cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.82250/3003519
title: Pichia sp. yHMH446 translation elongation factor 1-alpha gene, partial cds

description: A novel budding yeast species was isolated from a soil sample collected in the United States of America. Phylogenetic analyses of multiple loci and phylogenomic analyses conclusively placed the species within the genus Pichia. Strain yHMH446 falls within a clade that includes Pichia norvegensis, Pichia pseudocactophila, Candida inconspicua, and Pichia cactophila. Whole genome sequence data were analyzed for the presence of genes known to be important for carbon and nitrogen metabolism, and the phenotypic data from the novel species were compared to all Pichia species with publicly available genomes. Across the genus, including the novel species candidate, we found that the inability to use many carbon and nitrogen sources correlated with the absence of metabolic genes. Based on these results, Pichia galeolata sp. nov. is proposed to accommodate yHMH446(T) (=NRRL Y-64187 = CBS 16864). This study shows how integrated taxogenomic analysis can add mechanistic insight to species descriptions.
DOI: 10.82250/3003522
title: Genomic and transcriptomic analysis of Saccharomyces eubayanus isolates

description: WGS and RNA-seq of Saccharomyces eubayanus strain yHRVM108 and derivatives
DOI: 10.82250/3003523
title: The Genetics of Aerotolerant Growth in Zymomonas mobilis

description: Reduced genome bacteria are genetically simplified systems that facilitate biological study and industrial use. The free-living Alphaproteobacterium, Zymomonas mobilis, has a naturally reduced genome containing fewer than 2000 protein coding genes. Despite its small genome, Z. mobilis thrives in diverse conditions including the presence or absence of atmospheric oxygen. However, insufficient characterization of essential and conditionally essential genes has limited broader adoption of Z. mobilis as a model Alphaproteobacterium. Here, we use genome-scale CRISPRi-seq to systematically identify and characterize Z. mobilis genes that are conditionally essential for aerotolerant or anaerobic growth, or are generally essential across both conditions. Comparative genomics revealed that the essentiality of most "generally essential" genes was shared between Z. mobilis and other Alphaproteobacteria, validating Z. mobilis as reduced genome model. Among conditionally essential genes, we found that the DNA repair gene, recJ, was critical only for aerobic growth but reduced the mutation rate under both conditions. Further, we show that genes encoding the F1FO ATP synthase and Rnf respiratory complex are required for anaerobic growth of Z. mobilis. Combining CRISPRi partial knockdowns with metabolomics and membrane potential measurements, we determined that the ATP synthase generates membrane potential that is consumed by Rnf to power downstream processes. Rnf knockdown strains accumulated isoprenoid biosynthesis intermediates, suggesting a key role for Rnf in powering essential biosynthetic reactions. Our work establishes Z. mobilis as a streamlined model for alphaproteobacterial genetics, has broad implications in bacterial energy coupling, and informs Z. mobilis genome manipulation for optimized production of valuable isoprenoid-based bioproducts
DOI: 10.82250/3003527
title: Properties of soil pore space regulate pathways of plant residue decomposition and community structure of associated bacteria

description: The goal of this study is to explore interactions between plant detritus and the micro-scale characteristics of physical micro-environments, that is, soil pores, and their influence on decomposition, on CO2 emission, and on composition of bacterial communities associated with the detritus. The study consisted of a series of soil incubation experiments with samples of contrasting pore characteristics with/without plant residue, accompanied by analyses of soil pores and phylogenetic analysis of microbial communities with rRNA genes via pyrosequencing.
DOI: 10.82250/3003528
title: Terpene addition Sorghum

description: Examining the effects of terpene addition on the microbial community in Sorghum belowground compartments
DOI: 10.82250/3003529
title: Kellogg Biological Station, Biofuel Cropping System Experiment 

description: High-throughput amplicon sequencing of the ITS, 16S and 18S regions from soil, roots and leaves DNAs of the 50 plots present in the BCSE (Biofuel Cropping System Experiment) experiment at Kellogg Biological Station.
DOI: 10.82250/3003533
title:  Arabidopsis thaliana strain:Col-3 Raw sequence reads

description: We performed RNA sequencing (RNA-seq) analyses in Col-0 and tgnap1-2 at 24 h of treatment with Pst DC3000 in three biological replicates. Mock controls, which were treated with 10 mM MgCl2, were included.
DOI: 10.82250/3003535
title: Arabidopsis thaliana strain:Col-0 Raw sequence reads

description: To investigate transcriptome changes in pir1-1 mutants, we performed RNA sequencing (RNA-seq) analyses in Col-0 and pir1-1at 24 h of adaptive endoplasmic reticulum stress in three biological replicates. Mock controls, which were treated with DMSO, are included.
DOI: 10.82250/3003537
title: Natural variation in the consequences of gene overexpression during osmotic stress [BAR-Seq]

description: We conducted a barcode sequencing experiment examining 4 yeast strains expressing a high copy number plasmid library. For each strain, we took samples at generation 0 (start of experiment) and generation 10 to quantify how plasmid abundance changes over time when strains were grown under osmotic and ionic stress induced by 0.7M of sodium chloride (NaCl). Each strain was measured in biological triplicate for a total of 24 samples.
DOI: 10.82250/3003538
title: Natural variation in the consequences of gene overexpression during osmotic stress [RNA-Seq]

description: RNA-seq and transcriptome analysis of 4 strains (BY4743, BC187, NCYC3290, and YPS128) that were grown in YPD+ 0.7M NaCl. For each strain, 3 samples were collected: T0 (unstressed cells), T30 (30 mins after cells placed in 0.7M NaCl), and T3h (3 hours after cells placed in NaCl). These strains were collected in 3 biological replicates. The library for sample YPS128 Rep 3 T30 failed so this sample is missing and there are a total of 35 samples in the dataset.
DOI: 10.82250/3003539
title: PKA regulatory subunit Bcy1 couples growth, lipid metabolism, and fermentation during anaerobic xylose growth in Saccharomyces cerevisiae

description: Past work from our lab, focused on engineering the budding yeast Saccharomyces cerevisiae for fermentation of the non-native pentose sugar xylose, discovered that hyperactivation of the RAS/Protein Kinase A (PKA) pathway was needed for rapid anaerobic xylose fermentation. Interestingly, the mechanism of PKA hyperactivation has a dramatic impact on growth and metabolism on xylose; deletion of the RAS inhibitor IRA2 permits rapid growth and fermentation, while deletion of the PKA regulatory subunit BCY1 allows for fermentation without growth on xylose. To understand how a single deletion in the PKA pathway can decouple growth and metabolism, we performed transcriptomic analysis of these strains, predicting that altered PKA activity would impact global gene expression and identify pathways important for growth and metabolism coordination.
DOI: 10.82250/3003542
title: Aureobasidium pullulans strain CRUB 1823, whole genome shotgun sequencing project

description: Aureobasidium pullulans strain CRUB 1823, whole genome shotgun sequencing project.
DOI: 10.82250/3003543
title: Aureobasidium pullulans strain CRUB 1823

description: Aureobasidium pullulans strain CRUB 1823 de novo genome assembly and annotation
DOI: 10.82250/3003546
title: Aureobasidium pullulans strain CRUB 1823 mtDNA annotation

description: Aureobasidium pullulans strain CRUB 1823 mtDNA annotation
DOI: 10.82250/3003548
title: bioreactor sludge metagenome

description: Anaerobic fermentation bioreactor microbial communities from Madison, Wisconsin, United States. The goal of this study is to characterize a central set of genes relevant to medium chain fatty acid (MCFA) production to guide screens of putative MCFA-producing microorganisms from additional environments or grown on different substrates.
DOI: 10.82250/3003549
title: Soil and root bacterial communities of Switchgrass and other biofuel grasses in the Michigan and Wisconsin (2018)

description: Meta-amplicon sequencing of the soil bacterial community of Switchgrass (var. Cave-n-Rock) along with other biofuel grasses with the Great Lakes Bioenergy Research Center Marginal Lands Experiment. Samples were collected in 2018.
DOI: 10.82250/3003550
title: Soil and root bacterial communities of Switchgrass and other biofuel grasses in the Michigan and Wisconsin (2018)

description: Meta-amplicon sequencing of the soil fungal community of Switchgrass (var. Cave-n-Rock) of the Great Lakes Bioenergy Research Center Marginal Lands Experiment. Samples were collected in 2018.
DOI: 10.82250/3003553
title: Sorghum epicuticular wax and aerial root mucilage microbiomes

description: Phyllosphere exudates select for distinct microbiome members in sorghum epicuticular wax and aerial root mucilage. We investigated the microbial communities associated with field-grown energy sorghum epicuticular wax and aerial root mucilage. Sequence data includes 16S rRNA amplicons and ITS amplicons.
DOI: 10.82250/3003557
title: Piromyces sp. TSL-2022a strain:E1

description: ITS1 and LSU regions from Piromyces macparvus
DOI: 10.82250/3003558
title: Three de novo Lamiaceae genomes

description: 10X de novo sequencing of Prunella vulgaris, Leonotis leonurus, and Plectranthus barbatus.
DOI: 10.82250/3003560
title: Seasonal dynamics of switchgrass and miscanthus phyllosphere microbiota: community structure and function
DOI: 10.82250/3003561
title: phyllosphere metagenome

description: Genome-centric analyses of seasonal phyllosphere microbiome activities in perennial crops
DOI: 10.15468/dl.twbnjf
title: Occurrence Download

description: A dataset containing 26577 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Miniopterus schreibersii",
 "HasCoordinate is true"
 ]
}

 The dataset includes 26577 records from 173 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0045471-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.82250/3003565
title: Genome characterization of Saccharomyces genus

description: Genome sequencing of multiple lineages from the Saccharomyces genus
DOI: 10.15468/dl.ew4smz
title: Occurrence Download

description: A dataset containing 116 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Ecuador",
 "Geometry POLYGON((-79.92029 -3.17641,-80.2673 -3.36003,-80.12503 -3.91758,-79.40326 -3.90027,-79.43102 -3.34617,-79.92029 -3.17641))",
 "HasGeospatialIssue is false",
 "TaxonKey is Cactaceae"
 ]
}

 The dataset includes 116 records from 14 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0045470-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.82250/3003566
title: Macroevolutionary diversity of traits and genomes in the model yeast genus Saccharomyces

description: Here, we show the geographies, hosts, substrates, and phylogenetic relationships for approximately 1,800 Saccharomyces strains, covering the complete genus with unprecedented breadth and depth.
DOI: 10.82250/3003569
title: The stem cell-type transcriptome of bioenergy sorghum reveals the spatial regulation of secondary cell wall networks  

description: Stems accumulate high levels of sucrose that could be used to synthesize bioethanol and useful biopolymers if information about stem cell-type gene expression and regulation was available to enable engineering. To obtain this information, Laser Capture Microdissection (LCM) was used to isolate and collect transcriptome profiles from five major cell types that are present in stems of the sweet sorghum Wray. Transcriptome analysis identified genes with cell-type specific and cell-preferred expression patterns that reflect the distinct metabolic, transport, and regulatory functions of each cell type.
DOI: 10.15468/dl.wk3jbq
title: Occurrence Download

description: A dataset containing 6805 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry MULTIPOLYGON(((0.32417 47.64218,0.33737 47.64698,0.3558 47.67127,0.36965 47.67589,0.36826 47.67868,0.36078 47.68537,0.35613 47.68386,0.3521 47.68604,0.33347 47.702,0.31814 47.7029,0.31344 47.70165,0.30038 47.69723,0.29204 47.70055,0.29364 47.6936,0.28083 47.66321,0.27229 47.6595,0.25832 47.66246,0.24606 47.6565,0.2679 47.64864,0.31289 47.65336,0.32145 47.64509,0.32417 47.64218)))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 6805 records from 47 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0045473-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.adj3px
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Lepus saxatilis",
 "Country is Brazil",
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 },
 {
 "or" : [
 "CoordinateUncertaintyInMeters is less than 10000",
 "CoordinateUncertaintyInMeters is null"
 ]
 }
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0045472-251025141854904/datasets/export for details.
DOI: 10.82250/3003572
title: Stable isotope probing of the glucose added soils(total DNA)

description: The objective of this project is to investigate the effect of plant diversity and the soil pore sizes on the active microorganisms utilizing the newly added carbon.
DOI: 10.82250/3003573
title: Stable isotope probing of the glucose added soils (fraction)

description: The objective of this study is to investigate the effect of plant diversity and soil pore sizes on the active microorganisms utilizing the newly added carbon.
DOI: 10.82250/3003574
title: Scheffersomyces xylosifermentans CBS 12540 Transcriptome - 10G3

description: Scheffersomyces xylosifermentans CBS 12540 Transcriptome; Cultures grown on xylose
DOI: 10.82250/3003575
title: Scheffersomyces coipomoensis NRRL Y-17651 Transcriptome - 7G7

description: Scheffersomyces coipomensis NRRL Y-17651 Transcriptome; Cultures grown on xylose
DOI: 10.82250/3003576
title: Scheffersomyces xylosifermentans CBS 12540 Standard Draft genome sequencing

description: Genome sequencing of yeast species that harbor traits desirable for biofuel production
DOI: 10.82250/3003577
title: Scheffersomyces coipomoensis NRRL Y-17651 Standard Draft genome sequencing

description: Genome sequencing of yeast species that harbor traits desirable for biofuel production
DOI: 10.82250/3003578
title: Tracking alternative versions of the galactose gene network in the genus Saccharomyces and their expansion after domestication

description: In this yeast, the study of trait variation at the population level led to the detection of distinct sets of GAL structural genes. Besides the reference version, present in most strains, alternative highly divergent alleles supporting faster growth on galactose were recently uncovered in strains associated with dairy products and also in some wild strains.
DOI: 10.82250/3003579
title: Nucleotide sequence

description: Saccharomyces kudriavzevii isolate AH052 alpha-1,2-mannosyltransferase MNN2 (MNN2) and Transportin (KAP104) genes, complete cds; GAL7, GAL10, and GAL1 pseudogenes, complete sequence; and Plasma membrane localized uracil permease (FUR4), Phosphatase Of ADP-ribose 1'-phosphate (POA1), and chitin synthase CHS3 (CHS3) genes, complete cds
DOI: 10.82250/3003584
title: Cropland abandonment between 1986 and 2018 across the United States: spatiotemporal patterns and current land uses

description: The data that support the findings of this study are openly available at the following URL/DOI: https://atlas.glbrc.org/.
DOI: 10.82250/3003585
title: PagMYB128 RNA-seq

description: PagMYB128 RNA-seq contains WT, SRDX and OE plants xylem RNA.
DOI: 10.15468/dl.etm9y9
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Microtus oeconomus mehelyi",
 "HasCoordinate is true"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0045474-251025141854904/datasets/export for details.
DOI: 10.82250/3003587
title: Lignin engineering in poplar via heterologous expression of dehydroshikimate dehydratase induces distinct transcriptional and metabolic changes in the shikimate and phenylpropanoid pathways

description: Understanding how crops respond to such genetic modifications at the transcriptional and metabolic levels is needed to facilitate further improvement and field deployment. In this work, we gathered some fundamental knowledge on lignin-modified QsuB poplar grown in a greenhouse using RNA-seq and metabolomics.
DOI: 10.82250/3003591
title: Effect of temperature and pH on microbial communities fermenting a dairy coproduct mixture

description: Metagenome-Assembled-Genomes from Microbiomes Fermenting Dairy Coproducts
DOI: 10.82250/3003592
title: <html>RNA-seq studying the catabolism of β-5 linked aromatics by <i>Novosphingobium aromaticivorans</i></html>

description: RNA-seq comparison of transcript abundance in a PDC-producing N. aromaticivorans strain (12444PDC) grown in the presence of dehydrodiconiferyl alcohol (DC-A) and glucose, vanillin and glucose, ferulic acid and glucose, or glucose alone
DOI: 10.82250/3003594
title: Population genomics identify the requirement of BAP2 in the sufficiency of IRE1 in the UPR

description: Sequencing reads archived here are part of a project studying natural variation in ER stress responses in Arabidopsis reported in Pastor-Cantizano et al. 2024. The project focused on contrasting alleles derived from Na-1 (tolerant) and Est-0 (susceptible) accessions when exposed to a ER stress inducer. These accession were crossed, F3 progeny were phenotyped, and the top and bottom 10% of relative performance under ER stress (42 individuals from each tail) were pooled and sequenced. Candidate genomic regions were identified by looking for allele frequency differences among the two pools in a standard QTL-seq approach
DOI: 10.82250/3003597
title: Measuring surface albedo for various crops

description: Surface albedo can affect the energy budget and subsequently cause localized warming or cooling
of the climate. When we convert a substantial portion of lands to agriculture, land surface
properties are consequently altered, including albedo. Through crop selection and management,
one can increase crop albedo to obtain higher levels of localized cooling effects to mitigate global
warming. Still, there is little understanding about how distinctive features of a cropping system
may be responsible for elevated albedo and consequently for the cooling potential of cultivated
lands. To address this pressing issue, we conducted seasonal measurements of surface reflectivity
during five growing seasons on annual crops of corn-soybean–winter wheat
DOI: 10.82250/3003595
title: CYP76BK1 orthologs catalyze furan and lactone ring formation in clerodane diterpenoids across the mint family

description: CYP76BK1 orthologs catalyze furan and lactone ring formation in clerodane diterpenoids across the mint family
DOI: 10.82250/3003596
title: 16S rRNA squencing to identify microbiomes associated with different crops and different growing conditions

description:  The microbiome associated with plant roots, the rhizobiome, can harbor beneficial microbes that alleviate stress, but the factors influencing their recruitment are unclear. We conducted a greenhouse experiment using field soil with a legacy of growing switchgrass and common bean to investigate the impact of short-term drought severity on the recruitment of active bacterial rhizobiome members. We applied 16S rRNA and 16S rRNA gene sequencing for both crops and metabolite profiling for switchgrass. We included planted and unplanted conditions to distinguish environment- versus plant-mediated rhizobiome drivers.
DOI: 10.82250/3003601
title: RNA-seq of Hanseniaspora, a yeast in the Saccharomycotina subphylum

description: Comparison of gene expression in fermentable vs nonfermentable carbon source across 2 Hanseniaspora species representing divergent metabolic traits.
DOI: 10.82250/3003603
title: <html>Genetic modification of the shikimate pathway to reduce lignin content in switchgrass (<i>Panicum virgatum</i> L.) significantly impacts plant microbiomes</html>

description: QsuB transgenic switchgrass associated 16S microbiome of different compartments
DOI: 10.82250/3003604
title: <html>Genetic modification of the shikimate pathway to reduce lignin content in switchgrass (<i>Panicum virgatum</i> L.) significantly impacts plant microbiomes</html>

description: QsuB transgenic switchgrass associated ITS microbiome of different compartments
DOI: 10.82250/3003610
title: Comparative modeling reveals the molecular determinants of aneuploidy fitness cost in a wild yeast model

description: gene duplication screen raw sequencing and barcode counts, on GEO
DOI: 10.82250/3003608
title: Bioenergy sorghum nodal root bud development: morphometric, transcriptomic and gene regulatory network analysis

description: Sorghum bicolor TX08001 Nodal Root Tissue Development Gene Expression Profiling
DOI: 10.82250/3003609
title: Comparative modeling reveals the molecular determinants of aneuploidy fitness cost in a wild yeast model

description: YPS1009-derivative strain genome assembly in NCBI, BioProject
DOI: 10.82250/3003612
title: Novosphingobium rhizosphaerae strain:LY

description: Whole genome sequencing of a pinoresinol-degrading bacterium
DOI: 10.82250/3003613
title: Novosphingobium rhizosphaerae strain LY chromosome, complete genome

description: Novosphingobium rhizosphaerae strain LY chromosome, complete genome
DOI: 10.82250/3003617
title: yHQL494_Lachancea_sp_nov_plate34_PLATANUS (SRR16988996)

description: yHQL494_Lachancea_sp_nov_plate34_PLATANUS (SRR16988996)
DOI: 10.82250/3003615
title: Novosphingobium rhizosphaerae strain LY plasmid pLY2, complete sequence

description: Novosphingobium rhizosphaerae strain LY plasmid pLY2, complete sequence
DOI: 10.82250/3003619
title: MTBLS12808: Physiological and Metabolic Responses of Zymomonas mobilis to Lignocellulosic Hydrolysate

description: <html>This study provides a systems-level evaluation of how <i>Zymomonas mobilis</i> responds to hydrolysate stress, revealing distinct physiological and lipid membrane remodeling responses.</html>
DOI: 10.82250/3003614
title: Novosphingobium rhizosphaerae strain LY plasmid pLY1, complete sequence

description: Novosphingobium rhizosphaerae strain LY plasmid pLY1, complete sequence
DOI: 10.82250/3003620
title: Physiological and Metabolic Responses of Zymomonas mobilis to Lignocellulosic Hydrolysate

description: This study provides a systems-level evaluation of how Zymomonas mobilis responds to hydrolysate stress, revealing distinct physiological and lipid membrane remodeling responses.
DOI: 10.82250/3003616
title: Lachancea sp. yHQL494, whole genome shotgun sequencing project

description: Lachancea sp. yHQL494, whole genome shotgun sequencing project
DOI: 10.82250/3003622
title: Tilletia maclaganii Tm001 NY21 standard draft genome sequencing

description: Tilletia maclaganii Tm001 NY21 genome; sample from smut-infected switchgrass cultivar 'Shawnee'