Fungal Genetics and Biology最新文献

{"title":"Unravelling fungal pathogenesis: Advances in CRISPR-Cas9 for understanding virulence and adaptation","authors":"Ajay Nair ,&nbsp;Archana S. Rao ,&nbsp;M.A. Surabhi ,&nbsp;M. Gnanika ,&nbsp;Sunil S. More","doi":"10.1016/j.fgb.2025.104006","DOIUrl":"10.1016/j.fgb.2025.104006","url":null,"abstract":"<div><div>Fungi, with their billion-year evolutionary history, have adapted to diverse ecological niches, including pathogenic roles that threaten global health, agriculture, and ecosystems. Fungal pathogenicity is shaped by the dynamic evolution of genetic traits that enable fungi to infect hosts, evade immune defenses, and develop resistance to antifungal treatments. Despite their significant clinical and ecological impact, the evolutionary processes underlying fungal virulence and adaptation remain incompletely understood. This review emphasizes the transformative role of CRISPR-Cas9 genome editing in revealing these mechanisms. By allowing precise manipulation of fungal genomes, CRISPR technologies have provided key insights into virulence factors, stress response mechanisms, immune evasion, and antifungal resistance pathways. These advances demonstrate how fungi adapt to selective pressures, repurpose conserved genetic pathways, and exploit genomic plasticity to thrive in host environments. This review explores the intersection of CRISPR technology and fungal biology, shedding light on its implications for understanding fungal pathogenesis and the potential to develop innovative therapeutic strategies against fungal infections. The integration of CRISPR applications into mycology holds promise for furthering our understanding of fungal evolutionary trajectories and enhancing the development of novel therapeutic approaches.</div></div>","PeriodicalId":55135,"journal":{"name":"Fungal Genetics and Biology","volume":"179 ","pages":"Article 104006"},"PeriodicalIF":2.4,"publicationDate":"2025-05-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144138361","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}

{"title":"Nearly telomere-to-telomere genome assembly of the L. edodes diploid genome","authors":"Kazutoshi Yoshitake ,&nbsp;Kenta Shirasawa ,&nbsp;Kenji K. Kojima ,&nbsp;Shuichi Asakawa ,&nbsp;Norio Tanaka ,&nbsp;Hiroyuki Kurokochi","doi":"10.1016/j.fgb.2025.104005","DOIUrl":"10.1016/j.fgb.2025.104005","url":null,"abstract":"<div><div><em>Lentinula edodes</em> (shiitake mushroom) possesses substantial nutritional and medicinal value. Even though the genomes of several strains have been reported, some essential observations, including the exact chromosome number, still need validation. This study reports a near-telomere-to-telomere assembly of the complete diploid genome of L. <em>edodes</em> strain XR1, a commercially important Japanese strain. We employed the PacBio HiFi long-read sequencing technology combined with single-cell genotyping data and manual curation. The assembled diploid genome comprised 20 chromosomes (10 per haplotype), and significant inter-haplotype variation was observed. Additionally, we identified a novel Penelope-like retrotransposon—Coprina-1_LeEd—specifically localized to the telomeres. This study marks the first report of telomere elongation by the transposition of Coprina. Our findings provide a high-resolution genome resource for L. <em>edodes</em>, consequently elucidating its evolution, genomic structure, and breeding potential. Furthermore, this study establishes a foundation for further research on edible mushroom genetics and biotechnology.</div></div>","PeriodicalId":55135,"journal":{"name":"Fungal Genetics and Biology","volume":"179 ","pages":"Article 104005"},"PeriodicalIF":2.4,"publicationDate":"2025-05-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144144519","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}

{"title":"Phenotypic analyses of ΔwcoA and ΔwcoB mutants in Fusarium fujikuroi reveal dark and light-dependent functions as a white-collar complex","authors":"Julia Marente ,&nbsp;Philipp Wiemann ,&nbsp;Adrián Perera-Bonaño ,&nbsp;Bettina Tudzynski ,&nbsp;M. Carmen Limón ,&nbsp;Javier Avalos","doi":"10.1016/j.fgb.2025.104004","DOIUrl":"10.1016/j.fgb.2025.104004","url":null,"abstract":"<div><div>The <em>Fusarium fujikuroi</em> fungus<em>,</em> known as a biotechnological source of gibberellins, has a complex secondary metabolism that responds to various environmental signals, including the availability of light and nitrogen. White collar complex proteins, consisting of the flavoprotein WC1 and its partner WC2, are widespread in fungi where they play a central role in the regulation of numerous genes in response to light. <em>Fusarium</em> fungi possess one copy of each WC gene, named <em>wcoA</em> and <em>wcoB</em> in <em>F. fujikuroi</em>. Function of WcoA was previously investigated for the phenotypic effects of its mutation and the consequences on the transcriptome. In this work we have obtained deletion mutants of the <em>wcoA</em> and <em>wcoB</em> genes in IMI58289 genetic background and the expression of some light-regulated genes related to photobiology, development, and stress, as well as genes for key enzymes of secondary metabolism have been analyzed. The results show that several investigated genes require both WcoA and WcoB to be induced by light, and in some cases, also to be correctly expressed in darkness. The regulatory alterations observed in the <em>wcoA</em> or <em>wcoB</em> mutants are mostly coincidental, indicating the functioning of the encoded proteins as a complex. On the other hand, the diversity of effects on different genes of secondary metabolism, as well as the differences of these effects with those previously observed in another wild-type strain, indicate a high functional versatility of the predicted white-collar complex in the genus <em>Fusarium</em>.</div></div>","PeriodicalId":55135,"journal":{"name":"Fungal Genetics and Biology","volume":"179 ","pages":"Article 104004"},"PeriodicalIF":2.4,"publicationDate":"2025-05-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144120150","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}

{"title":"Identification of a novel genetic locus conferring virulence in the wheat tan spot pathogen Pyrenophora tritici-repentis","authors":"Jingwei Guo ,&nbsp;Gongjun Shi ,&nbsp;Md. Mukul Islam ,&nbsp;Gayan Kariyawasam ,&nbsp;Paula Moolhuijzen ,&nbsp;Pao-Theen See ,&nbsp;Shaobin Zhong ,&nbsp;Reem Aboukhaddour ,&nbsp;Justin D. Faris ,&nbsp;Timothy Friesen ,&nbsp;Zhaohui Liu","doi":"10.1016/j.fgb.2025.104002","DOIUrl":"10.1016/j.fgb.2025.104002","url":null,"abstract":"<div><div>The ascomycete <em>Pyrenophora tritici-repentis</em> (Ptr) is the causal agent of tan spot, a common and economically important wheat disease worldwide. Three necrotrophic effectors (NEs), known as Ptr ToxA, Ptr ToxB, and Ptr ToxC, have been identified from the fungal pathogen as major virulence factors. The race 2 isolate 86-124 which produces Ptr ToxA is capable of causing disease on wheat lines that is insensitive to Ptr ToxA, suggesting the use of additional NEs during the infection. To identify new NE gene(s) from 86-124, we developed a biparental fungal population from a cross between this isolate and the race 5 isolate DW5 using genetically modified heterothallic strains. The fungal population was genotyped with SNP and SSR markers as well as the <em>ToxA</em> gene, the mating type genes, and six <em>ToxB</em> loci. Each progeny was phenotyped onto the hard red spring wheat line CDC-Osler, which is insensitive to both Ptr ToxA and Ptr ToxB, but is highly susceptible to 86-124. The constructed genetic map consisted of 11 linkage groups that corresponded to the 11 chromosomes (chr) of the Ptr reference genome. <em>ToxA</em> and mating type genes mapped to the expected positions. Five of the six <em>ToxB</em> copies were tightly linked, residing at the distal end of chr 11, while the sixth copy was localized to the distal end of chr 5. Composite interval mapping revealed a major QTL on the distal end of chr 2 conferring virulence toward CDC-Osler by 86-124. This locus was designated as <em>VirOsler1</em>. Genomic sequence alignment at the locus showed a region of approximately 900 kb at the end of chr 2 absent in DW5. The identification of <em>VirOsler1</em> locus provides clear evidence that the wheat tan spot pathogen uses additional virulence factors that interact with unidentified host factors for disease susceptibility.</div></div>","PeriodicalId":55135,"journal":{"name":"Fungal Genetics and Biology","volume":"179 ","pages":"Article 104002"},"PeriodicalIF":2.4,"publicationDate":"2025-05-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144089419","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}

{"title":"Endocytosis in filamentous Fungi: Coordinating polarized hyphal growth and membrane recycling","authors":"Caleb Oliver Bedsole ,&nbsp;Joseph G. Vasselli ,&nbsp;Brian D. Shaw","doi":"10.1016/j.fgb.2025.104000","DOIUrl":"10.1016/j.fgb.2025.104000","url":null,"abstract":"<div><div>Filamentous fungi rely on a finely tuned balance between exocytosis and endocytosis to maintain polarized growth. This review highlights the essential role of the subapical endocytic collar in recycling excess plasma membrane and key proteins, enabling sustained hyphal extension. It distinguishes between clathrin-mediated and AP-2–dependent clathrin-independent pathways, emphasizing their unique contributions to membrane homeostasis and cargo trafficking. The synthesis of quantitative imaging and genetic analyses provides a comprehensive framework for understanding vesicle dynamics, with implications for addressing fungal pathogenicity and industrial applications.</div></div>","PeriodicalId":55135,"journal":{"name":"Fungal Genetics and Biology","volume":"179 ","pages":"Article 104000"},"PeriodicalIF":2.4,"publicationDate":"2025-05-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143942267","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}

{"title":"Colony differentiation of saprobic and pathogenic fungi in relation to carbon utilization","authors":"Ronald P. de Vries","doi":"10.1016/j.fgb.2025.104001","DOIUrl":"10.1016/j.fgb.2025.104001","url":null,"abstract":"<div><div>Carbon utilization is crucial for the cellular functions of all fungi and is highly dependent on the prevalent carbon sources in the environment. In natural environments, plant biomass is a major carbon source for most saprobic and pathogenic filamentous fungi and its utilization requires a complex process involving extracellular enzymes, sugar transporters and metabolic pathways, governed by a network of transcriptional regulators.</div><div>Filamentous fungi form extensive colonies that encounter highly diverse environmental conditions and available carbon levels, which raises the question if, and to which extent, parts of the colony exposed to sufficient carbon source levels can support other parts that are under carbon limitation or starvation. While it is difficult to mimic the heterogenic natural conditions in a laboratory experiment, several studies into carbon translocation, and colony and hyphal differentiation have provided insights into this complex biological process. These studies are reviewed here and their insights are re-assessed and combined into a current state of the art of this field.</div></div>","PeriodicalId":55135,"journal":{"name":"Fungal Genetics and Biology","volume":"179 ","pages":"Article 104001"},"PeriodicalIF":2.4,"publicationDate":"2025-05-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143928257","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}

{"title":"Fungal cell wall biogenesis: structural complexity, regulation and inhibition","authors":"Neil A.R. Gow","doi":"10.1016/j.fgb.2025.103991","DOIUrl":"10.1016/j.fgb.2025.103991","url":null,"abstract":"<div><div>The cell wall is the defining organelle of filamentous and yeast-like fungi. It is responsible for morphology, biotic and abiotic interactions and its components confer its unique and variable signature, making it a natural target for antifungal drugs, but a moving target for immune recognition. The wall is however more than the sum of its many parts. The polysaccharides and proteins of the cell wall must be made at the right time and the right place, but also linked together and remodelled throughout the cell cycle and in response to environmental challenges, nutrient availability, damage after predation and to be complaint to the need to establish mutualistic and parasitic associations. This review summarises recent advances in our understanding of the complex and vital process of fungal cell wall biogenesis using the human pathogens <em>Candida albicans</em> and <em>Aspergillus fumigatus</em> as the principal model fungi.</div></div>","PeriodicalId":55135,"journal":{"name":"Fungal Genetics and Biology","volume":"179 ","pages":"Article 103991"},"PeriodicalIF":2.4,"publicationDate":"2025-05-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143918033","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}

{"title":"Analysis of the genetic diversity of the soybean rust pathogen Phakopsora pachyrhizi reveals two major evolutionary lineages","authors":"Vinicius Delgado da Rocha ,&nbsp;Everton Geraldo Capote Ferreira ,&nbsp;Fernanda Machado Castanho ,&nbsp;Marcia Kamogae Kuwahara ,&nbsp;Cláudia Vieira Godoy ,&nbsp;Maurício Conrado Meyer ,&nbsp;Kerry F. Pedley ,&nbsp;Ralf T. Voegele ,&nbsp;Anna Lipzen ,&nbsp;Kerrie Barry ,&nbsp;Igor V. Grigoriev ,&nbsp;Marco Loehrer ,&nbsp;Ulrich Schaffrath ,&nbsp;Catherine Sirven ,&nbsp;Sebastien Duplessis ,&nbsp;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}

{"title":"Transcription factors Fst8, Ftr3 and Gat1 are regulators of the immune system of the mushroom Schizophyllum commune","authors":"Erik P.W. Beijen,&nbsp;Marieke H. van Maanen,&nbsp;Esther S. van den Bergh,&nbsp;Rose Brouns,&nbsp;Ioana M. Marian,&nbsp;Thomas J. de Vries,&nbsp;Peter Jan Vonk,&nbsp;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}

{"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,&nbsp;Satoshi Mimura,&nbsp;Kozue Hatanaka,&nbsp;Tetsuya Kakizaki,&nbsp;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}