cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.12312101.v1
title: <i>Commelinaceomyces</i>, gen. nov., for four clavicipitaceous species misplaced in <i>Ustilago</i> that infect Commelinaceae

description: A fungus causing false smut in the flowers of <i>Murdannia keisak</i> (Commelinaceae, Commelinales, Monocots) in Japan was morphologically identical to <i>Ustilago aneilematis</i>. The fungus infected ovaries of most flowers of host plants. Infected flowers were filled with yellow to orange thick-walled conidia that became olivaceous green at maturity. However, multilocus phylogenetic analysis of DNA sequences (18S, 28S, translation elongation factor 1α [<i>TEF</i>], the largest [<i>RPB1</i>] and the second largest [<i>RPB2</i>] subunit of RNA polymerase II) showed that the fungus belonged to the tribe Ustilaginoideae (Clavicipitaceae, Hypocreales, Ascomycota). Microscopic examination showed that the fungus developed conidia at the apex of conidiogenous cells, in contrast to other species in the Ustilaginoideae that develop conidia pleurogenously. A new genus, <i>Commelinaceomyces</i>, is formally proposed in the Ustilaginoideae to accommodate this fungus. Four species previously misplaced in <i>Ustilago</i> (Ustilaginales, Basidiomycota) are transferred to <i>Commelinaceomyces</i>, including the type of the genus, <i>C. aneilematis</i>, on <i>Murdannia keisak</i>. This is the first report of a clavicipitaceous species infecting host plants in the Commelinaceae.
DOI: 10.6084/m9.figshare.12168069
title: Purple haze: Cryptic purple sequestrate <i>Cortinarius</i> in New Zealand

description: is a species-rich ectomycorrhizal genus containing taxa that exhibit agaricoid or sequestrate basidiome morphologies. In New Zealand, one of the most recognizable and common <i>Cortinarius</i> species is the purple sequestrate fungus, <i>C. porphyroideus</i>. We used genome skimming of the almost 100-y-old type specimen from <i>C. porphyroideus</i> to obtain the nuc rDNA internal transcribed spacer region ITS1-5.8S-ITS2 (ITS barcode) and partial nuc rDNA 28S (28S) sequences. The phylogenetic position of <i>C. porphyroideus</i> was established, and we found that it represents a rarely collected species. Purple sequestrate <i>Cortinarius</i> comprise multiple cryptic species in several lineages. We describe four new species of <i>Cortinarius</i> with strong morphological similarity to <i>C. porphyroideus: Cortinarius diaphorus, C. minorisporus, C. purpureocapitatus</i>, and <i>C. violaceocystidiatus</i>. Based on molecular evidence, <i>Thaxterogaster viola</i> is recognized as <i>Cortinarius violaceovolvatus</i> var. <i>viola</i>. These species are associated with <i>Nothofagus</i> (southern beech) and have very similar morphology to <i>C. porphyroideus</i> but are all phylogenetically distinct based on molecular data.
DOI: 10.6084/m9.figshare.12168069.v1
title: Purple haze: Cryptic purple sequestrate <i>Cortinarius</i> in New Zealand

description: is a species-rich ectomycorrhizal genus containing taxa that exhibit agaricoid or sequestrate basidiome morphologies. In New Zealand, one of the most recognizable and common <i>Cortinarius</i> species is the purple sequestrate fungus, <i>C. porphyroideus</i>. We used genome skimming of the almost 100-y-old type specimen from <i>C. porphyroideus</i> to obtain the nuc rDNA internal transcribed spacer region ITS1-5.8S-ITS2 (ITS barcode) and partial nuc rDNA 28S (28S) sequences. The phylogenetic position of <i>C. porphyroideus</i> was established, and we found that it represents a rarely collected species. Purple sequestrate <i>Cortinarius</i> comprise multiple cryptic species in several lineages. We describe four new species of <i>Cortinarius</i> with strong morphological similarity to <i>C. porphyroideus: Cortinarius diaphorus, C. minorisporus, C. purpureocapitatus</i>, and <i>C. violaceocystidiatus</i>. Based on molecular evidence, <i>Thaxterogaster viola</i> is recognized as <i>Cortinarius violaceovolvatus</i> var. <i>viola</i>. These species are associated with <i>Nothofagus</i> (southern beech) and have very similar morphology to <i>C. porphyroideus</i> but are all phylogenetically distinct based on molecular data.
DOI: 10.6084/m9.figshare.12063996.v1
title: Nitrogen-obtaining and -conserving strategies in xylotrophic basidiomycetes

description: Nitrogen in sufficient quantities is strictly necessary for all living organisms. In this study, the ability of some xylotrophic basidiomycetes to grow extremely long on a solid growth medium full of carbon nutrition but lacking a nitrogen source in its composition was discovered. The nitrogen oligotrophy of wood-decaying fungi is associated with their adaptation to live in a wood substrate, which is also deficient in nitrogen content. This nitrogen-depleted cultural growth is called “pseudo-foraging” and can be used as a simplified model of wood-decaying growth. Four main nitrogen-obtaining and -conserving strategies (nitrogen concentration, using alternative sources of nitrogen, economy of growth, and nutritional recycling), which are attributed to wood-colonizing xylotrophs in the literature, were revised studying the pseudo-foraging model. Based on the results, some aspects of the behavior of xylotrophs deep in undecomposed wood were predicted. For example, one of the results is that for pseudo-foraging xylotrophs, the main way to obtain nitrogen is its concentration in their mycelium from the nutrient medium in which nitrogen is contained in the impurities of the components of the medium. The result suggests that in bulk solid wood, the nitrogen concentration strategy also dominates the strategy of using diazotrophic and other alternative nitrogen. In addition, three individual unprecedented mechanisms, which supposedly help the xylotrophic fungi to colonize wood in nature (generation of fine mycelium, macrovesicular endocytosis, formation and conversion of super-elongated mitochondria), were investigated in the laboratory.
DOI: 10.6084/m9.figshare.12103419
title: <i>Quaeritorhiza haematococci</i> is a new species of parasitic chytrid of the commercially grown alga, <i>Haematococcus pluvialis</i>

description: Aquaculture companies grow the green alga <i>Haematococcus pluvialis</i> (Chlorophyta) to extract the carotenoid astaxanthin to sell, which is used as human and animal dietary supplements. We were requested to identify an unknown pathogen of <i>H. pluvialis</i> from an alga growing facility in the southwestern United States. To identify this zoosporic fungus and determine its phylogenetic placement among other chytrids, we isolated it into pure culture, photographed its morphology and zoospore ultrastructure, and sequenced and analyzed portions of nuc rDNA 18S and 28S genes. The organism belongs in the Chytridiomycota, but a comparison of rDNA with available representatives of the phylum did not convincingly place it in any described order. The unique zoospore ultrastructure supports its indeterminate ordinal position, and the morphology, as determined by light microscopy, did not match any described species. Consequently, we have placed this chytrid in the new genus, <i>Quaeritorhiza</i>, and described it as the new species <i>Q. haematococci</i> in the family Quaeritorhizaceae but otherwise incertae sedis in the Chytridiomycetes. This new taxon is important because it increases the known diversity of Chytridiomycota and the organism has the ability to disrupt agricultural production of an algal monoculture.
DOI: 10.6084/m9.figshare.12103419.v1
title: <i>Quaeritorhiza haematococci</i> is a new species of parasitic chytrid of the commercially grown alga, <i>Haematococcus pluvialis</i>

description: Aquaculture companies grow the green alga <i>Haematococcus pluvialis</i> (Chlorophyta) to extract the carotenoid astaxanthin to sell, which is used as human and animal dietary supplements. We were requested to identify an unknown pathogen of <i>H. pluvialis</i> from an alga growing facility in the southwestern United States. To identify this zoosporic fungus and determine its phylogenetic placement among other chytrids, we isolated it into pure culture, photographed its morphology and zoospore ultrastructure, and sequenced and analyzed portions of nuc rDNA 18S and 28S genes. The organism belongs in the Chytridiomycota, but a comparison of rDNA with available representatives of the phylum did not convincingly place it in any described order. The unique zoospore ultrastructure supports its indeterminate ordinal position, and the morphology, as determined by light microscopy, did not match any described species. Consequently, we have placed this chytrid in the new genus, <i>Quaeritorhiza</i>, and described it as the new species <i>Q. haematococci</i> in the family Quaeritorhizaceae but otherwise incertae sedis in the Chytridiomycetes. This new taxon is important because it increases the known diversity of Chytridiomycota and the organism has the ability to disrupt agricultural production of an algal monoculture.
DOI: 10.6084/m9.figshare.12063996
title: Nitrogen-obtaining and -conserving strategies in xylotrophic basidiomycetes

description: Nitrogen in sufficient quantities is strictly necessary for all living organisms. In this study, the ability of some xylotrophic basidiomycetes to grow extremely long on a solid growth medium full of carbon nutrition but lacking a nitrogen source in its composition was discovered. The nitrogen oligotrophy of wood-decaying fungi is associated with their adaptation to live in a wood substrate, which is also deficient in nitrogen content. This nitrogen-depleted cultural growth is called “pseudo-foraging” and can be used as a simplified model of wood-decaying growth. Four main nitrogen-obtaining and -conserving strategies (nitrogen concentration, using alternative sources of nitrogen, economy of growth, and nutritional recycling), which are attributed to wood-colonizing xylotrophs in the literature, were revised studying the pseudo-foraging model. Based on the results, some aspects of the behavior of xylotrophs deep in undecomposed wood were predicted. For example, one of the results is that for pseudo-foraging xylotrophs, the main way to obtain nitrogen is its concentration in their mycelium from the nutrient medium in which nitrogen is contained in the impurities of the components of the medium. The result suggests that in bulk solid wood, the nitrogen concentration strategy also dominates the strategy of using diazotrophic and other alternative nitrogen. In addition, three individual unprecedented mechanisms, which supposedly help the xylotrophic fungi to colonize wood in nature (generation of fine mycelium, macrovesicular endocytosis, formation and conversion of super-elongated mitochondria), were investigated in the laboratory.
DOI: 10.6084/m9.figshare.12314426
title: Mycelial biomass and concentration of loline alkaloids driven by complex population structure in <i>Epichloë uncinata</i> and meadow fescue (<i>Schedonorus pratensis</i>)

description: Many efforts have been made to select and isolate naturally occurring animal-friendly <i>Epichloë</i> strains for later reinfection into elite cultivars. Often this process involves large-scale screening of <i>Epichloë</i>-infected wild grass populations where strains are characterized and alkaloids measured. Here, we describe for the first time the use of genotyping-by-sequencing (GBS) on a collection of 217 <i>Epichloë</i>-infected grasses (7 <i>S. arundinaceum</i>, 4 <i>L. perenne</i>, and 206 <i>S. pratensis</i>). This genotyping strategy is cheaper than complete genome sequencing, is suitable for a large number of individuals, and, when applied to endophyte-infected grasses, conveniently genotypes both organisms. In total, 6273 single nucleotide polymorphisms (SNPs) in the endophyte data set and 38 323 SNPs in the host data set were obtained. Our findings reveal a composite structure with three distinct endophyte clusters unrelated to the three main <i>S. pratensis</i> gene pools that have most likely spread from different glacial refugia in Eurasia. All three gene pools can establish symbiosis with <i>E. uncinata</i>. A comparison of the endophyte clusters with microsatellite-based fingerprinting of the same samples allows a quick test to discriminate between these clusters using two simple sequence repeats (SSRs). Concentrations of loline alkaloids and mycelial biomass are correlated and differ significantly among the plant and endophyte subpopulations; one endophyte strain has higher levels of lolines than others, and one specific host genotype is particularly suitable to host <i>E. uncinata</i>. These findings pave the way for targeted artificial inoculations of specific host-endophyte combinations to boost loline production in the symbiota and for genome association studies with the aim of isolating genes involved in the compatibility between meadow fescue and <i>E. uncinata</i>.
DOI: 10.6084/m9.figshare.12314426.v1
title: Mycelial biomass and concentration of loline alkaloids driven by complex population structure in <i>Epichloë uncinata</i> and meadow fescue (<i>Schedonorus pratensis</i>)

description: Many efforts have been made to select and isolate naturally occurring animal-friendly <i>Epichloë</i> strains for later reinfection into elite cultivars. Often this process involves large-scale screening of <i>Epichloë</i>-infected wild grass populations where strains are characterized and alkaloids measured. Here, we describe for the first time the use of genotyping-by-sequencing (GBS) on a collection of 217 <i>Epichloë</i>-infected grasses (7 <i>S. arundinaceum</i>, 4 <i>L. perenne</i>, and 206 <i>S. pratensis</i>). This genotyping strategy is cheaper than complete genome sequencing, is suitable for a large number of individuals, and, when applied to endophyte-infected grasses, conveniently genotypes both organisms. In total, 6273 single nucleotide polymorphisms (SNPs) in the endophyte data set and 38 323 SNPs in the host data set were obtained. Our findings reveal a composite structure with three distinct endophyte clusters unrelated to the three main <i>S. pratensis</i> gene pools that have most likely spread from different glacial refugia in Eurasia. All three gene pools can establish symbiosis with <i>E. uncinata</i>. A comparison of the endophyte clusters with microsatellite-based fingerprinting of the same samples allows a quick test to discriminate between these clusters using two simple sequence repeats (SSRs). Concentrations of loline alkaloids and mycelial biomass are correlated and differ significantly among the plant and endophyte subpopulations; one endophyte strain has higher levels of lolines than others, and one specific host genotype is particularly suitable to host <i>E. uncinata</i>. These findings pave the way for targeted artificial inoculations of specific host-endophyte combinations to boost loline production in the symbiota and for genome association studies with the aim of isolating genes involved in the compatibility between meadow fescue and <i>E. uncinata</i>.
DOI: 10.6084/m9.figshare.12311837
title: Bambusicolous <i>Fomitiporia</i> revisited: multilocus phylogeny reveals a clade of host-exclusive species

description: is a genus of wood-inhabiting Hymenochaetaceae (Agaricomycetes) that includes pathogens and decomposers occurring on a wide array of plant substrates. Some species decay culms of woody bamboos, a poorly known biotic interaction. Four bambusicolous species of <i>Fomitiporia</i> are currently known. However, no studies concerning their phylogenetic relationships have been performed. In order to assess species boundaries and their relationships to each other, we conducted molecular phylogenetic analyses of nuc rDNA internal transcribed spacer region ITS1-5.8S-ITS2 (ITS) and portions of nuc 28S rDNA (28S), RNA polymerase II second largest subunit (<i>RPB2</i>), and translation elongation factor 1-α (<i>TEF1</i>), as well as morphological analyses. Four species that occur on culms of woody bamboos, <i>F. bambusarum, F. spinescens, F. uncinata</i>, and the new species <i>F. bambusipileata</i>, grouped together in an exclusive clade within a primarily Neotropical lineage. The new species differs from all other species in the group by the pileate basidiomata. Hypotheses regarding host-exclusivity are discussed.
DOI: 10.6084/m9.figshare.12311837.v1
title: Bambusicolous <i>Fomitiporia</i> revisited: multilocus phylogeny reveals a clade of host-exclusive species

description: is a genus of wood-inhabiting Hymenochaetaceae (Agaricomycetes) that includes pathogens and decomposers occurring on a wide array of plant substrates. Some species decay culms of woody bamboos, a poorly known biotic interaction. Four bambusicolous species of <i>Fomitiporia</i> are currently known. However, no studies concerning their phylogenetic relationships have been performed. In order to assess species boundaries and their relationships to each other, we conducted molecular phylogenetic analyses of nuc rDNA internal transcribed spacer region ITS1-5.8S-ITS2 (ITS) and portions of nuc 28S rDNA (28S), RNA polymerase II second largest subunit (<i>RPB2</i>), and translation elongation factor 1-α (<i>TEF1</i>), as well as morphological analyses. Four species that occur on culms of woody bamboos, <i>F. bambusarum, F. spinescens, F. uncinata</i>, and the new species <i>F. bambusipileata</i>, grouped together in an exclusive clade within a primarily Neotropical lineage. The new species differs from all other species in the group by the pileate basidiomata. Hypotheses regarding host-exclusivity are discussed.
DOI: 10.6084/m9.figshare.13754770
title: Genome sequencing and annotation and phylogenomic analysis of the medicinal mushroom <i>Amauroderma rugosum</i>, a traditional medicinal species in the family Ganodermataceae

description: <i>Amauroderma rugosum</i> is one of the traditional Chinese medicinal mushrooms and is used to reduce inflammation, treat diuretic and upset stomach, and prevent cancer. Here, we present a genomic resource of <i>Amauroderma rugosum</i> (ACCC 51706) for further understanding its biology and exploration of the synthesis pathway of bioactive compounds. Genomic DNA was extracted and then subjected to Illumina HiSeq X Ten and PacBio Sequel I sequencing. The final genome is 40.66 Mb in size, with an N<sub>50</sub> scaffold size of 36.6 Mb, and encodes 10 181 putative predicted genes. Among them, 6931 genes were functionally annotated. Phylogenomic analysis suggested that <i>A. rugosum</i> and <i>Ganoderma sinense</i> were not clustered together into a group and the latter was grouped with the Polyporaceae. Further, we also identified 377 carbohydrate-active enzymes (CAZymes) and 15 secondary metabolite biosynthetic gene clusters. This is the first genome-scale assembly and annotation for an <i>Amauroderma</i> species. The identification of novel secondary metabolite biosynthetic gene clusters would promote pharmacological research and development of novel bioactive compounds in the future.
DOI: 10.6084/m9.figshare.13754770.v1
title: Genome sequencing and annotation and phylogenomic analysis of the medicinal mushroom <i>Amauroderma rugosum</i>, a traditional medicinal species in the family Ganodermataceae

description: <i>Amauroderma rugosum</i> is one of the traditional Chinese medicinal mushrooms and is used to reduce inflammation, treat diuretic and upset stomach, and prevent cancer. Here, we present a genomic resource of <i>Amauroderma rugosum</i> (ACCC 51706) for further understanding its biology and exploration of the synthesis pathway of bioactive compounds. Genomic DNA was extracted and then subjected to Illumina HiSeq X Ten and PacBio Sequel I sequencing. The final genome is 40.66 Mb in size, with an N<sub>50</sub> scaffold size of 36.6 Mb, and encodes 10 181 putative predicted genes. Among them, 6931 genes were functionally annotated. Phylogenomic analysis suggested that <i>A. rugosum</i> and <i>Ganoderma sinense</i> were not clustered together into a group and the latter was grouped with the Polyporaceae. Further, we also identified 377 carbohydrate-active enzymes (CAZymes) and 15 secondary metabolite biosynthetic gene clusters. This is the first genome-scale assembly and annotation for an <i>Amauroderma</i> species. The identification of novel secondary metabolite biosynthetic gene clusters would promote pharmacological research and development of novel bioactive compounds in the future.
DOI: 10.6084/m9.figshare.13755239.v1
title: Two new species and one new record of <i>Xenosporium</i> with ellipsoidal or ovoid conidia from Taiwan

description: Three species of <i>Xenosporium</i> producing ellipsoidal or ovoid conidia were collected from decaying culms of <i>Miscanthus floridulus</i> submerged in freshwater streams of Alishan area, Chiayi County, Taiwan. <i>Xenosporium formosiforme</i> and <i>X. parvulum</i> are described and illustrated as new species. <i>Xenosporium africanum</i> is described in this paper as a new record for Taiwan. The phylogenetic relationships of <i>Xenosporium</i> species and related taxa were sought by comparing the sequences of their internal transcribed spacer (ITS) barcode, 28S rDNA, and RNA polymerase II second largest subunit (<i>RPB2</i>) gene segments. Phylogenetic analysis of these <i>Xenosporium</i> species supports their placement in the Tubeufiaceae. A synopsis of <i>Xenosporium</i> species producing ellipsoidal or ovoid conidia is given. The criteria used to differentiate species are discussed.
DOI: 10.6084/m9.figshare.13755239
title: Two new species and one new record of <i>Xenosporium</i> with ellipsoidal or ovoid conidia from Taiwan

description: Three species of <i>Xenosporium</i> producing ellipsoidal or ovoid conidia were collected from decaying culms of <i>Miscanthus floridulus</i> submerged in freshwater streams of Alishan area, Chiayi County, Taiwan. <i>Xenosporium formosiforme</i> and <i>X. parvulum</i> are described and illustrated as new species. <i>Xenosporium africanum</i> is described in this paper as a new record for Taiwan. The phylogenetic relationships of <i>Xenosporium</i> species and related taxa were sought by comparing the sequences of their internal transcribed spacer (ITS) barcode, 28S rDNA, and RNA polymerase II second largest subunit (<i>RPB2</i>) gene segments. Phylogenetic analysis of these <i>Xenosporium</i> species supports their placement in the Tubeufiaceae. A synopsis of <i>Xenosporium</i> species producing ellipsoidal or ovoid conidia is given. The criteria used to differentiate species are discussed.