Pestalotiopsis-like taxa encompass a diverse group of fungi that are often associated with plant diseases, unique ecological interactions such as endophytism, and the production of novel chemical metabolites. Traditionally, classifying pestalotiopsis-like taxa has been challenging due to their significant phenotypic plasticity and the overlapping morphological characteristics among species. Identifying certain isolates at the species level remains problematic, or even impossible, with current DNA sequencing methods, which highlights issues with defining species boundaries. To refine species boundaries, we integrated evidence from single-gene phylogenies (ITS, tef1, and tub2), multi-gene phylogenetic analyses combined with species delimitation methods (GCPSR—genealogical concordance phylogenetic species recognition; PTP—Poisson tree processes; mPTP—multi-rate Poisson tree processes; ABGD—automatic barcode gap discovery; and ASAP—assemble species by automatic partitioning), and genomic metrics including average nucleotide identity (ANI) and the proportion of shared core gene clusters within the pangenome. Two novel species, Neopestalotiopsis camelliae and Pseudopestalotiopsis dasymaschalonis, are introduced based on integrative analyses. Evidence of over-splitting was detected across all three genera. Consequently, five species complexes—Pe. adusta species complex, Pe. brassicae species complex, Pe. clavata species complex, Pe. rosea species complex, and Ps. cocos species complex—are established to accommodate lineages that form monophyletic clades in both multi-gene and genome-scale phylogenies but exhibit short internal branches, low statistical support, and indistinct species boundaries. Furthermore, 28 species are synonymized, including seven in Neopestalotiopsis, 18 in Pestalotiopsis, and three in Pseudopestalotiopsis. Overall, our findings highlight the necessity of integrating genomic evidence with traditional phylogenetic approaches to achieve reliable species delimitation and prevent taxonomic inflation in pestalotiopsis-like fungi.

Euglenids are an important group of free-living phototrophic, osmotrophic, or phagotrophic protists, with most of the phylogenetic diversity represented by phagotrophs. One major subgroup of phagotrophs is the petalomonads: rigid, often relatively small cells with few pellicle strips (usually 4-8). They have been proposed to be sisters to other euglenids, a pivotal evolutionary position supported by multigene phylogenies. Most described petalomonads are assigned to either Petalomonas or Notosolenus; however, neither is monophyletic, and existing genera clearly do not reflect phylogenetic diversity within petalomonads. We report 14 Petalomonas or Notosolenus-like isolates and characterize them using light microscopy, scanning electron microscopy (for most), and SSU rDNA phylogenetics. Most isolates branch in/with three of the five known major clades within petalomonads; however, a new major clade is revealed that houses an isolate identified as Petalomonas poosilla, plus five freshwater Notosolenus isolates, including the type species Notosolenus apocamptus. Overall, we report five new species, plus five new combinations that transfer Notosolenus-like species assigned to other clades to two new genera, Tonotosolenus and Unotosolenus. Over half of the isolates are monoprotistan cultures, markedly increasing the availability of tractable petalomonads for examining euglenid biology in a comparative evolutionary framework.

Abstract Inonotus is a hymenochaetoid genus with worldwide distribution, known for its wood-decaying species. Since Karsten proposed it in 1879, significant revisions have been made to its circumscription, and several species complexes are currently being reevaluated through integrative taxonomic approaches. Although rare, some species in the genus have a described anamorphic stage. Historically, dense, ferruginous, pulvinate masses of chlamydospores attached to trunks and branches have been attributed to Ptychogaster cubensis , the anamorph of Inonotus rickii . However, during a survey of wood-inhabiting fungi in Central Brazil, similar structures were found on living and dead trees. Long-term observations revealed that the fungus grew annually on the same host and adjacent trees and exhibited an ecological relationship with beetles that fed on its structures and dispersed chlamydospores to nearby hosts. The collected sporomata were isolated and characterized morphologically and phylogenetically using ITS, LSU, RPB2 , and TEF1-α partial sequences. Based on these analyses, we describe a new species represented in its anamorphic stage, Inonotus cerradensis sp. nov. The new species is characterized by sporomata formed by beard-like rhizomorphs bearing dense clusters of globose, soft, fragile chlamydospores that easily disintegrate upon touch, rhizomorphs cylindrical to flattened, with superficial outward-projecting and hyphal setae. We also conducted a detailed review of specimens representing both stages of I. rickii to refine its morphological circumscription. Both species form distinct and well-defined clades within Inonotus s. str. and differ mainly in sporomata organization: loose, rhizomorph-supported structures characterize the new species, whereas compact, stratified, and concentrically organized sporomata correspond to the anamorph of I. rickii . This study highlights how integrative taxonomy clarifies species boundaries within Inonotus and advances the understanding of the genus and its ecology in Neotropical environments.

Poales is one of the largest orders of monocotyledonous plants, comprising families such as Cyperaceae, Poaceae, and Typhaceae. These plant families dominate the macrophytes found in tropical lentic and lotic wetlands habitat in Prachuap Khiri Khan Thailand. This study investigated microfungi associated with wetland-dwelling Poales and revealed taxa belonging to Chaetomiaceae, Naviculisporaceae, Pleurotheciaceae, and Schizotheciaceae in Sordariomycetes were prominent. Submerged and decaying plant material from Cyperaceae and Typhaceae were gathered from the Pran Buri marshlands and the Pran Buri River, Thailand. The spatial distribution of the locations was significantly influenced by fluctuations in ocean water levels. Fungal characterization was performed using morphological analysis and multigene phylogeny, incorporating nuclear ribosomal DNA (ITS, LSU, SSU) and protein-coding loci (rpb2, tub2, tef1-α). This study introduces two novel species, Corynascus fluvialis and Pseudorhypophila hyalibasiconica from Carex sp. along with two new host records: Dematipyriforma aquilariae from Typha sp. and Triangularia allahabadensis from Carex sp. Pseudorhypophila hyalibasiconica is characterized by ovoid to limoniform upper cells and a hyaline conical lower cell. Corynascus fluvialis differs from other members of Corynascus by possessing angular pedicellate asci, and ascospores with a single apical germ pore. The comparisons using morphology and phylogeny of newly described taxa are provided. This study investigates the role of sustainably managed forests in the conservation of terrestrial ecosystems.

Introduction Caloneis egena is a species of diatom originally described from Campeche Bay (Mexico) that is regarded as cosmopolitan, with several reports from the Pacific region. Methods A strain of diatom from the genus Caloneis was isolated from the Gulf of Tomini, Sulawesi (Indonesia). It was subjected to an integrated approach combining microscopy, genomic analyses, and phylogeny. Results Although looking similar to C. egena , the strain from Tomini was found to be a new species, hereby described as Caloneis paraegena sp. nov. The complete mitochondrial and plastid genomes were sequenced and annotated and represent the first organellar genomes made available for the genus Caloneis . The multigene phylogeny inferred from these results positions C. paraegena as sister to a clade that associates Caloneis fontinalis , C. silicula , and C. lewisii . Discussion A survey of the literature dedicated to C. egena led to questioning its distribution, suggesting that records from the Pacific region might, in fact, represent C. paraegena based on morphology. Because of the absence of a molecular reference for C. egena , the exact relationship between these two species remains to be verified.

In this article, we describe a new cave‐associated fungus belonging to Nectriaceae (Hypocreales), collected from the air in Swallow Cave, Yunnan Province, China. Initial morphological observations confirmed that our collection exhibits characteristics typical of an acremonium‐like species. Phylogenetic analyses of the combined internal transcribed spacer (ITS), large subunit ribosomal RNA (LSU), and β‐tubulin ( TUB ) sequence dataset confirmed that our fungus forms an independent lineage within Paracremonium , sister to P. bendijkiorum , P. apiculatum , and P. variiforme . Based on morphology and multigene phylogeny, we describe our fungus as a new species, Paracremonium yunnanense . A comprehensive description, micrographs, and a phylogenetic tree showing the placement of the new species are provided. Moreover, our results contribute to understanding the genus Paracremonium and expand the knowledge of cave‐associated fungi in China.

Increased demand for cultivated oyster mushrooms (Pleurotus species) in Aotearoa New Zealand has led to the importation of exotic species, which pose potential invasion risks. Gaps in taxonomic knowledge of this genus have complicated biosecurity decisions and cultivation efforts. To address this, we collected 84 wild and cultivated New Zealand Pleurotus specimens for multi-locus phylogenetic analysis (ITS, LSU, RPB1, RPB2, and Tef) and morphological examination. We describe Pleurotus pulmonarius var. aotearoa as a new variety indigenous to New Zealand, distinct from imported P. pulmonarius sens. str. We establish that Pleurotus purpureo-olivaceus has no anamorphic stage and falls outside the subgenus Coremiopleurotus, unlike Pleurotus australis, a species sometimes found on living trees. The close monophyletic relationship between P. parsonsiae and Pleurotus djamor underscores the need to reconsider the presence of the exotic P. djamor in the country. The refined species boundaries between the indigenous P. australis, P. parsonsiae, P. pulmonarius var. aotearoa and P. purpureo-olivaceus have important implications for conservation and biosecurity, and support the potential of using indigenous strains for cultivation in New Zealand.

Hydnum species are called "hedgehogs" or "tooth fungi" because of their spinose hymenophores. Considering its edible and ectomycorrhizal nature, Hydnum has been found to possess high economic and ecological values. In the present study, a multi-gene (ITS-nLSU-tef1α) phylogenetic analysis and detailed morphological observations of the genus Hydnum were carried out. Based on the distinctive morphological characteristics and the phylogenetic evidence, two new species were described: H. flosculoides sp. nov. and H. robustum sp. nov. from China. Moreover, ITS is the most frequently used DNA region for identification of Hydnum species, but its effectiveness is uncertain. A total of 1,293 ITS sequences of Hydnum could be attributed to six subgenera and four clades with uncertain position (Clade Insulana and Incertae sedis 1, 2, 3), representing 84 morphologically and phylogenetically identified species, 14 putatively new phylospecies and 17 singletons. Furthermore, two new species were described and provided with illustrations. The morphological characters, phylogenetic delimitation, geographic distribution and habitat preferences of Hydnum were discussed, and the effectiveness of the ITS region was also evaluated to enhance rapid identification.

Abstract Omethidae are a small family of soft‐bodied beetles, which are classified in the superfamily Elateroidea. The family is composed of 13 extant and one fossil genera and 69 species described from the Americas and East Asia. Members of Omethidae have a particularly heterogeneous morphology, with current members originally described in Cantharidae, Drilidae, Lampyridae, Telegeusidae and Phengodidae. Morphological and molecular‐based phylogenetic hypotheses are still highly divergent, with morphology‐based phylogenies recovering Telegeusinae related to Phengodidae, and multigene phylogenies recovering Telegeusinae as closely related to Omethidae. We implemented a genome skimming sequencing approach to produce genomic data for representatives of all Omethidae subfamilies. The resulting dataset is the first phylogenomic study produced for the family. Our results corroborated previous multigene phylogenies, and recovered Omethidae sister to Artematopodidae, and Telegeusinae as a subfamily of Omethidae, and also rejected the relationships of Telegeusinae with Phengodidae. In contrast to previous molecular‐based hypotheses, Driloniinae were recovered as a sister group to the remaining Omethidae, rendering the following topology: (Artematopodidae + (Driloniinae + (Telegeusinae + (Omethinae + Matheteinae)))). We reviewed the family and presented an updated diagnosis for Omethidae and its subfamilies, as well as identification keys for the subfamilies and genera, and a checklist for all described extant and extinct species.

Morphology and multigene phylogeny uncover association of new Pestalotiopsis allied genera with grey leaf blight disease of coconut (Cocos nucifera) in India

The morphology, morphogenesis, and multi-gene phylogeny of a new hypotrich, Stichotricha koreana sp. nov., from a temporary pond in Gangneung-si, South Korea, were investigated. The new species inhabits a gelatinous lorica that is often branched, forming a colony. Diagnostic features include two frontal cirri, one buccal cirrus, a short parabuccal row, two frontoventral cirral rows, a single marginal row on each side, and three dorsal kineties, each with a caudal cirrus. The frontoventral rows, marginal rows, and dorsal kineties spiral by half to one turn around the long body axis. Detailed morphogenesis is documented in the genus for the first time: the oral primordium arises close to the left frontoventral row; the parental adoral zone is fully retained; frontoventral rows, both marginal rows, and all dorsal kineties develop at two levels via within-row anlagen formation; and the parabuccal row originates from the oral primordium. Phylogenetic analyses of 18S rDNA place Stichotricha koreana sp. nov. within Chaetospiridae, forming a sister group to members of the family Gonostomatidae and the core urostylids. A concatenated rDNA gene dataset shows that Chaetospiridae is sister to hypotrichs with gonostomatid oral apparatus. These data refine the diagnosis of Chaetospiridae and confirm the generic assignment of S. koreana sp. nov.

Multi-gene phylogeny and morphological study reveal three new species of Amanita in the Russian Far East

Pyracantha fortuneana (H. L. Li, Rosaceae), valued for ornamental and ecological uses, is widely distributed in southern/southwestern China. Its polysaccharides exhibit antioxidant and anticancer potential, driving commercial juice development (Yao et al. 2020). On 10 October 2024, fruit rot symptoms were observed on P. fortuneana at Qujing Normal University, Yunnan, China (25.52°N, 103.75°E). Symptomatic fruits displayed circular to subcircular black lesions; internal tissues were necrotic and brown. Disease incidence averaged 10.4% ± 2.07% (SD) across 500 fruits from five replicates (100 fruits each). Pathogen isolation utilized four replicate 9-cm PDA plates. Three lesion-margin fragments (0.2 × 0.5 cm) per replicate were surface-sterilized (75% ethanol, 4 min), triple-rinsed in sterile water, and incubated at 28 °C in darkness. Hyphal tips from emerging white mycelia were transferred to PDA medium plate after 24 h. Colonies developed gray-green centers with regular white margins within 3 days, covering plates fully by day 9. Nine morphologically similar strains were isolated; a representative (BHB) was characterized morphologically and molecularly. After 14 days, colonies produced solitary or catenate conidia (5.28–13.52 μm × 8.90–28.38 μm; mean 8.66 × 15.50 μm, n=50). Conidia were pyriform to elliptical, with 1–6 transverse and 0–1 longitudinal septa, exhibiting slight septal constrictions, consistent with Alternaria spp. (Simmons 2007). For molecular identification, genomic DNA was extracted, and eight loci were amplified/sequenced: SSU (NS1/NS4), LSU (LSU1Fd/LR5), ITS (ITS1/ITS4), TEF1 (EF1-728F/EF1-986R), Alt a 1 (Alt-for/Alt-rev), EndoPG (PG3/PG2b), OPA10-2 (OPA10-2R/OPA10-2L), H3 (H3-1a/H3-1b) (Zhang et al. 2023; Zheng et al. 2015). Sequences (SSU: PQ895780; LSU: PQ895777; ITS: PQ895770; TEF1: PV082022; Alt a 1: PV082020; EndoPG: PV092677; OPA10-2: PV092678; H3: PV082021) showed 95–100% homology to Alternaria alternata reference strains (GenBank accessions: PP190241 [1,010/1,010 bp], PP190242 [858/858 bp], PP189927 [544/544 bp], PP196558 [251/252 bp], PP196559 [462/481 bp], PP196560 [439/439 bp], PP196561 [670/702 bp], ON375577 [407/407 bp]). Maximum-likelihood and Bayesian phylogenetic analyses (PhyloSuite v1.2.3) using concatenated loci placed BHB within the A. alternata clade. Combined morphology and multigene phylogeny identified BHB as A. alternata. Pathogenicity was confirmed by inoculating needle-wounded fruits with mycelial plugs and conidial suspensions (1×10⁶ conidia/ml). Unwounded fruits inoculated with suspensions/plugs served as positive controls; needle-wounded fruits treated with sterile water were negative controls. After 7 days, lesions matching field symptoms developed on all plug-inoculated fruits (wounded/unwounded), but only on wounded suspension-inoculated fruits. Negative controls remained symptom-free. Reisolation from lesions yielded cultures morphologically and molecularly identical to A. alternata. To our knowledge, this is the first report of A. alternata causing P. fortuneana fruit rot in China. These findings provide critical insights for monitoring disease spread and developing control strategies.

IntroductionThe genus Trichoderma encompasses cosmopolitan fungi that play key ecological and biotechnological roles, including mycoparasitism, plant growth promotion, and tolerance to abiotic stress. As the catalog of undescribed species continues to expand, the need for precise species delimitation is increasingly evident.MethodsIn this work, we isolated strain BMH-0061 as a root endophyte of chili (Capsicum annuum) and assessed its phenotypic and antagonistic potential. This strain originated from Mexico’s milpa agroecosystem, an underexplored reservoir of microbial diversity. To robustly evaluate its taxonomic status, we generated a near-complete, telomere-to-telomere genome assembly and assessed its completeness with BUSCO. Subsequently, we evaluated a comprehensive set of genomic coherence metrics, including Average Nucleotide Identity (ANI), Average Amino Acid Identity (AAI), Percentage of Conserved Proteins (POCP), and k-mer composition.ResultsIntegrative phylogenomic analyses, supported by Bayesian speciation models and clustering-based comparisons, consistently recovered BMH-0061 as an independent lineage. The strain exhibited broad-spectrum mycoparasitism against phytopathogens and tolerance to moderate abiotic stress. Morphological characterization, growth profiles, and multi-gene phylogenies suggested its placement within the Trichoderma genus, but it is distinct from known species. A near-complete telomere-to-telomere genome assembly was obtained, showing a BUSCO completeness of 99.08%. Genomic coherence analyses revealed that strain BMH-0061 shared ANI values ranging from 83.93% to 94.43% with its closest Trichoderma relatives, supporting its distinction as a separate lineage.DiscussionWe formally describe this new taxon as Trichoderma tlahuicanensis sp. nov., in honor of the indigenous pre-Hispanic Tlahuica people of Morelos, Mexico. Our work demonstrates how a phylophenetic framework, combining genomic, phylogenetic, genetic diversity, and evolutionary analyses, provides a powerful approach to species delimitation. This integrative strategy confirms the recognition of T. tlahuicanensis as a distinct species while offering a methodological pathway for peers engaged in fungal systematics

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.

A paper by Johnston and others published in 2019 provided three Leotiomycetes-wide phylogenies, one based on genomes, one a multigene phylogeny with up to 15 genes, and one based on ITS sequences. The genomic and multigene phylogenies provided a backbone phylogeny for the class that has proven to be robust, providing a phylogenetically stable concept for the large order Helotiales. However, a lack of genomic data for the clades outside of Helotiales, towards the root of the tree, meant that relationships in this part of the tree remained somewhat poorly resolved. The ITS phylogeny, although phylogenetically much less informative, provided a wider taxon coverage, focussing on the type species of genera not otherwise treated for which ITS data was available. This paper treats genera listed as Leotiomycetes in the Outline of Fungi 2024. It incorporates newly available DNA sequence data and taxonomic changes, especially for genera, families, and orders published since 2019, into the 2019 multigene and ITS analyses. The genomic phylogeny is not updated. Citation: Johnston PR, Park D (2025). An updated multigene phylogeny of Leotiomycetes. Persoonia 55: 527-566. doi: 10.3114/persoonia.2025.55.13.

A 40-year taxonomic enigma: multigene phylogeny resolves the polyphyly of <i>Plectranthias</i> (Perciformes: Anthiadidae) and supports a revised taxonomy

Morpho-cultural and molecular characterization based on multigene phylogeny of Colletotrichum truncatum associated with leaf blight of linseed (Linum usitatissimum L.)

The whole genome of fungal isolate EMM_F5, isolated from the phyllosphere of Magnolia grandiflora, was sequenced, assembled, and annotated. Preliminary phylogenomic analysis places EMM_F5 in the Cystobasidiomycetes class within Basidiomycota fungi, with multigene phylogenies placing it in Microsporomycetaceae family.

Ranunculi ternati Radix is a perennial herb of Ranunculaceae Ranunculus plant Ranunculus ternatus Thunb.. It is the only medicinal plant of the buttercup genus included in the 1977 edition of the Chinese Pharmacopoeia. As an important traditional medicinal plant,Ranunculus ternatus Thunb. is rich in organic acids, sugars, esters, sterols, volatile oils,alkaloids, flavonoids, triterpenoids, total saponins and other components. It is mainly distributed in Guangxi, Taiwan, Jiangsu, Zhejiang, Jiangxi, Hunan, Anhui, Hubei, Henan another provinces in China. In November of 2024, a severe outbreak of Ranunculus ternatus Thunb. soft rot disease occurred in Lichun Town, Pengzhou City, Sichuan Province of China (103°10′-103°40′ E, 30°54′-31°26′ N), causing symptoms such as water-soaked lesions on stems and leaves that turn brown and rot inward. Affected plants gradually wilt, defoliate, emit a foul odor, and eventually die (Figure 1). In a field of 0.8 ha,the disease incidence was 30% . Symptomatic samples were surface sterilized in 75% ethanol for 30 seconds and then in 2% NaClO for 60 seconds. After sterilization, the samples were rinsed three times with sterile water and dried on sterilized filter paper. The samples were then cut into pieces and suspended in sterile water. Finally, the suspension was spread onto culture plates containing nutrient agar medium (NA) and incubated for 2 days at 28 °C in the dark. Representative strain (fy02-1) was convex, circular with smooth margins on NA medium. The bacteria were gram-negative, short straight rods, 0.5 to 0.9 × 1.5 to 3.0 μm, single polar flagellum. The bacterium grew at temperatures up to 42 °C. The purified bacterial strain was inoculated into NA liquid medium and cultured at 28°C for 18-24 h. The bacterial concentration was adjusted to 108 CFU/mL with sterile water, and 20 μL was injected into the stem base of Ranunculus ternatus Thunb., with sterile water as the control. The plants were grown under conditions of 28°C and 70% humidity, and disease symptoms were observed, with the color, size, location, and severity of lesions recorded at different stages of disease development. Symptoms appeared on the second day after inoculation, with initial lesions appearing brown. By the third day, the entire plant had rotted and withered, while the control group showed no symptoms (Figure 2). Pathogenic bacteria was reisolated from the infected plants, confirming Koch’s postulates and the pathogenicity on Ranunculus ternatus Thunb. For bacterial species identification, a single-colony culture was subjected to genomic DNA extraction, gene amplification, and sequencing of 16S rRNA, rpoD, and gyrB. The universal primers 27F/1492R (Lane 1991) were used to amplify the 16S rRNA gene, and the specific primers 70F/70R and UP-1E/APrU (Hwang et al. 2005) were used to amplify the rpoD and gyrB genes, respectively. In the BLAST analysis, the 16S rRNA sequence (GenBank PV926360.1) of the isolate shared 99% similarity (1428/1527 bp) with the Pseudomonas fluorescens strain MFAF76a (KT350501.1), and the rpoD ( PV963828.1) and gyrB (PV963827.1) sequences showed &gt;98% identity to rpoD (695/1260 bp; KT350504.1) and gyrB (657/940 bp; KT350502.1) of the P. fluorescens strain MFAF76a. Based on the multigene phylogeny, the isolated bacterium was identified as P. fluorescens. P. fluorescens has also been shown to cause certain plant diseases, such as stem rot disease on melon (Zhang et al. 2016), bacterial head rot on broccoli (Li et al. 2009), and head rot on Brassica oleracea convar. botrytis var. italica (Catore et al. 2007). As far as we know, this is the first report of P. fluorescens causing Ranunculus ternatus Thunb. soft rot disease in China. Soft rot caused by P. fluorescens may be a threat to Ranunculus ternatus Thunb. cultivation,and this report of its occurrence is the first step in determining potential spread and effective control measures.