cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15156/bio/sh0164019.10fu
title: SH0164019.10FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh0164020.10fu
title: SH0164020.10FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh0164021.10fu
title: SH0164021.10FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh0164022.10fu
title: SH0164022.10FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh0164023.10fu
title: SH0164023.10FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh0164024.10fu
title: SH0164024.10FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh0164025.10fu
title: SH0164025.10FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh0164026.10fu
title: SH0164026.10FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh0164027.10fu
title: SH0164027.10FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh0164028.10fu
title: SH0164028.10FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15468/dl.au237e
title: Occurrence Download

description: A dataset containing 1076 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is one of (South Georgia and the South Sandwich Islands, Antarctica, Australia)",
 {
 "or" : [
 "Geometry POLYGON((-180 -90,180 -90,180 -3,-180 -3,-180 -90))",
 "Geometry POLYGON((-180 -90,180 -90,180 90,-180 90,-180 -90))",
 "Geometry POLYGON((-180 -30,180 -30,180 0,-180 0,-180 -30))"
 ]
 },
 "TaxonKey is Electrona carlsbergi (Tåning, 1932)",
 "Year 2000-2023"
 ]
}

 The dataset includes 1076 records from 11 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0251421-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.nh67hc
title: Occurrence Download

description: A dataset containing 40 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Heterophleps confusa (Wileman, 1911)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 40 records from 11 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0129379-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.3yqasx
title: Occurrence Download

description: A dataset containing 124 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Thladiantha henryi Hemsl."
 ]
}

 The dataset includes 124 records from 19 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0251424-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.m529nj
title: Occurrence Download

description: A dataset containing 221 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Polygala caudata Rehder & E.H.Wilson"
 ]
}

 The dataset includes 221 records from 21 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0240163-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.s5qbwy
title: Occurrence Download

description: A dataset containing 282 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Hydrophis torquatus Günther, 1864"
 ]
}

 The dataset includes 282 records from 17 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0139333-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.cuukf9
title: Occurrence Download

description: A dataset containing 6359 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Arabis collina Ten.",
 "HasCoordinate is true",
 "Year is greater than or equal to 1900",
 "BasisOfRecord is one of (Human Observation, Specimen, Unknown evidence)"
 ]
}

 The dataset includes 6359 records from 111 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0047846-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.yw8uhp
title: Occurrence Download

description: A dataset containing 303 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Tephrocactus articulatus (Pfeiff. ex Otto) Backeb."
 ]
}

 The dataset includes 303 records from 26 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0047771-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.7nnryf
title: Occurrence Download

description: A dataset containing 21 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Acanthis hornemanni (Holböll, 1843)",
 "HasCoordinate is true",
 "Country is Norway",
 "DatasetKey is Norwegian Species Observation Service",
 "Year is 1998",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 21 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0252704-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.kh3nar
title: Occurrence Download

description: A dataset containing 61135 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "Country is Spain",
 "Geometry POLYGON((-5.45487 35.89569,-4.82518 36.01079,-4.45955 36.9093,-4.82518 37.45951,-5.41424 37.45951,-6.1658 37.45951,-6.73456 36.95801,-7.01893 36.42049,-5.45487 35.89569))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Plantae"
 ]
}

 The dataset includes 61135 records from 119 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0240124-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.rgncvd
title: Occurrence Download

description: A dataset containing 169 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Incilius leucomyos (McCranie & Wilson, 2000)"
 ]
}

 The dataset includes 169 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0123466-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.7760650
title: Haplotype-resolved telomere-to-telomere assembly of the African catfish Clarias gariepinus provides insights for semi-terrestrial adaptation of airbreathing catfishes

description: Airbreathing catfishes (clariids) are a group of stenohaline freshwater fish that can withstand various environmental conditions and farming practices, including the ability to breathe atmospheric oxygen. This unique ability has allowed them to thrive in semi-terrestrial habitats. However, the underlying genomic and adaptive mechanisms remain poorly investigated. Here, we sequenced the genome of the African catfish Clarias gariepinus, one of the most commonly farmed clariids, and generated a gapless telomere-to-telomere (T2T) chromosome-level assembly with high-resolution haplotypes, by integrating long-range sequencing (Hi-C) with PacBio single-molecule (HiFi), Oxford Nanopore, and Illumina sequencing data. The diploid genome assembly yielded 58 contigs with a total length of 969.72 Mb and a contig N50 of 33.71 Mb. We report 25,655 predicted protein-coding genes and 49.94% repetitive elements in the African catfish genome. Our genome assembly provides the first comprehensive gene annotation and haplotype information, such as the male-specific haplotype, enabling us to identify putative genes and molecular mechanisms underlying amphibious traits and terrestrial adaptation of airbreathing catfishes. Several gene families involved in ion transport, osmoregulation, oxidative stress response, and muscle metabolism were expanded or positively selected in clariids, suggesting a potential role in their transition to terrestrial life. The reported findings expand our understanding of the genomic mechanisms underpinning the resilience and adaptive mechanisms of C. gariepinus to adverse ecological conditions. They will serve as a valuable resource for future studies in elucidating these unique biological traits in related teleosts and leverage these insights for aquaculture improvement
DOI: 10.5281/zenodo.7760649
title: Haplotype-resolved and near-T2T assembly of the African catfish (Clarias gariepinus)

description: Airbreathing catfishes are a group of stenohaline freshwater fish that can withstand various environmental conditions and farming practices, including the ability to breathe atmospheric oxygen. This unique ability has allowed them to thrive in semi-terrestrial habitats. However, the genomic mechanisms underlying their adaptation to adverse ecological conditions remain to fully investigate, due to the absence of gold standard reference genomes. The present study aimed to sequence and characterize the genome of the African catfish (Clarias gariepinus), a representative air-breathing catfish, to elucidate the genomic underpinnings of its remarkable adaptability. By generating a near telomere-to-telomere (T2T) assembly with high-resolution haplotypes, we sought to identify genomic and evolutionary features that may have contributed to its ability to withstand adverse conditions and transition to semi-terrestrial life. \textbf{Methods:} We conducted a comprehensive genomic analysis of the African catfish using a multi-platform sequencing approach, integrating Oxford Nanopore, PacBio HiFi, Illumina, and Hi-C technologies to achieve a haplotype-resolved chromosome-scale genome assembly. Functional annotations and comparative genomic analyses, including gene family evolution and positive selection studies, were performed to identify the genomic mechanisms underlying the species' resilience and adaptation to diverse environments. Results: This multifaceted approach has provided novel insights into the African catfish's complex genomic architecture and adaptive strategies. The near-T2T diploid assembly yielded 48 contigs spanning 969.62 Mb with a contig N50 of 33.71 Mb. We report 25,655 predicted protein-coding genes and 43.94\% repetitive elements in the African catfish genome. Several gene families involved in ion transport, osmoregulation, oxidative stress response, and muscle metabolism were expanded and positively selected in clariids, suggesting a potential role in their transition and adaptation to semi-terrestrial habitats. Conclusion: Our study provides a comprehensive genomic resource for \textit{Clarias gariepinus}, shedding light on the genetic and genomic mechanisms of clariids' adaptation to adverse ecological environments. The findings enhance our understanding of resilience in C. gariepinus and offer valuable insights for improving aquaculture and studying related teleosts.
DOI: 10.15468/dl.kyw5kn
title: Occurrence Download

description: A dataset containing 227946 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Gymnadenia conopsea (L.) R.Br."
 ]
}

 The dataset includes 227946 records from 811 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0240136-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.4gwtm5
title: Occurrence Download

description: A dataset containing 110 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Tribulopis solandri R.Br."
 ]
}

 The dataset includes 110 records from 13 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000735-230530130749713/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.mua2y8
title: Occurrence Download

description: A dataset containing 5 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Longithorax nouveli O.Tattersall, 1955"
 ]
}

 The dataset includes 5 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0123483-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.r9syj2
title: Occurrence Download

description: A dataset containing 2099 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "Country is one of (Colombia, Mexico, United States of America, New Zealand, Costa Rica, Argentina, Réunion, Puerto Rico, Panama, Spain)",
 "TaxonKey is Persea americana Mill.",
 "Year 2011-2022"
 ]
}

 The dataset includes 2099 records from 53 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0190944-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.