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Although Xylaria hypoxylon is one of the most familiar fungi of temperate regions, the basionym of the
name, Clavaria hypoxylon of Linnaeus, has remained untypified. Here we assess the original five elements included in the 1753 protologue; no candidate specimen was located but two illustrations Linnaeus cited were considered, one a mixture of spec...
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Context 1
... Ehret. tab." would appear to be a reference to illustrations in a work of either Micheli or Ehret. We could not locate this name in Micheli (1729: 104), where he uses the descriptive phrase "Lichen Agaricus, nigricans, lingo adnacens, plreumque multifidus, & compressus, ima parte villosus, summa vero glaber, albidus, & pulvenulentus Tab. 15. fig. 55" for what is clearly the species of concern as: (a) he cites Ray (1724: 15) amongst numerous synonyms, and (b) the illustration indicated shows white horn-like apices of the stromata with perithecia in the lower ...Context 2
... Linnean binominal had sanctioned status under the Code as Fries (1823: 327; Fig. 5) adopted the name Sphaeria hypoxylon (L.) Pers. 1796. Fries recognized three infraspecific taxa, of which the first is pertinent here. The literature on such a common fungus had grown considerably since the time of Linnaeus, and Fries cites 18 works, including many references to plates and also to several exsiccatae, herbals, and 17 th ...Similar publications
Four new Keratinophyton species (Ascomycota, Pezizomycotina, Onygenales), K. gollerae, K. lemmensii, K. straussii, and K. wagneri, isolated from soil samples originating from Europe (Austria, Italy, and Slovakia) are described and illustrated. The new taxa are well supported by phylogenetic analysis of the internal transcribed spacer region (ITS) r...
Citations
... To then extend synonymy to citations by the sanctioning author further increases the likelihood for error manyfold: without examining either the author's specimen or the specimen he cites, a sanctioner cannot be expected to form consistently accurate opinions of their identity, let alone true synonymy, from his desk. As long as such errors can be corrected, making the sanctioner's citations a valid alternate source for original material may produce a felicitous selection, where the author's material falls short (e.g., Stadler & al. 2014) or is missing. However, legislating that such material, with a built-in markedly elevated likelihood for error, is an obligAToRy choice for typification (Art. ...
Comparison of the protologue of Agaricus umbellifer L. with specimens and descriptions of the basidiolichen Lichenomphalia umbellifera (L.) Redhead & al. revealed that the epithet umbellifera was grossly misapplied to the basidiolichen, causing several major conflicts with Linnaeus’s species concept. In the region where Linnaeus collected A. umbellifer we discovered a species of Marasmius sect. Epiphylli, congruent with Linnaeus’s protologue. Because M. sect. Epiphylli arises from an evolutionary pathway divergent from that leading to Marasmius s. str., we erected a new genus, Owingsia, to accommodate it, and recombined A. umbellifer as O. umbellifera, type species of the genus, naming our collection epitype for this species. Molecular studies cemented the concinnity of A. umbellifer with our collection: O. umbellifera is the most common of several similar species in a complex prevalent in Lapland, where Linnaeus first encountered it, and in the complex, O. umbellifera shares the pileal shape of its lectotype and most closely resembles it regarding stipe length, is widely distributed beyond the regions where Linnaeus found it, encompassing the regions of its lecto- and epitype, and sharing substrates with both. The earliest legitimate description of the basidiolichen previously known as L. umbellifera is A. pseudoandrosaceus Bull., a name superseded by the sanctioned later synonym, A. ericetorum Pers. We recombined this basionym as L. ericetorum, and epitypified it with a modern sequenced specimen.
... Among the dominant genera, Clavaria (also known as Xylaria) and Oryza were detected in summer samples. Clavaria was one of the most common fungi in temperate regions (Stadler et al. 2014), and some had high nutritional and biological activity (Sharma and Gautam 2017). However, a small amount of this genus in summer samples was found. ...
In recent years, the impact of biological aerosols produced by sewage treatment plants on air quality and human health has become a hot spot of concern. Airborne fungi were characterized via KC-1000 large-flow air sampler and Anderson-type six-stage sampler, at free-surface flowing reeds constructed wetland located in Qingdao City, Shandong Province. The high-throughput sequencing technology and fungal culture-dependent method were selected to analyze the composition and dynamic changes of the fungal community attached to the atmospheric particulate matter in the free surface flow constructed wetland. The results showed that the aerosol concentration of fungi in the constructed wetlands varied from 587~3382 CFU m-3, with a peak at the range of 1.10 to 2.10 μm particle size, and the particles (＜4.70 μm) that easily entered the lungs accounted for 57.03~96.03%. Significant seasonal differences in fungal richness and community diversity were found. The particle size distribution of fungi in atmospheric particles was not obvious. Fungal genera in the atmospheric particulate matter were mainly driven by humidity. However, other factors i.e. temperature, NO2, SO2, and PM10 contents also contributed.
... With the introduction of DNA sequence analysis and multiple gene genealogies, the Phylogenetic Species Concept has been widely applied (Stadler et al., 2014;Taylor et al., 2000) in the description of novel taxa and has unveiled cryptic species in Diaporthe (Udayanga et al., 2014a). The most recent taxonomic studies in this genus have relied mostly on the analysis of five loci: ITS rDNA (internal transcribed spacer region of the nuclear ribosomal DNA) and the protein coding genes tef1-a (translation elongation factor 1-alpha), tub2 (b-tubulin), his3 (histone 3) and cal (calmodulin) (Gomes et al., 2013;Santos et al., 2017a), which provide a robust approach to resolve Diaporthe species . ...
... Moreover, it was shown that these ITS types, even if belonging to sibling ascospores, reflected an intraindividual sequence divergence of 6.2%. Interestingly, Stadler et al. (2014) have also observed the same in Xylaria hypoxylon, where single ascospore isolates were also derived from the same perithecium, resulting in three different ITS genotypes. Two other ITS types referred to in this study as VII and VIII were recovered from D. malorum isolated from 3 different hosts (V. ...
Species in Diaporthe are largely reported as important plant pathogens. Identification of species in this genus has been complemented by morphological and molecular features. However, one important factor delaying this process is the struggle to formulate robust species concepts to create adequate international phytosanitary measures. Regardless of the wide use of the internal transcribed spacer (ITS) rDNA region, established as the primary DNA barcode for fungi, the tendency for intraspecific variation has been reported, misleading interpretation of phylogenetic analyses. Therefore, the present study aimed to illustrate, using specific examples, how the ITS region may be problematic for species delimitation. We showed that the ITS region is highly variable, with strains of Diaporthe malorum and Diaporthe novem falling into more than one clade, which if analyzed on their own, would be likely recognized as distinct taxa. Divergent ITS paralogs were also proven to coexist within the genome of D. novem. We also suggest that ITS may have escaped from concerted evolution or has undergone a duplication event. Furthermore, this study reports for the first time the existence of a putative hybrid in the genus Diaporthe. Our findings offer new clues towards the intraspecific and intragenomic variation in the ITS region, raising questions about its value for barcoding, i.e., identifying species in the genus Diaporthe. Therefore, we recommend that the ITS region be analyzed cautiously and always compared for congruence prior to description of novel taxa.
... This approach allows broader applicability of published keys and descriptions. I made specific reference to Rappaz (1987), Chlebicki (2005), Glawe and Rogers (1984), and Stephenson (2004, 2006) for Diatrypaceae; to Ju et al. (1998), Laessøe et al. (1989), and Barr et al. (1993) for Graphostromataceae; to Jaklitsch et al. (2014) and Daranagama et al. (2018) for Lopadostomataceae; to Wendt et al. (2018), Miller (1961), Ju and Rogers (1996), and Stadler et al. (2014a) for Hypoxylaceae; to many works from Jack D. Rogers and Yu-Ming Ju (Ju and Rogers 2002, as well as works in collaboration with Brenda Callan (Rogers and Callan 1986) and those in collaboration with Larissa Vasilyeva and Andrew Miller (Rogers et al. 2008, Vasilyeva et al. 2007 for Xylariaceae; and the recent monograph by Petrini (2013) for Rosellinia. ...
The Xylariales (Sordariomycetes, Ascomycota) is an order of mostly stromatic perithecial fungi generally inhabiting wood and other plant debris, as well as some impor- tant plant pathogenic species. As a follow-up to an extensive fungal inventory conducted by D. Haelewaters and colleagues since December 2012 at the Boston Harbor Islands National Recreation Area in Massachusetts, I examined members of the Xylariales in detail, including previously unreported collections. I constructed keys for included taxa, and I provide species notes, references, substrate, and collecting data of the following Xylarialean genera: Diatrype, Eutypa, Eutypella (Diatrypaceae); Biscogniauxia, Camil- lea, Graphostroma (Graphostromataceae); Annulohypoxylon, Daldinia, Hypomontagnella, Hypoxylon, Jackrogersella (Hypoxylaceae); Lopadostoma (Lopadostomataceae); and Entoleuca, Kretzschmaria, Nemania, Rosellinia, Xylaria (Xylariaceae). I herein formally describe a new species, Xylaria nismundoensis sp. nov., based on combined morphology and multi-locus phylogenetic analysis. This taxon provides the rst evidence of a saprotrophic lifestyle for members of the E9 phylogenetic clade of Xylaria, previously only known as endophytes.
... En esta oportunidad las investigaciones se centraron en las especies de Xylaria Hill ex Schrank, siendo éste el género más diverso y complejo de la Familia Xylariaceae (Fournier, Flessa, Persoh, y Stadler, 2011;Stadler, Hawsworth, y Fournier, 2014). Sus miembros son un componente dominante de la comunidad endófita de los bosques alrededor del mundo y desempeñan una función importante como saprótrofos en estos ecosistemas (Rodrigues y Samuels, 1990;Rodrigues, Leuchtmann, y Petrini, 1993). ...
Se presentan registros sobre los hongos xilariales que habitan en corteza y madera de Ocotea porphyria, un árbol endémico de la selva montana de Argentina y Bolivia. Se registran por primera vez seis especies del género Xylaria, incluyéndose descripcio- nes, ilustraciones y comentarios sobre las mismas. Se proveen dos claves dicotómicas, una sobre los géneros y la otra sobre las especies presentes en este hospedante.
... For the genome sequencing, twelve morphologically well characterized ascospore-derived strains of the order Xylariales were chosen. The selection was comprised of eleven representatives of the Hypoxylaceae ( (Stadler et al. 2014a;Kuhnert et al. 2014aKuhnert et al. , 2017Wendt et al. 2018) except for D. concentrica, E. liquescens, H. lienhwacheense, Hypomontagnella monticulosa MUCL 54604 and H. pulicicidum, which do not represent type strains. Regarding upcoming studies, two endosymbiontic isolates of Hypomontagnella were included as well. ...
The Hypoxylaceae (Xylariales, Ascomycota) is a diverse family of mainly saprotrophic fungi, which commonly occur in angiosperm-dominated forests around the world. Despite their importance in forest and plant ecology as well as a prolific source of secondary metabolites and enzymes, genome sequences of related taxa are scarce and usually derived from environmental isolates. To address this lack of knowledge thirteen taxonomically well-defined representatives of the family and one member of the closely related Xylariaceae were genome sequenced using combinations of Illumina and Oxford nanopore technologies or PacBio sequencing. The workflow leads to high quality draft genome sequences with an average N50 of 3.0 Mbp. A backbone phylogenomic tree was calculated based on the amino acid sequences of 4912 core genes reflecting the current accepted taxonomic concept of the Hypoxylaceae. A Percentage of Conserved Proteins (POCP) analysis revealed that 70% of the proteins are conserved within the family, a value with potential application for the definition of family boundaries within the order Xylariales. Also, Hypomontagnella spongiphila is proposed as a new marine derived lineage of Hypom. monticulosa based on in-depth genomic comparison and morphological differences of the cultures. The results showed that both species share 95% of their genes corresponding to more than 700 strain-specific proteins. This difference is not reflected by standard taxonomic assessments (morphology of sexual and asexual morph, chemotaxonomy, phylogeny), preventing species delimitation based on traditional concepts. Genetic changes are likely to be the result of environmental adaptations and selective pressure, the driving force of speciation. These data provide an important starting point for the establishment of a stable phylogeny of the Xylariales; they enable studies on evolution, ecological behavior and biosynthesis of natural products; and they significantly advance the taxonomy of fungi.
... NIBRGR0000180467. D. childiae is a widely distributed wood-inhabiting ascomycete fungus belonging to the family Hypoxylaceae and the order Xylariales (7). Although many studies of this fungus have focused on taxonomy and ecology, little is known about the bioactivity of its metabolites and its genomics. ...
The fungus Daldinia childiae strain JS-1345, isolated from stem tissue of Abies koreana (Korean fir), has shown strong anti-inflammatory activity. Here, we report the genome sequence of D. childiae JS-1345. The final assembly consisted of 133 scaffolds totaling 38,652,569 bp (G+C content, 44.07%).
... On the other hand, many species of Xylariales that were erected based on specimens from North America have never been recollected and subjected to DNA sequencing. Mycologists have in the past also frequently used European species names for North American fungi that were later shown to be misapplied (see, e.g., Fournier et al. 2012 for Xylaria;Stadler et al. 2014a, b for Daldinia). Therefore, the species identification of these endophytes remains tentative. ...
The internal transcribed spacer (ITS) region of the ribosomal DNA (rDNA) has been established (and is generally accepted) as a primary "universal" genetic barcode for fungi for many years, but the actual value for taxonomy has been heavily disputed among mycologists. Recently, twelve draft genome sequences, mainly derived from type species of the family Hypoxylaceae (Xylariales, Ascomycota) and the ex-epitype strain of Xylaria hypoxylon have become available during the course of a large phylogenomic study that was primarily aimed at establishing a correlation between the existing multi-gene-based genealogy with a genome-based phylogeny and the discovery of novel biosynthetic gene clusters encoding for secondary metabolites. The genome sequences were obtained using combinations of Illumina and Oxford nanopore technologies or PacBio sequencing, respectively, and resulted in high-quality sequences with an average N50 of 3.2 Mbp. While the main results will be published concurrently in a separate paper, the current case study was dedicated to the detection of ITS nrDNA copies in the genomes, in an attempt to explain certain incongruities and apparent mismatches between phenotypes and genotypes that had been observed during previous polyphasic studies. The results revealed that all of the studied strains had at least three copies of rDNA in their genomes, with Hypoxylon fragiforme having at least 19 copies of the ITS region, followed by Xylaria hypoxylon with at least 13 copies. Several of the genomes contained 2-3 copies that were nearly identical, but in some cases drastic differences, below 97% identity were observed. In one case, ascribable to the presence of a pseudogene, the deviations of the ITS sequences from the same genome resulted in only ca. 90% of overall homology. These results are discussed in the scope of the current trends to use ITS data for species recognition and segregation of fungi. We propose that additional genomes should be checked for such ITS polymorphisms to reassess the validity of this non-coding part of the fungal DNA for molecular identification.
... On the other hand, many species of Xylariales that were erected based on specimens from North America have never been recollected and subjected to DNA sequencing. Mycologists have in the past also frequently used European species names for North American fungi that were later shown to be misapplied (see, e.g., Fournier et al. 2012 for Xylaria;Stadler et al. 2014a, b for Daldinia). Therefore, the species identification of these endophytes remains tentative. ...
The internal transcribed spacer (ITS) region of the ribosomal DNA (rDNA) has been established (and is generally accepted) as a primary "universal" genetic barcode for fungi for many years, but the actual value for taxonomy has been heavily disputed among mycologists. Recently, twelve draft genome sequences, mainly derived from type species of the family Hypoxylaceae (Xylariales, Ascomycota) and the ex-epitype strain of Xylaria hypoxylon have become available during the course of a large phylogenomic study that was primarily aimed at establishing a correlation between the existing multi-gene based genealogy with a genome based phylogeny and the discovery of novel biosynthetic gene clusters encoding for secondary metabolites. The genome sequences were obtained using combinations of Illumina and Oxford nanopore technologies or PacBio sequencing, respectively and resulted in high quality sequences with an average N50 of 3.2 Mbp. While the main results will be published concurrently in a separate paper, the current case study was dedicated to the detection of ITS nrDNA copies in the genomes, in an attempt to explain certain incongruities and apparent mismatches between phenotypes and genotypes that had been observed during previous polyphasic studies. The results revealed that all of the studied strains had at least three copies of rDNA in their genomes, with Hypoxylon fragiforme having at least 19 copies of the ITS region, followed by Xylaria hypoxylon with at least 13 copies. Several of the genomes contained 2-3 copies that were nearly identical, but in some cases drastic differences, below 97% identity were observed. In one case, ascribable to the presence of a pseudogene, the deviations of the ITS sequences from the same genome resulted in only ca. 90% of overall homology. These results are discussed in the scope of the current trends to use ITS data for species recognition and segregation of fungi. We propose that additional genomes should be checked for such ITS polymorphisms to reassess the validity of this non-coding part of the fungal DNA for molecular identification.
... Xylaria hypoxylon; wood-rotting fungus; mitochondrial genome; phylogenetic analysis Xylaria hypoxylon belongs to the order Xylariales, which is one of the famous fungus widely distributed in temperate regions. It is usually buried in the soil on stumps or woody materials, and always distributed in a humid environment throughout Asia, Europe, and America (Stadler et al. 2014). A large number of researches have shown that X. hypoxylon fruit body and culture mycelial possess a variety of chemical compounds, such as inhibiting various pathogenic bacteria related to humans, inhibitory activity of HIV-1 reverse transcriptase, inhibiting the proliferation of various tumor cell lines and also as adjuvant to enhance the cellular immune response (Liu et al. 2006;Sch€ uffler et al. 2007;Gu and Ding 2008;Hu et al. 2012;Kang et al. 2015;Canli et al. 2016). ...
Xylaria hypoxylon is a noticeable black fungus, and also habitual to cluster on rotting wood. In this study, the high-quality whole-genome of X. hypoxylon strain SFY20170806 was sequenced on the Illumina sequencing platform. The complete mitochondrial genome of X. hypoxylon was assembled and annotated. The single circular structure of 129,366 bp length is the largest species found in the order Xylariales. The overall GC content is 29.7% and gene composition includes 13 protein-coding genes (PCGs), 30 transfer RNA genes(tRNA), 2 ribosomal RNA genes(rRNA) and 6 open reading frames (ORF). Phylogenetic tree was constructed to validate the evolutionary relationship based on the complete mitogenomes from twelve taxa of four species of Xylariales, four species of Hypocreales, two species of Helotiales, one species of Microascales and X. hypoxylon. Phylogenetic analysis demonstrated that X. hypoxylon has a special evolutionary status and close genetic relationship with Annulohypoxylon stygium.
