Fungal Genetics and Biology最新文献_第3页

Benchmarking fungal species classification using Oxford Nanopore Technologies long-read ITS metabarcodes 使用牛津纳米孔技术长读ITS元条形码对真菌物种分类进行基准测试

IF 2.3 3区生物学

Fungal Genetics and Biology Pub Date : 2025-12-01 Epub Date: 2025-10-25 DOI: 10.1016/j.fgb.2025.104042

Abigail Graetz , Jinghang Feng , Alex Ringeri , Austin Bird , Duong Vu , Camille Truong , Benjamin Schwessinger

{"title":"Benchmarking fungal species classification using Oxford Nanopore Technologies long-read ITS metabarcodes","authors":"Abigail Graetz , Jinghang Feng , Alex Ringeri , Austin Bird , Duong Vu , Camille Truong , Benjamin Schwessinger","doi":"10.1016/j.fgb.2025.104042","DOIUrl":"10.1016/j.fgb.2025.104042","url":null,"abstract":"<div><div>The gold standard for fungal classification has long been specimen or culture-based, however, many Fungi display simple morphological characteristics, or are unculturable by current methods. Using DNA metabarcodes, many taxa can be identified from a single sample simultaneously, but annotating these sequences with species-level taxonomy often requires more information than short-read sequences afford. Oxford Nanopore Technologies (ONT) long-read sequencing has achieved species-level resolution in metabarcoding of bacteria and invertebrates, but the application of this technology has not been extensively benchmarked for Fungi. In this work, we use a mock community of real ONT long-read metabarcodes from 54 fungi from the Dikarya subkingdom to extensively benchmark classification approaches to assign species-level taxonomy. We compare eight classification approaches spanning alignment and <em>k</em>-mer based algorithms, to emerging machine learning methods, and assess the sensitivity, precision, and diversity estimation of each classifier at the species level. Our results indicate that classifiers which determine informed thresholds of sequence similarity based on a provided reference database are not only more accurate at the species level, but more consistent to correct species abundance distributions, and better able to place sequences from ‘unknown’ species taxonomically closer to their true origin. We demonstrate the power of machine learning classifiers to leverage long-read metabarcodes, and discuss their potential as emerging methods in DNA sequence classification. We present our results in the context of real-world use cases, to demonstrate that species-level taxonomic inference is achievable, precise, and reliable with ONT long-read fungal metabarcodes.</div></div>","PeriodicalId":55135,"journal":{"name":"Fungal Genetics and Biology","volume":"181 ","pages":"Article 104042"},"PeriodicalIF":2.3,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145417061","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

A nitric oxide reductase is a key enzyme target for eliminating fungal emissions of nitrous oxide 一氧化氮还原酶是消除真菌排放的氧化亚氮的关键酶目标。

IF 2.3 3区生物学

Fungal Genetics and Biology Pub Date : 2025-12-01 Epub Date: 2025-09-23 DOI: 10.1016/j.fgb.2025.104038

Blake A. Oakley , Trevor R. Mitchell , Quentin D. Read , Garrett T. Hibbs , Thomas T. Baldwin , Larry J. Pierce , Scott E. Gold , Anthony E. Glenn

{"title":"A nitric oxide reductase is a key enzyme target for eliminating fungal emissions of nitrous oxide","authors":"Blake A. Oakley , Trevor R. Mitchell , Quentin D. Read , Garrett T. Hibbs , Thomas T. Baldwin , Larry J. Pierce , Scott E. Gold , Anthony E. Glenn","doi":"10.1016/j.fgb.2025.104038","DOIUrl":"10.1016/j.fgb.2025.104038","url":null,"abstract":"<div><div>Nitrous oxide (N<sub>2</sub>O) derived from agricultural activity is a major contributor to Earth's greenhouse effect. Synthetic nitrogen fertilizer applied at high levels, particularly combined with heavy rainfall events, generates hot spots of N<sub>2</sub>O emissions in agricultural fields due to the process of microbial denitrification. Here, a key conserved fungal denitrification enzyme necessary for N<sub>2</sub>O emissions was identified. Phylogenetic analysis revealed that fungal <em>NOR1</em>-like genes, with rare exceptions, are highly conserved and confined to the phylum Ascomycota. Plant pathogenic <em>Fusarium</em> species that possess <em>NOR1</em> exhibited drastic differences in N<sub>2</sub>O production based on denitrification potential. Functional characterization of the p450nor nitric oxide reductase encoding gene, <em>NOR1</em>, in the soil-borne denitrifying maize pathogen, <em>Fusarium verticillioides,</em> showed that this enzyme is critical for fungal N<sub>2</sub>O production. Deletion of the single copy <em>NOR1</em> gene in <em>F. verticillioides</em> eliminated N<sub>2</sub>O emissions. Complementation of deletion mutants via the <em>NOR1</em> gene add-back restored wild type N<sub>2</sub>O emission levels and segregation analysis further corroborated the pivotal role of <em>NOR1</em> for N<sub>2</sub>O emissions. We suggest targeting of the NOR1 enzyme as an effective strategy to reduce fungal-based N<sub>2</sub>O emissions.</div></div>","PeriodicalId":55135,"journal":{"name":"Fungal Genetics and Biology","volume":"181 ","pages":"Article 104038"},"PeriodicalIF":2.3,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145152100","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

Genetics of avirulence and interacting inhibitors in Puccinia striiformis f. sp. tritici 小麦纹状锈菌的毒力及相互作用抑制剂的遗传。

IF 2.3 3区生物学

Fungal Genetics and Biology Pub Date : 2025-12-01 Epub Date: 2025-09-16 DOI: 10.1016/j.fgb.2025.104037

My Livbjerg , Julian Rodriguez-Algaba , James K.M. Brown , Chris K. Sørensen , Mogens Hovmøller , Annemarie Fejer Justesen

{"title":"Genetics of avirulence and interacting inhibitors in Puccinia striiformis f. sp. tritici","authors":"My Livbjerg , Julian Rodriguez-Algaba , James K.M. Brown , Chris K. Sørensen , Mogens Hovmøller , Annemarie Fejer Justesen","doi":"10.1016/j.fgb.2025.104037","DOIUrl":"10.1016/j.fgb.2025.104037","url":null,"abstract":"<div><div>The segregation of molecular markers and avirulence was investigated in three progeny populations of <em>Puccinia striiformis</em> f. sp. <em>tritici</em> (<em>Pst</em>)<em>,</em> derived from selfing of the three European isolates DK09_11(PstS7), DK02d_12 (PstS8) and DK219_19 (PstS15). Progeny isolates were genotyped using 19 Single Sequence Repeat (SSR) markers and phenotyped for avirulence on a differential set of 34 wheat lines including at least two independent lines per <em>Yr</em>-gene considered. All three progeny populations were virulent to most of the tested <em>Yr</em>-genes and were largely homozygous for either virulence or avirulence. Segregation was observed for avirulence to <em>Yr4</em>, <em>YrSp, Yr8</em> and a resistance specificity in Avocet S (<em>AvS)</em>. In one population (DK219_19, PstS15), segregation ratios indicated that avirulence to <em>Yr4</em> was a dominant trait controlled by a single gene. For <em>YrSp,</em> the observed ratios were consistent with both 13:3 and 3:1 (avirulence: virulence) suggesting that avirulence was a dominant trait, potentially controlled by either one or two interacting genes. In another population (DK02d_12, PstS8), most progeny isolates were virulent to <em>Yr8</em> and <em>AvS,</em> and segregation ratios were consistent with both 1:3 and 3:13, suggesting the presence of dominant inhibition of avirulence or alternatively, avirulence being a recessive trait controlled by either one or two genes. The third population (DK09_11, PstS7) showed no segregation at known avirulence loci, indicating that these were homozygous either for avirulence or virulence to each <em>Yr</em>-gene tested.</div></div>","PeriodicalId":55135,"journal":{"name":"Fungal Genetics and Biology","volume":"181 ","pages":"Article 104037"},"PeriodicalIF":2.3,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145088452","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

Structural and regulatory dynamics of septum development in fungal hyphae 真菌菌丝中隔发育的结构和调控动力学

IF 2.4 3区生物学

Fungal Genetics and Biology Pub Date : 2025-09-01 Epub Date: 2025-06-03 DOI: 10.1016/j.fgb.2025.104008

Olga A. Callejas-Negrete , Alejandro Fajardo-Peralta , Rosa R. Mouriño-Pérez

{"title":"Structural and regulatory dynamics of septum development in fungal hyphae","authors":"Olga A. Callejas-Negrete , Alejandro Fajardo-Peralta , Rosa R. Mouriño-Pérez","doi":"10.1016/j.fgb.2025.104008","DOIUrl":"10.1016/j.fgb.2025.104008","url":null,"abstract":"<div><div>Filamentous fungi grow through hyphae, divided by septa with central pores that allow cytoplasmic flow, supporting coenocytic behavior. Septa provide structural rigidity, contain damage by plugging pores during injury, and aid in developmental processes like conidiation. Septum formation is tightly regulated, involving selection of the septation site, actomyosin ring assembly and cell wall deposition. Recent advances in microscopy and molecular studies have clarified many aspects of septation, however some mechanisms remain unclear. This review examines the roles, structure, and regulation of hyphal septa, emphasizing their dynamic functions in structural support, damage control, and differentiation. Septa are multilayered structures composed of chitin and β-1,3-glucan, with Woronin bodies (WB) acting as emergency plugs in ascomycetes. The actin cytoskeleton, septins, and microtubule-organizing centers (MTOCs) are crucial for septum formation, with actin and associated proteins driving the contractile actomyosin ring (CAR). Septins organize into higher-order structures, regulating septation and fungal development. Regulatory networks, including the septation initiation network (SIN), coordinate mitosis and septation, with Rho GTPases playing key role. Despite progress, questions remain about protein transport, septum regulation, and evolutionary adaptations. This review highlights the complexity of septation and the need for further research to fully understand this essential process in filamentous fungi.</div></div>","PeriodicalId":55135,"journal":{"name":"Fungal Genetics and Biology","volume":"180 ","pages":"Article 104008"},"PeriodicalIF":2.4,"publicationDate":"2025-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144220973","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

Influence of environmental temperature on the phenotypic variation of Batrachochytrium dendrobatidis isolates from Mexico 环境温度对墨西哥石斛壶菌表型变异的影响。

IF 2.4 3区生物学

Fungal Genetics and Biology Pub Date : 2025-09-01 Epub Date: 2025-06-20 DOI: 10.1016/j.fgb.2025.104017

Andrea P. Angeles-Vázquez , Mirna G. García-Castillo , Gabriela Parra-Olea , Marco T. Solano de la Cruz , M. Delia Basanta

{"title":"Influence of environmental temperature on the phenotypic variation of Batrachochytrium dendrobatidis isolates from Mexico","authors":"Andrea P. Angeles-Vázquez , Mirna G. García-Castillo , Gabriela Parra-Olea , Marco T. Solano de la Cruz , M. Delia Basanta","doi":"10.1016/j.fgb.2025.104017","DOIUrl":"10.1016/j.fgb.2025.104017","url":null,"abstract":"<div><div>Chytridiomycosis, caused by <em>Batrachochytrium dendrobatidis</em> (<em>Bd</em>), is a major emerging disease contributing to the global decline of amphibians. Phenotypic variations in <em>Bd</em>, such as zoosporangia size and zoospore production, may be linked to differences in pathogenicity among isolates and adaptation to temperatures. <em>Bd</em> has been detected in various regions in Mexico, but its phenotypic variability and relationship to pathogenicity remain unexplored. Here, we examine phenotypic characteristics of <em>Bd</em> such as the growth rate, carrying capacity, zoospore production, and zoosporangia size of ten <em>Bd</em> isolates representing different sublineages within the <em>Bd</em> Global Panzootic Lineage, collected from diverse temperature regimes in Mexico. We found high phenotypic variability between isolates, with growth rate and zoosporangia size influenced by the environmental temperature of their respective sites. Other traits, such as carrying capacity and zoospore production, did not show clear patterns related to environmental temperature. Our findings provide insights into the phenotypic variability of <em>Bd</em> in Mexico and highlight the complexity of pathogen-environment interactions suggesting local adaptations.</div></div>","PeriodicalId":55135,"journal":{"name":"Fungal Genetics and Biology","volume":"180 ","pages":"Article 104017"},"PeriodicalIF":2.4,"publicationDate":"2025-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144369600","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

The role of NLRP3/caspase−/GSDMD signal axis mediated cell pyroptosis in the pathogenicity of T. asahii NLRP3/caspase-/GSDMD信号轴介导的细胞焦亡在日本血吸虫致病性中的作用

IF 2.4 3区生物学

Fungal Genetics and Biology Pub Date : 2025-09-01 Epub Date: 2025-07-02 DOI: 10.1016/j.fgb.2025.104021

Yuekun Zou , Shuang Bai , Minna Han , Xin Yang , Xiaoxian Cheng , Jiamin Wu , Zhikuan Xia , Rongya Yang

{"title":"The role of NLRP3/caspase−/GSDMD signal axis mediated cell pyroptosis in the pathogenicity of T. asahii","authors":"Yuekun Zou , Shuang Bai , Minna Han , Xin Yang , Xiaoxian Cheng , Jiamin Wu , Zhikuan Xia , Rongya Yang","doi":"10.1016/j.fgb.2025.104021","DOIUrl":"10.1016/j.fgb.2025.104021","url":null,"abstract":"<div><div>Cell pyroptosis serves as a critical regulatory mechanism by which host cells respond to fungal infections. However, whether pyroptosis contributes to alterations in fungal pathogenicity during microevolution remains unclear. In this study, we investigated the role of pyroptosis in the pathogenicity of <em>Trichosporon asahii</em> (<em>T. asahii</em>) intraspecies variation, as well as the underlying mechanisms. An in vitro model was established by co-culturing a strain (Ori 2.2174) and a intraspecies variation (Evo 1403.3) of <em>T. asahii</em> with mouse macrophages, while an in vivo model was developed by inoculating immunosuppressed ICR mice with these strains. Survival analysis was performed to assess mortality differences between groups. In vitro experiments revealed that the macrophages infected with Evo 1403.3 exhibited significantly lower lysis rates, pyroptosis levels, and inflammatory cytokine production compared to those infected with Ori 2.2174. Similarly, mice inoculated with Evo 1403.3 showed significantly higher survival rates and reduced fungal burden and lesion areas in organ tissues compared to those infected with Ori 2.2174. Furthermore, pyroptosis mediated by the NLRP3/Caspase-1/GSDMD signaling axis was observed in macrophages infected with both strains, with the extent of pyroptosis positively correlating with strain pathogenicity. Collectively, these findings indicate that cell pyroptosis mediated through the NLRP3/Caspase-1/GSDMD pathway plays a pivotal role in regulating the pathogenicity of <em>T. asahii</em> intraspecies variation.</div></div>","PeriodicalId":55135,"journal":{"name":"Fungal Genetics and Biology","volume":"180 ","pages":"Article 104021"},"PeriodicalIF":2.4,"publicationDate":"2025-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144565522","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

Functional characterization of endo-β-1,3-glucanase in Trichoderma reesei 里氏木霉内切-β-1,3-葡聚糖酶的功能表征。

IF 2.4 3区生物学

Fungal Genetics and Biology Pub Date : 2025-09-01 Epub Date: 2025-06-30 DOI: 10.1016/j.fgb.2025.104022

Haiyan Wang , Peiya Chen , Yun Wang , Babar Khan , Ai-Ping Pang , Fu-Gen Wu , Fengming Lin

{"title":"Functional characterization of endo-β-1,3-glucanase in Trichoderma reesei","authors":"Haiyan Wang , Peiya Chen , Yun Wang , Babar Khan , Ai-Ping Pang , Fu-Gen Wu , Fengming Lin","doi":"10.1016/j.fgb.2025.104022","DOIUrl":"10.1016/j.fgb.2025.104022","url":null,"abstract":"<div><div>While <em>endo</em>-β-1,3-glucanases, crucial for hydrolyzing β-1,3-glucan in cell wall, play significant roles in cellular activities of filamentous fungi, research on these enzymes in <em>Trichoderma reesei</em> remains scarce. In this study, we explored the cellular functions and molecular properties of a novel <em>endo</em>-β-glucanase, GLU1, in <em>T</em>. <em>reesei</em>. The mRNA level of <em>glu1</em> was noticeably upregulated under cellulase-producing condition as compared to non-cellulase-producing condition. Moreover, the deletion of <em>glu1</em> significantly repressed cellulase production, primarily by reducing the transcript levels of key genes involved in cellulase synthesis during the early stages of fermentation. This deletion further led to weakened cell growth, diminished sporulation, and mutated colony morphology. These suggest that <em>glu1</em> plays a crucial positive role in cellulase biosynthesis, cell growth, and sporulation. Additionally, the absence of <em>glu1</em> led to increased β-glucan content within cell wall, making <em>T</em>. <em>reesei</em> more susceptible to Congo red but less sensitive to NaCl. This suggests that GLU1 is involved in modulating the composition and functionality of cell wall. Bioinformatic analyses classified GLU1 within the GH64 family, while the cellular distribution analysis revealed GLU1 was located in the cytoplasm. These experimental data broaden our understanding of the roles and molecular characteristics of <em>endo</em>-β-1,3-glucanases in filamentous fungi.</div></div>","PeriodicalId":55135,"journal":{"name":"Fungal Genetics and Biology","volume":"180 ","pages":"Article 104022"},"PeriodicalIF":2.4,"publicationDate":"2025-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144555885","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

The effect of exogenous addition of metformin hydrochloride on lipid synthesis in Mucor circinelloides WJ11 外源添加二甲双胍对环毛霉WJ11脂质合成的影响。

IF 2.4 3区生物学

Fungal Genetics and Biology Pub Date : 2025-09-01 Epub Date: 2025-07-13 DOI: 10.1016/j.fgb.2025.104023

Xinai Liu , Xiuwen Wang , Yueping Yang , Kang Li , Wenrong Liu , Qing Liu , Yuanda Song

{"title":"The effect of exogenous addition of metformin hydrochloride on lipid synthesis in Mucor circinelloides WJ11","authors":"Xinai Liu , Xiuwen Wang , Yueping Yang , Kang Li , Wenrong Liu , Qing Liu , Yuanda Song","doi":"10.1016/j.fgb.2025.104023","DOIUrl":"10.1016/j.fgb.2025.104023","url":null,"abstract":"<div><div>As a well-established oleaginous model fungus, <em>Mucor circinelloides</em> has been extensively employed in lipid metabolism research due to its high lipid accumulation capacity and genetic tractability. Metformin hydrochloride, a biguanide drug, exerts significant effects on glucose and lipid metabolism in animal model, however, its effect on lipid metabolism in oleaginous microorganism is unclear. This investigation elucidates the regulatory effects of metformin hydrochloride on lipid biosynthesis in the model oleaginous fungus <em>M. circinelloides</em>. The findings revealed that metformin hydrochloride suppresses fatty acid biosynthesis in <em>M. circinelloides</em>. Addition of 4 g/L metformin hydrochloride to the growth medium of the fungus reduced the total fatty acid content from 29.57 % to 23.27 %, representing a decrease of 21.30 %. Furthermore, metformin hydrochloride significantly upregulated the transcriptional levels of <em>AMPK</em> subunits (such as Snf-α1, Snf-γ1, and Snf-γ3) while suppressing the expression of key genes involved in lipid synthesis, including <em>acl</em>, <em>acc1</em>, and <em>acc2</em>. Our enzymatic assays revealed that metformin hydrochloride treatment markedly inhibited ACC and 6PGDH activities, thereby restricting the availability of both acetyl-CoA precursors and NADPH reducing equivalents required for lipid biosynthesis. This study provided evidence supporting the relationship between metformin hydrochloride and lipid synthesis and validated metformin hydrochloride as a targeted drug for inhibiting lipid synthesis in <em>M. circinelloides</em>.</div></div>","PeriodicalId":55135,"journal":{"name":"Fungal Genetics and Biology","volume":"180 ","pages":"Article 104023"},"PeriodicalIF":2.4,"publicationDate":"2025-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144644190","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

Highly dynamic supernumerary mini-chromosomes in a Magnaporthe oryzae strain contributes to cellular variance of genomic content 稻瘟病菌株中高度动态的额外小染色体有助于基因组内容的细胞变异

IF 2.4 3区生物学

Fungal Genetics and Biology Pub Date : 2025-09-01 Epub Date: 2025-06-27 DOI: 10.1016/j.fgb.2025.104020

Guifang Lin , Huakun Zheng , Dal-Hoe Koo , Zonghua Wang , David Cook , Barbara Valent , Sanzhen Liu

{"title":"Highly dynamic supernumerary mini-chromosomes in a Magnaporthe oryzae strain contributes to cellular variance of genomic content","authors":"Guifang Lin , Huakun Zheng , Dal-Hoe Koo , Zonghua Wang , David Cook , Barbara Valent , Sanzhen Liu","doi":"10.1016/j.fgb.2025.104020","DOIUrl":"10.1016/j.fgb.2025.104020","url":null,"abstract":"<div><div><em>Magnaporthe oryzae</em> (syn. <em>Pyricularia oryzae</em>), the causative agent of devastating crop diseases, exhibits remarkable genomic plasticity that contributes to its adaptability and pathogenicity. Individual <em>M. oryzae</em> strains may contain supernumerary mini-chromosomes, which are dispensable and highly repetitive. Here, we explored the stability of two mini-chromosomes of a <em>Lolium</em> strain isolated in the US, TF05–1, in which one mini-chromosome contains sequences nearly identical to the mini-chromosome of the wheat isolate B71 from Bolivia. The discordance of their phylogenetic relationships based on genomic polymorphisms in core chromosomes and polymorphisms in mini-chromosomes indicated horizontal transfer of the mini-chromosome. Contour-clamped homogeneous electric field (CHEF) karyotyping and genome sequencing analysis found variation in numbers and sizes of mini-chromosomes among asexual monoconidial progeny of TF05–1. Optimization of a fluorescence in situ hybridization (FISH) protocol enabled single-cell karyotyping and revelation of drastic cellular variation in numbers of mini-chromosomes. In addition, rearrangement within mini-chromosomes occurred frequently in the TF05–1 progeny. We characterized an intrachromosomal rearrangement presumably mediated by a palindrome repeat. The rearrangement resulted in a 300-kb deletion and a 900-kb duplication. We found that, in contrast to Long Terminal Repeat (LTR) retrotransposons in core chromosomes, LTR retrotransposons in mini-chromosomes were more recently inserted, less methylated, and with higher G + C content. The data indicated that most LTR retrotransposons in mini-chromosomes retain high activity and have yet to be silenced by fungal genome defense mechanisms such as repeat-induced point mutation, which may contribute to highly dynamic mini-chromosome content in fungi.</div></div>","PeriodicalId":55135,"journal":{"name":"Fungal Genetics and Biology","volume":"180 ","pages":"Article 104020"},"PeriodicalIF":2.4,"publicationDate":"2025-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144517737","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

Duplicating the mold: Branching of fungal hyphae 复制霉菌：真菌菌丝的分支

IF 2.3 3区生物学

Fungal Genetics and Biology Pub Date : 2025-09-01 Epub Date: 2025-08-29 DOI: 10.1016/j.fgb.2025.104025

Steven D. Harris

引用次数: 0