The genus Micromonospora, a globally distributed actinomycete inhabiting diverse ecosystems, is widely recognized for its remarkable biosynthetic capacity and role as a prolific source of bioactive natural products. However, the members of the genus Micromonospora from extreme environments remain largely unstudied. In this study, we isolated 15 Micromonospora spp. strains from samples collected in desert and marine habitats. Based on polyphasic taxonomy approaches eight strains were identified and represent four novel species. Genome mining of the newly isolated strains revealed substantial biosynthetic potential for terpenes (n = 70, 22.9% of total biosynthetic gene clusters [BGCs]) and polyketides (n = 60, 19.6% of total BGCs). Subsequent pan-genomic analysis identified substantial numbers of terpene-related (n = 745, 33.8% of total biosynthetic genes [BGs]) and polyketide-related (n = 728, 33.0%) BGs in the core genome, highlighting their core biosynthetic potential. To further investigate their metabolic capacity, fermentation and metabolomic profiling were conducted to assess the secondary metabolite production capacity of all 15 strains. The results revealed a diverse array of alkaloids (averaging 75.3, 33.4% of total annotated secondary metabolites) and amino acid-derived peptides (averaging 56.3, 25.0% of total). These findings also highlight significant metabolic variations among strains and underscore the pivotal role of fermentation conditions in shaping their metabolic profiles. This study advances the taxonomic and functional understanding of Micromonospora spp. and presents a multi-omics framework combining genome mining and metabolomics to explore the biosynthetic potential of wild-type strains from extreme habitats.

Gene loss is a widespread phenomenon in species evolution, yet the evolutionary significance of large-scale gene loss—whether arising through neutral processes or adaptive evolution—remains a subject of ongoing debate. Agaricus bisporus, a globally distributed macrofungus, serves as an ideal model to investigate this phenomenon. Utilizing the “map-to-pan” method, we constructed a high-resolution pangenome comprising 30 793 genes and 143 Mb of additional sequences, including 21 370 genes absent in the reference genome. Phylogenetic and admixture analyses identified four genetic lineages: the globally distributed MIX and region-specific European, America, and Highland lineages. Core gene analyses revealed a substantially lower genetic load in MIX lineage, accompanied by a marked reduction in the frequency of deleterious mutations compared with other lineages. Presence–absence variation (PAV) analyses further demonstrated extensive gene loss in MIX lineage, with functional enrichment analyses associating these PAVs with DNA damage repair pathways. This finding suggests that gene loss could enhance tolerance to DNA damage, thereby mitigating mutation accumulation. A significantly higher proportion of lost PAVs in MIX lineage was under selective pressure, supporting gene loss as an adaptive strategy. Our findings highlight two key mechanisms facilitating the MIX lineage's broad distribution: (1) the reduction of deleterious mutations, thereby lowering genetic load, and (2) the selective loss of redundant, non-essential genes, enhancing adaptability across diverse environments. This study not only underscores the adaptive significance of large-scale gene loss in the evolution of A. bisporus but also offers a broader framework for understanding how gene loss events shape the evolutionary trajectories of other fungal species.

In the Mountains of Southwest China (MSC), accelerated diversification triggered by mountain uplift and monsoon intensification in the Miocene is widely revealed, but less is known about the stage after the Pliocene. Thus, the tempo‐spatial evolution of the endemism of Gaoligong Shan (GLGS), a young and isolated mountain with the highest biodiversity in the MSC, was determined. Temporal patterns were inferred by the stem ages of the endemic species and spatial patterns were inferred through ancestral area reconstructions and the distributions of the sister taxa. Temporally, the calibrated origin times of 114 phylogenetically well resolved endemic species (75 plants, 33 animals and six fungi) ranged from the early Miocene to the Holecene. Spatially, 82 centric origin species (mean = 3.08 Ma) were significantly younger than 32 eccentric origin species (6.84 Ma). Eccentric origins accumulated smoothly while centric origins burst after the late Pliocene, especially after the Pleistocene (n = 52). In centric origins, most of the sister taxa showed sympatric (n = 47) or allopatric (n = 23) distributions in the GLGS. The eccentric origins were mainly dispersed from the southern lower latitude region (n = 20). Principle component analysis indicated that niche conservatism exerted greater contribution to the speciation of the endemic species. Uplift of the GLGS and monsoon intensification during the late Pliocene accelerated the formation of its endemism. The “Species pump” effect of the Pleistocene climatic fluctuations is further revealed. Speciation triggered by geological isolation by mountain and river barriers through niche conservatism exceeds adaptive evolution.

The genus Xylaria comprises a diverse group of fungi with a global distribution and significant ecological importance, known for being a source of bioactive secondary metabolites with antibacterial, antioxidative, anticarcinogenic, and additional properties. In this study, we present a comprehensive taxonomic revision of the species of Xylaria found in some parts of southern China, characterized by an extensive multilocus phylogeny analysis based on internal transcribed spacer (ITS), TUB2 (β-tubulin), and DNA-directed RNA polymerase II subunit 2 (rpb2) gene regions. Morphological examination and detailed comparative analyses of the collected specimens were conducted to determine the distinctiveness of each species. The multilocus phylogeny approach allowed us to infer evolutionary relationships and assess species boundaries accurately, leading to the identification of 40 novel Xylaria species hitherto unknown to science. The newly described species are: X. baoshanensis, X. bawanglingensis, X. botryoidalis, X. dadugangensis, X. doupengshanensis, X. fanglanii, X. glaucae, X. guizhouensis, X. japonica, X. jinghongensis, X. jinshanensis, X. kuankuoshuiensis, X. liboensis, X. negundinis, X. orbiculati, X. ovata, X. pseudoanisopleura, X. pseudocubensis, X. pseudobambusicola, X. pseudoglobosa, X. pseudohemisphaerica, X. pseudohypoxylon, X. puerensis, X. qianensis, X. qiongzhouensis, X. rhombostroma, X. serratifoliae, X. shishangensis, X. shuqunii, X. shuangjiangensis, X. sinensis, X. tongrenensis, X. umbellata, X. xishuiensis, X. yaorenshanensis, X. yinggelingensis, X. yumingii, X. yunnanensis, X. zangmui, and X. zonghuangii. The study's findings shed light on the distinctiveness of the newly described species, supported by both morphological distinctions and phylogenetic relationships with their close relatives. This taxonomic revision significantly contributes to our understanding the diversity of Xylaria in China and enriches the knowledge of fungal biodiversity worldwide.

Plants, insects, and fungi have successfully colonized almost all terrestrial ecosystems, and their interactions have been the subject of numerous studies in recent decades. Plant-associated fungi include endophytic, arbuscular mycorrhizal, ambrosia, saprotrophic, pathogenic, and floral fungi. These fungi interact with insects through various mechanisms, including the modification of plant nutritional quality and degradation of plant defensive allelochemicals that are toxic to insects. Additionally, certain fungi assist plants in defending against insect attacks. Correspondingly, insects have evolved sophisticated nervous, digestive, and muscular systems that assist them in recognizing, preying on, and dispersing plant-associated fungi; these organ systems allow insects to detect and respond to various chemical signatures in the environment. Insects can be nourished, attracted, repelled, poisoned, and killed by chemical molecules produced by plant-associated fungi, which could be beneficial or detrimental to plants. This review summarizes the functions of different chemicals from the perspective of plant-fungus-insect interactions and discusses the challenges and future perspectives in this chemical ecology research field.

The unique co-occurrence of thyriothecia belonging to three fossil genera of epiphyllous fungi, Stomiopeltites Alvin & Muir (Micropeltidaceae), Callimothallus Dilcher, and Trichothyrites Rosendahl (Microthyriaceae), are reported on the leaves of the same host plant, Cunninghamia shangcunica Kodrul, Gordenko & Sokolova from the Oligocene Shangcun Formation of the Maoming Basin, South China. In China, Stomiopeltites is identified for the first time, Callimothallus is known from the Oligocene and Miocene of Guangxi and Zhejiang provinces, and Trichothyrites previously has been found only in the Eocene palynological assemblages of the Maoming Basin. The presence of abundant and diverse epiphyllous micromycetes, together with the taxonomic composition of the Shangcun megaflora and pollen assemblage, as well as quantitative climatic estimates obtained using Climate Leaf Analysis Multivariate Program, confirm the existence of a warm and humid climate in this region during the late early Oligocene. The geographic and stratigraphic distributions, comparisons with extant analogues, as well as ecological and paleoclimatic implications of the fossil fungi are discussed.

Since the discovery of the Pleurocordyceps/ “Polycephalomyces” clade unaffiliated with the clades of Clavicipitaceae s. str., Ophiocordycipitaceae, and Cordycipitaceae of clavicipitaceous fungi, some taxa have been published and more fungal material relevant to the group have become available for further study. Here, a multigene phylogeny using nrSSU, nrLSU, tef1, rpb1, and rpb2 was constructed with some of the recently discovered additional taxa using maximum likelihood and Bayesian analyses (BI) to test and refine the current phylogenetic framework for Cordyceps s. lat. and other clavicipitaceous fungi. In addition to the well supported major Pleurocordyceps/“Polycephalomyces” clade revealed previously, another clade with newly added taxa referred to as “Polycephalomyces formosus-like” from Japan was found to be sister to the Pleurocordyceps/“Polycephalomyces” clade. Extensive investigation revealed that strains named “P. formosus-like” grouped in this new clade and do indeed represent the true P. formosus and that species previously included in the genus Polycephalomyces required a new generic name. Based on the phylogenetic analyses and morphological characteristics, including both sexual and asexual morphs when available, the new generic name Pleurocordyceps is introduced and relevant new combinations are made. A newly designated lectotype and a supporting epitype for P. formosus is selected and the circumscription of Polycephalomyces is discussed.

Plants play important roles as habitat and food for a tremendous diversity of specialist animals and fungi. The disappearance of any plant species can lead to extinction cascades of its associated biota. In consequence, documenting the diversity and specificity of plant-associated organisms is of high practical relevance in biodiversity conservation. Here, we present the first large-scale molecular investigation into the diversity, host specificity, and cophylogenetic congruence of an especially rich plant–fungal association, the rust fungi (Pucciniaceae) of Cyperaceae and Juncaceae. Using the largest rust fungi DNA barcoding dataset published to date (252 sequences, 82 taxa), we reject the presence of a global ITS2-28S barcode gap, but find a local gap in Cyperaceae–Juncaceae rusts, and suggest the existence of many cryptic species in North America, with some broadly circumscribed species possibly corresponding to >10 cryptic species. We test previous hypotheses of correlations between the phylogenies of rust fungi and their Cyperaceae–Juncaceae hosts using a combination of global-fit and event-based cophylogenetic methods. A significant cophylogenetic signal is detected between rusts and their hosts, but the small number of cospeciations argues for preferential host jumps as the driving process behind these correlations. In addition, temporal congruence between the origin of major Carex clades and their rusts suggests that host diversification may have promoted parasite diversification. Finally, we discuss the relevance of rust infection patterns to the systematics of Cyperaceae, highlight some taxonomic problems uncovered by the analyses, and call attention to the promise of DNA barcoding for bridging knowledge gaps in poorly studied plant-associated microorganisms.

The genus Phaeolus holds significant economic and ecological value as an important pathogen of coniferous trees. Although species diversity within this genus has been described in recent years, there were limited studies of its origin, evolution, and biogeography. In this study, we collected new specimens from China and the United States, and reconstructed the phylogeny, divergence times, and biogeography of Phaeolus based on internal transcribed spacers (ITS) and nuclear large ribosomal subunit (nLSU) sequences. Phylogenetic analyses identified two new species, Phaeolus himalayanus and Phaeolus occidentiamericanus, one new combination, Phaeolus hispidoides, one synonym, Phaeolus fragilis (treated as Phaeolus schweinitzii), and one new record from China, Phaeolus sharmae. Phaeolus himalayanus is characterized by pileate, imbricate basidiomata, round to irregular pores of two to three per millimeter, abundant gloeoplerous hyphae, mango-shaped to ellipsoid basidiospores (5.5–7 × 4–4.5 µm), and distribution in Xizang of China. Phaeolus occidentiamericanus is characterized by pileate, imbricate basidiomata, round to irregular pores of two to three per millimeter, mango-shaped to ellipsoid basidiospores (6.5–7.8 × 4–5 µm), and distribution in the western United States. Molecular clock analyses indicated that the genus Phaeolus likely originated in the Late Cretaceous, with species divergence occurring between 9–71 Ma. Ancestral state reconstruction suggested that the genus originated in the Himalaya–Hengduan Mountains region and subsequently dispersed to Europe and North America. The earliest host trees of Phaeolus were probably Abies and Pinus, with all known species capable of growing on Pinus, demonstrating a strong host trees preference. Additionally, a key of the genus Phaeolus is added. This study provides a crucial foundation in pathogen control and ecological conservation of this genus in the future.