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Marc Stadler - One of the best experts on this subject based on the ideXlab platform.
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Recent progress in biodiversity research on the Xylariales and their secondary metabolism
The Journal of Antibiotics, 2021Co-Authors: Kevin Becker, Marc StadlerAbstract:The families Xylariaceae and Hypoxylaceae (Xylariales, Ascomycota) represent one of the most prolific lineages of secondary metabolite producers. Like many other fungal taxa, they exhibit their highest diversity in the tropics. The stromata as well as the mycelial cultures of these fungi (the latter of which are frequently being isolated as endophytes of seed plants) have given rise to the discovery of many unprecedented secondary metabolites. Some of those served as lead compounds for development of pharmaceuticals and agrochemicals. Recently, the endophytic Xylariales have also come in the focus of biological control, since some of their species show strong antagonistic effects against fungal and other pathogens. New compounds, including volatiles as well as nonvolatiles, are steadily being discovered from these ascomycetes, and polythetic taxonomy now allows for elucidation of the life cycle of the endophytes for the first time. Moreover, recently high-quality genome sequences of some strains have become available, which facilitates phylogenomic studies as well as the elucidation of the biosynthetic gene clusters (BGC) as a starting point for synthetic biotechnology approaches. In this review, we summarize recent findings, focusing on the publications of the past 3 years.
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Intragenomic polymorphisms in the ITS region of high-quality genomes of the Hypoxylaceae (Xylariales, Ascomycota)
Mycological Progress, 2020Co-Authors: Marc Stadler, Miroslav Kolařik, Christopher Lambert, Daniel Wibberg, Jörn Kalinowski, Russell J. Cox, Eric KuhnertAbstract: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.
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natonodosa speciosa gen et sp nov and rediscovery of poroisariopsis inornata neotropical anamorphic fungi in Xylariales
Mycological Progress, 2020Co-Authors: Gabriela Heredia, Marc Stadler, Marcela Gamboaangulo, Lucile Wendt, Martina Reblova, Rosa Ma Arias, Vaclav Stěpanek, Rafael F CastanedaruizAbstract:Natonodosa is introduced as new genus based on morphology and multigene phylogenetic data, and the monotypic genus Natonodosa, typified by N. speciosa, is characterized by mononematous conidiophores, polyblastic, nodose conidiogenous cells and unicellular, fusiform, hyaline conidia. The other freshly collected material was identified as Poroisariopsis inornata, a species that since its original description had not been reported; it is characterized by synnematous conidiophores with polytretic, cylindrical and uncinate conidiogenous cells with percurrent extensions, and distoseptate, obclavate, brown conidia. A lectotype and an epitype for the species are established and referred since the original specimen of this microfungus has not been found in any herbarium. Placement of both taxa in Xylariales was ascertained by BLASTn searches. Maximum likelihood analysis of the combined sequence data of the ribosomal rDNA (ITS and partial LSU region), as well as partial gene regions coding for the second largest subunit of RNA polymerase II (RPB2) and beta-tubulin (TUB2), was performed. In addition, a new name, Guarroa, is proposed for replacing the illegitimate genus name Phaeobotrys M. Calduch, Gene & Guarro. A dichotomous key to the new genus and morphologically similar taxa is provided.
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A novel species and a new combination of Daldinia from Ban Hua Thung community forest in the northern part of Thailand
Mycological Progress, 2019Co-Authors: Sarunyou Wongkanoun, Marc Stadler, Lucile Wendt, Jennifer Luangsa-ard, Prasert SrikitikulchaiAbstract:During a survey of Xylariales in northern Thailand, several specimens with affinities to the genus Daldinia were found and examined for morphological characters, secondary metabolites, and molecular phylogenetic traits. Aside from morphological and chemotaxonomic studies, a multi-locus phylogenetic analysis using internal transcribed spacers regions (ITS) and the large subunit (LSU) of the ribosomal DNA, the second largest subunit of the RNA polymerase (RPB2), and beta-tubulin (TUB2) genes was performed. Among the specimens was a new species and a new record of a species that had previously never been sequenced and studied for its anamorphic morphology. This species, previously described by Ju and Rogers as Hypoxylon kretzschmarioides based on a single record from Indonesia, showed secondary metabolite profiles reminiscent of those of the genus Daldinia and even clustered in the latter genus in the phylogenetic tree. Therefore, it is transferred to Daldinia as D. kretzschmarioides comb. nov. A second new species, D. subvernicosa sp. nov., was found to have a close relationship with D . vernicosa based on morphological and molecular evidence, but differs from D. vernicosa by long-stipitate asci with mostly subglobose ascospores, and the basal ascospores are often elongated.
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volatiles from the hypoxylaceous fungi hypoxylon griseobrunneum and hypoxylon macrocarpum
Beilstein Journal of Organic Chemistry, 2018Co-Authors: Jan Rinkel, Alexander Babczyk, Marc Stadler, Jeroen S DickschatAbstract:The volatiles emitted by the ascomycetes Hypoxylon griseobrunneum and Hypoxylon macrocarpum (Hypoxylaceae, Xylariales) were collected by use of a closed-loop stripping apparatus (CLSA) and analysed by GC–MS. The main compound class of both species were polysubstituted benzene derivatives. Their structures could only be unambiguously determined by comparison to all isomers with different substitution patterns. The substitution pattern of the main compound from H. griseobrunneum, the new natural product 2,4,5-trimethylanisole, was explainable by a polyketide biosynthesis mechanism that was supported by a feeding experiment with (methyl-2H3)methionine.
Kevin D Hyde - One of the best experts on this subject based on the ideXlab platform.
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multigene phylogeny reveals haploanthostomella elaeidis gen et sp nov and familial replacement of endocalyx Xylariales sordariomycetes ascomycota
Life, 2021Co-Authors: Sirinapa Konta, Milan C. Samarakoon, Saisamorn Lumyong, Samantha C. Karunarathna, Kevin D Hyde, Prapassorn D Eungwanichayapant, Lucas A P Dauner, Sasith Tharanga Aluthwattha, Saowaluck TibprommaAbstract:During our investigation of palm fungi in Thailand, two interesting taxa from Elaeis guineensis and Metroxylon sagu (Arecaceae) were collected. Based on phylogenetic analyses of a combined dataset of ITS, LSU, rpb2, and tub2 nucleotide sequences as well as unique morphological characteristics, we introduce the new genus Haploanthostomella within Xylariales, and a new species Endocalyx metroxyli. Additionally, in our study, the genus Endocalyx is transferred to the family Cainiaceae based on its brown conidia and molecular phylogenetic evidence.
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vamsapriya yunnana a new species of vamsapriya xylariaceae Xylariales associated with bamboo from yunnan china
Phytotaxa, 2018Co-Authors: Hongbo Jiang, R. Phookamsak, Darbhe J Bhat, Ali H Bahkali, Sehroon Khan, Abdallah M Elgorban, Kevin D HydeAbstract:Vamsapriya yunnana sp. nov., collected from dead bamboo in Yunnan Province of China, is described and illustrated in this paper. The new taxon is characterized by synnematous conidiophores, with enteroblastic, monotretic conidiogenous cells and brown to dark brown, 4–9-septate, fusiform conidia with a long, apical, appendage-like region. The species differs from the type and other species in the genus in having a wider fertile region and rostrate apex of the conidia. Maximum likelihood and Bayesian inference analyses of a combined ITS, LSU and RPB2 DNA sequence dataset show that V. yunnana is a new species, belonging to the genus Vamsapriya in Xylariaceae.
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towards a natural classification and backbone tree for graphostromataceae hypoxylaceae lopadostomataceae and xylariaceae
Fungal Diversity, 2018Co-Authors: Eric H. C. Mckenzie, Esteban Benjamin Sir, Milan C. Samarakoon, Dinushani A Daranagama, Kevin D Hyde, Kasun M Thambugala, Qing Tian, Subashini C Jayasiri, Saowaluck TibprommaAbstract:Species and generic recognition in the order Xylariales has been uncertain due to lack of molecular data from authentic cultures, as well as overlapping morphological characteristics. In this study, we revise the families Graphostromataceae, Hypoxylaceae, Lopadostomataceae and Xylariaceae in Xylariales. Our study is based on DNA sequence data derived from living cultures of fresh isolates, data from GenBank and morphological observation of type and worldwide herbarium specimens. We also collected new specimens from Germany, Italy and Thailand. Combined analyses of ITS, LSU, RPB2 and β-tubulin sequence data were used to reconstruct the molecular phylogeny of the above families. Generic and familiar boundaries between these families are revised and presented in an updated combined phylogenetic tree. We accept six genera in Graphostromataceae, 19 genera in Hypoxylaceae, four in Lopadostomataceae and 37 genera in Xylariaceae. Five genera previously treated in Xylariaceae are placed in Amphisphaeriales genera incertae sedis and seven genera are placed in Xylariales genera incertae sedis. Two genera are placed in Sordariomycetes genera incertae sedis, while four genera are placed as Xylariomycetidae genera incertae sedis. Three genera are considered as doubtful. Barrmaelia and Cannonia, presently included in Xylariaceae are transferred to Diatrypaceae and Coniochaetales respectively, based on their morphology and phylogeny. Areolospora and Myconeesia are excluded from Xylariaceae and synonymized with Phaeosporis and Anthostomella respectively. Updated descriptions and illustrations are provided for all taxa with notes provided on each genus. Excluded and doubtful genera are listed with notes on their taxonomy and phylogeny. Taxonomic keys are provided for all revised families with morphological details for genera within the families.
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establishment of zygosporiaceae fam nov Xylariales sordariomycetes based on rdna sequence data to accommodate zygosporium
Mycosphere, 2017Co-Authors: R. Phookamsak, Rajesh Jeewon, Saisamorn Lumyong, Darbhe J Bhat, Kevin D Hyde, Saowaluck Tibpromma, Ekachai Chukeatirote, Sajeewa S N Maharachchikumbura, E H C MckenzieAbstract:Zygosporium species are widespread on hosts and usually associated with monocotyledonous plants including Arecaceae (palms) and Pandanaceae. Zygosporium forms colonies as darkened spots on the host surface. This study recovers two Zygosporium species from China and Thailand and makes an attempt to clarify the systematic placement of Zygosporium based on morphological characteristics and phylogenetic analyses based on rDNA sequence data. Phylogenetic analyses of a combined LSU and ITS sequence data generated under Maximum Likelihood and Bayesian criteria indicate that Zygosporium species form a strongly supported monophyletic lineage basal to the Coniocessiaceae and not to the Microdochiaceae as previously assumed. Given the distinct morphological features of Zygosporium and its strongly supported monophyletic nature, a new family, Zygosporiaceae is introduced within the Xylariales.
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tristratiperidium microsporum gen et sp nov Xylariales on dead leaves of arundo plinii
Mycological Progress, 2016Co-Authors: Marc Stadler, Dinushani A Daranagama, Erio Camporesi, Xingzhong Liu, Darbhe J Bhat, Sunita Chamyuang, Ali H Bahkali, Kevin D HydeAbstract:Tristratiperidium microsporum gen. et sp. nov. (Xylariales) is introduced to accommodate a taxon isolated from dead leaves of Arundo plinii, collected in Italy. The sexual and asexual morphs are described and illustrated and compared with similar taxa. Phylogenetic analysis of combined Internal Transcribed Spacer (ITS) and Large Subunit (LSU) rRNA sequence data show the relationships of T. microsporum with other genera in the Xylariales. Tristratiperidium microsporum clusters with the hyphomycete Subramaniomyces fusisaprophyticus in the order Xylariales, in the clade comprising Apiosporaceae, Hyponectriaceae, Melogrammataceae, and Pseudomassariaceae. The phylogenetic relationships of T. microsporum and allied fungi are discussed and its placement in the Xylariales genera incertae sedis is suggested.
Eric Kuhnert - One of the best experts on this subject based on the ideXlab platform.
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Intragenomic polymorphisms in the ITS region of high-quality genomes of the Hypoxylaceae (Xylariales, Ascomycota)
Mycological Progress, 2020Co-Authors: Marc Stadler, Miroslav Kolařik, Christopher Lambert, Daniel Wibberg, Jörn Kalinowski, Russell J. Cox, Eric KuhnertAbstract: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.
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discovery of new mitorubrin derivatives from hypoxylon fulvo sulphureum sp nov ascomycota Xylariales
Mycological Progress, 2015Co-Authors: Eric Kuhnert, Frank Surup, Marc StadlerAbstract:A specimen of the Hypoxylon rubiginosum complex featuring unusual bicoloured stromata was collected in northern Thailand and examined by means of classical morphological methodology, complemented by studies of its secondary metabolites using high performance liquid chromatography coupled with diode array and electrospray mass spectrometric detection (HPLC-DAD/MS), and molecular phylogenetic analysis of its ITS and partial beta-tubulin DNA sequences. In addition, the ultrastructure of its ascospores was examined by SEM. The chemotaxonomic studies revealed the presence of two putatively unknown, apparently specific azaphilone pigments in the stromata. These metabolites were consequently isolated to purity by preparative HPLC and identified by means of nuclear magnetic resonance spectroscopy and high resolution mass spectrometry as the novel natural products, (+)-6″-hydroxymitorubrinol acetate (1) and (+)-6″-hydroxymitorubrinol (3).
Dinushani A Daranagama - One of the best experts on this subject based on the ideXlab platform.
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towards a natural classification and backbone tree for graphostromataceae hypoxylaceae lopadostomataceae and xylariaceae
Fungal Diversity, 2018Co-Authors: Eric H. C. Mckenzie, Esteban Benjamin Sir, Milan C. Samarakoon, Dinushani A Daranagama, Kevin D Hyde, Kasun M Thambugala, Qing Tian, Subashini C Jayasiri, Saowaluck TibprommaAbstract:Species and generic recognition in the order Xylariales has been uncertain due to lack of molecular data from authentic cultures, as well as overlapping morphological characteristics. In this study, we revise the families Graphostromataceae, Hypoxylaceae, Lopadostomataceae and Xylariaceae in Xylariales. Our study is based on DNA sequence data derived from living cultures of fresh isolates, data from GenBank and morphological observation of type and worldwide herbarium specimens. We also collected new specimens from Germany, Italy and Thailand. Combined analyses of ITS, LSU, RPB2 and β-tubulin sequence data were used to reconstruct the molecular phylogeny of the above families. Generic and familiar boundaries between these families are revised and presented in an updated combined phylogenetic tree. We accept six genera in Graphostromataceae, 19 genera in Hypoxylaceae, four in Lopadostomataceae and 37 genera in Xylariaceae. Five genera previously treated in Xylariaceae are placed in Amphisphaeriales genera incertae sedis and seven genera are placed in Xylariales genera incertae sedis. Two genera are placed in Sordariomycetes genera incertae sedis, while four genera are placed as Xylariomycetidae genera incertae sedis. Three genera are considered as doubtful. Barrmaelia and Cannonia, presently included in Xylariaceae are transferred to Diatrypaceae and Coniochaetales respectively, based on their morphology and phylogeny. Areolospora and Myconeesia are excluded from Xylariaceae and synonymized with Phaeosporis and Anthostomella respectively. Updated descriptions and illustrations are provided for all taxa with notes provided on each genus. Excluded and doubtful genera are listed with notes on their taxonomy and phylogeny. Taxonomic keys are provided for all revised families with morphological details for genera within the families.
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tristratiperidium microsporum gen et sp nov Xylariales on dead leaves of arundo plinii
Mycological Progress, 2016Co-Authors: Marc Stadler, Dinushani A Daranagama, Erio Camporesi, Xingzhong Liu, Darbhe J Bhat, Sunita Chamyuang, Ali H Bahkali, Kevin D HydeAbstract:Tristratiperidium microsporum gen. et sp. nov. (Xylariales) is introduced to accommodate a taxon isolated from dead leaves of Arundo plinii, collected in Italy. The sexual and asexual morphs are described and illustrated and compared with similar taxa. Phylogenetic analysis of combined Internal Transcribed Spacer (ITS) and Large Subunit (LSU) rRNA sequence data show the relationships of T. microsporum with other genera in the Xylariales. Tristratiperidium microsporum clusters with the hyphomycete Subramaniomyces fusisaprophyticus in the order Xylariales, in the clade comprising Apiosporaceae, Hyponectriaceae, Melogrammataceae, and Pseudomassariaceae. The phylogenetic relationships of T. microsporum and allied fungi are discussed and its placement in the Xylariales genera incertae sedis is suggested.
Saowaluck Tibpromma - One of the best experts on this subject based on the ideXlab platform.
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multigene phylogeny reveals haploanthostomella elaeidis gen et sp nov and familial replacement of endocalyx Xylariales sordariomycetes ascomycota
Life, 2021Co-Authors: Sirinapa Konta, Milan C. Samarakoon, Saisamorn Lumyong, Samantha C. Karunarathna, Kevin D Hyde, Prapassorn D Eungwanichayapant, Lucas A P Dauner, Sasith Tharanga Aluthwattha, Saowaluck TibprommaAbstract:During our investigation of palm fungi in Thailand, two interesting taxa from Elaeis guineensis and Metroxylon sagu (Arecaceae) were collected. Based on phylogenetic analyses of a combined dataset of ITS, LSU, rpb2, and tub2 nucleotide sequences as well as unique morphological characteristics, we introduce the new genus Haploanthostomella within Xylariales, and a new species Endocalyx metroxyli. Additionally, in our study, the genus Endocalyx is transferred to the family Cainiaceae based on its brown conidia and molecular phylogenetic evidence.
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towards a natural classification and backbone tree for graphostromataceae hypoxylaceae lopadostomataceae and xylariaceae
Fungal Diversity, 2018Co-Authors: Eric H. C. Mckenzie, Esteban Benjamin Sir, Milan C. Samarakoon, Dinushani A Daranagama, Kevin D Hyde, Kasun M Thambugala, Qing Tian, Subashini C Jayasiri, Saowaluck TibprommaAbstract:Species and generic recognition in the order Xylariales has been uncertain due to lack of molecular data from authentic cultures, as well as overlapping morphological characteristics. In this study, we revise the families Graphostromataceae, Hypoxylaceae, Lopadostomataceae and Xylariaceae in Xylariales. Our study is based on DNA sequence data derived from living cultures of fresh isolates, data from GenBank and morphological observation of type and worldwide herbarium specimens. We also collected new specimens from Germany, Italy and Thailand. Combined analyses of ITS, LSU, RPB2 and β-tubulin sequence data were used to reconstruct the molecular phylogeny of the above families. Generic and familiar boundaries between these families are revised and presented in an updated combined phylogenetic tree. We accept six genera in Graphostromataceae, 19 genera in Hypoxylaceae, four in Lopadostomataceae and 37 genera in Xylariaceae. Five genera previously treated in Xylariaceae are placed in Amphisphaeriales genera incertae sedis and seven genera are placed in Xylariales genera incertae sedis. Two genera are placed in Sordariomycetes genera incertae sedis, while four genera are placed as Xylariomycetidae genera incertae sedis. Three genera are considered as doubtful. Barrmaelia and Cannonia, presently included in Xylariaceae are transferred to Diatrypaceae and Coniochaetales respectively, based on their morphology and phylogeny. Areolospora and Myconeesia are excluded from Xylariaceae and synonymized with Phaeosporis and Anthostomella respectively. Updated descriptions and illustrations are provided for all taxa with notes provided on each genus. Excluded and doubtful genera are listed with notes on their taxonomy and phylogeny. Taxonomic keys are provided for all revised families with morphological details for genera within the families.
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establishment of zygosporiaceae fam nov Xylariales sordariomycetes based on rdna sequence data to accommodate zygosporium
Mycosphere, 2017Co-Authors: R. Phookamsak, Rajesh Jeewon, Saisamorn Lumyong, Darbhe J Bhat, Kevin D Hyde, Saowaluck Tibpromma, Ekachai Chukeatirote, Sajeewa S N Maharachchikumbura, E H C MckenzieAbstract:Zygosporium species are widespread on hosts and usually associated with monocotyledonous plants including Arecaceae (palms) and Pandanaceae. Zygosporium forms colonies as darkened spots on the host surface. This study recovers two Zygosporium species from China and Thailand and makes an attempt to clarify the systematic placement of Zygosporium based on morphological characteristics and phylogenetic analyses based on rDNA sequence data. Phylogenetic analyses of a combined LSU and ITS sequence data generated under Maximum Likelihood and Bayesian criteria indicate that Zygosporium species form a strongly supported monophyletic lineage basal to the Coniocessiaceae and not to the Microdochiaceae as previously assumed. Given the distinct morphological features of Zygosporium and its strongly supported monophyletic nature, a new family, Zygosporiaceae is introduced within the Xylariales.
