Fungal Diversity最新文献

{"title":"A re-evaluation of Diaporthe: refining the boundaries of species and species complexes","authors":"Asha J. Dissanayake, Jin-Tao Zhu, Ya-Ya Chen, Sajeewa S. N. Maharachchikumbura, Kevin D. Hyde, Jian-Kui Liu","doi":"10.1007/s13225-024-00538-7","DOIUrl":"https://doi.org/10.1007/s13225-024-00538-7","url":null,"abstract":"<p><i>Diaporthe</i> is an important plant pathogenic genus, which also occurs as endophytes and saprobes. Many <i>Diaporthe</i> species that are morphologically similar proved to be genetically distinct. The current understanding of <i>Diaporthe</i> taxonomy by applying morphological characters, host associations and multi-gene phylogeny are problematic leading to overestimation/underestimation of species numbers of this significant fungal pathogenic genus. Currently, there are no definite boundaries for the accepted species. Hence, the present study aims to re-structure the genus <i>Diaporthe</i>, based on single gene phylogenies (ITS, <i>tef</i>, <i>tub</i>, <i>cal</i> and <i>his</i>), multi-gene phylogeny justified by applying GCPSR (Genealogical Concordance Phylogenetic Species Recognition) methodology as well as the coalescence-based models (PTP—Poisson Tree Processes and mPTP—multi-rate Poisson Tree Processes). Considering all available type isolates of <i>Diaporthe</i>, the genus is divided into seven sections while boundaries for 13 species and 15 species-complexes are proposed. To support this re-assessment of the genus, 82 <i>Diaporthe</i> isolates obtained from woody hosts in Guizhou Province in China were investigated and revealed the presence of two novel species and 17 previously known species. Synonymies are specified for 31 species based on molecular data and morphological studies. Dividing <i>Diaporthe</i> into several specific sections based on phylogenetic analyses can avoid the construction of lengthy phylogenetic trees of the entire genus in future taxonomic studies. In other words, when one conducts research related to the genus, only species from the appropriate section need to be selected for phylogenetic analysis.</p>","PeriodicalId":12471,"journal":{"name":"Fungal Diversity","volume":"9 1","pages":""},"PeriodicalIF":20.3,"publicationDate":"2024-07-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141561350","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Phylogenomics, divergence times and notes of orders in Basidiomycota","authors":"Mao-Qiang He, Bin Cao, Fei Liu, Teun Boekhout, Teodor T. Denchev, Nathan Schoutteten, Cvetomir M. Denchev, Martin Kemler, Sergio P. Gorjón, Dominik Begerow, Ricardo Valenzuela, Naveed Davoodian, Tuula Niskanen, Alfredo Vizzini, Scott A. Redhead, Virginia Ramírez-Cruz, Viktor Papp, Vasiliy A. Dudka, Arun Kumar Dutta, Ricardo García-Sandoval, Xin-Zhan Liu, Teeratas Kijpornyongpan, Anton Savchenko, Leho Tedersoo, Bart Theelen, Larissa Trierveiler-Pereira, Fang Wu, Juan Carlos Zamora, Xiang-Yu Zeng, Li-Wei Zhou, Shi-Liang Liu, Masoomeh Ghobad-Nejhad, Admir J. Giachini, Guo-Jie Li, Makoto Kakishima, Ibai Olariaga, Danny Haelewaters, Bobby Sulistyo, Junta Sugiyama, Sten Svantesson, Andrey Yurkov, Pablo Alvarado, Vladimír Antonín, André Felipe da Silva, Irina Druzhinina, Tatiana B. Gibertoni, Laura Guzmán-Dávalos, Alfredo Justo, Samantha C. Karunarathna, Mahesh C. A. Galappaththi, Merje Toome-Heller, Tsuyoshi Hosoya, Kare Liimatainen, Rodrigo Márquez, Armin Mešić, Jean-Marc Moncalvo..","doi":"10.1007/s13225-024-00535-w","DOIUrl":"https://doi.org/10.1007/s13225-024-00535-w","url":null,"abstract":"<p>Basidiomycota is one of the major phyla in the fungal tree of life. The outline of Basidiomycota provides essential taxonomic information for researchers and workers in mycology. In this study, we present a time-framed phylogenomic tree with 487 species of Basidiomycota from 127 families, 47 orders, 14 classes and four subphyla; we update the outline of Basidiomycota based on the phylogenomic relationships and the taxonomic studies since 2019; and we provide notes for each order and discuss the history, defining characteristics, evolution, justification of orders, problems, significance, and plates. Our phylogenomic analysis suggests that the subphyla diverged in a time range of 443–490 Myr (million years), classes in a time range of 312–412 Myr, and orders in a time range of 102–361 Myr. Families diverged in a time range of 50–289 Myr, 76–224 Myr, and 62–156 Myr in Agaricomycotina, Pucciniomycotina, and Ustilaginomycotina, respectively. Based on the phylogenomic relationships and divergence times, we propose a new suborder Mycenineae in Agaricales to accommodate Mycenaceae. In the current outline of Basidiomycota, there are four subphyla, 20 classes, 77 orders, 297 families, and 2134 genera accepted. When building a robust taxonomy of Basidiomycota in the genomic era, the generation of molecular phylogenetic data has become relatively easier. Finding phenotypical characters, especially those that can be applied for identification and classification, however, has become increasingly challenging.</p>","PeriodicalId":12471,"journal":{"name":"Fungal Diversity","volume":"39 1","pages":""},"PeriodicalIF":20.3,"publicationDate":"2024-07-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141566298","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Selection dictates the distance pattern of similarity in trees and soil fungi across forest ecosystems","authors":"Yue-Hua Hu, Daniel J. Johnson, Zhen-Hua Sun, Lian-Ming Gao, Han-Dong Wen, Kun Xu, Hua Huang, Wei-Wei Liu, Min Cao, Ze-Wei Song, Peter G. Kennedy","doi":"10.1007/s13225-024-00537-8","DOIUrl":"https://doi.org/10.1007/s13225-024-00537-8","url":null,"abstract":"<p>How the four major processes affecting community assembly—selection, dispersal, drift, and diversification—solely or jointly shape co-occurring assemblages of macro- and microorganisms at the same scales remains poorly understood. Here, we delved into the distance pattern of similarity (DPS) in tree and soil fungal communities in three <i>c.</i> 20-hectare forest plots spanning tropical to temperate climates in Yunnan province, Southwest China. Specifically, we decrypted the assembly contribution of individual-based random sampling, selection and/or dispersal using drift-inexplicit ordination and drift-explicit baseline models. Surprisingly, our findings demonstrated that most soil fungal realized distribution ranges (RDR) were shorter than most trees. Because of explicitly integrating drift and the range of DPS is broader than the RDR of most trees and fungi, selection baseline models overwhelmingly captured the DPS structures in trees and fungi across spatial scales in tropical, subtropical, and subalpine forest ecosystems and that for fungi across taxonomic levels and fungal guilds. Under the premise that modeling frameworks, ecosystems, spatial scales, sample intensities, selection variables, and dispersal variables are well unified, the ubiquitous dominance of selection elucidates no fundamental difference in the assembly mechanism between trees and soil fungi.</p>","PeriodicalId":12471,"journal":{"name":"Fungal Diversity","volume":"51 1","pages":""},"PeriodicalIF":20.3,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141489552","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Current trends, limitations and future research in the fungi?","authors":"Kevin D. Hyde, Petr Baldrian, Yanpeng Chen, K. W. Thilini Chethana, Sybren De Hoog, Mingkwan Doilom, Antonio R. Gomes de Farias, Micael F. M. Gonçalves, Didsanutda Gonkhom, Heng Gui, Sandra Hilário, Yuwei Hu, Ruvishika S. Jayawardena, Sabin Khyaju, Paul M. Kirk, Petr Kohout, Thatsanee Luangharn, Sajeewa S. N. Maharachchikumbura, Ishara S. Manawasinghe, Peter E. Mortimer, Allen Grace T. Niego, Monthien Phonemany, Birthe Sandargo, Indunil C. Senanayake, Marc Stadler, Frank Surup, Naritsada Thongklang, Dhanushka N. Wanasinghe, Ali H. Bahkali, Arttapon Walker","doi":"10.1007/s13225-023-00532-5","DOIUrl":"https://doi.org/10.1007/s13225-023-00532-5","url":null,"abstract":"<p>The field of mycology has grown from an underappreciated subset of botany, to a valuable, modern scientific discipline. As this field of study has grown, there have been significant contributions to science, technology, and industry, highlighting the value of fungi in the modern era. This paper looks at the current research, along with the existing limitations, and suggests future areas where scientists can focus their efforts, in the field mycology. We show how fungi have become important emerging diseases in medical mycology. We discuss current trends and the potential of fungi in drug and novel compound discovery. We explore the current trends in phylogenomics, its potential, and outcomes and address the question of how phylogenomics can be applied in fungal ecology. In addition, the trends in functional genomics studies of fungi are discussed with their importance in unravelling the intricate mechanisms underlying fungal behaviour, interactions, and adaptations, paving the way for a comprehensive understanding of fungal biology. We look at the current research in building materials, how they can be used as carbon sinks, and how fungi can be used in biocircular economies. The numbers of fungi have always been of great interest and have often been written about and estimates have varied greatly. Thus, we discuss current trends and future research needs in order to obtain more reliable estimates. We address the aspects of machine learning (AI) and how it can be used in mycological research. Plant pathogens are affecting food production systems on a global scale, and as such, we look at the current trends and future research needed in this area, particularly in disease detection. We look at the latest data from High Throughput Sequencing studies and question if we are still gaining new knowledge at the same rate as before. A review of current trends in nanotechnology is provided and its future potential is addressed. The importance of Arbuscular Mycorrhizal Fungi is addressed and future trends are acknowledged. Fungal databases are becoming more and more important, and we therefore provide a review of the current major databases. Edible and medicinal fungi have a huge potential as food and medicines, especially in Asia and their prospects are discussed. Lifestyle changes in fungi (e.g., from endophytes, to pathogens, and/or saprobes) are also extremely important and a current research trend and are therefore addressed in this special issue of Fungal Diversity.</p>","PeriodicalId":12471,"journal":{"name":"Fungal Diversity","volume":"31 1","pages":""},"PeriodicalIF":20.3,"publicationDate":"2024-03-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140182799","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Species diversity of fungal pathogens on cultivated mushrooms: a case study on morels (Morchella, Pezizales)","authors":"Feng-Ming Yu, Ruvishika S. Jayawardena, Thatsanee Luangharn, Xiang-Yu Zeng, Cui-Jin-Yi Li, Shu-Xin Bao, Hong Ba, De-Qun Zhou, Song-Ming Tang, Kevin D. Hyde, Qi Zhao","doi":"10.1007/s13225-023-00531-6","DOIUrl":"https://doi.org/10.1007/s13225-023-00531-6","url":null,"abstract":"&lt;p&gt;Mushrooms are important organisms because of their human nutritional and medicinal value. With the expansion of the cultivation of edible mushrooms, fungal diseases have become a major problem in limiting their production. Numerous fungi can cause mushroom deformation or rots. In this publication we report on fungal diseases found during &lt;i&gt;Morchella&lt;/i&gt; cultivation in China, with emphasis on morphology and phylogeny to characterise species. The key findings include 1) establishment of a new family &lt;i&gt;Albomorchellophilaceae&lt;/i&gt; in &lt;i&gt;Hypocreales&lt;/i&gt;, and a novel monotypic genus &lt;i&gt;Albomorchellophila&lt;/i&gt; with the type species &lt;i&gt;A. morchellae&lt;/i&gt;. Divergence time estimates indicate that &lt;i&gt;Albomorchellophilaceae&lt;/i&gt; diverged from its sister family &lt;i&gt;Calcarisporiaceae&lt;/i&gt; at ca. 105 (92–120) MYA; 2) the phylogeny and morphology of the family &lt;i&gt;Pseudodiploosporeaceae&lt;/i&gt; (&lt;i&gt;Hypocreales&lt;/i&gt;) is revised. The family contains a single genus &lt;i&gt;Pseudodiploospora&lt;/i&gt;. Intraspecific genetic analyses of &lt;i&gt;Pseudodiploospora longispora&lt;/i&gt; reveals significant base differences within strains, especially in the regions of protein-coding genes &lt;i&gt;RPB&lt;/i&gt; 2 and &lt;i&gt;TEF&lt;/i&gt;; 3) four fungicolous taxa, i.e., &lt;i&gt;Cylindrodendrum alicantinum&lt;/i&gt;, &lt;i&gt;Hypomyces aurantius&lt;/i&gt;, &lt;i&gt;Hypomyces rosellus&lt;/i&gt;, and &lt;i&gt;Trichothecium roseum&lt;/i&gt;, are reported as putative pathogens on cultivated morels for the first time. In addition, the previously reported pathogens of morels, &lt;i&gt;Clonostachys rosea&lt;/i&gt;, &lt;i&gt;Clonostachys solani&lt;/i&gt;, &lt;i&gt;Hypomyces odoratus&lt;/i&gt;, and &lt;i&gt;Pseudodiploospora longispora&lt;/i&gt; are also detailed in their symptoms and morphology; 4) the phylogeny and morphology of “&lt;i&gt;Zelopaecilomyces&lt;/i&gt;” previously placed within &lt;i&gt;Pseudodiploosporeaceae&lt;/i&gt; are re-assessed. “&lt;i&gt;Zelopaecilomyces&lt;/i&gt;” is proved to be introduced through a chimerism of gene fragments sourced from two distinct organisms. Consequently, it is recommended that “&lt;i&gt;Zelopaecilomyces&lt;/i&gt;” should not be recognised due to the mixed up molecular data in phylogeny and a lack of support from morphological evidence. Furthermore, this study discusses the voucher specimen &lt;i&gt;Paecilomyces penicillatus&lt;/i&gt; (CBS 448.69), which may contain two mixed taxa, i.e., &lt;i&gt;Pseudodiploospora longispora&lt;/i&gt; and a member of &lt;i&gt;Penicillium&lt;/i&gt;. Publications on pathogenic fungi of cultivated mushrooms is sporadically, which leads to a lack of understanding of causal agents. As a follow up to the diseases of morel cultivation, we also review the fungal diseases of cultivated mushrooms reported over the last four decades. More than 130 pathogens affect the growth and development of the main cultivated mushrooms. The taxonomic diversity of these pathogens is high, distributed in 58 genera, 40 families, 20 orders, 12 classes and six phyla. The host infected are from Ascomycota to Basidiomycota, mainly being reported from &lt;i&gt;Agaricus bisporus&lt;/i&gt;, &lt;i&gt;Cordyceps militaris&lt;/i&gt;, &lt;i&gt;Morchella&lt;/i&gt; spp., and &lt;i&gt;Pleurotus&lt;/i&gt; spp. This s","PeriodicalId":12471,"journal":{"name":"Fungal Diversity","volume":"14 1","pages":""},"PeriodicalIF":20.3,"publicationDate":"2024-03-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140032232","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Class-wide genomic tendency throughout specific extremes in black fungi","authors":"Claudia Coleine, Tania Kurbessoian, Giulia Calia, Manuel Delgado-Baquerizo, Alessandro Cestaro, Massimo Pindo, Federica Armanini, Francesco Asnicar, Daniela Isola, Nicola Segata, Claudio Donati, Jason E. Stajich, Sybren de Hoog, Laura Selbmann","doi":"10.1007/s13225-024-00533-y","DOIUrl":"https://doi.org/10.1007/s13225-024-00533-y","url":null,"abstract":"<p>The classes <i>Dothideomycetes</i> and <i>Eurotiomycetes</i> include constitutively melanized fungi adapted to extreme conditions and they are widely distributed in diverse hostile habitats worldwide. Yet, despite the growing interest in these fungi, there is a considerable gap of knowledge on their functionality. Their genomic analysis is still in its infancy and the possibility to understand their adaptive strategies and exploit their potentialities in bioremediation is very limited. Here, we supply a genome catalog of 118 black fungi, encompassing different ecologies, phylogenies and lifestyles, as a first example of a comparative genomic study at high level of diversity. Results indicate that, as a rule, <i>Dothideomycetes</i> show more variable genome size and that larger genomes are associated with harshest conditions; low temperature tolerance and DNA repair capacity are overrepresented in their genomes. In <i>Eurotiomycetes</i> high temperature tolerance and capacity to metabolize hydrocarbons are more frequently present and these abilities are positively correlated with the human presence. The genomic features are consistent with the prevalent ecologies in the two classes. Indeed, <i>Dothideomycetes</i> are more common in cold and dry environments with high capacity for DNA repair being consistent with the normally highly UV-impacted conditions in their habitats; in contrast, <i>Eurotiomycetes</i> spread mainly in hot human-impacted sites with industrial pollution. Mean annual temperature and isothermality are positively correlated with tolerance to high temperatures in <i>Dothideomycetes</i>, suggesting that, despite their preference for the cold, they are potentially equipped to survive even when temperatures rise due to the global warming.</p>","PeriodicalId":12471,"journal":{"name":"Fungal Diversity","volume":"6 1","pages":""},"PeriodicalIF":20.3,"publicationDate":"2024-02-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139967382","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Fungal diversity notes 1717–1817: taxonomic and phylogenetic contributions on genera and species of fungal taxa","authors":"Shi-Liang Liu, Xue-Wei Wang, Guo-Jie Li, Chun-Ying Deng, Walter Rossi, Marco Leonardi, Kare Liimatainen, Tapio Kekki, Tuula Niskanen, Matthew E. Smith, Joe Ammirati, Dimitar Bojantchev, Mohamed A. Abdel-Wahab, Ming Zhang, Enjing Tian, Yong-Zhong Lu, Jing-Yi Zhang, Jian Ma, Arun Kumar Dutta, Krishnendu Acharya, Tian-Ye Du, Jize Xu, Ji Seon Kim, Young Woon Lim, Alice Gerlach, Nian-Kai Zeng, Yun-Xiao Han, Parisa Razaghi, Mubashar Raza, Lei Cai, Mark S. Calabon, E. B. Gareth Jones, Rituparna Saha, T. K. Arun Kumar, K. Krishnapriya, Anjitha Thomas, Malarvizhi Kaliyaperumal, Kezhocuyi Kezo, Sugantha Gunaseelan, Sanjay Kumar Singh, Paras Nath Singh, Ajay Chandrakant Lagashetti, Kadambari Subhash Pawar, Shuhua Jiang, Chao Zhang, Huang Zhang, Yun Qing, Tolgor Bau, Xing-Can Peng, Ting-Chi Wen, Natalia A. Ramirez, Nicolás Niveiro, Mei-Xiang Li, Zhu L. Yang, Gang Wu, Entaj Tarafder, Danushka S. Tennakoon, Chang-Hsin Kuo, Tatiane M. da Silva, Cristina M. Souza-Motta, Jadson D. P. Bezerra,..","doi":"10.1007/s13225-023-00529-0","DOIUrl":"https://doi.org/10.1007/s13225-023-00529-0","url":null,"abstract":"&lt;p&gt;As the continuation of Fungal Diversity Notes series, the current paper is the 16th contribution to this series. A total of 103 taxa from seven classes in &lt;i&gt;Ascomycota&lt;/i&gt; and &lt;i&gt;Basidiomycota&lt;/i&gt; are included here. Of these 101 taxa, four new genera, 89 new species, one new combination, one new name and six new records are described in detail along with information of hosts and geographic distributions. The four genera newly introduced are &lt;i&gt;Ascoglobospora&lt;/i&gt;, &lt;i&gt;Atheliella&lt;/i&gt;, &lt;i&gt;Rufoboletus&lt;/i&gt; and &lt;i&gt;Tenuimyces&lt;/i&gt;. Newly described species are &lt;i&gt;Akanthomyces xixiuensis&lt;/i&gt;, &lt;i&gt;Agaricus agharkarii&lt;/i&gt;, &lt;i&gt;A. albostipitatus&lt;/i&gt;, &lt;i&gt;Amphisphaeria guttulata&lt;/i&gt;, &lt;i&gt;Ascoglobospora marina&lt;/i&gt;, &lt;i&gt;Astrothelium peudostraminicolor&lt;/i&gt;, &lt;i&gt;Athelia naviculispora&lt;/i&gt;, &lt;i&gt;Atheliella conifericola&lt;/i&gt;, &lt;i&gt;Athelopsis &lt;/i&gt;&lt;i&gt;subglaucina&lt;/i&gt;, &lt;i&gt;Aureoboletus minimus&lt;/i&gt;, &lt;i&gt;A. nanlingensis&lt;/i&gt;, &lt;i&gt;Autophagomyces incertus&lt;/i&gt;, &lt;i&gt;Beltrania liliiferae&lt;/i&gt;, &lt;i&gt;Beltraniella jiangxiensis&lt;/i&gt;, &lt;i&gt;Botryobasidium coniferarum&lt;/i&gt;, &lt;i&gt;Calocybella sribuabanensis&lt;/i&gt;, &lt;i&gt;Calonarius caesiofulvus&lt;/i&gt;, &lt;i&gt;C. nobilis&lt;/i&gt;, &lt;i&gt;C. pacificus&lt;/i&gt;, &lt;i&gt;C. pulcher&lt;/i&gt;, &lt;i&gt;C. subcorrosus&lt;/i&gt;, &lt;i&gt;Cortinarius flaureifolius&lt;/i&gt;, &lt;i&gt;C. floridaensis&lt;/i&gt;, &lt;i&gt;C. subiodes&lt;/i&gt;, &lt;i&gt;Crustomyces juniperi&lt;/i&gt;, &lt;i&gt;C. scytinostromoides&lt;/i&gt;, &lt;i&gt;Cystostereum subsirmaurense&lt;/i&gt;, &lt;i&gt;Dimorphomyces seemanii&lt;/i&gt;, &lt;i&gt;Fulvoderma microporum&lt;/i&gt;, &lt;i&gt;Ginnsia laricicola&lt;/i&gt;, &lt;i&gt;Gomphus zamorinorum&lt;/i&gt;, &lt;i&gt;Halobyssothecium sichuanense&lt;/i&gt;, &lt;i&gt;Hemileccinum duriusculum&lt;/i&gt;, &lt;i&gt;Henningsomyces hengduanensis&lt;/i&gt;, &lt;i&gt;Hygronarius californicus&lt;/i&gt;, &lt;i&gt;Kneiffiella pseudoabdita&lt;/i&gt;, &lt;i&gt;K. pseudoalutacea&lt;/i&gt;, &lt;i&gt;Laboulbenia bifida&lt;/i&gt;, &lt;i&gt;L. tschirnhausii&lt;/i&gt;, &lt;i&gt;L. tuberculata&lt;/i&gt;, &lt;i&gt;Lambertella dipterocarpacearum&lt;/i&gt;, &lt;i&gt;Laxitextum subrubrum&lt;/i&gt;, &lt;i&gt;Lyomyces austro-occidentalis&lt;/i&gt;, &lt;i&gt;L. crystallina&lt;/i&gt;, &lt;i&gt;L. guttulatus&lt;/i&gt;, &lt;i&gt;L. niveus&lt;/i&gt;, &lt;i&gt;L. tasmanicus&lt;/i&gt;, &lt;i&gt;Marasmius centrocinnamomeus&lt;/i&gt;, &lt;i&gt;M. ferrugineodiscus&lt;/i&gt;, &lt;i&gt;Megasporoporia tamilnaduensis&lt;/i&gt;, &lt;i&gt;Meruliopsis crystallina&lt;/i&gt;, &lt;i&gt;Metuloidea imbricata&lt;/i&gt;, &lt;i&gt;Moniliophthora atlantica&lt;/i&gt;, &lt;i&gt;Mystinarius ochrobrunneus&lt;/i&gt;, &lt;i&gt;Neomycoleptodiscus alishanense&lt;/i&gt;, &lt;i&gt;Nigrograna kunmingensis&lt;/i&gt;, &lt;i&gt;Paracremonium aquaticum&lt;/i&gt;, &lt;i&gt;Parahelicomyces dictyosporus&lt;/i&gt;, &lt;i&gt;Peniophorella sidera&lt;/i&gt;, &lt;i&gt;P. subreticulata&lt;/i&gt;, &lt;i&gt;Phlegmacium fennicum&lt;/i&gt;, &lt;i&gt;P. pallidocaeruleum&lt;/i&gt;, &lt;i&gt;Pholiota betulicola&lt;/i&gt;, &lt;i&gt;P. subcaespitosa&lt;/i&gt;, &lt;i&gt;Pleurotheciella hyalospora&lt;/i&gt;, &lt;i&gt;Pleurothecium aseptatum&lt;/i&gt;, &lt;i&gt;Resupinatus porrigens&lt;/i&gt;, &lt;i&gt;Russula chlorina&lt;/i&gt;, &lt;i&gt;R. chrysea&lt;/i&gt;, &lt;i&gt;R. cruenta&lt;/i&gt;, &lt;i&gt;R. haematina&lt;/i&gt;, &lt;i&gt;R. luteocarpa&lt;/i&gt;, &lt;i&gt;R. sanguinolenta&lt;/i&gt;, &lt;i&gt;Synnemellisia punensis&lt;/i&gt;, &lt;i&gt;Tenuimyces bambusicola&lt;/i&gt;, &lt;i&gt;Thaxterogaster americanoporphyropus&lt;/i&gt;, &lt;i&gt;T. obscurovibratilis&lt;/i&gt;, &lt;i&gt;Thermoascus endophyticus&lt;/i&gt;, &lt;i&gt;Trechispora alba&lt;/i&gt;, &lt;i&gt;T. perminispora&lt;/i&gt;, &lt;i&gt;T. subfarinacea&lt;/i&gt;, &lt;i&gt;T. tuberculata&lt;/i&gt;, &lt;i&gt;Tremella sairandhriana&lt;/i&gt;, &lt;i&gt;Tropico","PeriodicalId":12471,"journal":{"name":"Fungal Diversity","volume":"6 1","pages":""},"PeriodicalIF":20.3,"publicationDate":"2024-02-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139739323","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Lifestyle changes in Botryosphaeriaceae as evidenced by ancestral genome expansion and horizontal gene transfer","authors":"Xuncheng Wang, Wei Zhang, Junbo Peng, Ishara S. Manawasinghe, Linna Wu, Yonghua Li, Qikai Xing, Xinghong Li, Jiye Yan","doi":"10.1007/s13225-023-00530-7","DOIUrl":"https://doi.org/10.1007/s13225-023-00530-7","url":null,"abstract":"<p><i>Botryosphaeriaceae</i> (Botryosphaeriales, Dothideomycetes, Ascomycota) encompasses commonly encountered opportunistic pathogens that cause stem cankers on woody plants. Lifestyles of <i>Botryosphaeriaceae</i> species could vary as endophytes, pathogens and saprobes and one species can have one or more lifestyles. Therefore, this family is an excellent candidate to study the relationships among lifestyles and lifestyle changes. It is postulated that this family has saprobic ancestors, and the mechanisms by which they evolved from nonpathogenic ancestors to woody pathogens remain unclear. Here, we present an analysis of 18 <i>Botryosphaeriaceae</i> genomes, including four newly generated high-quality genomes of <i>Botryosphaeriaceae</i> strains. We compared <i>Botryosphaeriaceae</i> genomes with phylogenetically closely related Dothideomycetes taxa including plant pathogens and saprobes which revealed significant net gene family expansion in <i>Botryosphaeriaceae</i>. This gene expansion is prominent in the early ancestors before the divergence of genera of <i>Botryosphaeriaceae</i>. This expansion affected the pathogenicity-related genes and detoxification genes. Furthermore, we analysed horizontal gene transfer, which is a mechanism of transfer to genetic material between organisms that are not in a parent–offspring relationship and identified widespread putative intra-kingdom horizontal gene transfer events in this family. Most were transferred during the evolution of ancient ancestors of <i>Botryosphaeriaceae</i>, before the divergence of the modern genera and were enriched in pathogenicity-related genes and detoxification genes. Furthermore, The RNA sequencing analysis of the <i>Botryosphaeriaceae</i> species <i>Lasiodiplodia theobromae</i> revealed that pathogenicity-related genes and detoxification genes, including those obtained through gene family expansion and horizontal gene transfers, were significantly induced after the infection of plant hosts rather than before infection. These insights reveal critical roles for gene family expansion and horizontal gene transfers in the evolutionary adaptation of <i>Botryosphaeriaceae</i> in the infection of woody plants. We postulate that the pathogenic lifestyle of <i>Botryosphaeriaceae</i> species evolved from saprobic or endophytic lifestyles in the early divergence of this family. However, there are few endophytic genomes available for closely related species of <i>Botryosphaeriaceae</i>, thus further studies are necessary to clarify the evolutionary relationships of the endophytes.</p>","PeriodicalId":12471,"journal":{"name":"Fungal Diversity","volume":"65 1","pages":""},"PeriodicalIF":20.3,"publicationDate":"2023-12-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138571359","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"ASF1 regulates asexual and sexual reproduction in Stemphylium eturmiunum by DJ-1 stimulation of the PI3K/AKT signaling pathway","authors":"Shi Wang, Xiaoman Liu, Chenlin Xiong, Susu Gao, Wenmeng Xu, Lili Zhao, Chunyan Song, Xiaoyong Liu, Timothy Y. James, Zhuang Li, Xiuguo Zhang","doi":"10.1007/s13225-023-00528-1","DOIUrl":"https://doi.org/10.1007/s13225-023-00528-1","url":null,"abstract":"<p>Most fungi display a mixed mating system with both asexual and sexual reproduction. The timing of the two modes of reproduction must be carefully coordinated through signal perception and coordination in the cell along with chromatin modification. Here, we investigated coordination of reproductive output by investigating the function of the histone chaperone anti-silencing factor 1 (ASF1) in a fungal species amenable to characterization of both asexual and sexual reproduction. We used knockout approach to show that SeASF1 influenced asexual and sexual reproduction in <i>Stemphylium eturmiunum</i>. SeASF1-deleted strains failed to produce pseudothecia, but produce abnormal conidia and showed an irregular distribution of nuclei in mycelium. Transcriptome sequencing was then used to identify genes with altered expression in the SeASF1-deleted strains. The transcriptional expression of the identified SeDJ-1 was strongly regulated by SeASF1. The interaction of SeDJ-1 and SeASF1 was confirmed using Y2H, Co-IP, and pull-down. Due to some components of phosphatidylinositol 3-kinase/protein kinase B (PI3K/AKT) signaling pathway were known to interact with DJ-1 in mammals, we verified SePI3K, an element of PI3K/AKT signaling pathway in <i>S. eturmiunum</i>, was directly linked to SeDJ-1 and then these two proteins were defined as a coordinator of reproduction. However, knockout of SeDJ-1 or SePI3K altered the asexual and sexual reproduction, but SePI3K recovered the asexual and sexual development of ∆<i>Sedj-1</i>. The SeDJ-1-M6 segment of SeDJ-1 was essential for its interaction with SePI3K and played a critical role in restoring sexual reproduction in the ∆<i>Sepi3k</i>, providing a deep understanding of the regulatory mechanism of SeDJ-1 in <i>S. eturmiunum</i> development. Summarily, SeASF1 is able to trigger SeDJ-1 and SeDJ-1can also activate SePI3K, which is orchestrally involved in asexual and sexual reproduction in <i>S. eturmiunum</i>. All these results reveal that SeASF1 manipulates asexual and sexual reproduction in <i>S. eturmiunum</i> by SeDJ-1 perception of PI3K/AKT signaling pathway. These data highlight the deep similarities in coordinating asexual and sexual processes in both fungi and eukaryotes in general.</p>","PeriodicalId":12471,"journal":{"name":"Fungal Diversity","volume":" December","pages":""},"PeriodicalIF":20.3,"publicationDate":"2023-12-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138481014","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Systematic arrangement within the family Clitocybaceae (Tricholomatineae, Agaricales): phylogenetic and phylogenomic evidence, morphological data and muscarine-producing innovation","authors":"Zheng-Mi He, Zuo-Hong Chen, Tolgor Bau, Geng-Shen Wang, Zhu L. Yang","doi":"10.1007/s13225-023-00527-2","DOIUrl":"https://doi.org/10.1007/s13225-023-00527-2","url":null,"abstract":"<p>The Clitocybaceae is a recently established family. Currently, the infrafamilial divisions and relationships within the family are vague due to limited sampling and genes employed for phylogenetic analysis. Some mushrooms of the family contain the neurotoxic muscarine, which has caused many severe and even deadly poisonings worldwide. However, the taxonomic distribution and evolution of the toxin within the family is largely unknown. In this study, phylogenetic analyses based on nucleotide sequences of ITS and of six molecular loci (ITS, LSU, <i>TEF1</i>, <i>RPB1</i>, <i>RPB2</i> and <i>ATP6</i>), plus a phylogenomic analysis based on 485 single-copy orthologous genes, were performed to reconstruct the framework of Clitocybaceae. BEAST analysis was used to estimate the divergence times within the family. Additionally, biochemical analysis for muscarine was conducted of 32 representative species. Based on these analyses, an updated classification of Clitocybaceae into six genera (<i>Clitocybe</i>, <i>Collybia</i>, <i>Dendrocollybia</i>, <i>Lepista</i>, <i>Pseudolyophyllum</i>, and <i>Singerocybe</i>) is proposed. The genus <i>Collybia</i> is emended to accommodate four subgenera (<i>Collybia</i>, <i>Crassicybe</i>, <i>Leucocalocybe</i>, and <i>Macrosporocybe</i>). Seventeen new Chinese species and 15 new combinations are proposed. Keys to the genera of Clitocybaceae and the subgenera of <i>Collybia</i>, as well as to the known species of <i>Clitocybe</i> and <i>Collybia</i> subgen. <i>Collybia</i> in China, are presented. In addition, muscarine was detected in 18 species, and these muscarine-containing species formed a major monophyletic clade within <i>Collybia</i> subgen. <i>Collybia</i>. Finally, our phylogenetic, phylogenomic, chemotaxonomic and molecular dating results indicate that the Clitocybaceae is a natural group estimated to have arisen some 60 million years ago, and in this family, muscarine has evolved only once circa 20 million years ago without later losses.</p>","PeriodicalId":12471,"journal":{"name":"Fungal Diversity","volume":"71 6","pages":""},"PeriodicalIF":20.3,"publicationDate":"2023-11-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138449723","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}