Akira Hashimoto's research while affiliated with Bioresource Research Centre and other places
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Antherospora vaillantii is an anther smut fungus that was originally considered occurring on Muscari spp. around the world; however, cryptic species were revealed during recent taxonomic investigations, thus emphasizing the importance of host specificity. In Japan, A. vaillantii was identified on Barnardia japonica in 1936. Although the recent revelations indicate that it may be part of a complex based on the host plant genus, the phylogenetic placement of this Japanese species is currently unresolved. In this investigation, seven specimens of the A. vaillantii complex were collected from the Kanto area of Japan, and six new single teliospore isolates were established. Molecular phylogenetic analyses based on the internal transcribed spacer sequences and large subunit nuclear ribosomal DNA (28S) region indicated that the new samples formed a monophyletic clade with other Antherospora spp. among Floromycetaceae lineage. Our samples were separated from other known species of Antherospora and formed a robust monophyletic clade in any analysis. Detailed morphological observations revealed that the new samples could be distinguished from other known Antherospora species. As a result, it is proposed that Antherospora barnardiae can accommodate B. japonica parasites.
The generic variety and habitats of Camptophora species, generally known as black yeasts have not been clarified. Here, we re-evaluated Camptophora based on morphological observations and phylogenetic analyses. Because investigations on Camptophora relied only on a few strains/specimens, twenty-four Camptophora -related strains were newly obtained from 13 leaf samples from various plant species to redefine the generic and species concepts of Camptophora . Their molecular phylogenetic relationships were examined based on the small subunit nuclear ribosomal DNA (nSSU, 18S rDNA), internal transcribed spacer rDNA operon (ITS), large subunit nuclear ribosomal DNA (LSU, 28S rDNA), β-tubulin ( tub ), the second largest subunit of RNA polymerase II ( rpb2 ), and mitochondrial small subunit DNA (mtSSU). Single- and multi-locus analyses using SSU-ITS-LSU- rpb2 -mtSSU revealed a robust phylogenetic relationship among Camptophora within the Chaetothyriaceae. Camptophora can be distinguished from other chaetothyriaceous genera by its snake-shaped conidia with microcyclic conidiation and loosely interwoven mycelial masses. Based on the results of the phylogenetic analyses, two undescribed lineages were recognised, and Ca. schimae was considered to be excluded from the genus. ITS sequence comparison with environmental DNA (eDNA) sequences revealed the distribution of the genus limited to the Asia-Pacific region. Camptophora has been isolated or detected from abrupt sources, and the reason for this was inferred to be their microcycle. Mechanisms driving genetic diversity within species are discussed with respect to their phyllosphere habitats.
Harmoniella junipericola, a new hyphomycete inhabiting on leaf litter of Juniperus chinensis (Cupressaceae) in Japan is described based on morphological characters on natural substrates and in culture and phylogenetic analyses using the sequences of internal transcribed spacer (ITS), large subunit nrRNA gene (LSU; 28S), DNA-directed RNA polymerase I largest subunit gene (RPB1), and DNA-directed RNA polymerase II second largest subunit gene (RPB2). The fungus belongs to the monotypic/monogeneric family Strobiloscyphaceae (one genus with two species; Pezizales) typified by Strobiloscypha. Brief notes are added on morphological and ecological comparisons among H. chrysocephala (type species, in Ukraine), H. campanaensis (in Chile), and H. junipericola. Using the ITS sequences deposited in the DNA Data Bank, additional operational taxonomic units (OTUs) of Harmoniella and phylogenetically related sequences are briefly discussed based on the data from East Asia (Japan, China), Middle East (Israel), Europe (France, Italy, Portugal), and North America (USA).
Antherospora vaillantii is an anther smut fungus that was originally considered occurring on Muscari spp. around the world; however, cryptic species were revealed during recent taxonomic investigations, thus emphasizing the importance of host specificity. In Japan, A. vaillantii was identified on Barnardia japonica in 1936. Although the recent revelations indicate that it may be part of a complex based on the host plant genus, the phylogenetic placement of this Japanese species is currently unresolved. In this investigation, seven specimens of the A. vaillantii complex were collected from the Kanto area of Japan, and six new single teliospore isolates were established. Molecular phylogenetic analyses based on the internal transcribed spacer sequences and large subunit nuclear ribosomal DNA (28S) region indicated that the new samples formed a monophyletic clade with other Antherospora spp. among Floromycetaceae lineage. Our samples were separated from other known species of Antherospora and formed a robust monophyletic clade in any analysis. Detailed morphological observations revealed that the new samples could be distinguished from other known Antherospora species. As a result, it is proposed that A. barnardiae can accommodate B. japonica parasites. The evolutionary processes of Floromycetaceae in relation to their Asparagaceous host plants have also been carefully discussed. Based on the morphological observations of the basidiospore ontogenic patterns, the familial concept of Floromycetaceae was redefined.
The phylogenetic affinities of four representative Endocalyx taxa at the species and variety levels are studied based on materials collected on different palm hosts in Japan and the states of Hawaii and Texas, USA. They include specimens and their isolates belonging to E. cinctus, E. indumentum, E. melanoxanthus var. grossus, and E. melanoxanthus var. melanoxanthus. Phylogenetic analyses of nuclear ribosomal DNA sequence data (ITS-LSU nrDNA) confirmed that Endocalyx belongs to the order Xylariales (Sordariomycetes) where all species and varieties treated form a strongly supported monophyletic lineage within the family Cainiaceae. They were also phylogenetically well resolved and consistent with their morphological and ecological circumscription. Species status is proposed for E. melanoxanthus var. grossus under the name E. grossus comb. et stat. nov. on the basis of its distinct morphological, molecular, cultural, and ecological characteristics. The putative placement of Endocalyx within the family Apiosporaceae (Amphisphaeriales), based on the presence of basauxic conidiophores, is rejected considering that all species treated clustered within the distant Cainiaceae (Xylariales). This characteristic mode of conidiophore elongation is determined to have evolved independently within distantly related ascomycetous lineages. Novel morphological and cultural features of Endocalyx taxa based on new isolates are described and commented. The recently
described E. metroxyli is reduced to a synonym with E. melanoxanthus.
The diversity of sporocarp-inhabiting fungi (SCIF) was examined using six samples of xylarialean fungi from two different forests in Ibaraki Prefecture, Japan: a moist forest in the Sakuragawa area and an urban dry forest in the Tsukuba area. These fungi were enumerated using direct observation and dilution plate methods. We obtained 44 isolates, and careful morphological and molecular phylogenetic studies of these isolates revealed that approximately 30% of the operating taxonomic units were undescribed or cryptic species related to known fungi. Although typical mycoparasitic fungi, such as helotialean fungi and Trichoderma spp., were not isolated, the genera Acremonium, Acrodontium, and Simplicillium were detected. Comparisons of SCIF communities between the two forests suggested that the number of isolated species in the Sakuragawa area was lower than that in the Tsukuba area. Soil-borne fungi, such as Aspergillus, Beauveria, Penicillium, and Talaromyces, or polypores/corticioid mushrooms, are frequently detected in the Tsukuba area. Factors affecting SCIF communities in the two forests are discussed. Some noteworthy fungi are briefly described with notes on taxonomy, ecology, and molecular phylogeny.
Recent publications have argued that there are potentially serious consequences for researchers in recognising distinct genera in the terminal fusarioid clade of the family Nectriaceae. Thus, an alternate hypothesis, namely a very broad concept of the genus Fusarium was proposed. In doing so, however, a significant body of data that supports distinct genera in Nectriaceae based on morphology, biology, and phylogeny is disregarded. A DNA phylogeny based on 19 orthologous protein-coding genes was presented to support a very broad concept of Fusarium at the F1 node in Nectriaceae. Here, we demonstrate that re-analyses of this dataset show that all 19 genes support the F3 node that represents Fusarium sensu stricto as defined by F. sambucinum (sexual morph synonym Gibberella pulicaris). The backbone of the phylogeny is resolved by the concatenated alignment, but only six of the 19 genes fully support the F1 node, representing the broad circumscription of Fusarium. Furthermore, a re-analysis of the concatenated dataset revealed alternate topologies in different phylogenetic algorithms, highlighting the deep divergence and unresolved placement of various Nectriaceae lineages proposed as members of Fusarium. Species of Fusarium s. str. are characterised by Gibberella sexual morphs, asexual morphs with thin- or thick-walled macroconidia that have variously shaped apical and basal cells, and trichothecene mycotoxin production, which separates them from other fusarioid genera. Here we show that the Wollenweber concept of Fusarium presently accounts for 20 segregate genera with clear-cut synapomorphic traits, and that fusarioid macroconidia represent a character that has been gained or lost multiple times throughout Nectriaceae. Thus, the very broad circumscription of Fusarium is blurry and without apparent synapomorphies, and does not include all genera with fusarium-like macroconidia, which are spread throughout Nectriaceae (e.g., Cosmosporella, Macroconia, Microcera). In this study four new genera are introduced, along with 18 new species and 16 new combinations. These names convey information about relationships, morphology, and ecological preference that would otherwise be lost in a broader definition of Fusarium. To assist users to correctly identify fusarioid genera and species, we introduce a new online identification database, Fusarioid-ID, accessible at www.fusarium.org. The database comprises partial sequences from multiple genes commonly used to identify fusarioid taxa (act1, CaM, his3, rpb1, rpb2, tef1, tub2, ITS, and LSU). In this paper, we also present a nomenclator of names that have been introduced in Fusarium up to January 2021 as well as their current status, types, and diagnostic DNA barcode data. In this study, researchers from 46 countries, representing taxonomists, plant pathologists, medical mycologists, quarantine officials, regulatory agencies, and students, strongly support the application and use of a more precisely delimited Fusarium (= Gibberella) concept to accommodate taxa from the robust monophyletic node F3 on the basis of a well-defined and unique combination of morphological and biochemical features. This F3 node includes, among others, species of the F. fujikuroi, F. incarnatum-equiseti, F. oxysporum, and F. sambucinum species complexes, but not species of Bisifusarium [F. dimerum species complex (SC)], Cyanonectria (F. buxicola SC), Geejayessia (F. staphyleae SC), Neocosmospora (F. solani SC) or Rectifusarium (F. ventricosum SC). The present study represents the first step to generating a new online monograph of Fusarium and allied fusarioid genera (www.fusarium.org).
The phylogenetic affinities of four representative Endocalyx taxa, including three species and two varieties, are studied based on materials collected on different palm hosts in Japan and the states of Hawaii and Texas, USA. They include specimens and their isolates belonging to E. cinctus , E. indumentum , E. melanoxanthus var. grossus and E. melanoxanthus var. melanoxanthus . Phylogenetic analyses of nuclear ribosomal DNA sequence data (ITS-LSU nrDNA) confirmed that Endocalyx belongs to the order Xylariales (Sordariomycetes) where all species and varieties treated form a strongly supported monophyletic lineage within the family Cainiaceae. They were also phylogenetically well resolved and consistent with their morphological and ecological circumscription. Species status is proposed for E. melanoxanthus var. grossus under the name E. grossus comb. et stat. nov. on the basis of its distinct morphological, molecular, cultural and ecological characteristics. The putative placement of Endocalyx within the family Apiosporaceae (Amphisphaeriales) based on the presence of basauxic conidiophores is rejected considering that all species treated clustered within the distant Cainiaceae (Xylariales). This characteristic mode of conidiophore elongation is determined to have evolved independently within unrelated or distant ascomycetous lineages. Novel morphological and cultural features of Endocalyx taxa based on new isolates are commented. The recently described E. metroxyli is reduced to synonym with E. melanoxanthus .
The resinicolous fungi Sarea difformis and S. resinae (Sareomycetes) were taxonomically revised on the basis of morphological observations and phylogenetic analyses of the nucleotide sequences of the nSSU-LSU-rpb1-rpb2-mtSSU genes. The results of phylogenetic analyses show that S. difformis and S. resinae are grouped with members of Xylonomycetes. According to the results of phylogenetic analyses and their sexual and asexual morphs resemblance, Sareomycetes is synonymized with Xylonomycetes. Although Tromera has been considered a synonym of Sarea based on the superficial resemblance of the sexual morph, we show that they are distinct genera and Tromera should be resurrected to accommodate T. resinae (= S. resinae). Xylonomycetes was morphologically re-circumscribed to comprise a single family (Xylonaceae) with four genera (Sarea, Trinosporium, Tromera, and Xylona) sharing an endophytic or plant saprobic stage in their lifecycle, ascostroma-type ascomata with paraphysoid, Lecanora-type bitunicate asci, and pycnidial asexual morphs. Phylogenetic analyses based on ITS sequences and environmental DNA (eDNA) implied a worldwide distribution of the species. Although Symbiotaphrinales has been treated as a member of Xylonomycetes in previous studies, it was shown to be phylogenetically, morphologically, and ecologically distinct. We, therefore, treated Symbiotaphrinales as Pezizomycotina incertae sedis.
... Newly generated sequences and their closest hits in GenBank were selected and downloaded to build separate datasets for Sporidesmiaceae and Chaetosphaeriaceae, including additional sequences from Bao et al. (2021), Réblová et al. (2022), and Wu and Diao (2022) (Ronquist et al. 2012). Analyses were run following the settings outlined in Delgado et al. (2022). Separate phylogenies were topologically compatible for the most part (Supplementary Information Figs. ...
... A. luzulae was identified as one of the most common fungi in spruce samples, which is known as a cosmopolitan saprotrophic species of fungicolous fungi or plant decomposers [115]. The fungus was isolated from dead Luzula sylvatica leaves in England, rust on Carex sp. in Netherlands, and from Annulohypoxylon sp. and Hypoxylon sp. in Japan [115,116]. ...
... The genomic DNA was obtained following the CTAB protocol recommended by O'Donnell et al. [16] and diluted with 100 µL PCR grade water (Lonza) and stored at −18 • C for further use. Translation elongation factor (TEF1-α) and the second largest protein subunit of RNA polymerase II (RPB2) genes were amplified using the primers, EF1/EF2 and RPB2-5f2/fRPB2-7cr, respectively [17]. The PCR reaction mixture contained 5 µL of buffer (10X Green Buffer, DreamTaq Green DNA Polymerase, Thermo-Scientific, Waltham, MA, USA), 2 µL of dNTPs mixture (10 mM each, Thermo Scientific, Waltham, MA, USA), 1 µL of forward and reverse primers (10 pmol·µL −1 ), 0.25 µL of Taq polymerase (DreamTaq Green DNA Polymerase, Thermo-Scientific), 39.75 µL PCR grade water and 1 µL genomic DNA (100 ng·µL −1 ). ...
... The L+LE topology was first recovered by Beimforde et al. 16 using representatives of three of the seven lineages we recovered as Lichinomycetes. Hashimoto et al. 25 recovered all seven lineages in the topology we recover here but focused on the position of Xylonomycetes without exploring the implications of a monophyletic group sibling to LE. In the only two genome-scale studies to include relevant taxa, Shen et al. 5 and Li et al. 26 Given that lineages recovered here as part of the lichinomycete clade have been widely sampled, how did it go overlooked for so long? ...
... Regarding the molecular data characterizing this species, only one Japanese specimen collected from Chloranthus serratus Roem & Schult has been used to obtain nucleotide sequences of the internal transcribed spacer (ITS) regions, large subunit (LSU), and MCM7 genes of rDNA in phylogenetic studies of Erysiphaceae [6]. Here, we describe the morphological characteristics of the holomorph and indicate the phylogenetic position of the fungus based on newly obtained sequences from Korean specimens. ...
... The Longiostiolaceae was introduced by Phukhamsakda et al. (2020) to accommodate Longiostiolum and Crassiperidium. These genera were introduced by Li et al. (2016) and Matsumura et al. (2018), respectively, as Pleosporales genera incertae sedis. Wanasinghe et al. (2020) updated the taxonomic placement for Shearia in Longiostiolaceae by designating a neotype for S. formosa. ...
... A third of the novel taxa (7/21) listed in Table 1 were isolated from various subcutaneous infections or ulcerative skin lesions and include novels species in Alternaria (11), Gloniopsis (12), Knoxdaviesia (13), and Microascus (14) and the only novel genus described during this period, with three isolates of Gambiomyces profunda from clinical specimens (15). Similarly, four of the species listed in Table 1 were associated with cases of keratitis and included two novel taxa in each of the genera Curvularia (16) and Diaporthe (17). While Curvularia spp. ...
... Thambugala et al. (2015) accepted 16 genera in this family, including eleven new genera. Subsequently, another 13 genera, viz., Crassiclypeus, Desertiserpentica, Flabellascoma, Kiskunsagia, Lentistoma, Leptoparies, Lophiomurispora, Magnopulchromyces, Neopaucispora, Neovaginatispora, Parapaucispora, Pseudopaucispora, and Pseudocapulatispora were introduced to Lophiostomataceae (Wanasinghe et al. 2018Hashimoto et al. 2018;Crous et al. 2019;Mapook et al. 2020;Yuan et al. 2020;Maharachchikumbura et al. 2021). However, Wijayawardene et al. (2022) listed only 28 genera under Lophiostomataceae, including Decaisnella and Quintaria, but excluding Desertiserpentica, Lophiomurispora, and Magnopulchromyces. ...
... A comprehensive study of the genera in Pleosporales was carried out by Zhang et al. (2012), based on morphological studies of the type specimens coupled with phylogenetic analyses. Consequently, the taxonomic treatment of numerous Pleosporales was updated by various authors, based on polyphasic taxonomic approaches, mainly using morphology-phylogeny-based taxonomy (Ariyawansa et al. 2014(Ariyawansa et al. , 2015aPhookamsak et al. 2014Phookamsak et al. , 2015Tanaka et al. 2015;Thambugala et al. 2015;Boonmee et al. 2016;Jaklitsch and Voglmayr 2016;Jaklitsch et al. 2016aJaklitsch et al. , b, 2018Su et al. 2016;Chen et al. 2017;Hashimoto et al. 2017;Wanasinghe et al. 2017a, b). Even though novel taxa of Pleosporales have been dramatically increasing over the last ten years after the taxonomic circumscription provided by Zhang et al. (2012) and Hyde et al. (2013), there is still over a quarter of the total known species lacking molecular data and/or reliable phylogenetic markers for clarifying the placements in Pleosporales. ...
... Neohendersoniaceae was established by Giraldo et al. (2017) to accommodate a monotypic genus Neohendersonia typified by N. kickxii. The study conducted by Tanaka et al. (2017) accepted four genera, namely Brevicollum, Crassiparies, Medicopsis, and Neohendersonia in Neohendersoniaceae. Subsequently, Muriformispora and Neomedicopsis were assigned to this family (Crous et al. 2019, de Silva et al. 2022. ...
