Yufei Zhang, Wenbin Yu, Yi Lu, Yichuan Wu, Zhiwei Ouyang, Yayi Tu, Bin He
Secondary metabolism is one of the important mechanisms by which fungi adapt to their living environment and promote survival and reproduction. Recent studies have shown that epigenetic regulation, such as DNA methylation, histone modifications, and non-coding RNAs, plays key roles in fungal secondary metabolism and affect fungal growth, survival, and pathogenicity. This review describes recent advances in the study of epigenetic regulation of fungal secondary metabolism. We discuss the way in which epigenetic markers respond to environmental changes and stimulate the production of biologically active compounds by fungi, and the feasibility of these new findings applied to develop new antifungal strategies and optimize secondary metabolism. In addition, we have deliberated on possible future directions of research in this field. A deeper understanding of epigenetic regulatory networks is a key focus for future research.
{"title":"Epigenetic Regulation of Fungal Secondary Metabolism","authors":"Yufei Zhang, Wenbin Yu, Yi Lu, Yichuan Wu, Zhiwei Ouyang, Yayi Tu, Bin He","doi":"10.3390/jof10090648","DOIUrl":"https://doi.org/10.3390/jof10090648","url":null,"abstract":"Secondary metabolism is one of the important mechanisms by which fungi adapt to their living environment and promote survival and reproduction. Recent studies have shown that epigenetic regulation, such as DNA methylation, histone modifications, and non-coding RNAs, plays key roles in fungal secondary metabolism and affect fungal growth, survival, and pathogenicity. This review describes recent advances in the study of epigenetic regulation of fungal secondary metabolism. We discuss the way in which epigenetic markers respond to environmental changes and stimulate the production of biologically active compounds by fungi, and the feasibility of these new findings applied to develop new antifungal strategies and optimize secondary metabolism. In addition, we have deliberated on possible future directions of research in this field. A deeper understanding of epigenetic regulatory networks is a key focus for future research.","PeriodicalId":15878,"journal":{"name":"Journal of Fungi","volume":null,"pages":null},"PeriodicalIF":4.7,"publicationDate":"2024-09-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142223798","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Punicic acid (PuA) is a conjugated fatty acid with a wide range of nutraceutical properties naturally present in pomegranate seed oil. To meet the rising demand for pomegranate seed oil, a single-cell oil enriched in PuA provides a sustainable biomass-derived alternative. This study describes the production of a PuA-enriched single-cell oil through the engineering of the red yeast Rhodotorula toruloides grown in glucose and a low-cost substrate, crude glycerol. The gene for Punica granatum fatty acid conjugase, PgFADX, was randomly integrated into the genome of R. toruloides without disrupting the carotenoid synthesis. In shake flask studies, the effects of three promoters (PPGI1, PNAR1, and PPMA1) on PuA production were evaluated. PuA titers of 105.77 mg/L and 72.81 mg/L were obtained from engineered cells expressing PgFADX from the PPMA1 promoter cultivated for 72 h in glucose and for 168 h in crude glycerol, respectively. Furthermore, the detailed lipid analysis revealed a high enrichment PuA in the triacylglycerol lipid structures, even without substantial modifications to the metabolic pathways. This report demonstrates the high potential of R. toruloides in the upcycling of a low-cost substrate, crude glycerol, into a value-added product such as PuA. The findings support the feasibility of using engineered R. toruloides for sustainable production of PuA-enriched single-cell oil.
{"title":"The Plasma Membrane H+-ATPase Promoter Driving the Expression of FADX Enables Highly Efficient Production of Punicic Acid in Rhodotorula toruloides Cultivated on Glucose and Crude Glycerol","authors":"Daniela Krajciova, Roman Holic","doi":"10.3390/jof10090649","DOIUrl":"https://doi.org/10.3390/jof10090649","url":null,"abstract":"Punicic acid (PuA) is a conjugated fatty acid with a wide range of nutraceutical properties naturally present in pomegranate seed oil. To meet the rising demand for pomegranate seed oil, a single-cell oil enriched in PuA provides a sustainable biomass-derived alternative. This study describes the production of a PuA-enriched single-cell oil through the engineering of the red yeast Rhodotorula toruloides grown in glucose and a low-cost substrate, crude glycerol. The gene for Punica granatum fatty acid conjugase, PgFADX, was randomly integrated into the genome of R. toruloides without disrupting the carotenoid synthesis. In shake flask studies, the effects of three promoters (PPGI1, PNAR1, and PPMA1) on PuA production were evaluated. PuA titers of 105.77 mg/L and 72.81 mg/L were obtained from engineered cells expressing PgFADX from the PPMA1 promoter cultivated for 72 h in glucose and for 168 h in crude glycerol, respectively. Furthermore, the detailed lipid analysis revealed a high enrichment PuA in the triacylglycerol lipid structures, even without substantial modifications to the metabolic pathways. This report demonstrates the high potential of R. toruloides in the upcycling of a low-cost substrate, crude glycerol, into a value-added product such as PuA. The findings support the feasibility of using engineered R. toruloides for sustainable production of PuA-enriched single-cell oil.","PeriodicalId":15878,"journal":{"name":"Journal of Fungi","volume":null,"pages":null},"PeriodicalIF":4.7,"publicationDate":"2024-09-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142182986","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Ma. Irene Morelos-Martínez, Horacio Cano-Camacho, Karla Morelia Díaz-Tapia, June Simpson, Everardo López-Romero, María Guadalupe Zavala-Páramo
Colletotrichum lindemuthianum is the most frequent pathogenic fungus of the common bean Phaseolus vulgaris. This filamentous fungus employs a hemibiotrophic nutrition/infection strategy, which is characteristic of many Colletotrichum species. Due to host–pathogen coevolution, C. lindemuthianum includes pathotypes with a diversity of virulence against differential common bean varieties. In this study, we performed comparative genomic analyses on three pathotypes with different virulence levels and a non-pathogenic pathotype, isolated from different geographical areas in Mexico. Our results revealed large genomes with high transposable element contents that have undergone expansions, generating intraspecific diversity. All the pathotypes exhibited a similar number of clusters of orthologous genes (COGs) and Gene Ontology (GO) terms. TFomes contain families that are typical in fungal genomes; however, they show different contents between pathotypes, mainly in transcription factors with the fungal-specific TF and Zn2Cys6 domains. Peptidase families mainly contain abundant serine peptidases, metallopeptidases, and cysteine peptidases. In the secretomes, the number of genes differed between the pathotypes, with a high percentage of candidate effectors. Both the virulence gene and CAZyme gene content for each pathotype was abundant and diverse, and the latter was enriched in hemicellulolytic enzymes. We provide new insights into the nature of intraspecific diversity among C. lindemuthianum pathotypes and the origin of their ability to rapidly adapt to genetic changes in its host and environmental conditions.
{"title":"Comparative Genomic Analyses of Colletotrichum lindemuthianum Pathotypes with Different Virulence Levels and Lifestyles","authors":"Ma. Irene Morelos-Martínez, Horacio Cano-Camacho, Karla Morelia Díaz-Tapia, June Simpson, Everardo López-Romero, María Guadalupe Zavala-Páramo","doi":"10.3390/jof10090651","DOIUrl":"https://doi.org/10.3390/jof10090651","url":null,"abstract":"Colletotrichum lindemuthianum is the most frequent pathogenic fungus of the common bean Phaseolus vulgaris. This filamentous fungus employs a hemibiotrophic nutrition/infection strategy, which is characteristic of many Colletotrichum species. Due to host–pathogen coevolution, C. lindemuthianum includes pathotypes with a diversity of virulence against differential common bean varieties. In this study, we performed comparative genomic analyses on three pathotypes with different virulence levels and a non-pathogenic pathotype, isolated from different geographical areas in Mexico. Our results revealed large genomes with high transposable element contents that have undergone expansions, generating intraspecific diversity. All the pathotypes exhibited a similar number of clusters of orthologous genes (COGs) and Gene Ontology (GO) terms. TFomes contain families that are typical in fungal genomes; however, they show different contents between pathotypes, mainly in transcription factors with the fungal-specific TF and Zn2Cys6 domains. Peptidase families mainly contain abundant serine peptidases, metallopeptidases, and cysteine peptidases. In the secretomes, the number of genes differed between the pathotypes, with a high percentage of candidate effectors. Both the virulence gene and CAZyme gene content for each pathotype was abundant and diverse, and the latter was enriched in hemicellulolytic enzymes. We provide new insights into the nature of intraspecific diversity among C. lindemuthianum pathotypes and the origin of their ability to rapidly adapt to genetic changes in its host and environmental conditions.","PeriodicalId":15878,"journal":{"name":"Journal of Fungi","volume":null,"pages":null},"PeriodicalIF":4.7,"publicationDate":"2024-09-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142182989","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Anthracnose is one of the destructive diseases of pitaya that seriously affects the plant growth and fruit quality and causes significant yield and economic losses worldwide. However, information regarding the species of pathogens that cause anthracnose in pitaya (Hylocereus undatus) fruits in Gansu Province, China, and its pathogenic mechanism is unknown. Thus, the purposes of our present study were to identify the species of pathogens causing H. undatus fruits anthracnose based on the morphological and molecular characteristics and determine its pathogenic mechanism by physiological and biochemical methods. In our present study, forty-six isolates were isolated from the collected samples of diseased H. undatus fruits and classified as three types (named as H-1, H-2, and H-3), according to the colony and conidium morphological characteristics. The isolation frequencies of H-1, H-2, and H-3 types were 63.04%, 21.74%, and 15.22%, respectively. The representative single-spore isolate of HLGTJ-1 in H-1 type has significant pathogenicity, and finally we identified Colletotrichum truncatum as the pathogen based on the morphological characteristics as well as multi-locus sequence analysis. Moreover, the H. undatus fruits inoculated with C. truncatum had a significantly increased activity of cell wall-degrading enzymes (CWDEs) cellulase (Cx), β-glucosidase (β-Glu), polygalacturonase (PG), and pectin methylgalacturonase (PMG), while having a decreased level of cell wall components of original pectin and cellulose in comparison to control. The average increased activities of Cx, β-Glu, PG, and PMG were 30.73%, 40.40%, 51.55%, and 32.23% from day 0 to 6 after inoculation, respectively. In contrast, the average decreased contents of original pectin and cellulose were 1.82% and 16.47%, respectively, whereas the average increased soluble pectin content was 38.31% in comparison to control. Our results indicate that C. truncatum infection increased the activities of CWDEs in H. undatus fruits to disassemble their cell wall components, finally leading to the fruits’ decay and deterioration. Thus, our findings will provide significant evidence in the controlling of pitaya anthracnose in the future.
{"title":"Characterization and Pathogenicity of Colletotrichum truncatum Causing Hylocereus undatus Anthracnose through the Changes of Cell Wall-Degrading Enzymes and Components in Fruits","authors":"Shuwu Zhang, Yun Liu, Jia Liu, Enchen Li, Bingliang Xu","doi":"10.3390/jof10090652","DOIUrl":"https://doi.org/10.3390/jof10090652","url":null,"abstract":"Anthracnose is one of the destructive diseases of pitaya that seriously affects the plant growth and fruit quality and causes significant yield and economic losses worldwide. However, information regarding the species of pathogens that cause anthracnose in pitaya (Hylocereus undatus) fruits in Gansu Province, China, and its pathogenic mechanism is unknown. Thus, the purposes of our present study were to identify the species of pathogens causing H. undatus fruits anthracnose based on the morphological and molecular characteristics and determine its pathogenic mechanism by physiological and biochemical methods. In our present study, forty-six isolates were isolated from the collected samples of diseased H. undatus fruits and classified as three types (named as H-1, H-2, and H-3), according to the colony and conidium morphological characteristics. The isolation frequencies of H-1, H-2, and H-3 types were 63.04%, 21.74%, and 15.22%, respectively. The representative single-spore isolate of HLGTJ-1 in H-1 type has significant pathogenicity, and finally we identified Colletotrichum truncatum as the pathogen based on the morphological characteristics as well as multi-locus sequence analysis. Moreover, the H. undatus fruits inoculated with C. truncatum had a significantly increased activity of cell wall-degrading enzymes (CWDEs) cellulase (Cx), β-glucosidase (β-Glu), polygalacturonase (PG), and pectin methylgalacturonase (PMG), while having a decreased level of cell wall components of original pectin and cellulose in comparison to control. The average increased activities of Cx, β-Glu, PG, and PMG were 30.73%, 40.40%, 51.55%, and 32.23% from day 0 to 6 after inoculation, respectively. In contrast, the average decreased contents of original pectin and cellulose were 1.82% and 16.47%, respectively, whereas the average increased soluble pectin content was 38.31% in comparison to control. Our results indicate that C. truncatum infection increased the activities of CWDEs in H. undatus fruits to disassemble their cell wall components, finally leading to the fruits’ decay and deterioration. Thus, our findings will provide significant evidence in the controlling of pitaya anthracnose in the future.","PeriodicalId":15878,"journal":{"name":"Journal of Fungi","volume":null,"pages":null},"PeriodicalIF":4.7,"publicationDate":"2024-09-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142183035","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Kunzhi Jia, Yipu Jia, Qianhua Zeng, Zhaoqi Yan, Shihua Wang
Conidia are important for the dispersal of Aspergillus flavus, which usually generates aflatoxin B1 (AFB1) and poses a threat to the safety of agricultural food. The development of conidia is usually susceptible to changes in environmental conditions, such as nutritional status and light. However, how the light signal is involved in the conidiation in A. flavus is still unknown. In this study, LreA was identified to respond to blue light and mediate the promotion of conidiation in A. flavus, which is related to the central development pathway. At the same time, blue light inhibited the biosynthesis of AFB1, which was mediated by LreA and attributed to the transcriptional regulation of aflR and aflS expression. Our findings disclosed the function and mechanism of the blue light sensor LreA in regulating conidiation and AFB1 biosynthesis, which is beneficial for the prevention and control of A. flavus and mycotoxins.
{"title":"Regulation of Conidiation and Aflatoxin B1 Biosynthesis by a Blue Light Sensor LreA in Aspergillus flavus","authors":"Kunzhi Jia, Yipu Jia, Qianhua Zeng, Zhaoqi Yan, Shihua Wang","doi":"10.3390/jof10090650","DOIUrl":"https://doi.org/10.3390/jof10090650","url":null,"abstract":"Conidia are important for the dispersal of Aspergillus flavus, which usually generates aflatoxin B1 (AFB1) and poses a threat to the safety of agricultural food. The development of conidia is usually susceptible to changes in environmental conditions, such as nutritional status and light. However, how the light signal is involved in the conidiation in A. flavus is still unknown. In this study, LreA was identified to respond to blue light and mediate the promotion of conidiation in A. flavus, which is related to the central development pathway. At the same time, blue light inhibited the biosynthesis of AFB1, which was mediated by LreA and attributed to the transcriptional regulation of aflR and aflS expression. Our findings disclosed the function and mechanism of the blue light sensor LreA in regulating conidiation and AFB1 biosynthesis, which is beneficial for the prevention and control of A. flavus and mycotoxins.","PeriodicalId":15878,"journal":{"name":"Journal of Fungi","volume":null,"pages":null},"PeriodicalIF":4.7,"publicationDate":"2024-09-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142182987","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Fungal secondary metabolites (SMs) represent an invaluable source of therapeutic drugs. Genomics-based approaches to SM discovery have revealed a vast and largely untapped biosynthetic potential within fungal genomes. Here, we used the publicly available fungal genome sequences from the NCBI public database, as well as tools such as antiSMASH, BIG-SLiCE, etc., to analyze a total of 11,598 fungal genomes, identifying 293,926 biosynthetic gene clusters (BGCs), which were subsequently categorized into 26,825 gene cluster families (GCFs). It was discovered that only a tiny fraction, less than 1%, of these GCFs could be mapped to known natural products (NPs). Some GCFs that only contain a single BGC internally are crucial for the biodiversity of fungal biosynthesis. Evident patterns emerged from our analysis, revealing popular taxa as prominent sources of both actual and potential biosynthetic diversity. Our study also suggests that the genus rank distribution of GCF is generally consistent with NP diversity. It is noteworthy that genera Xylaria, Hypoxylon, Colletotrichum, Diaporthe, Nemania, and Calonectria appear to possess a higher potential for SM synthesis. In addition, 7213 BGCs match possible known compound structures, and homologous gene clusters of well-known drugs can be located in different genera, facilitating the development of derivatives that share structural similarity to these drugs and may potentially possess similar biological activity. Our study demonstrated the various types of fungi with mining potential, assisting researchers in prioritizing their research efforts and avoiding duplicate mining of known resources to further explore fungal NP producers.
{"title":"Global Analysis of Natural Products Biosynthetic Diversity Encoded in Fungal Genomes","authors":"Shu Zhang, Guohui Shi, Xinran Xu, Xu Guo, Sijia Li, Zhiyuan Li, Qi Wu, Wen-Bing Yin","doi":"10.3390/jof10090653","DOIUrl":"https://doi.org/10.3390/jof10090653","url":null,"abstract":"Fungal secondary metabolites (SMs) represent an invaluable source of therapeutic drugs. Genomics-based approaches to SM discovery have revealed a vast and largely untapped biosynthetic potential within fungal genomes. Here, we used the publicly available fungal genome sequences from the NCBI public database, as well as tools such as antiSMASH, BIG-SLiCE, etc., to analyze a total of 11,598 fungal genomes, identifying 293,926 biosynthetic gene clusters (BGCs), which were subsequently categorized into 26,825 gene cluster families (GCFs). It was discovered that only a tiny fraction, less than 1%, of these GCFs could be mapped to known natural products (NPs). Some GCFs that only contain a single BGC internally are crucial for the biodiversity of fungal biosynthesis. Evident patterns emerged from our analysis, revealing popular taxa as prominent sources of both actual and potential biosynthetic diversity. Our study also suggests that the genus rank distribution of GCF is generally consistent with NP diversity. It is noteworthy that genera Xylaria, Hypoxylon, Colletotrichum, Diaporthe, Nemania, and Calonectria appear to possess a higher potential for SM synthesis. In addition, 7213 BGCs match possible known compound structures, and homologous gene clusters of well-known drugs can be located in different genera, facilitating the development of derivatives that share structural similarity to these drugs and may potentially possess similar biological activity. Our study demonstrated the various types of fungi with mining potential, assisting researchers in prioritizing their research efforts and avoiding duplicate mining of known resources to further explore fungal NP producers.","PeriodicalId":15878,"journal":{"name":"Journal of Fungi","volume":null,"pages":null},"PeriodicalIF":4.7,"publicationDate":"2024-09-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142182991","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Zoe L. Tyree, Kimberly Bellingham-Johnstun, Jessica Martinez-Baird, Caroline Laplante
Cytokinesis is driven in part by the constriction of a ring of actin filaments, myosin motors and other proteins. In fission yeast, three myosins contribute to cytokinesis including a Myosin-V Myo51. As Myosin-Vs typically carry cargo along actin filaments, the role of Myo51 in cytokinesis remains unclear. The previous work suggests that Myo51 may crosslink actin filaments. We hypothesized that if Myo51 crosslinks actin filaments, cells carrying double deletions of ain1, which encodes the crosslinker alpha-actinin, and myo51 (∆ain1 ∆myo51 cells) will exhibit more severe cytokinesis phenotypes than cells with the single ∆ain1 mutation. Contrary to our expectations, we found that the loss of Myo51 in ∆ain1 cells partially rescued the severity of the node clumping phenotype measured in ∆ain1 cells. Furthermore, we describe a normal process of contractile ring “shedding”, the appearance of fragments of ring material extending away from the contractile ring along the ingressing septum that occurs in the second half of constriction. We measured that ∆ain1 ∆myo51 cells exhibit premature and exaggerated shedding. Our work suggests that Myo51 is not a simple actin filament crosslinker. Instead, a role in effective node motion better recapitulates its function during ring assembly and disassembly.
{"title":"The Myosin-V Myo51 and Alpha-Actinin Ain1p Cooperate during Contractile Ring Assembly and Disassembly in Fission Yeast Cytokinesis","authors":"Zoe L. Tyree, Kimberly Bellingham-Johnstun, Jessica Martinez-Baird, Caroline Laplante","doi":"10.3390/jof10090647","DOIUrl":"https://doi.org/10.3390/jof10090647","url":null,"abstract":"Cytokinesis is driven in part by the constriction of a ring of actin filaments, myosin motors and other proteins. In fission yeast, three myosins contribute to cytokinesis including a Myosin-V Myo51. As Myosin-Vs typically carry cargo along actin filaments, the role of Myo51 in cytokinesis remains unclear. The previous work suggests that Myo51 may crosslink actin filaments. We hypothesized that if Myo51 crosslinks actin filaments, cells carrying double deletions of ain1, which encodes the crosslinker alpha-actinin, and myo51 (∆ain1 ∆myo51 cells) will exhibit more severe cytokinesis phenotypes than cells with the single ∆ain1 mutation. Contrary to our expectations, we found that the loss of Myo51 in ∆ain1 cells partially rescued the severity of the node clumping phenotype measured in ∆ain1 cells. Furthermore, we describe a normal process of contractile ring “shedding”, the appearance of fragments of ring material extending away from the contractile ring along the ingressing septum that occurs in the second half of constriction. We measured that ∆ain1 ∆myo51 cells exhibit premature and exaggerated shedding. Our work suggests that Myo51 is not a simple actin filament crosslinker. Instead, a role in effective node motion better recapitulates its function during ring assembly and disassembly.","PeriodicalId":15878,"journal":{"name":"Journal of Fungi","volume":null,"pages":null},"PeriodicalIF":4.7,"publicationDate":"2024-09-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142183004","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
An in-depth study of the phylogenetic relationships of Xylaria species associated with nutshells of fruits and seeds within the genus Xylaria and related genera of Xylaceaecea was conducted in China. The multi-gene phylogenetic analyses were carried out based on ITS, RPB2, and TUB sequences of 100 species of 16 known genera in Xylariaceae around the world. Based on molecular phylogenetic analyses, morphological observations, and ecological habitats, a new genus, Heteroxylaria, is established to accommodate four new species, viz. H. cordiicola, H. juglandicola, H. meliicola, and H. terminaliicola, and four new combinations, viz. H. oxyacanthae, H. palmicola, H. reevesiae, and H. rohrensis. The genus is characterized by cylindrical stromata with conspicuous to inconspicuous perithecial mounds, surface black, having brown to dark brown ascospores with a germ slit, and it grows on nutshell of fruits. The combined ITS+RPB2+TUB sequence dataset of representative taxa in the Xylariaceae demonstrate that Heteroxylaria is grouped with Hypocreodendron but forms a monophyletic lineage. All novelties described herein are morphologically illustrated and compared to similar species and phylogeny is investigated to establish new genera and species.
在中国对木犀属（Xylaria）和木犀科（Xylaceaecea）相关属中与果实和种子果壳相关的木犀属（Xylaria）物种的系统发生关系进行了深入研究。基于ITS、RPB2和TUB序列，对全球已知的16个木犀属100个物种进行了多基因系统发育分析。根据分子系统进化分析、形态观察和生态习性，建立了一个新属 Heteroxylaria，包括四个新种，即 H. cordiicola、H. juglandicola、H. meliicola 和 H. terminaliicola，以及四个新组合，即 H. oxyacanthae、H. palmicola、H. reevesiae 和 H. rohrensis。该属的特征是圆柱形基质，有明显至不明显的壳丘，表面黑色，有褐色至深褐色的带胚芽裂缝的放线孢子，生长在果实的果壳上。木犀科代表性类群的 ITS+RPB2+TUB 序列组合数据集表明，Heteroxylaria 与 Hypocreodendron 同属一个类群，但形成一个单系。本文描述的所有新种都有形态学图解，并与相似种进行了比较，通过系统发育研究建立了新属和新种。
{"title":"Multi-Gene Phylogenetic Analyses Reveals Heteroxylaria Gen. Nov. and New Contributions to Xylariaceae (Ascomycota) from China","authors":"An-Hong Zhu, Zi-Kun Song, Jun-Fang Wang, Hao-Wen Guan, Zhi Qu, Hai-Xia Ma","doi":"10.3390/jof10090645","DOIUrl":"https://doi.org/10.3390/jof10090645","url":null,"abstract":"An in-depth study of the phylogenetic relationships of Xylaria species associated with nutshells of fruits and seeds within the genus Xylaria and related genera of Xylaceaecea was conducted in China. The multi-gene phylogenetic analyses were carried out based on ITS, RPB2, and TUB sequences of 100 species of 16 known genera in Xylariaceae around the world. Based on molecular phylogenetic analyses, morphological observations, and ecological habitats, a new genus, Heteroxylaria, is established to accommodate four new species, viz. H. cordiicola, H. juglandicola, H. meliicola, and H. terminaliicola, and four new combinations, viz. H. oxyacanthae, H. palmicola, H. reevesiae, and H. rohrensis. The genus is characterized by cylindrical stromata with conspicuous to inconspicuous perithecial mounds, surface black, having brown to dark brown ascospores with a germ slit, and it grows on nutshell of fruits. The combined ITS+RPB2+TUB sequence dataset of representative taxa in the Xylariaceae demonstrate that Heteroxylaria is grouped with Hypocreodendron but forms a monophyletic lineage. All novelties described herein are morphologically illustrated and compared to similar species and phylogeny is investigated to establish new genera and species.","PeriodicalId":15878,"journal":{"name":"Journal of Fungi","volume":null,"pages":null},"PeriodicalIF":4.7,"publicationDate":"2024-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142182988","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Zongjun Tong, Xing Han, Xinlian Duan, Junbin Lin, Jie Chen, Jihong Xiao, Ying Gan, Bingcheng Gan, Junjie Yan
Zinc finger proteins (ZFPs) are essential transcription factors in eukaryotes, particularly the extensively studied C2H2 family, which is known for its involvement in various biological processes. This research provides a thorough examination and analysis of the C2H2-ZFP gene family in Flammulina filiformis. Using bioinformatics tools, 58 FfC2H2-ZFP genes spread across 11 chromosomes were identified and scrutinized in detail for their gene structures, protein characteristics, and phylogenetic relationships. The study of phylogenetics and synteny sheds light on the evolutionary relationships among C2H2-ZFPs in F. filiformis and other fungi, revealing a complex evolutionary past. The identification of conserved cis-regulatory elements in the gene promoter regions suggests intricate functionalities, particularly in the developmental and stress response pathways. By utilizing RNA-seq and qRT-PCR techniques, the expression patterns of these genes were explored across different developmental stages and tissues of F. filiformis, unveiling distinct expression profiles. Notably, significant expression variations were observed in the stipe elongation region and pilei of various sizes, indicating potential roles in fruiting body morphogenesis. This study enhances our knowledge of the C2H2-ZFP gene family in F. filiformis and lays the groundwork for future investigations into their regulatory mechanisms and applications in fungal biology and biotechnology.
{"title":"Genome-Wide Identification and Expression Analysis of the Cys2His2 Zinc Finger Protein Gene Family in Flammulina filiformis","authors":"Zongjun Tong, Xing Han, Xinlian Duan, Junbin Lin, Jie Chen, Jihong Xiao, Ying Gan, Bingcheng Gan, Junjie Yan","doi":"10.3390/jof10090644","DOIUrl":"https://doi.org/10.3390/jof10090644","url":null,"abstract":"Zinc finger proteins (ZFPs) are essential transcription factors in eukaryotes, particularly the extensively studied C2H2 family, which is known for its involvement in various biological processes. This research provides a thorough examination and analysis of the C2H2-ZFP gene family in Flammulina filiformis. Using bioinformatics tools, 58 FfC2H2-ZFP genes spread across 11 chromosomes were identified and scrutinized in detail for their gene structures, protein characteristics, and phylogenetic relationships. The study of phylogenetics and synteny sheds light on the evolutionary relationships among C2H2-ZFPs in F. filiformis and other fungi, revealing a complex evolutionary past. The identification of conserved cis-regulatory elements in the gene promoter regions suggests intricate functionalities, particularly in the developmental and stress response pathways. By utilizing RNA-seq and qRT-PCR techniques, the expression patterns of these genes were explored across different developmental stages and tissues of F. filiformis, unveiling distinct expression profiles. Notably, significant expression variations were observed in the stipe elongation region and pilei of various sizes, indicating potential roles in fruiting body morphogenesis. This study enhances our knowledge of the C2H2-ZFP gene family in F. filiformis and lays the groundwork for future investigations into their regulatory mechanisms and applications in fungal biology and biotechnology.","PeriodicalId":15878,"journal":{"name":"Journal of Fungi","volume":null,"pages":null},"PeriodicalIF":4.7,"publicationDate":"2024-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142183041","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Claudia Cortimiglia, Javier Alonso-Del-Real, Mireya Viviana Belloso Daza, Amparo Querol, Giovanni Iacono, Pier Sandro Cocconcelli
Classifying a yeast strain into a recognized species is not always straightforward. Currently, the taxonomic delineation of yeast strains involves multiple approaches covering phenotypic characteristics and molecular methodologies, including genome-based analysis. The aim of this study was to evaluate the suitability of the Average Nucleotide Identity (ANI) calculation through FastANI, a tool created for bacterial species identification, for the assignment of strains to some yeast species. FastANI, the alignment of in silico-extracted D1/D2 sequences of LSU rRNA, and multiple alignments of orthologous genes (MAOG) were employed to analyze 644 assemblies from 12 yeast genera, encompassing various species, and on a dataset of hybrid Saccharomyces species. Overall, the analysis showed high consistency between results obtained with FastANI and MAOG, although, FastANI proved to be more discriminating than the other two methods applied to genomic sequences. In particular, FastANI was effective in distinguishing between strains belonging to different species, defining clear boundaries between them (cutoff: 94–96%). Our results show that FastANI is a reliable method for attributing a known yeast species to a particular strain. Moreover, although hybridization events make species discrimination more complex, it was revealed to be useful in the identification of these cases. We suggest its inclusion as a key component in a comprehensive approach to species delineation. Using this approach with a larger number of yeasts would validate it as a rapid technique to identify yeasts based on whole genome sequences.
{"title":"Evaluating the Genome-Based Average Nucleotide Identity Calculation for Identification of Twelve Yeast Species","authors":"Claudia Cortimiglia, Javier Alonso-Del-Real, Mireya Viviana Belloso Daza, Amparo Querol, Giovanni Iacono, Pier Sandro Cocconcelli","doi":"10.3390/jof10090646","DOIUrl":"https://doi.org/10.3390/jof10090646","url":null,"abstract":"Classifying a yeast strain into a recognized species is not always straightforward. Currently, the taxonomic delineation of yeast strains involves multiple approaches covering phenotypic characteristics and molecular methodologies, including genome-based analysis. The aim of this study was to evaluate the suitability of the Average Nucleotide Identity (ANI) calculation through FastANI, a tool created for bacterial species identification, for the assignment of strains to some yeast species. FastANI, the alignment of in silico-extracted D1/D2 sequences of LSU rRNA, and multiple alignments of orthologous genes (MAOG) were employed to analyze 644 assemblies from 12 yeast genera, encompassing various species, and on a dataset of hybrid Saccharomyces species. Overall, the analysis showed high consistency between results obtained with FastANI and MAOG, although, FastANI proved to be more discriminating than the other two methods applied to genomic sequences. In particular, FastANI was effective in distinguishing between strains belonging to different species, defining clear boundaries between them (cutoff: 94–96%). Our results show that FastANI is a reliable method for attributing a known yeast species to a particular strain. Moreover, although hybridization events make species discrimination more complex, it was revealed to be useful in the identification of these cases. We suggest its inclusion as a key component in a comprehensive approach to species delineation. Using this approach with a larger number of yeasts would validate it as a rapid technique to identify yeasts based on whole genome sequences.","PeriodicalId":15878,"journal":{"name":"Journal of Fungi","volume":null,"pages":null},"PeriodicalIF":4.7,"publicationDate":"2024-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142223800","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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