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Ascomycota: Diversity, Taxonomy and Phylogeny, 3rd Edition

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A special issue of Journal of Fungi (ISSN 2309-608X). This special issue belongs to the section "Fungal Evolution, Biodiversity and Systematics".

Deadline for manuscript submissions: closed (31 January 2026) | Viewed by 13609

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Prof. Dr. Jian-Kui Liu

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School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 611731, China
Interests: fungal diversity; fungal taxonomy; fungal phylogeny; plant pathogen (fungi); ascomycetes
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Special Issue Information

Dear Colleagues,

This Special Issue will be dedicated to Ascomycota, which is the most diverse and species-rich phylum in the Fungi kingdom, comprising ca. 110,000 species. A broad range of life modes such as pathogenic (agriculturally and clinically), saprobic, and endophytic have been extensively studied in Ascomycota. The concept of ‘one fungus, one name’ which was implemented in 2011, influences the nomenclature of pleomorphic taxa in Ascomycota, which reproduce both sexually and asexually. Precise species identification and establishment of generic/species boundaries, which were assisted by DNA-based phylogenetic analyses, resolved most of the confusion in this phylum. One of the topics that changes sporadically is the higher-level classification of Ascomycota, while some other interesting topics among mycologists are current species number, predicted species number, and discovering missing species in Ascomycota. Missing taxa could be discovered in less studied habitats, in species complexes, in biodiversity rich areas, and in existing collections. Recent studies confirmed that unculturable taxa are a vital group that needs to be studied, and environmental sequencing and metagenomics should assist in this regard. Hence, this volume is planned to embrace the aspects of diversity, taxonomy, and phylogeny of Ascomycota by providing timely needed updates to the phylum as well as to identify species from numerous locales all over the world.

Prof. Dr. Jian-Kui Liu
Guest Editor

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Keywords

asexual/sexual morph
classification
fungal ecology
molecular data
morphology
novel taxa
phylogeny

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Related Special Issues

Ascomycota: Diversity, Taxonomy and Phylogeny, 4th Edition in Journal of Fungi
Ascomycota: Diversity, Taxonomy and Phylogeny in Journal of Fungi (19 articles)
Ascomycota: Diversity, Taxonomy and Phylogeny, 2nd Edition in Journal of Fungi (12 articles)

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Research

28 pages, 10512 KB

Open AccessArticle

Sordariomycetes Taxa Associated with Dracaena in Karst Outcrops: Two Novel Species and Five New Host Records from Thailand

by Napalai Chaiwan, Saowaluck Tibpromma, Samantha C. Karunarathna, Dhanushka N. Wanasinghe, Kevin D. Hyde, Nakarin Suwannarach, Ruvishika S. Jayawardena and Itthayakorn Promputtha

J. Fungi 2026, 12(3), 168; https://doi.org/10.3390/jof12030168 - 26 Feb 2026

Viewed by 632

Abstract

Currently, our understanding of the fungi associated with Dracaena species is limited. There is a clear need for more comprehensive information, especially in the context of Thailand. In our study, we collected dead Dracaena leaves with fungal structures from limestone outcrops in seven Thai provinces: Chiang Mai, Kanchanaburi, Krabi, Nakhon Si Thammarat, Ratchaburi, Songkhla, and Tak. The fungi in these samples were isolated and identified using a combination of morphological characteristics and a multi-loci phylogeny (ACT, CHS-1, GAPDH, ITS, LSU, and TUB2). We are thrilled to introduce seven taxa belonging to four families within three orders (Chaetosphaeriales, Glomerellales, and Xylariales). Our detailed morphological descriptions and updated phylogenetic trees of two new species (Zygosporium dracaenae, and Z. dracaenicola) and five new host/geographical records (Colletotrichum dracaenophilum, C. gigasporum, C. truncatum, Malaysiasca phaii, and Neoleptosporella camporesiana) represent a significant step forward in our understanding of this field. Full article

(This article belongs to the Special Issue Ascomycota: Diversity, Taxonomy and Phylogeny, 3rd Edition)

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27 pages, 5092 KB

Open AccessArticle

Cladobotryum rhodochroum sp. nov. (Hypocreales, Ascomycota): A New Fungicolous Species Revealed by Morphology, Phylogeny, and Comparative Genomics

by Anastasia C. Christinaki, Dimitrios Floudas, Antonis I. Myridakis, Zacharoula Gonou-Zagou and Vassili N. Kouvelis

J. Fungi 2026, 12(2), 117; https://doi.org/10.3390/jof12020117 - 6 Feb 2026

Viewed by 863

Abstract

Species of the ascomycetous genus Cladobotryum (Hypocreales, Hypocreaceae) are ecologically and economically important mycoparasites that cause cobweb disease in cultivated and wild mushrooms. Despite their significance as fungal pathogens and producers of bioactive metabolites, the taxonomy of Cladobotryum remains unresolved due to extensive morphological plasticity, complex teleomorph–anamorph connections, and the presence of cryptic species. This study employs an integrative approach combining micro- and macromorphological characterization, multi-locus phylogeny (ITS, rpb2, and tef-1a), and comparative genomics to clarify the taxonomic position of the Greek isolate Cladobotryum sp. ATHUM 6904, previously designated as an unclassified red-pigmented (URP) strain. Phylogenetic analyses demonstrated that URP strains form a distinct, well-supported clade closely related to C. tenue and C. rubrobrunnescens, yet genetically and morphologically distinct from both. Comparative genomic analyses of isolate ATHUM 6904 and the ex-type strains of C. tenue and C. rubrobrunnescens revealed pronounced divergence in transposable element content, mitochondrial genome architecture, gene order, orthologous gene composition, secondary metabolite biosynthetic potential, and overall genomic distance. Micro- and macromorphological comparisons further supported the differentiation of isolate ATHUM 6904 from both reference species. Based on the combined molecular, morphological, and genomic evidence, the Greek isolate ATHUM 6904 is described as a novel species, Cladobotryum rhodochroum sp. nov. Full article

(This article belongs to the Special Issue Ascomycota: Diversity, Taxonomy and Phylogeny, 3rd Edition)

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35 pages, 5754 KB

Open AccessArticle

Novel Freshwater Ascomycetes from Submerged Plant Debris in the Zújar River (Extremadura Community, Spain)

by María Barnés-Guirado, Alberto Miguel Stchigel and José Francisco Cano-Lira

J. Fungi 2026, 12(2), 102; https://doi.org/10.3390/jof12020102 - 31 Jan 2026

Viewed by 759

Abstract

Freshwater fungi remain insufficiently documented in the Mediterranean river systems despite their key roles in organic-matter turnover. Here, we surveyed filamentous fungi associated with submerged decaying plant debris in the Zújar River (Extremadura, southwestern Spain) using a culture-based approach combined with phenotypic characterization and multilocus phylogenetic analyses (ITS, LSU, rpb1, rpb2 and tef-1α). A total of 49 strains were isolated and identified, revealing a diverse assemblage of Ascomycota. Five taxa are described as new to science: Arachnopeziza torrehermosensis, Conioscypha clavatispora, Neoanungitea torrehermosensis, Ophioceras diversisporum and Polyscytalum submersum. Notably, Polyscytalum submersum represents the first record of the genus for the Iberian Peninsula, while Arachnopeziza torrehermosensis, Neoanungitea torrehermosensis and Ophioceras diversisporum constitute the first records of their respective genera for Spain (and Neoanungitea torrehermosensis also for Europe). In addition, phylogenetic evidence supports taxonomic refinements within the orders Magnaporthales and Conioscyphales, including the establishment of Protophioceras to accommodate Ophioceras sichuanense and the establishment of Protoconioscypha for two previously misclassified Conioscypha species. Overall, this first mycological report of submerged plant debris in the Zújar River substantially expands knowledge of freshwater fungal diversity in the region and provides a refined framework for the taxonomy of several lineages of aquatic-associated ascomycetes. Full article

(This article belongs to the Special Issue Ascomycota: Diversity, Taxonomy and Phylogeny, 3rd Edition)

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21 pages, 5298 KB

Open AccessArticle

Morpho-Phylogenetic Evidence Reveals Neokeissleriella gen. nov. and Three Novel Species of Lentitheciaceae from Grasses (Poaceae)

by Yong-Xiu Yu, Asha J. Dissanayake and Jian-Kui Liu

J. Fungi 2026, 12(1), 12; https://doi.org/10.3390/jof12010012 - 24 Dec 2025

Cited by 1 | Viewed by 941

Abstract

The Poaceae family, commonly known as grasses, is one of the most strategically important plant groups on earth. They are globally distributed, found in virtually every terrestrial habitat on earth, from deserts and grasslands to forests and wetlands. An investigation was conducted on the fungi associated with grasses in Sichuan and Guizhou Provinces, China. Based on morphological characteristics and multi-locus phylogenetic analyses (from Maximum Likelihood (ML) and Bayesian Inference (BI)) of combined LSU, SSU, ITS, and tef1-α sequence data, a new genus, Neokeissleriella, and three novel species—Keissleriella guttata, K. sichuanensis, and Neokeissleriella fusispora—were introduced. Two new host records of Keissleriella caraganae, K. yunnanensis and a new geographical record of K. gloeospora in Sichuan Province, China, are reported. To substantiate the newly established taxa, detailed morphological descriptions and illustrations are provided and supported with molecular phylogenetic analysis. This study broadens the understanding of fungal diversity on Poaceae hosts in Sichuan and Guizhou provinces, China, revealing the high potential for identifying novel taxa. Full article

(This article belongs to the Special Issue Ascomycota: Diversity, Taxonomy and Phylogeny, 3rd Edition)

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37 pages, 18947 KB

Open AccessArticle

Diversity of Sordariales Fungi: Identification of Seven New Species of Naviculisporaceae Through Morphological Analyses and Genome Sequencing

by Narumon Tangthirasunun, Valérie Gautier, Christophe Lalanne, Lucas Bonometti, Sandrine Cros-Arteil, Richard D. Hayes, Sarah Calhoun, Robert Riley, Jasmyn Pangilinan, Anna Lipzen, Vivian Ng, Igor V. Grigoriev, Pierre Gladieux, Tatiana Giraud and Philippe Silar

J. Fungi 2025, 11(12), 880; https://doi.org/10.3390/jof11120880 - 12 Dec 2025

Viewed by 1150

Abstract

Thanks to next-generation sequencing (NGS) technologies, the diversity of fungi can now be investigated through the analysis of their genome sequences. Naviculisporaceae is a family within the Sordariales, whose diversity is not well-known, with only one genome sequence published for this family. Here, we report on the isolation and cultivation of 20 new strains of Naviculisporaceae. Their genome sequences, as well as those of the five commercially available strains, were determined, thus providing complete genome sequences for 25 new Naviculisporaceae strains. Species delimitation was conducted using a combination of (1) ITS + LSU phylogenetic analysis of the new isolates along with other known species of the family, (2) comparisons between DNA barcode sequences of the new strains with those of the known species, and (3) average genome-wide nucleotide identity calculation. We built a phylogenomic tree and studied the organization of the mating-type locus. In vitro fruiting was obtained for 16 strains, enabling the definition of seven new species, namely Pseudorhypophila gallica, Pseudorhypophila guyanensis Rhypophila alpibus, Rhypophila brasiliensis, Rhypophila camarguensis, Rhypophila reunionensis and Rhypophila thailandica, as well as two new combinations, namely Pseudorhypophila latipes and Pseudorhypophila oryzae. Eight strains for which in vitro fruiting was not obtained may belong to additional new species. These results expand the known diversity of the Naviculisporaceae and greatly enlarge the genomic data available for the family. Full article

(This article belongs to the Special Issue Ascomycota: Diversity, Taxonomy and Phylogeny, 3rd Edition)

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16 pages, 5868 KB

Open AccessArticle

Morphology and Updated Phylogeny Revealed Three New Species in Chlorencoelia (Cenangiaceae, Helotiales) from China

by Huan-Di Zheng and Wen-Ying Zhuang

J. Fungi 2025, 11(12), 855; https://doi.org/10.3390/jof11120855 - 1 Dec 2025

Viewed by 1086

Abstract

Morphological and molecular phylogenetic studies of Chlorencoelia in China revealed three novel species, which are described and illustrated as C. biguttulata, C. ellipsoidea, and C. sinensis. Chlorencoelia biguttulata is characterized by greyish green to blackish green hymenium surface, clavate tomentum hyphae on receptacle surface, and inequilateral ellipsoidal ascospores having two large guttules and 8.5–14.5 × 3.5–4.5 μm. Chlorencoelia ellipsoidea differs from the known species by distinctly stipitate apothecia with a dark green hymenium surface and ellipsoidal ascospores 7.2–9.1 × 3.5–4.2 μm. Chlorencoelia sinensis is characterized by substipitate apothecia, blackish receptacle surface, and fusoidal ascospores 9–13.7 × 2.2–3.5 μm. Sequence analyses of the ITS region supported recognition of them as separate species. All three new species occurred on rotten wood in montane forests. Morphological features for species delimitation and diversity of Chlorencoelia are discussed. An identification key to the known species of the genus is provided. Full article

(This article belongs to the Special Issue Ascomycota: Diversity, Taxonomy and Phylogeny, 3rd Edition)

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34 pages, 9872 KB

Open AccessArticle

Global Diversity, Host Associations, and New Insights into Aigialaceae, Astrosphaeriellaceae, and Pseudoastrosphaeriellaceae

by Danushka S. Tennakoon, Nimali I. de Silva, Ning Xie and Sinang Hongsanan

J. Fungi 2025, 11(12), 834; https://doi.org/10.3390/jof11120834 - 25 Nov 2025

Viewed by 1603

Abstract

During a survey of plant litter-associated microfungi in Guangdong and Jiangxi Provinces, China, several specimens that have carbonaceous ascomata were collected. Morphological characteristics combined with multi-gene (LSU, SSU, and tef1-α) phylogeny revealed that they belong to the Aigialaceae, Astrosphaeriellaceae, and Pseudoastrosphaeriellaceae families. Phylogenetic analyses were conducted using Maximum Likelihood (ML) and Bayesian Inference (BI) approaches. Caryospora pruni and Pseudoastrosphaeriella zingiberacearum are introduced as new species, and Astrosphaeriella bambusae, C. quercus, Fissuroma caryotae, and Neoastrosphaeriella aquatica are introduced as new host records. In addition, Caryospora minima is synonymized under C. aquatica based on close morphological and phylogenetic relationships. All the newly introduced species fit well with their respective generic concepts and can be distinguished from closely related species in their morphology and DNA molecular data. The new host records also provide similar morphological characteristics to their respective type species, and multi-gene phylogeny analyses also offer evidence for their placements. In addition, we compiled the geographical distribution and host associations of species in Aigialaceae, Astrosphaeriellaceae, and Pseudoastrosphaeriellaceae. This provides a database for future studies to understand the ecological interactions and geographical variations. Full article

(This article belongs to the Special Issue Ascomycota: Diversity, Taxonomy and Phylogeny, 3rd Edition)

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20 pages, 10422 KB

Open AccessArticle

Metagenomic Insights into Disease-Induced Microbial Dysbiosis and Elemental Cycling Alterations in Morchella Cultivation Soils: Evidence from Two Distinct Regions

by Zong-Lin Deng, Feng-Ming Yu, Xiang Ma, Qi Zhao and Jian-Kui Liu

J. Fungi 2025, 11(9), 663; https://doi.org/10.3390/jof11090663 - 10 Sep 2025

Viewed by 1433

Abstract

Soil-borne diseases represent a major constraint on the sustainable cultivation of morel mushrooms (Morchella spp.), yet the microbial ecological mechanisms driving disease occurrence and progression remain poorly understood. In this study, we conducted comparative metagenomic analyses of rhizosphere and root-adhering soils associated with healthy and diseased Morchella crops from two major production regions in China, aiming to elucidate shifts in microbial community composition, assembly processes, and functional potential. Disease conditions were linked to pronounced microbial dysbiosis, with community assembly shifting from stochastic to deterministic processes, particularly within fungal communities under host selection and pathogen pressure. Co-occurrence network analysis revealed substantial reductions in connectivity, modularity, and clustering coefficients in diseased soils, indicating the loss of ecological stability and keystone taxa. Functional annotations using CAZy, COG, and KEGG databases showed that healthy soils were enriched in genes related to carbohydrate metabolism, aerobic respiration, and ecosystem resilience, whereas diseased soils exhibited higher abundance of genes associated with stress responses, proliferation, and host defense. Furthermore, elemental cycling analysis demonstrated that healthy soils supported pathways involved in aerobic carbon degradation, nitrogen fixation, phosphate transport, and sulfur oxidation, while diseased soils favored fermentation, denitrification, phosphorus limitation responses, and reductive sulfur metabolism. Collectively, these results highlight the importance of microbial functional integrity in maintaining soil health and provide critical insights into microbiome-mediated disease dynamics, offering a foundation for developing microbiome-informed strategies for sustainable fungal crop management. Full article

(This article belongs to the Special Issue Ascomycota: Diversity, Taxonomy and Phylogeny, 3rd Edition)

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21 pages, 5077 KB

Open AccessArticle

Seven New Series and Four New Species in Sections Subinflati and Trachyspermi of Talaromyces (Trichocomaceae, Eurotiales)

by Lu-Yao Peng, Xin-Cun Wang, Yusufjon Gafforov and Wen-Ying Zhuang

J. Fungi 2025, 11(7), 508; https://doi.org/10.3390/jof11070508 - 4 Jul 2025

Cited by 4 | Viewed by 2239

Abstract

Species of Talaromyces C.R. Benj. are valuable biological resources for human beings as competent producers of enzymes, antibiotics, antifungal agents and biopigments, but a comprehensive taxonomic system at the series level has not been fully provided for this genus. In this study, three new series, Palmarum, Resedani and Subinflati, are proposed in section Subinflati. Section Trachyspermi is also restructured to include five series, in which Diversi, Erythromelles, Miniolutei and Resinarum are newly erected, and Trachyspermi is emended. Additionally, four new species are discovered: T. elephas, T. sinensis and T. xishuangbannaensis isolated from rotten fruit husk in Yunnan Province, China, belonging to the series Erythromelles, Subinflati and Miniolutei, respectively, and T. tianshanicus from soil in Uzbekistan, located in ser. Diversi. Morphological distinctions, including colony characteristics, conidiophore structures, and conidial morphologies, along with phylogenetic analyses based on multi-locus datasets (ITS, BenA, CaM and RPB2), confirm their novelty to science. Detailed descriptions and illustrations of the new species are given. The proposed classification of Talaromyces at the series level provides a refined infrageneric framework and facilitates taxonomic stability and future biodiversity studies. Full article

(This article belongs to the Special Issue Ascomycota: Diversity, Taxonomy and Phylogeny, 3rd Edition)

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17 pages, 3695 KB

Open AccessArticle

Molecular Characterisation of Fusarium Species Causing Common Bean Root Rot in Uganda

by Samuel Erima, Moses Nyine, Richard Edema, Allan Nkuboye, Nalule Habiba, Agnes Candiru and Pamela Paparu

J. Fungi 2025, 11(4), 283; https://doi.org/10.3390/jof11040283 - 3 Apr 2025

Cited by 2 | Viewed by 1995

Abstract

Recently, Fusarium root rot (FRR)-like symptoms were observed in Uganda’s agroecology zones, prompting the National Agricultural Organisation (NARO) to conduct a disease survey. The survey reports indicated FRR as the second most prevalent root rot disease of common bean in Uganda after Southern blight. Ninety nine Fusarium spp. strains were obtained from samples collected during the surveys. The strains were morphologically and pathogenically characterised and confirmed to cause Fusarium root rot as observed in the field. However, molecular characterization of the strains was not conducted. In this study, therefore, 80 of the strains were characterized using partial sequences of translation elongation factor 1-alpha (TEF-1α) gene, beta tubulin (β tubulin) gene and internal transcribed spacers (ITS) region of ribosomal RNA to determine species diversity. High-quality Sanger sequences from the target genes were compared to the sequences from Fusarium species available in the National Centre for Biotechnology Information coding sequences (NCBI-CDS) database to determine the most likely species the strains belonged. The sequences from our strains were deposited into the NCBI gene bank under ID#288420, 2883276, 2873058 for TEF-1α, β tubulin and ITS respectively. The Fusarium species identified included; F. oxysporum, F. solani, F. equiseti F. delphinoides, F. commune, F. subflagellisporum, F. fabacearum, F. falciforme, F. brevicaudatum, F. serpentimum, F. fredkrugeri and F. brachygibbosum. The diversity of these Fusarium species needs to be taken into consideration when developing breeding programs for management of the disease since currently there is no variety of common bean resistant to FRR in Uganda. Full article

(This article belongs to the Special Issue Ascomycota: Diversity, Taxonomy and Phylogeny, 3rd Edition)

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