb1 were suppressed by overexpression of the gene pkaR1 encoding the regulatory subunit 1 of PKA, indicating that this pathway is controlled by Gpg1 and Gpb1. Moreover, Δgpg1 and Δgpb1 show a downregulation of the transcription factors tec1 and tec2. Furthermore, tec-overexpression in Δgpg1, Δgpb1, and ΔpkaR1 restores the wild-type phenotype, indicating that both Tec are under control by the Gpb1, Gpg1, and PKA pathway. Moreover, the Δgpb1/Δgbg1(+)(−) exhibits lower aerobic germination, hyphal growth and downregulates NAD+-glutamate dehydrogenases (gdh2a/b), whereas virulence is similar to that of the wild-type (WT) strain. These alterations in Δgpb1/Δgbg1(+)(−) were reversed by the presence of glutamate during growth, suggesting that NAD+-Gdh2 could be under control of these subunits. Compared to the WT and Δgpb1/Δgbg1(+)(−) strains under aerobic growth, single deletion strains showed lower rhizoferrin levels, respiration and reactive oxygen species levels. Our results suggest that Gpg1 interacts with Gpb1 to positively control the hyphal development and virulence by repressing the PKA pathway, thereby regulating the mitochondrial oxidative metabolism in M. lusitanicus.
{"title":"Heterotrimeric G-gamma 1 (Gpg1) participates with G-beta 1 (Gpb1) in the induction of hyphal growth and virulence via the PKA pathway in Mucor lusitanicus","authors":"J. Alberto Patiño-Medina , David Vargas-Tejeda , Nancy Y. Reyes-Mares , Viridiana Alejandre-Castañeda , Cesar J. Torres-Cortes , Carlos Pérez-Arques , Leon F. Ruiz-Herrera , Joel Ramírez-Emiliano , Sandeep Vellanki , Marco I. Valle-Maldonado , Karla Viridiana Castro-Cerritos , Martha I. Ramirez-Diaz , Soo Chan Lee , Victoriano Garre , Víctor Meza-Carmen","doi":"10.1016/j.fgb.2025.103974","DOIUrl":"10.1016/j.fgb.2025.103974","url":null,"abstract":"<div><div>Previous work from our lab indicates that the heterotrimeric Gβ subunit 1 (Gpb1) enhances hyphal development and virulence in <em>Mucor lusitanicus</em>. In this study, three Gγ- and two additional Gβ-encoding genes were deleted to identify which ones might have a similar role as Gpb1. Deletion of <em>gpg1</em> reduces hyphal growth, virulence, cyclic adenosine monophosphate (cAMP) levels, and protein kinase A (PKA) activity, similar to <em>gpb1</em> deletion, suggesting that <em>gpg1</em> participates in the same regulatory pathway as <em>gpb1</em>. The defects observed in Δ<em>gpg1</em> or Δ<em>gpb1</em> were suppressed by overexpression of the gene <em>pkaR1</em> encoding the regulatory subunit 1 of PKA, indicating that this pathway is controlled by Gpg1 and Gpb1. Moreover, Δ<em>gpg1</em> and Δ<em>gpb1</em> show a downregulation of the transcription factors <em>tec1</em> and <em>tec2</em>. Furthermore, <em>tec</em>-overexpression in Δ<em>gpg1</em>, Δ<em>gpb1, and</em> Δ<em>pkaR1</em> restores the wild-type phenotype, indicating that both Tec are under control by the Gpb1, Gpg1, and PKA pathway. Moreover, the Δ<em>gpb1</em>/Δ<em>gbg1</em><sup><em>(+)(−)</em></sup> exhibits lower aerobic germination, hyphal growth and downregulates NAD<sup>+</sup>-glutamate dehydrogenases (<em>gdh</em>2a/b), whereas virulence is similar to that of the wild-type (WT) strain. These alterations in Δ<em>gpb1</em>/Δ<em>gbg1</em><sup><em>(+)(−)</em></sup> were reversed by the presence of glutamate during growth, suggesting that NAD<sup>+</sup>-Gdh2 could be under control of these subunits. Compared to the WT and Δ<em>gpb1</em>/Δ<em>gbg1</em><sup><em>(+)(−)</em></sup> strains under aerobic growth, single deletion strains showed lower rhizoferrin levels, respiration and reactive oxygen species levels. Our results suggest that Gpg1 interacts with Gpb1 to positively control the hyphal development and virulence by repressing the PKA pathway, thereby regulating the mitochondrial oxidative metabolism in <em>M. lusitanicus</em>.</div></div>","PeriodicalId":55135,"journal":{"name":"Fungal Genetics and Biology","volume":"178 ","pages":"Article 103974"},"PeriodicalIF":2.4,"publicationDate":"2025-03-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143574707","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}
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