cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.23786806.v1
title: Genomes and transcriptomes help unravel the complex life cycle of the blastoclad fungus, <i>Coelomomyces lativittatus</i>, an obligate parasite of mosquitoes and microcrustaceans

description: Species of the phylum Blastocladiomycota, early-diverging zoosporic (flagellated) lineages of fungi, are vastly understudied. This phylum includes the genus <i>Coelomomyces</i>, which consists of more than 80 fungal species that are obligate parasites of arthropods. Known <i>Coelomomyces</i> species lack a complete asexual life cycle, instead surviving through an obligate heterecious alternation of generations life cycle. Despite their global distribution and interesting life cycle, little is known about the genomics of any <i>Coelomomyces</i> species. To address this, we generated three draft-level genomes and annotations for <i>C. lativittatus</i> representing its haploid meiospore, orange gamete, and amber gamete life stages. These draft genome assemblies ranged in size from 5002 to 5799 contigs, with a total length of 19.8–22.8 Mb and a mean of 7416 protein-coding genes. We then demonstrated the utility of these genomes by combining the draft annotations as a reference for analysis of <i>C. lativittatus</i> transcriptomes. We analyzed transcriptomes from across host-associated life stages, including infected larvae and excised mature sporangia from the mosquito <i>Anopheles quadrimaculatus</i>. We identified differentially expressed genes and enriched GO terms both across and within life stages and used these to make hypotheses about <i>C. lativittatus</i> biology. Generally, we found the <i>C. lativittatus</i> transcriptome to be a complex and dynamic expression landscape; GO terms related to metabolism and transport processes were enriched during infection and terms related to dispersal were enriched during sporulation. We further identified five high mobility group (HMG)-box genes in <i>C. lativittatus</i>, three belonging to clades with mating type (MAT) loci from other fungi, as well as four ortholog expansions in <i>C. lativittatus</i> compared with other fungi. The <i>C. lativittatus</i> genomes and transcriptomes reported here are a valuable resource and may be leveraged toward furthering understanding of the biology of these and other early-diverging fungal lineages.
DOI: 10.6084/m9.figshare.23705631
title: Seeing double on <i>Cannabis</i>: Haploids and heteroploids of <i>Bipolaris gigantea</i> on hemp and other dicots

description: <i>Bipolaris gigantea</i> (= <i>Drechslera gigantea</i>) causes Bipolaris leaf spot (BLS), a devastating and widespread disease on industrial hemp (<i>Cannabis sativa</i>). An investigation of relationships of isolates from hemp and other plants indicated variation in ploidy that has not previously been reported for <i>Bipolaris</i>. Isolates were obtained from BLS lesions on hemp and nearby weeds in 11 Kentucky counties and were similar to each other in morphology and growth characteristics. In total, 23 isolates were analyzed by multilocus phylogenetics, of which seven were also chosen for whole genome shotgun sequencing. Genes for RNA polymerase II subunit 2 (<i>RPB2</i>), translation elongation factor 1-α (<i>TEF1</i>), and mating type (<i>MAT1</i>) indicated that 13 of the isolates were haploid with only a single allele each of <i>RPB2</i> and <i>TEF1</i> and either the <i>MAT1-1</i> or <i>MAT1-2</i> idiomorph, whereas 10 were apparently “heteroploid” with two alleles each of <i>RPB2</i> and <i>TEF1</i> and both <i>MAT1</i> idiomorphs. Haploids all had identical <i>RPB2</i> alleles except for a 1-bp difference in two isolates, identical <i>TEF1</i> alleles, and (if present) identical <i>MAT1-2</i> alleles. Those alleles were also present in each heteroploid along with either of two related but distinct alleles for each gene. In contrast, haploids and heteroploids shared allelic variation of <i>MAT1-1</i>. In total, four haploid and two heteroploid genotypes were identified. Genome sequence data assembled to 30–32 Mb for each of four haploid isolates, but 10–31 Mb larger sizes for each of three heteroploids depending on sequencing platform and assembly program. The haploids and heteroploids caused similar disease on hemp.
DOI: 10.6084/m9.figshare.23705631.v1
title: Seeing double on <i>Cannabis</i>: Haploids and heteroploids of <i>Bipolaris gigantea</i> on hemp and other dicots

description: <i>Bipolaris gigantea</i> (= <i>Drechslera gigantea</i>) causes Bipolaris leaf spot (BLS), a devastating and widespread disease on industrial hemp (<i>Cannabis sativa</i>). An investigation of relationships of isolates from hemp and other plants indicated variation in ploidy that has not previously been reported for <i>Bipolaris</i>. Isolates were obtained from BLS lesions on hemp and nearby weeds in 11 Kentucky counties and were similar to each other in morphology and growth characteristics. In total, 23 isolates were analyzed by multilocus phylogenetics, of which seven were also chosen for whole genome shotgun sequencing. Genes for RNA polymerase II subunit 2 (<i>RPB2</i>), translation elongation factor 1-α (<i>TEF1</i>), and mating type (<i>MAT1</i>) indicated that 13 of the isolates were haploid with only a single allele each of <i>RPB2</i> and <i>TEF1</i> and either the <i>MAT1-1</i> or <i>MAT1-2</i> idiomorph, whereas 10 were apparently “heteroploid” with two alleles each of <i>RPB2</i> and <i>TEF1</i> and both <i>MAT1</i> idiomorphs. Haploids all had identical <i>RPB2</i> alleles except for a 1-bp difference in two isolates, identical <i>TEF1</i> alleles, and (if present) identical <i>MAT1-2</i> alleles. Those alleles were also present in each heteroploid along with either of two related but distinct alleles for each gene. In contrast, haploids and heteroploids shared allelic variation of <i>MAT1-1</i>. In total, four haploid and two heteroploid genotypes were identified. Genome sequence data assembled to 30–32 Mb for each of four haploid isolates, but 10–31 Mb larger sizes for each of three heteroploids depending on sequencing platform and assembly program. The haploids and heteroploids caused similar disease on hemp.
DOI: 10.6084/m9.figshare.23727226
title: Patterns of basidiocarp growth in oak mazegill (<i>Daedalea quercina</i>, Polyporales) revealed by experimental and natural perturbations

description: In Polyporales, the pore field immediately behind the basidiocarp margin may configure the hymenophore. Basidiocarp growth is not restricted to the margin, however. Here, the importance of the pore field was assessed from two years’ of observations on naturally occurring oak mazegill (<i>Daedalea quercina</i>, Polyporales) basidiocarps and tested by experimental perturbations in natural habitats. Oak mazegill was chosen because the formed hymenophore has a unique and stable combination of poroid and lamellate features. Whether the pore field is required for basidiocarp growth was tested in 10 basidiocarps in which one side was resected. New growth was observed in six basidiocarps, and it occurred equally from the cut hymenophore and the intact pore field. New formation of hymenophore and pileus even occurred in seven out of 10 basidiocarps that had the entire pore field resected. Whether the hymenophore is configured permanently was tested on 54 basidiocarps on 10 trunks that were turned upside down. A new hymenophore grew through the old pileus, often far from the pore field, and its hymenophore configuration was invariably poroid despite the old hymenophore had lamellate features. In 48 experimentally banded basidiocarps, new hymenophore grew in the insertion hole of the band despite this being far from the pore field. The banded basidiocarps grew at an average rate of 5 mm per year. In conclusion, the capacity to configure the hymenophore is not confined to the pore field and it could be broadly present in the basidiocarp, possibly due to ubiquitous hyphal totipotency.
DOI: 10.6084/m9.figshare.23727226.v1
title: Patterns of basidiocarp growth in oak mazegill (<i>Daedalea quercina</i>, Polyporales) revealed by experimental and natural perturbations

description: In Polyporales, the pore field immediately behind the basidiocarp margin may configure the hymenophore. Basidiocarp growth is not restricted to the margin, however. Here, the importance of the pore field was assessed from two years’ of observations on naturally occurring oak mazegill (<i>Daedalea quercina</i>, Polyporales) basidiocarps and tested by experimental perturbations in natural habitats. Oak mazegill was chosen because the formed hymenophore has a unique and stable combination of poroid and lamellate features. Whether the pore field is required for basidiocarp growth was tested in 10 basidiocarps in which one side was resected. New growth was observed in six basidiocarps, and it occurred equally from the cut hymenophore and the intact pore field. New formation of hymenophore and pileus even occurred in seven out of 10 basidiocarps that had the entire pore field resected. Whether the hymenophore is configured permanently was tested on 54 basidiocarps on 10 trunks that were turned upside down. A new hymenophore grew through the old pileus, often far from the pore field, and its hymenophore configuration was invariably poroid despite the old hymenophore had lamellate features. In 48 experimentally banded basidiocarps, new hymenophore grew in the insertion hole of the band despite this being far from the pore field. The banded basidiocarps grew at an average rate of 5 mm per year. In conclusion, the capacity to configure the hymenophore is not confined to the pore field and it could be broadly present in the basidiocarp, possibly due to ubiquitous hyphal totipotency.
DOI: 10.6084/m9.figshare.23786803
title: Diversity of <i>Colletotrichum</i> species associated with torch ginger anthracnose

description: Anthracnose caused by <i>Colletotrichum</i> species is one of the most important diseases of torch ginger. The disease leads to loss of aesthetic and commercial value of torch ginger stems. This study aimed to characterize <i>Colletotrichum</i> species associated with torch ginger anthracnose in the production areas of Pernambuco and Ceará. A total of 48 <i>Colletotrichum</i> isolates were identified using molecular techniques. Pathogenicity tests were performed on torch ginger with representative isolates. Phylogenetic analyses based on seven loci—DNA lyase (<i>APN</i>2), intergenic spacer between DNA lyase and the mating-type locus <i>MAT1-2-1</i> (<i>APN</i>2/<i>MAT</i>-IGS), calmodulin (<i>CAL</i>), intergenic spacer between glyceraldehyde-3-phosphate dehydrogenase (<i>GAPDH</i>) and a hypothetical protein (<i>GAP</i>2-IGS), glutamine synthetase (<i>GS</i>), and β-tubulin (<i>TUB</i>2)—revealed that they belong to five known <i>Colletotrichum</i> species, namely, <i>C. chrysophilum, C. fructicola, C. siamense, C. theobromicola</i>, and <i>C. tropicale</i>, and three newly discovered species, described here as <i>C. atlanticum, C. floscerae</i>, and <i>C. zingibericola</i>. Of these, <i>C. atlanticum</i> was the most dominant. Pathogenicity assays showed that all isolates were pathogenic to torch ginger bracts. All species are reported for the first time associated with torch ginger in Brazil. The present study contributes to the current understanding of the diversity of <i>Colletotrichum</i> species associated with anthracnose on torch ginger and demonstrates the importance of accurate species identification for effective disease management strategies.
DOI: 10.6084/m9.figshare.23580292
title: Differential carbohydrate-active enzymes and secondary metabolite production by the grapevine trunk pathogen <i>Neofusicoccum parvum</i> Bt-67 grown on host and non-host biomass

description: <i>Neofusicoccum parvum</i> is one of the most aggressive Botryosphaeriaceae species associated with grapevine trunk diseases. This species may secrete enzymes capable of overcoming the plant barriers, leading to wood colonization. In addition to their roles in pathogenicity, there is an interest in taking advantage of <i>N. parvum</i> carbohydrate-active enzymes (CAZymes), related to plant cell wall degradation, for lignocellulose biorefining. Furthermore, <i>N. parvum</i> produces toxic secondary metabolites that may contribute to its virulence. In order to increase knowledge on the mechanisms underlying pathogenicity and virulence, as well as the exploration of its metabolism and CAZymes for lignocellulose biorefining, we evaluated the <i>N. parvum</i> strain Bt-67 capacity in producing lignocellulolytic enzymes and secondary metabolites when grown in vitro with two lignocellulosic biomasses: grapevine canes (GP) and wheat straw (WS). For this purpose, a multiphasic study combining enzymology, transcriptomic, and metabolomic analyses was performed. Enzyme assays showed higher xylanase, xylosidase, arabinofuranosidase, and glucosidase activities when the fungus was grown with WS. Fourier transform infrared (FTIR) spectroscopy confirmed the lignocellulosic biomass degradation caused by the secreted enzymes. Transcriptomics indicated that the <i>N. parvum</i> Bt-67 gene expression profiles in the presence of both biomasses were similar. In total, 134 genes coding CAZymes were up-regulated, where 94 of them were expressed in both biomass growth conditions. Lytic polysaccharide monooxygenases (LPMOs), glucosidases, and endoglucanases were the most represented CAZymes and correlated with the enzymatic activities obtained. The secondary metabolite production, analyzed by high-performance liquid chromatography–ultraviolet/visible spectophotometry–mass spectrometry (HPLC-UV/Vis-MS), was variable depending on the carbon source. The diversity of differentially produced metabolites was higher when <i>N. parvum</i> Bt-67 was grown with GP. Overall, these results provide insight into the influence of lignocellulosic biomass on virulence factor expressions. Moreover, this study opens the possibility of optimizing the enzyme production from <i>N. parvum</i> with potential use for lignocellulose biorefining.
DOI: 10.6084/m9.figshare.23580292.v1
title: Differential carbohydrate-active enzymes and secondary metabolite production by the grapevine trunk pathogen <i>Neofusicoccum parvum</i> Bt-67 grown on host and non-host biomass

description: <i>Neofusicoccum parvum</i> is one of the most aggressive Botryosphaeriaceae species associated with grapevine trunk diseases. This species may secrete enzymes capable of overcoming the plant barriers, leading to wood colonization. In addition to their roles in pathogenicity, there is an interest in taking advantage of <i>N. parvum</i> carbohydrate-active enzymes (CAZymes), related to plant cell wall degradation, for lignocellulose biorefining. Furthermore, <i>N. parvum</i> produces toxic secondary metabolites that may contribute to its virulence. In order to increase knowledge on the mechanisms underlying pathogenicity and virulence, as well as the exploration of its metabolism and CAZymes for lignocellulose biorefining, we evaluated the <i>N. parvum</i> strain Bt-67 capacity in producing lignocellulolytic enzymes and secondary metabolites when grown in vitro with two lignocellulosic biomasses: grapevine canes (GP) and wheat straw (WS). For this purpose, a multiphasic study combining enzymology, transcriptomic, and metabolomic analyses was performed. Enzyme assays showed higher xylanase, xylosidase, arabinofuranosidase, and glucosidase activities when the fungus was grown with WS. Fourier transform infrared (FTIR) spectroscopy confirmed the lignocellulosic biomass degradation caused by the secreted enzymes. Transcriptomics indicated that the <i>N. parvum</i> Bt-67 gene expression profiles in the presence of both biomasses were similar. In total, 134 genes coding CAZymes were up-regulated, where 94 of them were expressed in both biomass growth conditions. Lytic polysaccharide monooxygenases (LPMOs), glucosidases, and endoglucanases were the most represented CAZymes and correlated with the enzymatic activities obtained. The secondary metabolite production, analyzed by high-performance liquid chromatography–ultraviolet/visible spectophotometry–mass spectrometry (HPLC-UV/Vis-MS), was variable depending on the carbon source. The diversity of differentially produced metabolites was higher when <i>N. parvum</i> Bt-67 was grown with GP. Overall, these results provide insight into the influence of lignocellulosic biomass on virulence factor expressions. Moreover, this study opens the possibility of optimizing the enzyme production from <i>N. parvum</i> with potential use for lignocellulose biorefining.
DOI: 10.6084/m9.figshare.23727271
title: A contribution to the knowledge of the genus <i>Infundibulicybe</i> (Tricholomatineae, Agaricales) in China: Two new species and five redescribed taxa

description: In China, species of the genus <i>Infundibulicybe</i> are often confused with other taxa and misdetermined. Here we describe two newly discovered species, <i>I. bispora</i> and <i>I. ellipsospora</i>, and redescribe five known taxa of this genus present in China. These identifications are supported by both morphological and DNA-based phylogenetic evidence. Additionally, a key to all known species of <i>Infundibulicybe</i> is provided.
DOI: 10.6084/m9.figshare.23727271.v1
title: A contribution to the knowledge of the genus <i>Infundibulicybe</i> (Tricholomatineae, Agaricales) in China: Two new species and five redescribed taxa

description: In China, species of the genus <i>Infundibulicybe</i> are often confused with other taxa and misdetermined. Here we describe two newly discovered species, <i>I. bispora</i> and <i>I. ellipsospora</i>, and redescribe five known taxa of this genus present in China. These identifications are supported by both morphological and DNA-based phylogenetic evidence. Additionally, a key to all known species of <i>Infundibulicybe</i> is provided.
DOI: 10.6084/m9.figshare.24115995
title: <b>Contrasting effects of climate warming on host-parasitoid interactions: insights from Rocky Mountain aspen leaf miners and their parasitoids</b>

description: R code and data files for thermal tolerance, development, and thermal preference experiments. Microclimate modeling code and aspen location data points are also provided. Shape files and other data related to microclimate modeling are too large to deposit. They are available upon request (aashah@msu.edu).<br>
DOI: 10.5281/zenodo.8336072
title: Nanoindentation Datasets of Copper-Chromium Composits

description: This dataset contains supplementary material for the publication on Unsupervised Learning of Nanoindentation<br> Data - Inferring Microstructural Details of CuCr Alloys.
DOI: 10.5281/zenodo.8336071
title: Nanoindentation Datasets of Copper-Chromium Composits

description: This dataset contains supplementary material for the publication on Unsupervised Learning of Nanoindentation<br> Data - Inferring Microstructural Details of CuCr Alloys.
DOI: 10.5281/zenodo.8158745
title: Raw and metadata for: Substituting fossil-based with bio-based chemicals: the case of limonene as a greener pore expander for micellar templated silica

description: Raw and meta data for journal article : Substituting fossil-based with bio-based chemicals: the case of limonene as a greener pore expander for micellar templated silica DOI: 10.1039/D3SU00068K Abstract: Porous materials are widely used in applications such as adsorption, catalysis and separation. The use of expander molecules is a versatile route to enlarge the mesopore size in micellar templated mesoporous silica materials. Typical expanders used for this purpose are fossil-based organic molecules such as trimethylbenzene (TMB). In the course of making such syntheses greener and more sustainable, it is highly desirable to substitute such fossil-based chemicals with renewable ones. Here, we show that bio-based limonene can be used as an alternative expander molecule for the synthesis of large-pore templated silica. On the basis of electron microscopy, nitrogen physisorption and small angle X-ray scattering we show that the substitution of TMB by limonene leads to very similar material characteristics, reaching mean mesopore diameters of 17–19 nm. A comparative life-cycle assessment demonstrates the reduced environmental impact of limonene production from citrus peel waste compared to TMB production, supporting the call for more applications of renewable chemicals, ideally from waste-streams, also for the production of porous materials.
description: This project was funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation)– project-ID 416229255 – SFB 1411 and project-ID 431791331 – SFB 1452. Additional DFG support by NFDI 10/1 DAPHNE4NFDI.
DOI: 10.5281/zenodo.8158744
title: Raw and metadata for: Substituting fossil-based with bio-based chemicals: the case of limonene as a greener pore expander for micellar templated silica

description: Raw and meta data for journal article : Substituting fossil-based with bio-based chemicals: the case of limonene as a greener pore expander for micellar templated silica DOI: 10.1039/D3SU00068K Abstract: Porous materials are widely used in applications such as adsorption, catalysis and separation. The use of expander molecules is a versatile route to enlarge the mesopore size in micellar templated mesoporous silica materials. Typical expanders used for this purpose are fossil-based organic molecules such as trimethylbenzene (TMB). In the course of making such syntheses greener and more sustainable, it is highly desirable to substitute such fossil-based chemicals with renewable ones. Here, we show that bio-based limonene can be used as an alternative expander molecule for the synthesis of large-pore templated silica. On the basis of electron microscopy, nitrogen physisorption and small angle X-ray scattering we show that the substitution of TMB by limonene leads to very similar material characteristics, reaching mean mesopore diameters of 17–19 nm. A comparative life-cycle assessment demonstrates the reduced environmental impact of limonene production from citrus peel waste compared to TMB production, supporting the call for more applications of renewable chemicals, ideally from waste-streams, also for the production of porous materials.
description: This project was funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation)– project-ID 416229255 – SFB 1411 and project-ID 431791331 – SFB 1452. Additional DFG support by NFDI 10/1 DAPHNE4NFDI.
DOI: 10.17909/vjys-x251
title: JWSTCycle1Orion

description: All data from the JWST Cycle 1 GTO programme 1256 surveying the inner Orion Nebula and Trapezium Cluster with NIRCam.
DOI: 10.5281/zenodo.8335875
title: Rubin AOS Simulations and Trained AI Model

description: This deposit saves the simulations of the Rubin Observatory AOS used to train a machine learning model for wavefront estimation. The simulations are in <em>aos_sims_archive.gz</em>. You can use gzip to unpack this archive, and there is a README that describes the format that the data was saved in. This simulated data was generated using the code in this repo: https://github.com/jfcrenshaw/donut-sims The trained ML model is also saved here. This model is defined, trained, etc in the code in this repo: https://github.com/jfcrenshaw/ml-aos
DOI: 10.5281/zenodo.8335874
title: Rubin AOS Simulations and Trained AI Model

description: This deposit saves the simulations of the Rubin Observatory AOS used to train a machine learning model for wavefront estimation. The simulations are in <em>aos_sims_archive.gz</em>. You can use gzip to unpack this archive, and there is a README that describes the format that the data was saved in. This simulated data was generated using the code in this repo: https://github.com/jfcrenshaw/donut-sims The trained ML model is also saved here. This model is defined, trained, etc in the code in this repo: https://github.com/jfcrenshaw/ml-aos