cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.jrhrb2
title: Occurrence Download

description: A dataset containing 47 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Ornithogalum creticum Zahar.",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 47 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0298244-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.jszc52
title: Occurrence Download

description: A dataset containing 302 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Alchemilla impexa Buser",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 302 records from 12 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0286514-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.jtda67
title: Occurrence Download

description: A dataset containing 73 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Euphorbia cuneifolia Guss.",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 73 records from 15 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0296968-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.jtduck
title: Occurrence Download

description: A dataset containing 2096 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Delphinium pubescens DC.",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 2096 records from 47 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0295558-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.jtj28w
title: Occurrence Download

description: A dataset containing 620 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Festuca burnatii St.-Yves",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 620 records from 14 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0297203-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ju8cn4
title: Occurrence Download

description: A dataset containing 16 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Aconitum toxicum Rchb.",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 16 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0415171-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.juebvq
title: Occurrence Download

description: A dataset containing 151 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Viola ferrarinii Moraldo & Ricceri",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 151 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0285727-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.juh6sx
title: Occurrence Download

description: A dataset containing 6344 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Centaurea decipiens Thuill.",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 6344 records from 179 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0293153-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25345/c5cv4c45t
title: MassIVE MSV000098025 - Protein identification in Ph. vulgaris
title: "Potential antiglycating effect and antioxidant activity of bioactive peptides of the protein hydrolysate of common beans (Phaseolus vulgaris L.) genotypes race Chile". Enzymatic digestion with alcalase
DOI: 10.6084/m9.figshare.29765669
title: Annotated lipid feature table of Bos taurus milk from three farms

description: <b>Dataset overview</b><br>This CSV file contains 451 lipid features detected in untargeted LC-MS analysis of bovine (Bos taurus) milk from three farms (groups <b>P</b>, <b>PP</b>, <b>V</b>; three technical replicates per farm). Presence of a lipid in a farm was defined as signal detected in <b>≥ 2 of 3 replicates</b> (no cross-farm imputation).<b>Annotation strategy</b>Level 1 (L1) – Exact cross-references already present in the original matrix (<code>LM_ID</code>, <code>KEGG_ID</code>, <code>HMDB_ID</code>).Level 4 (L4) – Class-only annotation where no unique database ID was available.<br>Additional mass-based and fuzzy-name matching layers (L2, L3) will be published in a future update.<b>Column definitions</b>
DOI: 10.6084/m9.figshare.29765669.v1
title: Annotated lipid feature table of Bos taurus milk from three farms

description: <b>Dataset overview</b><br>This CSV file contains 451 lipid features detected in untargeted LC-MS analysis of bovine (Bos taurus) milk from three farms (groups <b>P</b>, <b>PP</b>, <b>V</b>; three technical replicates per farm). Presence of a lipid in a farm was defined as signal detected in <b>≥ 2 of 3 replicates</b> (no cross-farm imputation).<b>Annotation strategy</b>Level 1 (L1) – Exact cross-references already present in the original matrix (<code>LM_ID</code>, <code>KEGG_ID</code>, <code>HMDB_ID</code>).Level 4 (L4) – Class-only annotation where no unique database ID was available.<br>Additional mass-based and fuzzy-name matching layers (L2, L3) will be published in a future update.<b>Column definitions</b>
DOI: 10.15468/dl.h23ujf
title: Occurrence Download

description: A dataset containing 21 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Senecio inaequidens",
 "Country is Croatia",
 "HasCoordinate is true"
 ]
}

 The dataset includes 21 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0085135-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.7qvv8k
title: Occurrence Download

description: A dataset containing 2278 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Lonicera rupicola"
 ]
}

 The dataset includes 2278 records from 77 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0085136-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6084/m9.figshare.28879210.v1
title: Additional file 3 of Evidence of pathogens associated with travelers’ diarrhea in Thailand: a systematic review

description: Supplementary Material 3
DOI: 10.6084/m9.figshare.28879196
title: Additional file 6 of Recombination and transposition drive genomic structural variation potentially impacting life history traits in a host-generalist fungal plant pathogen

description: Additional file 6: Supplementary Table 1. A BUSCO scores for all strains used to construct the pan-genome graph. B. Gaps and telomeres in each chromosome of each assembly. In the TELOMERES column, L stands for ‘left’ and R stands for ‘right’, referring to the two (arbitrary) ends of the chromosome in the assembly FASTA.
DOI: 10.6084/m9.figshare.28879196.v1
title: Additional file 6 of Recombination and transposition drive genomic structural variation potentially impacting life history traits in a host-generalist fungal plant pathogen

description: Additional file 6: Supplementary Table 1. A BUSCO scores for all strains used to construct the pan-genome graph. B. Gaps and telomeres in each chromosome of each assembly. In the TELOMERES column, L stands for ‘left’ and R stands for ‘right’, referring to the two (arbitrary) ends of the chromosome in the assembly FASTA.
DOI: 10.6084/m9.figshare.28879199
title: Additional file 7 of Recombination and transposition drive genomic structural variation potentially impacting life history traits in a host-generalist fungal plant pathogen

description: Additional file 7: Supplementary Table 2. Strains, excluding the reference strain, 1980, used to create the Sclerotinia sclerotiorum pan-genome and call structural variants. Strains with Nanopore and Illumina data were used to create the pan-genome graph whereas strains with only Illumina data (previous or current study) were used for mapping and variant calling against the graph.
DOI: 10.6084/m9.figshare.28879199.v1
title: Additional file 7 of Recombination and transposition drive genomic structural variation potentially impacting life history traits in a host-generalist fungal plant pathogen

description: Additional file 7: Supplementary Table 2. Strains, excluding the reference strain, 1980, used to create the Sclerotinia sclerotiorum pan-genome and call structural variants. Strains with Nanopore and Illumina data were used to create the pan-genome graph whereas strains with only Illumina data (previous or current study) were used for mapping and variant calling against the graph.
DOI: 10.6084/m9.figshare.28879202
title: Additional file 8 of Recombination and transposition drive genomic structural variation potentially impacting life history traits in a host-generalist fungal plant pathogen

description: Additional file 8: Supplementary Table 3. Results of phipack tests for recombination across the 120 independent Sclerotinia sclerotiorum lineages. These include the Neighbour Similarity Score (NSS), the Maximum Chi^2 (MAX_CHI2), and the Pairwise Homoplasy Index (PHI) tests. All tests were significant, with a P value of zero, indicating increasing levels of recombination between alleles with distance.
DOI: 10.6084/m9.figshare.28879202.v1
title: Additional file 8 of Recombination and transposition drive genomic structural variation potentially impacting life history traits in a host-generalist fungal plant pathogen

description: Additional file 8: Supplementary Table 3. Results of phipack tests for recombination across the 120 independent Sclerotinia sclerotiorum lineages. These include the Neighbour Similarity Score (NSS), the Maximum Chi^2 (MAX_CHI2), and the Pairwise Homoplasy Index (PHI) tests. All tests were significant, with a P value of zero, indicating increasing levels of recombination between alleles with distance.
DOI: 10.6084/m9.figshare.28879205
title: Additional file 9 of Recombination and transposition drive genomic structural variation potentially impacting life history traits in a host-generalist fungal plant pathogen

description: Additional file 9: Supplementary Table 4. A Spearman's rank correlation between distance from chromosome end and estimated recombination rate across the four population sub-samples and chromosomes (summarised in Figure 2 B). Rows highlighted in orange show a negative correlation and in green a positive. Grey rows were not significant. In most instances, there was a significant negative correlation between recombination rate and distance from chromosome end. B Recombination hotspots identified relative to the Sclerotinia sclerotiorum reference genome. Four non-structured population subsamples were used to identify hotspots.
DOI: 10.6084/m9.figshare.28879205.v1
title: Additional file 9 of Recombination and transposition drive genomic structural variation potentially impacting life history traits in a host-generalist fungal plant pathogen

description: Additional file 9: Supplementary Table 4. A Spearman's rank correlation between distance from chromosome end and estimated recombination rate across the four population sub-samples and chromosomes (summarised in Figure 2 B). Rows highlighted in orange show a negative correlation and in green a positive. Grey rows were not significant. In most instances, there was a significant negative correlation between recombination rate and distance from chromosome end. B Recombination hotspots identified relative to the Sclerotinia sclerotiorum reference genome. Four non-structured population subsamples were used to identify hotspots.
DOI: 10.6084/m9.figshare.28879208
title: Additional file 10 of Recombination and transposition drive genomic structural variation potentially impacting life history traits in a host-generalist fungal plant pathogen

description: Additional file 10: Supplementary Table 5. Sheets 1-6 are Cytosine methylation data from alignment of bisulfite sequencing reads to the 1980 genome. The first column is the NCBI chromosome accession. The columns for these tables are described in the CLC genomic workbench manual here: https://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=Call_Methylation_Levels.html . Each spreadsheet represents one of the samples, for example, 0 HPI R1 is 0 hours post-inoculation replicate 1. Sheet 7 (labelled'hotspot t-tests') is the results of t-tests to assess the difference between windows containing, or not containing, recombination hotspots, for gene density, number of structural variants, repeat density and SVπ.
DOI: 10.6084/m9.figshare.28879208.v1
title: Additional file 10 of Recombination and transposition drive genomic structural variation potentially impacting life history traits in a host-generalist fungal plant pathogen

description: Additional file 10: Supplementary Table 5. Sheets 1-6 are Cytosine methylation data from alignment of bisulfite sequencing reads to the 1980 genome. The first column is the NCBI chromosome accession. The columns for these tables are described in the CLC genomic workbench manual here: https://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=Call_Methylation_Levels.html . Each spreadsheet represents one of the samples, for example, 0 HPI R1 is 0 hours post-inoculation replicate 1. Sheet 7 (labelled'hotspot t-tests') is the results of t-tests to assess the difference between windows containing, or not containing, recombination hotspots, for gene density, number of structural variants, repeat density and SVπ.
DOI: 10.6084/m9.figshare.28879211
title: Additional file 11 of Recombination and transposition drive genomic structural variation potentially impacting life history traits in a host-generalist fungal plant pathogen

description: Additional file 11: Supplementary Table 6. Results of Dunn’s post hoc test to determine whether LTR transposons were significantly closer to structural variants across all genomes than other transposons. Transposon classifications are taken from EDTA.
DOI: 10.6084/m9.figshare.28879211.v1
title: Additional file 11 of Recombination and transposition drive genomic structural variation potentially impacting life history traits in a host-generalist fungal plant pathogen

description: Additional file 11: Supplementary Table 6. Results of Dunn’s post hoc test to determine whether LTR transposons were significantly closer to structural variants across all genomes than other transposons. Transposon classifications are taken from EDTA.
DOI: 10.6084/m9.figshare.28879214
title: Additional file 12 of Recombination and transposition drive genomic structural variation potentially impacting life history traits in a host-generalist fungal plant pathogen

description: Additional file 12: Supplementary Table 7. Transposable element content of the 24 Sclerotinia sclerotiorum genomes based on EDTA annotations.
DOI: 10.6084/m9.figshare.28879214.v1
title: Additional file 12 of Recombination and transposition drive genomic structural variation potentially impacting life history traits in a host-generalist fungal plant pathogen

description: Additional file 12: Supplementary Table 7. Transposable element content of the 24 Sclerotinia sclerotiorum genomes based on EDTA annotations.
DOI: 10.6084/m9.figshare.28879217.v1
title: Additional file 13 of Recombination and transposition drive genomic structural variation potentially impacting life history traits in a host-generalist fungal plant pathogen

description: Additional file 13: Supplementary Table 8. Spearman’s correlation between estimated recombination rate and SVπ, SV count and transposon content of 50,000 bp sliding windows. Rows coloured in green are significant positive correlations, those in red are significant negative correlations and those not coloured are not significant. Overall, the majority of chromosomes and populations showed a correlation between recombination rate and both SVπ and SV count but not transposon content.
DOI: 10.6084/m9.figshare.28879220
title: Additional file 14 of Recombination and transposition drive genomic structural variation potentially impacting life history traits in a host-generalist fungal plant pathogen

description: Additional file 14: Supplementary Table 9. Functional terms associated with genes in the largest gene bubble. Results are from an InterProScan analysis. The Gene IDs are based on a cd-hit grouping of Braker3 annotations across all genomes.
DOI: 10.6084/m9.figshare.28879220.v1
title: Additional file 14 of Recombination and transposition drive genomic structural variation potentially impacting life history traits in a host-generalist fungal plant pathogen

description: Additional file 14: Supplementary Table 9. Functional terms associated with genes in the largest gene bubble. Results are from an InterProScan analysis. The Gene IDs are based on a cd-hit grouping of Braker3 annotations across all genomes.
DOI: 10.6084/m9.figshare.28879223
title: Additional file 15 of Recombination and transposition drive genomic structural variation potentially impacting life history traits in a host-generalist fungal plant pathogen

description: Additional file 15: Supplementary Table 10. Genetic and actual correlations between life history traits. Where genetic correlations are above 1, below -1 or ‘NA’, the model was likely poorly or over-fit.
DOI: 10.6084/m9.figshare.28879217
title: Additional file 13 of Recombination and transposition drive genomic structural variation potentially impacting life history traits in a host-generalist fungal plant pathogen

description: Additional file 13: Supplementary Table 8. Spearman’s correlation between estimated recombination rate and SVπ, SV count and transposon content of 50,000 bp sliding windows. Rows coloured in green are significant positive correlations, those in red are significant negative correlations and those not coloured are not significant. Overall, the majority of chromosomes and populations showed a correlation between recombination rate and both SVπ and SV count but not transposon content.
DOI: 10.6084/m9.figshare.28879223.v1
title: Additional file 15 of Recombination and transposition drive genomic structural variation potentially impacting life history traits in a host-generalist fungal plant pathogen

description: Additional file 15: Supplementary Table 10. Genetic and actual correlations between life history traits. Where genetic correlations are above 1, below -1 or ‘NA’, the model was likely poorly or over-fit.
DOI: 10.6084/m9.figshare.28879226
title: Additional file 16 of Recombination and transposition drive genomic structural variation potentially impacting life history traits in a host-generalist fungal plant pathogen

description: Additional file 16: Supplementary Table 11. Tests for overall impact of SVs on phenotype. Grey cells are for test statistics that were not significant. Green cells are for test statistics that indicate in increase in SV impact on phenotype. Red cells are for test statistics that indicate a decrease in SV impact on phenotype.
DOI: 10.6084/m9.figshare.28879226.v1
title: Additional file 16 of Recombination and transposition drive genomic structural variation potentially impacting life history traits in a host-generalist fungal plant pathogen

description: Additional file 16: Supplementary Table 11. Tests for overall impact of SVs on phenotype. Grey cells are for test statistics that were not significant. Green cells are for test statistics that indicate in increase in SV impact on phenotype. Red cells are for test statistics that indicate a decrease in SV impact on phenotype.
DOI: 10.6084/m9.figshare.28879229
title: Additional file 17 of Recombination and transposition drive genomic structural variation potentially impacting life history traits in a host-generalist fungal plant pathogen

description: Additional file 17: Supplementary Table 12. Linear mixed models testing improvement in predictive ability (Pearson’s ρ) from models with no SVs in the genomic relationship to matrix to models with two terms, one for SVs and the other for non-SVs, or to models with only SVs. Improvements in predictive ability were variable but some traits showed a relatively large improvement.
DOI: 10.6084/m9.figshare.28879229.v1
title: Additional file 17 of Recombination and transposition drive genomic structural variation potentially impacting life history traits in a host-generalist fungal plant pathogen

description: Additional file 17: Supplementary Table 12. Linear mixed models testing improvement in predictive ability (Pearson’s ρ) from models with no SVs in the genomic relationship to matrix to models with two terms, one for SVs and the other for non-SVs, or to models with only SVs. Improvements in predictive ability were variable but some traits showed a relatively large improvement.
DOI: 10.6084/m9.figshare.28879232
title: Additional file 18 of Recombination and transposition drive genomic structural variation potentially impacting life history traits in a host-generalist fungal plant pathogen

description: Additional file 18: Supplementary Table 13. A Results of a GWAS for 14 life history traits. B BLASTp hits for gene downstream of 48 bp InDel azoxystrobin QTL, which encodes a centrosomin. C BLASTp hits for gene upstream of 48 bp InDel azoxystrobin QTL, which encodes a protein with no known functional domains.
DOI: 10.6084/m9.figshare.28879232.v1
title: Additional file 18 of Recombination and transposition drive genomic structural variation potentially impacting life history traits in a host-generalist fungal plant pathogen

description: Additional file 18: Supplementary Table 13. A Results of a GWAS for 14 life history traits. B BLASTp hits for gene downstream of 48 bp InDel azoxystrobin QTL, which encodes a centrosomin. C BLASTp hits for gene upstream of 48 bp InDel azoxystrobin QTL, which encodes a protein with no known functional domains.
DOI: 10.6084/m9.figshare.28879235
title: Additional file 19 of Recombination and transposition drive genomic structural variation potentially impacting life history traits in a host-generalist fungal plant pathogen

description: Additional file 19: Supplementary Table 14. A RNA sequencing data used for Braker3 annotation of genomes. B The host genomes used for filtering RNA sequencing reads used in Braker3 annotation.
DOI: 10.6084/m9.figshare.28879235.v1
title: Additional file 19 of Recombination and transposition drive genomic structural variation potentially impacting life history traits in a host-generalist fungal plant pathogen

description: Additional file 19: Supplementary Table 14. A RNA sequencing data used for Braker3 annotation of genomes. B The host genomes used for filtering RNA sequencing reads used in Braker3 annotation.
DOI: 10.6084/m9.figshare.28879238.v1
title: Additional file 20 of Recombination and transposition drive genomic structural variation potentially impacting life history traits in a host-generalist fungal plant pathogen

description: Additional file 20: Supplementary File 1. Plots showing the same data as Figure 2 H for all populations and chromosomes.