cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.27655577
title: The biosynthesis and impacts of cytokinins on growth of the oyster mushroom, <i>Pleurotus ostreatus</i>

description: While a lot is known about cytokinins (CKs) and their actions at the molecular and cellular levels in plants, much less is known about the function of CKs in other kingdoms such as fungi. CKs have been detected in a wide range of fungal species where they play roles ranging from enhancing the virulence of phytopathogens to fortifying plant growth when secreted from fungal symbionts. However, the role of CKs where they concern fungal physiology, apart from plant associations, remains largely uncharacterized. Profiling by UHPLC-HRMS/MS (ultrahigh-performance liquid chromatography–high-resolution tandem mass spectrometry) revealed that <i>Pleurotus ostreatus</i> (oyster mushroom) produces CKs in vitro in both liquid and solid cultures. During fungal growth, CK profiling patterns were consistent with previous suggestions that tRNA degradation products might play a role in the physiological development of fungi. It confirms that those products are CKs that act as fungal growth regulators. Moreover, <i>P. ostreatus</i> was shown to respond to exogenous applications of aromatic and isoprenoid CKs, and their effects were dependent on the dose and CK type in a biphasic manner consistent with hormone action. <i>N</i><sup>6</sup>-benzyladenine (BAP), kinetin (KIN), <i>N</i><sup>6</sup>-isopentenyladenine (iP), and <i>trans</i>-zeatin (tZ) bioassays all revealed hormesis-type responses. Accordingly, at low doses, mycelium colony diameter, biomass accumulation, and changes in morphology were stimulated, whereas at high doses only inhibitory effects were observed. Thus, CKs may act as “mycohormones” and consequently have potential for applications in fungal agriculture and medicinal compound production.
DOI: 10.6084/m9.figshare.27655577.v1
title: The biosynthesis and impacts of cytokinins on growth of the oyster mushroom, <i>Pleurotus ostreatus</i>

description: While a lot is known about cytokinins (CKs) and their actions at the molecular and cellular levels in plants, much less is known about the function of CKs in other kingdoms such as fungi. CKs have been detected in a wide range of fungal species where they play roles ranging from enhancing the virulence of phytopathogens to fortifying plant growth when secreted from fungal symbionts. However, the role of CKs where they concern fungal physiology, apart from plant associations, remains largely uncharacterized. Profiling by UHPLC-HRMS/MS (ultrahigh-performance liquid chromatography–high-resolution tandem mass spectrometry) revealed that <i>Pleurotus ostreatus</i> (oyster mushroom) produces CKs in vitro in both liquid and solid cultures. During fungal growth, CK profiling patterns were consistent with previous suggestions that tRNA degradation products might play a role in the physiological development of fungi. It confirms that those products are CKs that act as fungal growth regulators. Moreover, <i>P. ostreatus</i> was shown to respond to exogenous applications of aromatic and isoprenoid CKs, and their effects were dependent on the dose and CK type in a biphasic manner consistent with hormone action. <i>N</i><sup>6</sup>-benzyladenine (BAP), kinetin (KIN), <i>N</i><sup>6</sup>-isopentenyladenine (iP), and <i>trans</i>-zeatin (tZ) bioassays all revealed hormesis-type responses. Accordingly, at low doses, mycelium colony diameter, biomass accumulation, and changes in morphology were stimulated, whereas at high doses only inhibitory effects were observed. Thus, CKs may act as “mycohormones” and consequently have potential for applications in fungal agriculture and medicinal compound production.
DOI: 10.6084/m9.figshare.27607010
title: Phylogeny and taxonomy of the genera of Erysiphaceae, part 6: <i>Erysiphe</i> (the “<i>Microsphaera</i> lineage” part 2)

description: This is the sixth contribution in a series devoted to the phylogeny and taxonomy of powdery mildews. This part includes our third treatment of the species of the genus <i>Erysiphe</i>. It continues the previous contribution on the phylogenetic-taxonomic assessment of the species belonging to the “<i>Microsphaera</i> lineage.” Since this is a large lineage, we have split the treatment of the “<i>Microsphaera</i> lineage” into two parts. Phylogenetic trees based on rDNA are supplemented by sequences of additional markers (<i>CAM, GAPDH, GS, RPB2</i>, and <i>TUB</i>). The “<i>Erysiphe trifoliorum</i> complex” is a challenging group that belongs to the “<i>Microsphaera</i> lineage.” Adequate clarification of this complex will be possible when additional worldwide multilocus sequence analyses are performed. The new species <i>Erysiphe acetosae, E. acmisponis, E. lathyrina, E. salmoniana</i>, and <i>E. santalicola</i> are described, and the new combinations <i>E. biuncinata</i> and <i>E. pavoniae</i> are introduced. Specimens of several species have been sequenced for the first time, particularly North American species, such as <i>Erysiphe caryae, E. ceanothi, E. juglandis-nigrae</i>, and <i>E. ravenelii. Erysiphe syringae</i> is lectotypified and 15 species names are epitypified in order to provide ex-epitype reference sequences. For other species, non-ex-type reference sequences are proposed for phylogenetic-taxonomic purposes. Ex-type sequences for <i>Erysiphe baptisiicola, E. sesbaniae, Microsphaera sydowiana, M. umbilici</i>, and <i>Oidium pavoniae</i> have been retrieved.
DOI: 10.6084/m9.figshare.27607010.v2
title: Phylogeny and taxonomy of the genera of Erysiphaceae, part 6: <i>Erysiphe</i> (the “<i>Microsphaera</i> lineage” part 2)

description: This is the sixth contribution in a series devoted to the phylogeny and taxonomy of powdery mildews. This part includes our third treatment of the species of the genus <i>Erysiphe</i>. It continues the previous contribution on the phylogenetic-taxonomic assessment of the species belonging to the “<i>Microsphaera</i> lineage.” Since this is a large lineage, we have split the treatment of the “<i>Microsphaera</i> lineage” into two parts. Phylogenetic trees based on rDNA are supplemented by sequences of additional markers (<i>CAM, GAPDH, GS, RPB2</i>, and <i>TUB</i>). The “<i>Erysiphe trifoliorum</i> complex” is a challenging group that belongs to the “<i>Microsphaera</i> lineage.” Adequate clarification of this complex will be possible when additional worldwide multilocus sequence analyses are performed. The new species <i>Erysiphe acetosae, E. acmisponis, E. lathyrina, E. salmoniana</i>, and <i>E. santalicola</i> are described, and the new combinations <i>E. biuncinata</i> and <i>E. pavoniae</i> are introduced. Specimens of several species have been sequenced for the first time, particularly North American species, such as <i>Erysiphe caryae, E. ceanothi, E. juglandis-nigrae</i>, and <i>E. ravenelii. Erysiphe syringae</i> is lectotypified and 15 species names are epitypified in order to provide ex-epitype reference sequences. For other species, non-ex-type reference sequences are proposed for phylogenetic-taxonomic purposes. Ex-type sequences for <i>Erysiphe baptisiicola, E. sesbaniae, Microsphaera sydowiana, M. umbilici</i>, and <i>Oidium pavoniae</i> have been retrieved.
DOI: 10.6084/m9.figshare.27607010.v1
title: Phylogeny and taxonomy of the genera of Erysiphaceae, part 6: <i>Erysiphe</i> (the “<i>Microsphaera</i> lineage” part 2 p.p.)

description: This is the sixth contribution in a series devoted to the phylogeny and taxonomy of powdery mildews. This part includes our third treatment of the species of the genus <i>Erysiphe</i>. It continues the previous contribution on the phylogenetic-taxonomic assessment of the species belonging to the “<i>Microsphaera</i> lineage.” Since this is a large lineage, we have split the treatment of the “<i>Microsphaera</i> lineage” into two parts. Phylogenetic trees based on rDNA are supplemented by sequences of additional markers (<i>CAM, GAPDH, GS, RPB2</i>, and <i>TUB</i>). The “<i>Erysiphe trifoliorum</i> complex” is a challenging group that belongs to the “<i>Microsphaera</i> lineage.” Adequate clarification of this complex will be possible when additional worldwide multilocus sequence analyses are performed. The new species <i>Erysiphe acetosae, E. acmisponis, E. lathyrina, E. salmoniana</i>, and <i>E. santalicola</i> are described, and the new combinations <i>E. biuncinata</i> and <i>E. pavoniae</i> are introduced. Specimens of several species have been sequenced for the first time, particularly North American species, such as <i>Erysiphe caryae, E. ceanothi, E. juglandis-nigrae</i>, and <i>E. ravenelii. Erysiphe syringae</i> is lectotypified and 15 species names are epitypified in order to provide ex-epitype reference sequences. For other species, non-ex-type reference sequences are proposed for phylogenetic-taxonomic purposes. Ex-type sequences for <i>Erysiphe baptisiicola, E. sesbaniae, Microsphaera sydowiana, M. umbilici</i>, and <i>Oidium pavoniae</i> have been retrieved.
DOI: 10.6084/m9.figshare.27902598
title: Cell morphological plasticity in response to substrate availability of a cosmopolitan polymorphic yeast from the open ocean

description: Polymorphic yeasts can switch between unicellular division and multicellular filamentous growth. Although prevalent in aquatic ecosystems, such as the open ocean, we have a limited understanding of the controlling factors on their morphological variation in an aquatic ecology context. Here we show that substrate concentration regulates cell morphogenesis in a cosmopolitan polymorphic yeast, <i>Aureobasidium pullulans</i>, isolated from the pelagic open ocean and analyzed in liquid batch culture. Filamentous cell development was triggered only under high initial substrate conditions, suggesting that hyphal growth could be more advantageous under eutrophic conditions and may influence pelagic fungal interactions with particulate organic matter. Filamentous growth proportionally declined before the exhaustion of substrate and before budding yeast-type cell division entered stationary phase, possibly modulated by quorum sensing as previously evidenced in other polymorphic yeasts. We also found that budding yeast-type unicells decreased in size and became more elongated in shape in response to substrate depletion, resulting in higher cell surface area to volume ratios, which could affect yeast dispersal and/or provide a nutrient uptake advantage under oligotrophic conditions. Our results demonstrate resource-responsive morphological plasticity in a marine-derived polymorphic yeast, providing mechanistic insight into the ability of fungi to survive fluctuating environmental conditions such as in the open ocean.
DOI: 10.6084/m9.figshare.27902598.v1
title: Cell morphological plasticity in response to substrate availability of a cosmopolitan polymorphic yeast from the open ocean

description: Polymorphic yeasts can switch between unicellular division and multicellular filamentous growth. Although prevalent in aquatic ecosystems, such as the open ocean, we have a limited understanding of the controlling factors on their morphological variation in an aquatic ecology context. Here we show that substrate concentration regulates cell morphogenesis in a cosmopolitan polymorphic yeast, <i>Aureobasidium pullulans</i>, isolated from the pelagic open ocean and analyzed in liquid batch culture. Filamentous cell development was triggered only under high initial substrate conditions, suggesting that hyphal growth could be more advantageous under eutrophic conditions and may influence pelagic fungal interactions with particulate organic matter. Filamentous growth proportionally declined before the exhaustion of substrate and before budding yeast-type cell division entered stationary phase, possibly modulated by quorum sensing as previously evidenced in other polymorphic yeasts. We also found that budding yeast-type unicells decreased in size and became more elongated in shape in response to substrate depletion, resulting in higher cell surface area to volume ratios, which could affect yeast dispersal and/or provide a nutrient uptake advantage under oligotrophic conditions. Our results demonstrate resource-responsive morphological plasticity in a marine-derived polymorphic yeast, providing mechanistic insight into the ability of fungi to survive fluctuating environmental conditions such as in the open ocean.
DOI: 10.6084/m9.figshare.27969728
title: Marine fungi degrade plastic and can be conditioned to do it faster

description: Plastics are a prevalent and persistent pollutant in the environment. As plastic production increases, finding ways to degrade these recalcitrant polymers is paramount. Many terrestrial fungi, across the kingdom, degrade various types of plastic. Plastics are the fastest-growing habitat in the oceans, and we hypothesized that fungi isolated from the ocean would demonstrate high success rates in degrading polyurethane (PU). To test this, visual degradation assays were performed by inoculating 1% PU medium with 68 different fungal strains cultured from marine habitats. The area of clearance of the fungus was measured periodically, to determine a relative degradation rate. Of the 68 fungal strains, 42 demonstrated the ability to degrade PU. We conditioned the nine fastest PU degraders through serial inoculations into liquid media with increasing concentrations of PU, starting at 1% and going up to 12%. The growth rates of the original and conditioned fungi were then compared in new inoculation trials, and results show that three of the nine conditioned fungi demonstrate higher PU degradation rates than their unconditioned counterparts. Marine fungi, coupled with conditioning, show promise for developing novel mycoremediation technologies.
DOI: 10.6084/m9.figshare.27969728.v1
title: Marine fungi degrade plastic and can be conditioned to do it faster

description: Plastics are a prevalent and persistent pollutant in the environment. As plastic production increases, finding ways to degrade these recalcitrant polymers is paramount. Many terrestrial fungi, across the kingdom, degrade various types of plastic. Plastics are the fastest-growing habitat in the oceans, and we hypothesized that fungi isolated from the ocean would demonstrate high success rates in degrading polyurethane (PU). To test this, visual degradation assays were performed by inoculating 1% PU medium with 68 different fungal strains cultured from marine habitats. The area of clearance of the fungus was measured periodically, to determine a relative degradation rate. Of the 68 fungal strains, 42 demonstrated the ability to degrade PU. We conditioned the nine fastest PU degraders through serial inoculations into liquid media with increasing concentrations of PU, starting at 1% and going up to 12%. The growth rates of the original and conditioned fungi were then compared in new inoculation trials, and results show that three of the nine conditioned fungi demonstrate higher PU degradation rates than their unconditioned counterparts. Marine fungi, coupled with conditioning, show promise for developing novel mycoremediation technologies.
DOI: 10.6084/m9.figshare.28009748
title: Chemotypic diversity of bioprotective grass endophytes based on genome analyses, with new insights from a Mediterranean-climate region in Isfahan Province, Iran

description: <i>Epichloë</i> species are systemic, often seed-transmissible symbionts (endophytes) of cool-season grasses (Poaceae subfam. Poöideae) that produce up to four classes of bioprotective alkaloids. Whereas haploid <i>Epichloë</i> species may reproduce sexually and transmit between host plants (horizontally), many <i>Epichloë</i> species are polyploid hybrids that are exclusively transmitted via seeds (vertically). Therefore, the generation of, and selection on, chemotypic (alkaloid) profiles and diversity should differ between haploids and hybrids. We undertook a genome-level analysis of haploids and polyploid hybrids, emphasizing hybrids that produce lolines, which are potent broad-spectrum anti-invertebrate alkaloids that can accumulate to levels up to 2% of plant dry mass. Prior phylogenetic analysis had indicated that loline alkaloid gene clusters (<i>LOL</i>) in many hybrids are from the haploid species <i>Epichloë bromicola</i>, but no <i>LOL</i>-containing <i>E. bromicola</i> strains were previously identified. We discovered <i>LOL</i>-containing <i>E. bromicola</i> from host grasses <i>Bromus tomentellus</i> and <i>Melica persica</i> in a Mediterranean-climate region (MCR) in Isfahan Province, Iran, and from <i>Thinopyrum intermedium</i> in Poland. The isolates from <i>B. tomentellus</i> and <i>M. persica</i> were closely related and had nearly identical alkaloid gene profiles, and their <i>LOL</i> clusters were most closely related to those of several <i>Epichloë</i> hybrids. In contrast, several <i>LOL</i> genes in the isolate from <i>T. intermedium</i> were phylogenetically more basal in genus <i>Epichloë</i>, indicating trans-species polymorphism. While identifying likely hybrid ancestors, this study also revealed novel host ranges in central Iran, with the first observation of <i>E. bromicola</i> in host tribe Meliceae and of <i>Epichloë festucae</i> in host tribe Bromeae. We discuss the possibility that MCRs may be hotspots for diversification of grass-<i>Epichloë</i> symbioses via extended host ranges and interspecific hybridization of the symbionts.
DOI: 10.6084/m9.figshare.28009748.v1
title: Chemotypic diversity of bioprotective grass endophytes based on genome analyses, with new insights from a Mediterranean-climate region in Isfahan Province, Iran

description: <i>Epichloë</i> species are systemic, often seed-transmissible symbionts (endophytes) of cool-season grasses (Poaceae subfam. Poöideae) that produce up to four classes of bioprotective alkaloids. Whereas haploid <i>Epichloë</i> species may reproduce sexually and transmit between host plants (horizontally), many <i>Epichloë</i> species are polyploid hybrids that are exclusively transmitted via seeds (vertically). Therefore, the generation of, and selection on, chemotypic (alkaloid) profiles and diversity should differ between haploids and hybrids. We undertook a genome-level analysis of haploids and polyploid hybrids, emphasizing hybrids that produce lolines, which are potent broad-spectrum anti-invertebrate alkaloids that can accumulate to levels up to 2% of plant dry mass. Prior phylogenetic analysis had indicated that loline alkaloid gene clusters (<i>LOL</i>) in many hybrids are from the haploid species <i>Epichloë bromicola</i>, but no <i>LOL</i>-containing <i>E. bromicola</i> strains were previously identified. We discovered <i>LOL</i>-containing <i>E. bromicola</i> from host grasses <i>Bromus tomentellus</i> and <i>Melica persica</i> in a Mediterranean-climate region (MCR) in Isfahan Province, Iran, and from <i>Thinopyrum intermedium</i> in Poland. The isolates from <i>B. tomentellus</i> and <i>M. persica</i> were closely related and had nearly identical alkaloid gene profiles, and their <i>LOL</i> clusters were most closely related to those of several <i>Epichloë</i> hybrids. In contrast, several <i>LOL</i> genes in the isolate from <i>T. intermedium</i> were phylogenetically more basal in genus <i>Epichloë</i>, indicating trans-species polymorphism. While identifying likely hybrid ancestors, this study also revealed novel host ranges in central Iran, with the first observation of <i>E. bromicola</i> in host tribe Meliceae and of <i>Epichloë festucae</i> in host tribe Bromeae. We discuss the possibility that MCRs may be hotspots for diversification of grass-<i>Epichloë</i> symbioses via extended host ranges and interspecific hybridization of the symbionts.
DOI: 10.6084/m9.figshare.27902597
title: Genome sequencing, phylogenomics, and population analyses of <i>Tilletia</i>, with recognition of one common bunt species, <i>T. caries</i> (synonym <i>T. laevis</i>), distinct from dwarf bunt, <i>T. controversa</i>

description: Some species of <i>Tilletia</i> are responsible for diseases in economically important crops, such as wheat and rice. In this study, we sequenced, assembled, and annotated 22 new genomes for <i>Tilletia</i>, with a focus on species causing dwarf bunt (DB; <i>T. controversa</i>), common bunt (CB; <i>T. caries</i> and <i>T. laevis</i>), and rice kernel smut (RKS; <i>T. horrida</i>). We present the first genomes for four other species (<i>T. bromi, T. fusca, T. goloskokovii</i>, and <i>T. rugispora</i>), resulting in the largest and most diverse sample of <i>Tilletia</i> genomes studied to date. Depending on the species and strain, the assembly size ranged from 24.3 to 30.5 Mb and gene prediction resulted in 7138 to 8261 gene models per genome. Phylogenomic analyses with hundreds to thousands of genes revealed significant support for the relationships among certain <i>Tilletia</i> taxa and validated findings of previous molecular studies that employed a small number of genes. Further population-level analyses showed two distinct populations of DB and CB: <i>T. controversa</i> (DB) as a single population and another intermixed population of <i>T. caries</i> and <i>T. laevis</i> (CB). No evidence of geographic isolation was observed within these populations. Our phylogenomic analyses also supported previous multigene hypotheses that multiple lineages of <i>Tilletia</i> may cause RKS. Collectively, our results suggest that taxonomic revisions are needed for the RKS-causing pathogens and provide convincing evidence for formally recognizing the CB-causing taxa as one species, named <i>T. caries</i> (synonym <i>T. laevis</i>). Overall, our study significantly enhances genomic resources for <i>Tilletia</i>, offers insights into phylogenetic relationships and population structure, and provides whole genome sequences for future studies.
DOI: 10.6084/m9.figshare.27902597.v1
title: Genome sequencing, phylogenomics, and population analyses of <i>Tilletia</i>, with recognition of one common bunt species, <i>T. caries</i> (synonym <i>T. laevis</i>), distinct from dwarf bunt, <i>T. controversa</i>

description: Some species of <i>Tilletia</i> are responsible for diseases in economically important crops, such as wheat and rice. In this study, we sequenced, assembled, and annotated 22 new genomes for <i>Tilletia</i>, with a focus on species causing dwarf bunt (DB; <i>T. controversa</i>), common bunt (CB; <i>T. caries</i> and <i>T. laevis</i>), and rice kernel smut (RKS; <i>T. horrida</i>). We present the first genomes for four other species (<i>T. bromi, T. fusca, T. goloskokovii</i>, and <i>T. rugispora</i>), resulting in the largest and most diverse sample of <i>Tilletia</i> genomes studied to date. Depending on the species and strain, the assembly size ranged from 24.3 to 30.5 Mb and gene prediction resulted in 7138 to 8261 gene models per genome. Phylogenomic analyses with hundreds to thousands of genes revealed significant support for the relationships among certain <i>Tilletia</i> taxa and validated findings of previous molecular studies that employed a small number of genes. Further population-level analyses showed two distinct populations of DB and CB: <i>T. controversa</i> (DB) as a single population and another intermixed population of <i>T. caries</i> and <i>T. laevis</i> (CB). No evidence of geographic isolation was observed within these populations. Our phylogenomic analyses also supported previous multigene hypotheses that multiple lineages of <i>Tilletia</i> may cause RKS. Collectively, our results suggest that taxonomic revisions are needed for the RKS-causing pathogens and provide convincing evidence for formally recognizing the CB-causing taxa as one species, named <i>T. caries</i> (synonym <i>T. laevis</i>). Overall, our study significantly enhances genomic resources for <i>Tilletia</i>, offers insights into phylogenetic relationships and population structure, and provides whole genome sequences for future studies.