cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.vw8usj
title: Occurrence Download

description: A dataset containing 85686 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is EOD – eBird Observation Dataset",
 "Geometry POLYGON((-87.168 40.29502,-86.5644 40.29502,-86.5644 40.51886,-87.168 40.51886,-87.168 40.29502))",
 "HasGeospatialIssue is false",
 "Month is one of (May, June, July)",
 "Year 2020-2022"
 ]
}

 The dataset includes 85686 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0289770-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.dr8c54
title: Occurrence Download

description: A dataset containing 110 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is iNaturalist Research-grade Observations",
 "MediaType is Audio",
 "TaxonKey is Gekko gecko (Linnaeus, 1758)"
 ]
}

 The dataset includes 110 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0196310-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15486/ngt/2382698
title: Tropical root traits in response to global changes from 1984 to 2023

description: This dataset is a compilation of tropical root traits data in response to different global changes in tropical sites, considering 23.50N and S as latitudinal boundaries. The global changes considered are warming, drought, flooding, cyclones, nitrogen addition, CO2 fertilization, and fire. This dataset contains 266 root trait observations from 93 studies across 24 tropical countries. The full citation from where the data was taken from is provided in the dataset, as well as the global change, the ecosystem type, location, coordinates, the root traits measured, and the direction of their response after the global change. Additional information such as the duration of the experiment, the intensity of the global change, the soil layers from where the roots were collected, the root orders, and the type of experiment are also shown. We obtained this dataset by performing a systematic literature review on Web of Science using standardized keywords in English, Spanish, and Portuguese (Yaffar, Lugli et al. in press).
DOI: 10.15486/ngt/2425967
title: Files and scripts to support manuscript Needham et al. Canopy Gradients of Respiration

description: This dataset includes the parameter files, relevant output files, and scripts to perform analysis with Jupyter notebooks that support the manuscript Needham et al 2025 “Canopy Gradients of Respiration Drive Plant Carbon Budgets and Leaf Area Index.” We add functionality to the Functionally Assembled Terrestrial Ecosystem Simulator (FATES) to allow flexible vertical gradients of leaf maintenance respiration (Rdark) and maximum carboxylation rate (Vcmax) through the canopy. We test the sensitivity of FATES to canopy gradients in Rdark, both in global simulations to assess broad scale impacts on leaf area index (LAI) and vegetation carbon, and in single site simulations where we assess impacts on plant functional type (PFT) competitive dynamics. Parameter files are netcdf files that can be converted to human readable .cdl files using NCO tools. Analysis scripts are Jupyter notebook files. These can be opened and run using the open source Jupyter notebook software. Model outputs are netcdf files.
DOI: 10.6084/m9.figshare.28389005
title: Diaozotroph MAGs recovered from global marine ecosystems

description: For each environment, clean reads were co-assembled using MEGAHIT v1.2.9 (parameters: --k-min 27 --k-max 147 --k-step 12) and then mapped to their assembly using Bowtie2 v2.4.4 (default parameters) to obtain the contigs coverage. The assembled metagenomic sequences were binned using MetaBAT2 v2.12.1 and CONCOCT v1.1.0 with 1.5 kb as contig length cut-offs. The two bin sets for each assembly were refined using the metaWRAP Bin_refinement module (parameters: -c 50). The identification of diazotroph MAGs was performed using the Diaiden pipeline (https://github.com/jchenek/Diaiden).
DOI: 10.15468/dl.q9gree
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 }
 ]
 },
 "TaxonKey is Letheobia sudanensis (Schmidt, 1923)"
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001233-240314170635999/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.urvdau
title: Occurrence Download

description: A dataset containing 9 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 }
 ]
 },
 "TaxonKey is Pithecia mittermeieri Marsh, 2014"
 ]
}

 The dataset includes 9 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0073055-240229165702484/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.wafqjm
title: Occurrence Download

description: A dataset containing 355 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Macadamia ternifolia F.Muell."
 ]
}

 The dataset includes 355 records from 42 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011732-171219132708484/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.s4j8ka
title: Occurrence Download

description: A dataset containing 54856 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Chondrilla juncea L."
 ]
}

 The dataset includes 54856 records from 704 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002308-240229165702484/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.gzbsju
title: Occurrence Download

description: A dataset containing 9983 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Chlorophonia occipitalis (Du Bus de Gisignies, 1847)"
 ]
}

 The dataset includes 9983 records from 63 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001270-240314170635999/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.dffbn6
title: Occurrence Download

description: A dataset containing 1738 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Panthera tigris (Linnaeus, 1758)"
 ]
}

 The dataset includes 1738 records from 80 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011733-160311141623029/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.wmsf8z
title: Occurrence Download

description: A dataset containing 65 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Alocasia sanderiana W.Bull"
 ]
}

 The dataset includes 65 records from 23 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002320-240229165702484/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.muhvt5
title: Occurrence Download

description: A dataset containing 297 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Mexico",
 "TaxonKey is Agave shawii subsp. goldmaniana (Trel.) Gentry"
 ]
}

 The dataset includes 297 records from 22 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0025058-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ejsvzs
title: Occurrence Download

description: A dataset containing 34 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Campanula vardariana Bocquet"
 ]
}

 The dataset includes 34 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0071050-240229165702484/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ix9ukb
title: Occurrence Download

description: A dataset containing 635 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Sturnira lilium (E.Geoffroy, 1810)",
 "Country is Brazil"
 ]
}

 The dataset includes 635 records from 24 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011734-160118175350007/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.k8zjht
title: Occurrence Download

description: A dataset containing 5 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Castanopsis arietina Hickel & A.Camus"
 ]
}

 The dataset includes 5 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001240-240314170635999/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ttio6y
title: Occurrence Download

description: A dataset containing 696 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "or" : [
 "PublishingOrg is 021121c0-f040-11d8-b22f-b8a03c50a862",
 "PublishingOrg is b4640710-8e03-11d8-b956-b8a03c50a862",
 "PublishingOrg is ff418020-1d67-11d9-8435-b8a03c50a862",
 "PublishingOrg is 49355de0-eb1f-11dc-ad06-b8a03c50a862",
 "PublishingOrg is 8edbbde0-055e-11d8-b850-b8a03c50a862",
 "PublishingOrg is b554c320-0560-11d8-b851-b8a03c50a862",
 "PublishingOrg is 7b8aff00-a9f8-11d8-944b-b8a03c50a862",
 "PublishingOrg is ff90b050-c256-11db-b71b-b8a03c50a862",
 "PublishingOrg is bc092ff0-02e4-11dc-991f-b8a03c50a862",
 "PublishingOrg is c76cf030-2a95-11da-9cc1-b8a03c50a862"
 ]
 },
 "TaxonKey is Campylopterus hemileucurus hemileucurus"
 ]
}

 The dataset includes 696 records from 16 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011734-170714134226665/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.uqnfjc
title: Occurrence Download

description: A dataset containing 2725 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Echinochloa crus-galli (L.) P.Beauv.",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Country is Japan"
 ]
}

 The dataset includes 2725 records from 60 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0010497-240216155721649/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ysw3fx
title: Occurrence Download

description: A dataset containing 10 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Clerodendrum urticifolium (Roxb.) Wall. ex Voigt"
 ]
}

 The dataset includes 10 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001281-240314170635999/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.gbyc0w
title: Occurrence Download

description: A dataset containing 456 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Agave salmiana Otto ex Salm-Dyck"
 ]
}

 The dataset includes 456 records from 29 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011735-160118175350007/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ad5czq
title: Occurrence Download

description: A dataset containing 63 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Centaurea soskae Hayek ex Kosanin"
 ]
}

 The dataset includes 63 records from 18 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001254-240314170635999/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.r2hjm7
title: Occurrence Download

description: A dataset containing 26 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Argentina",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Herpailurus yagouaroundi (É.Geoffroy Saint-Hilaire, 1803)"
 ]
}

 The dataset includes 26 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0010505-240216155721649/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.nbroav
title: Occurrence Download

description: A dataset containing 235962 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "or" : [
 "TaxonKey is Testudo graeca Perälä, 2002",
 "TaxonKey is Animalia"
 ]
 },
 "Country is Morocco"
 ]
}

 The dataset includes 235962 records from 420 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0059532-160910150852091/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.92nkwc
title: Occurrence Download

description: A dataset containing 1578 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Caeciliidae",
 "Continent is one of (North America, South America)"
 ]
}

 The dataset includes 1578 records from 116 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0020507-240216155721649/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.kh475u
title: Occurrence Download

description: A dataset containing 225989 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-19.17 20.09,44.08 20.09,44.08 58.75,-19.17 58.75,-19.17 20.09))",
 "OccurrenceStatus is Present",
 "TaxonKey is Testudines"
 ]
}

 The dataset includes 225989 records from 1545 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002859-250121130708018/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.9zmrhe
title: Occurrence Download

description: A dataset containing 2103550 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-19.17 20.09,44.08 20.09,44.08 58.75,-19.17 58.75,-19.17 20.09))",
 "OccurrenceStatus is Present",
 "TaxonKey is Squamata"
 ]
}

 The dataset includes 2103550 records from 6073 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002855-250121130708018/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.buppkg
title: Occurrence Download

description: A dataset containing 974 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Mexico",
 "TaxonKey is Leptonycteris yerbabuenae Martínez & Villa-R., 1940",
 "Year 2004-2024"
 ]
}

 The dataset includes 974 records from 27 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0036140-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.7z4caf
title: Occurrence Download

description: A dataset containing 8673 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Liatris aspera Michx."
 ]
}

 The dataset includes 8673 records from 153 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0036142-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25574/01110
title: Chandra X-ray Observatory ObsId 01110
DOI: 10.25345/c5gq6rd4s
title: MassIVE MSV000095439 - Non-targeted microbial metabolomics (DDA) of extracts from methanotroph cocultures
title: Non-targeted microbial metabolomics (DDA) of extracts from methanotroph cocultures
DOI: 10.15468/dl.zyzfqf
title: Occurrence Download

description: A dataset containing 148687 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Diospyros L."
 ]
}

 The dataset includes 148687 records from 924 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0036128-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.yk6vup
title: Occurrence Download

description: A dataset containing 176 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Lolium multiflorum x perenne)",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "HasGeospatialIssue is false",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Specimen)"
 ]
 }
 }
 ]
}

 The dataset includes 176 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0036144-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.s8t42y
title: Occurrence Download

description: A dataset containing 6537 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Liatris pycnostachya Michx."
 ]
}

 The dataset includes 6537 records from 143 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0036143-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.12751946
title: ZymoSoups: A high-throughput forward genetics method for rapid identification of virulence genes in Zymoseptoria tritici

description: These data were used to generate figures and summarise the number of mutations in 18 re-sequenced genomes of Zymoseptoria tritici. The isolates genotyped in this VCF file are all UV-mutegenized strains of the reference isolate IPO323.

Abstract

Septoria tritici blotch is caused by the fungus Zymoseptoria tritici and poses a major threat to wheat productivity. There are over twenty mapped loci in wheat that confer strong (gene-for-gene) resistance against this pathogen, however the corresponding genes in Z. tritici that confer virulence against distinct R genes remain largely unknown. In this study, we developed a rapid forward genetics methodology to identify genes that enable Z. tritici to gain virulence on previously resistant wheat varieties. We used the known gene-for-gene interaction between Stb6 and AvrStb6 as a proof of concept that this method could quickly recover single candidate virulence genes. We subjected the avirulent Z. tritici strain IPO323, which carries the recognized AvrStb6 allele, to UV mutagenesis and generated a library of over 66,000 surviving spores. We screened these survivors on leaves of the resistant wheat variety Cadenza, in mixtures (soups) ranging from 100-500 survivors per soup. We identified five soups with a gain-of-virulence (GoV) phenotype relative to the IPO323 parental strain and re-sequenced 18 individual isolates, including four control isolates and two isolates lacking virulence, when screened individually. Of the 12 confirmed GoV isolates, one had a single nucleotide polymorphism (SNP) in the AvrStb6 coding region. The other 11 GoV isolates exhibited large (~70Kb) deletions at the end of chromosome 5, including the AvrStb6 locus. Our findings demonstrate the efficiency of this forward genetic approach in elucidating the genetic basis of qualitative resistance to Z. tritici and the potential to rapidly identify other, currently unknown, Avr genes in this pathogen. 

Analysis pipeline

The pipeline used to generate this filtered vcf file and tab delimited file is publicly available at https://github.com/megancamilla/GATK4_Zymoseptoria

Isolate Data Accessibility

The individual fastq files for each isolate included in this study have been uploaded to NCBI's Short Read Archive (SRA), project number PRJNA1017776. This project contains 18 re-sequenced samples (SAMN37407989-SAMN37407972), which are UV mutagenized IPO323. Short Read Archive (SRA) accession numbers are SRR26072101-SRR26072118.
DOI: 10.5281/zenodo.12751947
title: ZymoSoups: A high-throughput forward genetics method for rapid identification of virulence genes in Zymoseptoria tritici

description: These data were used to generate figures and summarise the number of mutations in 18 re-sequenced genomes of Zymoseptoria tritici. The isolates genotyped in this VCF file are all UV-mutegenized strains of the reference isolate IPO323.

Abstract

Septoria tritici blotch is caused by the fungus Zymoseptoria tritici and poses a major threat to wheat productivity. There are over twenty mapped loci in wheat that confer strong (gene-for-gene) resistance against this pathogen, however the corresponding genes in Z. tritici that confer virulence against distinct R genes remain largely unknown. In this study, we developed a rapid forward genetics methodology to identify genes that enable Z. tritici to gain virulence on previously resistant wheat varieties. We used the known gene-for-gene interaction between Stb6 and AvrStb6 as a proof of concept that this method could quickly recover single candidate virulence genes. We subjected the avirulent Z. tritici strain IPO323, which carries the recognized AvrStb6 allele, to UV mutagenesis and generated a library of over 66,000 surviving spores. We screened these survivors on leaves of the resistant wheat variety Cadenza, in mixtures (soups) ranging from 100-500 survivors per soup. We identified five soups with a gain-of-virulence (GoV) phenotype relative to the IPO323 parental strain and re-sequenced 18 individual isolates, including four control isolates and two isolates lacking virulence, when screened individually. Of the 12 confirmed GoV isolates, one had a single nucleotide polymorphism (SNP) in the AvrStb6 coding region. The other 11 GoV isolates exhibited large (~70Kb) deletions at the end of chromosome 5, including the AvrStb6 locus. Our findings demonstrate the efficiency of this forward genetic approach in elucidating the genetic basis of qualitative resistance to Z. tritici and the potential to rapidly identify other, currently unknown, Avr genes in this pathogen. 

Analysis pipeline

The pipeline used to generate this filtered vcf file and tab delimited file is publicly available at https://github.com/megancamilla/GATK4_Zymoseptoria

Isolate Data Accessibility

The individual fastq files for each isolate included in this study have been uploaded to NCBI's Short Read Archive (SRA), project number PRJNA1017776. This project contains 18 re-sequenced samples (SAMN37407989-SAMN37407972), which are UV mutagenized IPO323. Short Read Archive (SRA) accession numbers are SRR26072101-SRR26072118.