Fungal Diversity最新文献

The burgeoning accumulation of genomic data in recent years has revolutionized our understanding of fungal phylogenies and classifications. However, the genomic era also brings new challenges, as phylogenetic incongruences make the appearance of monophyly in some phylogenetic trees questionable. Existing criteria for constructing taxonomic systems, such as diagnostic characters and divergence time, become insufficient to address this challenge. Through order-level analyses of genomic data of the Subkingdom Dikarya within the Kingdom Fungi, we introduce the extended quadripartition internode certainty (EQP-IC) value as a novel criterion for constructing high-level fungal classifications, with a recommended threshold of 0.1 for each taxonomic rank. Suprageneric taxa with an EQP-IC value exceeding 0.1 exhibit reduced topological variation, suggesting a stronger correspondence with natural taxonomic category. This new criterion was also put into practice to investigate the derived suborders of mushroom-forming Agaricales, including three suborders, Agaricineae, Pluteineae, and Tricholomatineae (APT), that had been long-standing problems in phylogenetic analyses. In total, 142 genomes, including 64 newly generated ones, were utilized to reconstruct the phylogenetic relationships and delve into the phylogenetic incongruencies and evolutionary histories of APT. Our data suggested widespread and high-level incomplete lineage sorting (ILS) and introgression/hybridization (IH) present among suborders within the APT. Therefore, a dichotomous phylogenetic tree may not reflect the real relationships among the clades within the APT. Instead, their natural relationships may be reticulate. Three newly named suborders, Amanitineae, Macrocystidiineae, and Omphalinineae are added to the clade including APT. The new combination Baisuzhenia humphreyi, new genus Baisuzhenia, new family Baisuzheniaceae, and new suborder Baisuzheniineae are proposed to accommodate Stereopsis humphreyi, which shows an independent, but close relationship, with the clade formed by the six above-mentioned derived suborders of Agaricales.

A complete taxonomic and phylogenetic study on corticioid and hydnoid (Hymenochaete and Hydnoporia) Hymenochaetaceae was carried out. Phylogenetic analyses were based on multigenes including the internal transcribed spacer regions (ITS), the large subunit of nuclear ribosomal RNA gene (nLSU) and the small subunit mitochondrial RNA gene (mtSSU). The mtSSU of Hymenochaete was amplified for the first time. A total of 660 sequences from 354 specimens representing 316 species was used in the phylogenetic analyses, of which 290 sequences were newly generated, including 125 ITS, 89 nLSU and 76 mtSSU sequences. Among 354 specimens, 297 represent 160 taxa from Hymenochaete and Hydnoporia. In this study, 44 new species, including five new species of Hydnoporia as Hydnoporia cinnamomea, H. conifera, H. fulvimarginata, H. imbricata and H. radiata, and 39 new species of Hymenochaete as Hymenochaete adnata, H. alpina, H. asiatica, H. atrobrunnea, H. austrosinensis, H. brunnea, H. cinerea, H. cinereoalba, H. conifericola, H. cylindrospora, H. dichotoma, H. erastii, H. flava, H. granulata, H. hainanensis, H. hubeiensis, H. leveillei, H. iliensis, H. luteomarginata, H. major, H. membranacea, H. moniliformis, H. montana, H. niveomarginata, H. piceae, H. puerensis, H. ramicola, H. rubrobrunnea, H. setulohypha, H. sichuanensis, H. stereoidea, H. subepichlora, H. subfissurata, H. subinnexa, H. subluteobadia, H. subrhabarbarina, H. variabilis, H. vitellina and H. vivida, are described. Illustrated descriptions, voucher specimens, hosts, distribution and remarks for these 44 new species are provided. The phylogenetic analyses confirmed that the two genera Hymenochaete and Hydnoporia formed two distinct clades within the Hymenochaetaceae. The phylogenetic relationships and morphological distinctions between these two genera are also discussed. This study recognizes 249 species in Hymenochaete and Hydnoporia and a worldwide annotated checklist is provided.

Diaporthales is an important group of fungi widely distributed worldwide as endophytes, pathogens, and saprobes on the various plants. Here, we collected and isolated 209 strains of the Diaporthales and then employed morphological characteristics and advanced techniques such as multigene phylogenetics, genomic phylogenetics, molecular clock estimates, and metabolic pathways annotations to explore the evolutionary diversification and metabolic pathways within the Diaporthales. Firstly, our study confirmed that Diaporthales occurred early with a mean stem age of 181.5 Mya and a mean crown age of 157.7 Mya. Secondly, two new families, Sinodisculaceae fam. nov. and Ternstroemiomycetaceae fam. nov., were introduced based on morphology, phylogeny, and divergence times. Thirdly, we further described multiple novel taxa or records including Anadiaporthostoma gen. nov. (Diaporthostomataceae), Lunatospora gen. nov. (Sinodisculaceae), Microphaeotubakia gen. nov. (Tubakiaceae), Neoplagiostoma gen. nov. (Pseudoplagiostomataceae), and Ternstroemiomyces gen. nov. (Ternstroemiomycetaceae), 55 new species, three new species complexes, 32 new host records, and three new combinations. Furthermore, we accepted 35 families within the Diaporthales based on analysis of multiple evidences. Additionally, high activity in universal pathways such as purine metabolism and ribosome across the order suggested a fundamental for robust growth and stress response in Diaporthales. These findings enrich fungal biodiversity and provide critical insights into the evolutionary processes in these communities.

Fungal endophytes have generally been considered as hidden microorganisms that reside asymptomatically within plant tissues and have been exploited for their potential in medicine and plant pathology. They are ubiquitous and associated with nearly all plant species sampled. Even though the exact roles of endophytic fungi within a plant is yet to be established, many speculate that they play important roles in obtaining nutrients and thus improve plant growth, confer plant immunity and promote resistance against biotic and abiotic stresses. It has been postulated that endophytes can exhibit different lifestyles and can even switch lifestyle (i.e., from endophytic to pathogenic or saprobic depending upon plant growth stages). However, there is limited evidence as to whether this switch really happens in vivo. Along the same line, with increasing knowledge of endophytic diversity, defining endophytes has not been easy given their multifaceted functions. The present study provides an updated account with comprehensive knowledge on several aspects including problems with existing definitions, isolation and identification techniques, theoretical and experimental evidence of the role of endophytes, contribution to fungal diversity as well as agenda for future research avenues. For years there has been a number of controversies and debates surrounding as to what exactly is an endophyte. Most of the previous definitions were ephemeral in nature and rather vague and could not realistically define an endophyte. Taking into account numerous biological aspects, we propose herein that endophytes can be defined as “asymptomatic microbial partners that are intimately associated and co-inhabit within healthy internal plant tissues with the ability to confer benefits, co-evolve and alter their lifestyle depending upon plant life stages and adverse conditions”. We also discuss the evolution of endophytes based on fossil data and their co-evolution with their host partners. Studies on fungal endophytes have relied mostly on culture-dependent methods to enable their characterization. However, it is generally well known that these methods suffer drawbacks and there is a need to address the challenges associated with lack of sporulation to enable morphological characterization, slow growth on artificial media, as well as contamination issues. These issues are discussed and addressed in detail here. The molecular mechanisms underlying endophytic colonization, avoidance of plant defense mechanisms, lifestyle changes, as well as their genomics and transcriptomics, are also reviewed. We analyze the possibility of endophytes being host-specific or associated with certain hosts and finally provide an account of their economic importance. This outline of fungal endophytes will provide a more comprehensive understanding of endophytes and can serve for boost research into the exploration and their potential applications in the future.

This paper represents the fifth One Stop Shop (OSS) series contribution. This series provides background, disease symptoms, pathogen biology and epidemiology (when available) distribution, hosts for the treated genera, and important gene regions for a better resolution. Species that have pathogenic data are also provided under each genus. This fifth OSS paper treats 25 genera of phytopathogenic fungi: Allophoma, Alternaria, Bipolaris, Boeremia, Calonectria, Calophoma, Campylocarpon, Clonastachys, Corynespora, Cryphonectria, Diaporthe, Diplocarpon, Epicoccum, Eutiarosporella, Ganoderma, Hypomyces, Lasiodiplodia, Monilinia, Neocordana, Phragmidium, Pileolaria, Pseudocercospora, Rhynchosporium, Scytalidium and Sphaeropsis.

Ips is a genus of bark beetles found throughout the Northern Hemisphere, many of which are highly destructive to coniferous forests and plantations. Fungal symbionts, especially ophiostomatoid fungi, have contributed to the success of Ips bark beetles. Recently, climate change accelerated tree mortality caused by bark beetles and their fungal symbionts. However, the knowledge of ophiostomatoid fungi associated with Ips bark beetles is inadequate in China. Therefore, this study investigated the ophiostomatoid fungal communities associated with different Ips bark beetles from various coniferous forest areas of China. A total of 14,512 ophiostomatoid fungal strains were isolated from 1265 vigorous adult beetles and 826 fresh galleries belonging to 11 Ips species infesting 16 coniferous tree species, including pines, spruces, and larches, from 42 sampling sites in nine provinces or autonomous regions in northeast, northwest and southwest China. Based on a combination of morphological features and phylogenetic analysis, 71 taxa belonging to eight genera were identified (Ceratocystiopsis, Graphilbum, Grosmannia, Leptographium, Masuyamyces, and Ophiostoma in Ophiostomatales; Endoconidiophora and Graphium in Microascales), of which 38 species were described as new. Comparing patterns of fungal assemblages indicated that fungal symbionts genetically co-differentiated with their vectors. Host trees possibly reinforce the coarse species-specific association between ophiostomatoid fungi and Ips bark beetles. This study further demonstrates the high diversity of ophiostomatoid fungi associated with Ips bark beetles and provides insights into their symbiotic associations.

Hyphomycetes are asexually reproducing parts in a fungal life cycle, and is an artificial classification. Hyphomycetes are fungi with diverse lifestyles, including saprobes, endophytes, plant and animal pathogens, hyperparasites, lichenized forms and extremophiles. Traditionally, morphological characters have been used to identify and classify hyphomycetes, which has led to many taxonomic controversies. Modern molecular methods based on DNA sequence data have developed a more reliable and natural classification of hyphomycetes. The present study revises the taxonomy of the brown-spored hyphomycetes based on both morphology and phylogeny. In total, 1,041 genera with brief notes are provided. Of these, 1,032 genera belong to Ascomycota (Dothideomycetes: 362; Eurotiomycetes: 34; Leotiomycetes: 22; Pezizomycetes: 7; Sordariomycetes: 210; Ascomycota genera incertae sedis: 397), and nine genera belong to Basidiomycota. In addition, 363 brown-spored hyphomycetous genera published since 2010 are listed. Multi-locus phylogeny, including 658 brown-spored hyphomycete genera within Ascomycota, are carried out using 28S nrDNA, 18S nrDNA and RNA polymerase II second largest subunit (rpb2), and the results show that 374 genera are phylogenetically placed in Dothideomycetes, 39 genera in Eurotiomycetes, 26 genera in Leotiomycetes, 6 genera in Pezizomycetes and 213 genera in Sordariomycetes. Based on the morphology and multi-gene phylogeny, 45 fresh collections are described in this study, including seven new genera, viz. Murihylinia, Pseudobrachysporiella, Saprosporodochifer, Solitariconidiophora, Tenebrosynnematica, Xenoberkleasmium, Xenostanjehughesia; 17 new species, viz. Acrodictys thailandica, Alfaria fusiformis, Conioscypha punctiformis, Gamsomyces breve, Murihylinia guizhouensis, Parafuscosporella atricolor, Pleocatenata thailandica, Polyplosphaeria appendiculata, Pseudobrachysporiella pyriforme, Saprosporodochifer fuscus, Solitariconidiophora guizhouensis, Sporidesmiella obovoidispora, Stachybotrys ellipsoidea, Tenebrosynnematica obclavata, Vanakripa obovoidea, Xenoberkleasmium chiangraiense, Yunnanomyces muriformis; one new combination, viz. Xenostanjehughesia polypora; nine new records, viz. Aquatisphaeria thailandica, Bahusandhika indica, Corynespora submersa, Fusariella sinensis, Helicodochium aquaticum, Pleopunctum ellipsoideum, Rhexoacrodictys erecta, Vikalpa dujuanhuensis, Virgaria nigra. Detailed descriptions and morphological illustrations are provided for these new taxa. Current taxonomic difficulties are discussed.