cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.29212964.v1
title: Fungal diversity in the Neotropics: update on the diversity and taxonomy of Hydnaceae in Costa Rica

description: Much progress documenting the diversity and relationships within the Hydnaceae has been made over the past decades. Nevertheless, the diversity of the family is far from completely known, especially in neotropical regions, which remain underexplored. Concentrated fieldwork to document the diversity and distribution of macrofungi in Costa Rica began in the late 1980s and continued through early 2000s. As most of the studies were morphology based, some species were identified only to genus level, provisionally named, or misidentified. This study provides morphological and molecular evidence of new species of Hydnaceae previously and newly collected in neotropical <i>Quercus</i>-dominated forests in Costa Rica. Molecular phylogenies support the proposal of five new species: a yellow chanterelle <i>Ca. neotropicalis</i>, three <i>Craterellus</i> species: <i>Cr. griseohymeninus</i>, sp. nov. <i>Cr. minutibrunneus</i>, sp. nov. and <i>Cr. lamelligracilis</i>, sp. nov. and a <i>Hydnum repandum</i> lookalike: <i>Hydnum pallideflavum</i>, sp. nov.
DOI: 10.6084/m9.figshare.29270582
title: <i>Didymellaceae</i> species associated with <i>Convolvulaceae</i> plants, with description of three new species

description: <i>Didymellaceae</i> is one of the largest families in the <i>Pleosporales</i>, encompassing main genera of <i>Phoma</i>-like fungi including <i>Ascochyta, Didymella</i>, and <i>Stagonosporopsis</i> and representing underestimated biodiversity. Plants in the <i>Convolvulaceae</i> often grow as weeds in many climates and host a wide range of fungi in the <i>Didymellaceae</i>. This study identified 22 <i>Didymellaceae</i> strains isolated from plants in the <i>Convolvulaceae</i> according to the consolidated species concept (CSC) using phylogenetic, micromorphological, and cultural features. Multilocus phylogenetic analysis inferred from nucleotide sequences of the internal transcribed spacer (ITS), large subunit (28S) of ribosomal DNA, partial DNA-directed RNA polymerase II subunit (<i>rpb2</i>), and β-tubulin (<i>tub2</i>) genes revealed well-supported monophyletic clades corresponding to 16 <i>Didymellaceae</i> species. Reported here for the first time from the <i>Convolvulaceae</i> hosts are <i>Didymella americana, D. bellidis, D. glomerata, D. pomorum, D. segeticola, D. sinensis, D. tanaceti, Nothophoma brennandiae, N. gossypiicola, Phomatodes nebulosa, Stagonosporopsis caricae, S. heliopsidis</i>, and <i>S. inoxydabilis</i>. Additionally, three new species were described: <i>Didymella pseudomacrophylla</i>, sp. nov. <i>Epicoccum convolvulicola</i>, sp. nov. and <i>Epicoccum pseudoplurivorum</i>, sp. nov. Seven species are reported for the first time from Russia: <i>D. bellidis, D. segeticola, D. sinensis, D. tanaceti, N. brennandiae, P. nebulosa</i>, and <i>S. caricae</i>, and one species, <i>S. heliopsidis</i>, for the first time from Kazakhstan.
DOI: 10.6084/m9.figshare.29270582.v1
title: <i>Didymellaceae</i> species associated with <i>Convolvulaceae</i> plants, with description of three new species

description: <i>Didymellaceae</i> is one of the largest families in the <i>Pleosporales</i>, encompassing main genera of <i>Phoma</i>-like fungi including <i>Ascochyta, Didymella</i>, and <i>Stagonosporopsis</i> and representing underestimated biodiversity. Plants in the <i>Convolvulaceae</i> often grow as weeds in many climates and host a wide range of fungi in the <i>Didymellaceae</i>. This study identified 22 <i>Didymellaceae</i> strains isolated from plants in the <i>Convolvulaceae</i> according to the consolidated species concept (CSC) using phylogenetic, micromorphological, and cultural features. Multilocus phylogenetic analysis inferred from nucleotide sequences of the internal transcribed spacer (ITS), large subunit (28S) of ribosomal DNA, partial DNA-directed RNA polymerase II subunit (<i>rpb2</i>), and β-tubulin (<i>tub2</i>) genes revealed well-supported monophyletic clades corresponding to 16 <i>Didymellaceae</i> species. Reported here for the first time from the <i>Convolvulaceae</i> hosts are <i>Didymella americana, D. bellidis, D. glomerata, D. pomorum, D. segeticola, D. sinensis, D. tanaceti, Nothophoma brennandiae, N. gossypiicola, Phomatodes nebulosa, Stagonosporopsis caricae, S. heliopsidis</i>, and <i>S. inoxydabilis</i>. Additionally, three new species were described: <i>Didymella pseudomacrophylla</i>, sp. nov. <i>Epicoccum convolvulicola</i>, sp. nov. and <i>Epicoccum pseudoplurivorum</i>, sp. nov. Seven species are reported for the first time from Russia: <i>D. bellidis, D. segeticola, D. sinensis, D. tanaceti, N. brennandiae, P. nebulosa</i>, and <i>S. caricae</i>, and one species, <i>S. heliopsidis</i>, for the first time from Kazakhstan.
DOI: 10.6084/m9.figshare.28891614
title: The enzymatic arsenal of <i>Discula destructiva</i>: strategies for understanding and managing the dogwood anthracnose pathogen

description: The increasing prevalence of fungal diseases poses major threats to agricultural productivity and biodiversity, particularly in the context of plant-pathogen interactions. Understanding the mechanisms by which pathogens such as <i>Discula destructiva</i> cause disease and losses in dogwoods, important forest plants and nursery ornamental crops, is crucial for developing effective management strategies. This study focuses on the enzymatic activities of <i>D. destructiva</i>, the causal agent of dogwood anthracnose, and their role in facilitating pathogenicity in <i>Cornus</i> spp. We hypothesized that <i>D. destructiva</i> produces higher levels of extracellular hydrolytic and oxidative enzymes compared with other <i>Discula</i> species, which could enhance its ability to invade and degrade host plant tissues. Our findings revealed that isolates of <i>D. destructiva</i> exhibit elevated enzymatic activities, specifically with abundant polyphenol oxidase activity. Additionally, we assessed the influence of environmental factors, such as pH and medium composition, on pathogen growth, demonstrated that optimal growth occurs at pH 4.5, whereas alkaline conditions inhibited growth dynamics. These insights suggest that managing environmental conditions or fungicide formulations could be an effective strategy for controlling the spread of dogwood anthracnose pathogen, thereby emphasizing the importance of enzymatic profiles in fungal pathogenicity.
DOI: 10.6084/m9.figshare.28891614.v1
title: The enzymatic arsenal of <i>Discula destructiva</i>: strategies for understanding and managing the dogwood anthracnose pathogen

description: The increasing prevalence of fungal diseases poses major threats to agricultural productivity and biodiversity, particularly in the context of plant-pathogen interactions. Understanding the mechanisms by which pathogens such as <i>Discula destructiva</i> cause disease and losses in dogwoods, important forest plants and nursery ornamental crops, is crucial for developing effective management strategies. This study focuses on the enzymatic activities of <i>D. destructiva</i>, the causal agent of dogwood anthracnose, and their role in facilitating pathogenicity in <i>Cornus</i> spp. We hypothesized that <i>D. destructiva</i> produces higher levels of extracellular hydrolytic and oxidative enzymes compared with other <i>Discula</i> species, which could enhance its ability to invade and degrade host plant tissues. Our findings revealed that isolates of <i>D. destructiva</i> exhibit elevated enzymatic activities, specifically with abundant polyphenol oxidase activity. Additionally, we assessed the influence of environmental factors, such as pH and medium composition, on pathogen growth, demonstrated that optimal growth occurs at pH 4.5, whereas alkaline conditions inhibited growth dynamics. These insights suggest that managing environmental conditions or fungicide formulations could be an effective strategy for controlling the spread of dogwood anthracnose pathogen, thereby emphasizing the importance of enzymatic profiles in fungal pathogenicity.
DOI: 10.6084/m9.figshare.29100292.v1
title: Phylogenetic and morphological studies of Meripilaceae (Polyporales) from South America: a reevaluation of the genera <i>Henningsia, Meripilus, and Physisporinus</i>

description: This study presents a comprehensive phylogenetic analysis of the genus <i>Meripilus</i> and its allied genera <i>Henningsia</i> and <i>Physisporinus</i> within the Meripilaceae family, in the broader context of the residual polyporoid clade. The three genera are morphologically similar and characterized by resupinate to pileate basidiomes that harden and often darken upon drying, a monomitic hyphal structure, simple-septate generative hyphae, and globose to ovoid basidiospores, with variable presence of cystidia. Species in <i>Henningsia</i> and <i>Meripilus</i>, in turn, present gloeopleurous hyphae in the context and large, multipileate basidiomes. Recent studies have indicated that <i>Physisporinus</i>, as currently defined, is not monophyletic, with <i>Meripilus</i> nested within it. Phylogenetic analysis based on four molecular markers confirmed the paraphyletic nature of <i>Physisporinus</i>, with <i>Meripilus</i> and <i>Henningsia</i> both nested within it. Morphological examinations of specimens collected in South America, along with revisions of type specimens, show that this segregation is not natural and causes nomenclatural problems. We propose to transfer all species currently placed in <i>Physisporinus</i> into <i>Meripilus</i>, thereby preventing the division of the genus into morphologically indistinguishable groups. As a result of this reclassification, we propose 35 new combinations in <i>Meripilus</i> and describe three new species from South America.
DOI: 10.6084/m9.figshare.29137325
title: Morphology and physicochemical properties of melanin particles from the lichen <i>Lobaria pulmonaria</i>

description: Melanins are the pigments with diverse protective functions in a wide range of organisms. The ability of lichens to synthesize melanins is an important adaptation in response to adverse light conditions, including ultraviolet (UV) irradiation and high light. Previously, we demonstrated that melanization of the lichen <i>Lobaria pulmonaria</i> is accompanied by the accumulation of melanin granules in the upper cortex. However, very little information is available on the morphology and physicochemical properties of these particles. Here, for the first time, we used polyclonal antibodies against eumelanin to visualize melanin in the upper cortex of <i>L. pulmonaria</i> and confirm its identity. Using scanning electron microscopy, we showed that extracted melanins are large, spherical aggregates, with an average size of 230 nm. The aggregates had an irregular and unstable structure and displayed high adhesive properties, according to atomic force microscopy. Purification using size exclusion chromatography showed that melanins coeluted with polysaccharides. Purified particles were visualized as discrete structures (subaggregates) with an average size of 42 nm and displayed higher stability and lower adhesive properties than non-purified aggregates. In colloidal aqueous systems, melanin particles formed aggregates with particle sizes of 279 and 212 nm for the non-purified and purified samples, respectively, suggesting that the removal of the polysaccharide component during purification causes the condensation of the polyaromatic structure of melanin. Taken together, our results suggest that melanin particles extracted from UV-melanized thalli of the lichen <i>L. pulmonaria</i> comprise a supramolecular assembly of melanin and polysaccharides. Analysis of the size, ζ-potential, and polydispersity index suggests that melanin particles are capable of structural rearrangements that lead to changes in their nanomechanical properties. The ability of the melanin to bind to polysaccharides may enhance the structural robustness of mycobiont cell walls and increase the tolerance of lichen thalli to stressful environments.
DOI: 10.6084/m9.figshare.29137325.v1
title: Morphology and physicochemical properties of melanin particles from the lichen <i>Lobaria pulmonaria</i>

description: Melanins are the pigments with diverse protective functions in a wide range of organisms. The ability of lichens to synthesize melanins is an important adaptation in response to adverse light conditions, including ultraviolet (UV) irradiation and high light. Previously, we demonstrated that melanization of the lichen <i>Lobaria pulmonaria</i> is accompanied by the accumulation of melanin granules in the upper cortex. However, very little information is available on the morphology and physicochemical properties of these particles. Here, for the first time, we used polyclonal antibodies against eumelanin to visualize melanin in the upper cortex of <i>L. pulmonaria</i> and confirm its identity. Using scanning electron microscopy, we showed that extracted melanins are large, spherical aggregates, with an average size of 230 nm. The aggregates had an irregular and unstable structure and displayed high adhesive properties, according to atomic force microscopy. Purification using size exclusion chromatography showed that melanins coeluted with polysaccharides. Purified particles were visualized as discrete structures (subaggregates) with an average size of 42 nm and displayed higher stability and lower adhesive properties than non-purified aggregates. In colloidal aqueous systems, melanin particles formed aggregates with particle sizes of 279 and 212 nm for the non-purified and purified samples, respectively, suggesting that the removal of the polysaccharide component during purification causes the condensation of the polyaromatic structure of melanin. Taken together, our results suggest that melanin particles extracted from UV-melanized thalli of the lichen <i>L. pulmonaria</i> comprise a supramolecular assembly of melanin and polysaccharides. Analysis of the size, ζ-potential, and polydispersity index suggests that melanin particles are capable of structural rearrangements that lead to changes in their nanomechanical properties. The ability of the melanin to bind to polysaccharides may enhance the structural robustness of mycobiont cell walls and increase the tolerance of lichen thalli to stressful environments.
DOI: 10.6084/m9.figshare.29100292
title: Phylogenetic and morphological studies of Meripilaceae (Polyporales) from South America: a reevaluation of the genera <i>Henningsia, Meripilus, and Physisporinus</i>

description: This study presents a comprehensive phylogenetic analysis of the genus <i>Meripilus</i> and its allied genera <i>Henningsia</i> and <i>Physisporinus</i> within the Meripilaceae family, in the broader context of the residual polyporoid clade. The three genera are morphologically similar and characterized by resupinate to pileate basidiomes that harden and often darken upon drying, a monomitic hyphal structure, simple-septate generative hyphae, and globose to ovoid basidiospores, with variable presence of cystidia. Species in <i>Henningsia</i> and <i>Meripilus</i>, in turn, present gloeopleurous hyphae in the context and large, multipileate basidiomes. Recent studies have indicated that <i>Physisporinus</i>, as currently defined, is not monophyletic, with <i>Meripilus</i> nested within it. Phylogenetic analysis based on four molecular markers confirmed the paraphyletic nature of <i>Physisporinus</i>, with <i>Meripilus</i> and <i>Henningsia</i> both nested within it. Morphological examinations of specimens collected in South America, along with revisions of type specimens, show that this segregation is not natural and causes nomenclatural problems. We propose to transfer all species currently placed in <i>Physisporinus</i> into <i>Meripilus</i>, thereby preventing the division of the genus into morphologically indistinguishable groups. As a result of this reclassification, we propose 35 new combinations in <i>Meripilus</i> and describe three new species from South America.
DOI: 10.6084/m9.figshare.29039152
title: Phylogeny and taxonomy of the genera of Erysiphaceae, part 7: Phyllactinieae

description: The seventh part of this series devoted to the phylogeny and taxonomy of powdery mildews presents the phylogeny and taxonomy of species assigned to the genera <i>Leveillula, Phyllactinia, Pleochaeta</i>, and <i>Queirozia</i> (Erysiphaceae tribe Phyllactinieae). Phylogenetic trees based on multiple loci (ITS+28S, <i>CAM, GADPH, GS</i>, IGS, <i>RPB2</i>, and <i>TUB</i>) are presented. All species with available sequence data are included. The present analyses aim at providing a reference for analyses of powdery mildews of tribe Phyllactinieae. A special focus is on the generic distinction at the base of tribe Phyllactinieae and between <i>Leveillula</i> and <i>Phyllactinia</i>. The inclusion of a larger number of phylogenetically basal <i>Phyllactinia</i> spp. and multiple loci allowed a better insight into the phylogeny of tribe Phyllactinieae and confirmed that <i>Leveillula</i> spp. are nested within the <i>Phyllactinia</i> clade. As a consequence, <i>Leveillula</i> is reduced to synonymy with <i>Phyllactinia</i>. Additionally, <i>Queirozia</i> was found to be nested within the <i>Pleochaeta</i> clade, and as such we have reduced <i>Queirozia</i> to synonymy with <i>Pleochaeta</i>. Multiple species have been sequenced for the first time, in particular multiple North American species. <i>Erysiphe betulae, E. orbicularis, E. polychaeta, E. saxaouli, Phyllactinia antarctica, Ph. broussonetiae-kaempferi, Ph. hamamelidis, Ph. kakicola, Ph. pyri-serotinae, Ph. salmonii, Ph. zanthoxylicola, Uncinula lynchii</i>, and <i>U. shiraiana</i> are epitypified. The new species <i>Ph. amelanchieris</i>, sp. nov. <i>Ph. fraxini-pennsylvanicae</i>, sp. nov. and <i>Ph. oemleriae</i>, sp. nov. are described, and the new combinations <i>Phyllactinia buddlejae, Ph. cleomes, Ph. cylindrospora, Ph. farinosa, Ph. golovinii, Ph. guilanensis, Ph. jaczewskii, Ph. lactucae-seriolae, Ph. lactucarum, Ph. lanugiosa, Ph. lappae, Ph. mindii, Ph. oxalidicola, Ph. picridis, Ph. rubiae, Ph. saxaoulii, Ph. taurica, Ph. thevenotiae, Ph. ulmi</i> (comb. et stat. nov.), <i>Ph. verbasci, Ph. wissadulae</i>, and <i>Pleochaeta erysiphoides</i> are introduced. Furthermore, <i>Phyllactinia</i> sect. <i>Basiphyllactinia</i>, sect. nov. <i>Phyllactinia</i> sect. <i>Leveillula</i>, comb. et stat. nov. and <i>Pleochaeta</i> sect. <i>Ovulariopsis</i>, comb. et stat. nov. are presented.
DOI: 10.6084/m9.figshare.29039152.v1
title: Phylogeny and taxonomy of the genera of Erysiphaceae, part 7: Phyllactinieae

description: The seventh part of this series devoted to the phylogeny and taxonomy of powdery mildews presents the phylogeny and taxonomy of species assigned to the genera <i>Leveillula, Phyllactinia, Pleochaeta</i>, and <i>Queirozia</i> (Erysiphaceae tribe Phyllactinieae). Phylogenetic trees based on multiple loci (ITS+28S, <i>CAM, GADPH, GS</i>, IGS, <i>RPB2</i>, and <i>TUB</i>) are presented. All species with available sequence data are included. The present analyses aim at providing a reference for analyses of powdery mildews of tribe Phyllactinieae. A special focus is on the generic distinction at the base of tribe Phyllactinieae and between <i>Leveillula</i> and <i>Phyllactinia</i>. The inclusion of a larger number of phylogenetically basal <i>Phyllactinia</i> spp. and multiple loci allowed a better insight into the phylogeny of tribe Phyllactinieae and confirmed that <i>Leveillula</i> spp. are nested within the <i>Phyllactinia</i> clade. As a consequence, <i>Leveillula</i> is reduced to synonymy with <i>Phyllactinia</i>. Additionally, <i>Queirozia</i> was found to be nested within the <i>Pleochaeta</i> clade, and as such we have reduced <i>Queirozia</i> to synonymy with <i>Pleochaeta</i>. Multiple species have been sequenced for the first time, in particular multiple North American species. <i>Erysiphe betulae, E. orbicularis, E. polychaeta, E. saxaouli, Phyllactinia antarctica, Ph. broussonetiae-kaempferi, Ph. hamamelidis, Ph. kakicola, Ph. pyri-serotinae, Ph. salmonii, Ph. zanthoxylicola, Uncinula lynchii</i>, and <i>U. shiraiana</i> are epitypified. The new species <i>Ph. amelanchieris</i>, sp. nov. <i>Ph. fraxini-pennsylvanicae</i>, sp. nov. and <i>Ph. oemleriae</i>, sp. nov. are described, and the new combinations <i>Phyllactinia buddlejae, Ph. cleomes, Ph. cylindrospora, Ph. farinosa, Ph. golovinii, Ph. guilanensis, Ph. jaczewskii, Ph. lactucae-seriolae, Ph. lactucarum, Ph. lanugiosa, Ph. lappae, Ph. mindii, Ph. oxalidicola, Ph. picridis, Ph. rubiae, Ph. saxaoulii, Ph. taurica, Ph. thevenotiae, Ph. ulmi</i> (comb. et stat. nov.), <i>Ph. verbasci, Ph. wissadulae</i>, and <i>Pleochaeta erysiphoides</i> are introduced. Furthermore, <i>Phyllactinia</i> sect. <i>Basiphyllactinia</i>, sect. nov. <i>Phyllactinia</i> sect. <i>Leveillula</i>, comb. et stat. nov. and <i>Pleochaeta</i> sect. <i>Ovulariopsis</i>, comb. et stat. nov. are presented.
DOI: 10.15468/dl.n397db
title: Occurrence Download

description: A dataset containing 153 records in GBIF matching the query:
SELECT
 kingdom,
 kingdomkey,
 phylum,
 phylumkey,
 class,
 classkey,
 "order",
 orderkey,
 family,
 familykey,
 genus,
 genuskey,
 species,
 specieskey,
 "year",
 IF(ISNULL(kingdomkey), NULL, SUM(COUNT(*)) OVER (
 PARTITION BY kingdomkey, "year")) kingdomcount,
 IF(ISNULL(phylumkey), NULL, SUM(COUNT(*)) OVER (
 PARTITION BY phylumkey, "year")) phylumcount,
 IF(ISNULL(classkey), NULL, SUM(COUNT(*)) OVER (
 PARTITION BY classkey, "year")) classcount,
 IF(ISNULL(orderkey), NULL, SUM(COUNT(*)) OVER (
 PARTITION BY orderkey, "year")) ordercount,
 IF(ISNULL(familykey), NULL, SUM(COUNT(*)) OVER (
 PARTITION BY familykey, "year")) familycount,
 IF(ISNULL(genuskey), NULL, SUM(COUNT(*)) OVER (
 PARTITION BY genuskey, "year")) genuscount,
 COUNT(*) occurrences,
 MIN(GBIF_TEMPORALUNCERTAINTY(eventdate, eventtime)) mintemporaluncertainty,
 MIN(COALESCE(coordinateuncertaintyinmeters, 1000)) mincoordinateuncertaintyinmeters
FROM
 occurrence
WHERE
 (occurrence.taxonkey = 5133088 OR occurrence.acceptedtaxonkey = 5133088 OR occurrence.kingdomkey = 5133088 OR occurrence.phylumkey = 5133088 OR occurrence.classkey = 5133088 OR occurrence.orderkey = 5133088 OR occurrence.familykey = 5133088 OR occurrence.genuskey = 5133088 OR occurrence.specieskey = 5133088)
 AND occurrence.hasgeospatialissues = FALSE
 AND NOT GBIF_STRINGARRAYCONTAINS(occurrence.issue, 'TAXON_MATCH_FUZZY', TRUE)
 AND (occurrence.distancefromcentroidinmeters &gt;= 2000.0 OR occurrence.distancefromcentroidinmeters IS NULL)
 AND NOT occurrence.basisofrecord IN ('FOSSIL_SPECIMEN', 'LIVING_SPECIMEN')
 AND occurrence.occurrencestatus = 'PRESENT'
 AND (occurrence.specieskey IS NOT NULL AND occurrence."year" IS NOT NULL)
GROUP BY
 occurrence.kingdom,
 occurrence.kingdomkey,
 occurrence.phylum,
 occurrence.phylumkey,
 occurrence.class,
 occurrence.classkey,
 occurrence."order",
 occurrence.orderkey,
 occurrence.family,
 occurrence.familykey,
 occurrence.genus,
 occurrence.genuskey,
 occurrence.species,
 occurrence.specieskey,
 occurrence."year"

 The dataset's 153 records were derived from 320 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0069011-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.qv32kz
title: Occurrence Download

description: A dataset containing 1214 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Parnassius apollo (Linnaeus, 1758)",
 "Country is Germany",
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "Year is greater than or equal to 1990"
 ]
}

 The dataset includes 1214 records from 15 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0069019-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.