Find research datasets worth reusing
Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.
4,144
datasets available to search
ShareScore release 0.9.0
Dataset results
4,144 results for “ITS barcode”
Figure 5 from: Pelingen AL, Freitag H (2020) Description of Neoperla mindoroensis sp. nov., the first record of a stonefly from Mindoro, Philippines (Plecoptera, Perlidae), and identification of its life stages using COI barcodes. ZooKeys 954: 47-63. https://doi.org/10.3897/zookeys.954.53746
Figure 5 Female larval habitus of Neoperla mindoroensis sp. nov. Scale bar: 4.0 mm.
Figure 1 from: Pelingen AL, Freitag H (2020) Description of Neoperla mindoroensis sp. nov., the first record of a stonefly from Mindoro, Philippines (Plecoptera, Perlidae), and identification of its life stages using COI barcodes. ZooKeys 954: 47-63. https://doi.org/10.3897/zookeys.954.53746
Figure 1 Paratype male adult habitus of Neoperla mindoroensis sp. nov. Scale bar: 2.00 mm.
Figure 2 from: Egger C, Neusser TP, Norenburg J, Leasi F, Buge B, Vannozzi A, Cunha RL, Cox CJ, Jörger KM (2020) Uncovering the shell game with barcodes: diversity of meiofaunal Caecidae snails (Truncatelloidea, Caenogastropoda) from Central America. ZooKeys 968: 1-42. https://doi.org/10.3897/zookeys.968.52986
Figure 2 Map of color-coded sampling sites (triangles) for Caecidae in Central American waters.
Figure 1 from: Yu H-J, Lin X-L, Zhang R-L, Wang Q, Wang X-H (2020) Species delimitation and life stage association of Propsilocerus Kieffer, 1923 (Diptera, Chironomidae) using DNA barcodes. ZooKeys 975: 79-86. https://doi.org/10.3897/zookeys.957.54668
Figure 1 Larva of Propsilocerus taihuensis (Wen, Zhou & Rong, 1994).
Evaluation of DNA barcode libraries used in the UK and developing an action plan to fill priority gaps: Appendices 3 and 4
<p>Supplementary data for the DEFRA Centre of Excellence for DNA Methods report: Evaluation of DNA barcode libraries used in the UK and developing an action plan to fill priority gaps. Appendix 3: Priority species identified during the survey and consultation Appendix 4: Raw data for gap analyses</p>
Figure 1 from: Kodada J, Jäch MA, Freitag H, Čiamporová-Zaťovičová Z, Goffová K, Selnekovič D, Čiampor Jr F (2020) Ancyronyx lianlabangorum sp. nov., a new spider riffle beetle from Sarawak, and new distribution records for A. pulcherrimus Kodada, Jäch & Čiampor based on DNA barcodes (Coleoptera, Elmidae). ZooKeys 1003: 31-55. https://doi.org/10.3897/zookeys.1003.55541
Figure 1 Maximum Likelihood tree inferred from aligned COI mtDNA nucleotides sequences.
Data from: A reliable DNA barcode reference library for the identification of the European shelf fish fauna
Valid fish species identification is an essential step both for fundamental science and fisheries management. The traditional identification is mainly based on external morphological diagnostic characters, leading to inconsistent results in many cases. Here, we provide a sequence reference library based on mitochondrial cytochrome c oxidase subunit I (COI) for a valid identification of 93 North Atlantic fish species originating from the North Sea and adjacent waters, including many commercially exploited species. Neighbour-joining analysis based on K2P genetic distances formed nonoverlapping clusters for all species with a ≥99% bootstrap support each. Identification was successful for 100% of the species as the minimum genetic distance to the nearest neighbour always exceeded the maximum intraspecific distance. A barcoding gap was apparent for the whole data set. Within-species distances ranged from 0 to 2.35%, while interspecific distances varied between 3.15 and 28.09%. Distances between congeners were on average 51-fold higher than those within species. The validation of the sequence library by applying BOLDs barcode index number (BIN) analysis tool and a ranking system demonstrated high taxonomic reliability of the DNA barcodes for 85% of the investigated fish species. Thus, the sequence library presented here can be confidently used as a benchmark for identification of at least two-thirds of the typical fish species recorded for the North Sea.
Data from: Scaling up DNA barcoding - primer sets for simple and cost efficient arthropod systematics by multiplex PCR and Illumina amplicon sequencing
1. The simplicity and cost efficiency of Illumina amplicon sequencing has greatly contributed to the advancement of DNA barcoding and metabarcoding applications. However, current amplicon sequencing based barcoding approaches are usually restricted to short, single-locus fragments, limiting their taxonomic and phylogenetic resolution. 2. Here, we establish a cost efficient and simple multiplex PCR protocol for arthropod systematics by Illumina amplicon sequencing. We introduce primer sets, including several new, generic primers, to reliably amplify nine loci across a wide range of arthropods. Using a diverse collection of arthropod species from 19 orders, we test loci for amplification efficiency and estimate the effect of cross-species amplification bias on taxon recovery from bulk community samples. We then explore the taxonomic and phylogenetic utility of the primer sets, focusing on a dataset of spiders that includes both deep and recent divergences. 3. The set of loci provides good phylogenetic support across a wide taxonomic spectrum, making it a useful addition to COI for resolving lineages within a comparative context. All loci recover sequences for the majority of arthropod taxa in separate PCRs. However, cross-species amplification bias in some primers prevents an exhaustive taxon recovery from bulk community samples. 4. Our protocol makes it possible to generate multilocus datasets for large numbers of arthropod taxa for a fraction of the price and workload of Sanger sequencing. This opens up the possibility for parallel phylogenetic and taxonomic analysis of large collections of arthropods, but also enables rapid exploratory analyses of target lineages. Primers for metabarcoding applications should be carefully evaluated for their performance in bulk community samples and chosen to minimize cross-species amplification bias.
Data from: A nuclear DNA barcode for eastern North American oaks and application to a study of hybridization in an Arboretum setting
DNA barcoding has proved difficult in a number of woody plant genera, including the ecologically important oak genus Quercus. In this study, we utilized restriction-site associated DNA sequencing (RAD-seq) to develop an economical single-nucleotide polymorphism (SNP) DNA barcoding system that suffices to distinguish eight common, sympatric eastern North American white oak species. Two de novo clustering pipelines, PyRAD and Stacks, were used in combination with post-clustering bioinformatic tools to generate a list of 291 potential SNPs, 80 of which were included in a barcoding toolkit that is easily implemented using MassARRAY mass spectrometry technology. As a proof-of-concept, we used the genotyping toolkit to infer potential hybridization between North American white oaks transplanted outside of their native range (Q. michauxii, Q. montana, Q muehlenbergii/ Q. prinoides and Q. stellata) among natural forests of locally native trees (Q. alba and Q. macrocarpa) in the living collection at The Morton Arboretum (Lisle, IL, USA). Phylogenetic and clustering analyses suggested low rates of hybridization between cultivated and native species, with the exception of one Q. michauxii mother tree, the acorns of which exhibited high admixture from either Q. alba or Q. stellata and Q. macrocarpa; and a hybrid between Q. stellata that appears to have backcrossed almost exclusively to Q. alba. Together, RAD-seq and MassARRAY technologies allow for efficient development and implementation of a multispecies barcode for one of the more challenging forest tree genera.
Data from: Sorting specimen-rich invertebrate samples with cost-effective NGS barcodes: validating a reverse workflow for specimen processing
Biologists frequently sort specimen-rich samples to species. This process is daunting when based on morphology, and disadvantageous if performed using molecular methods that destroy vouchers (e.g., metabarcoding). An alternative is barcoding every specimen in a bulk sample and then presorting the specimens using DNA barcodes, thus mitigating downstream morphological work on presorted units. Such a "reverse workflow" is too expensive using Sanger sequencing, but we here demonstrate that is feasible with an NGS barcoding pipeline that allows for cost-effective high throughput generation of short specimen-specific barcodes (313 bp of COI; lab cost <$0.50 per specimen) through Next Generation Sequencing of tagged amplicons. We applied our approach to a large sample of tropical ants, obtaining barcodes for 3290 of 4032 specimens (82%). NGS barcodes and their corresponding specimens were then sorted into molecular operational taxonomic units (mOTUs) based on objective clustering and Automated Barcode Gap Discovery (ABGD). High diversity of 88-90 mOTUs (4% clustering) was found and morphologically validated based on preserved vouchers. The mOTUs were overwhelmingly in agreement with morphospecies (match ratio 0.95 at 4% clustering). Because of lack of coverage in existing barcode databases, only 18 could be accurately identified to named species, but our study yielded new barcodes for 48 species, including 28 that are potentially new to science. With its low cost and technical simplicity, the NGS barcoding pipeline can be implemented by a large range of laboratories. It accelerates invertebrate species discovery, facilitates downstream taxonomic work, helps with building comprehensive barcode databases, and yields precise abundance information.
Data from: DNA barcoding reveals cryptic diversity in the peanut worm Sipunculus nudus
Peanut worm (Sipunculus nudus) is a cosmopolitan species mainly distributed in tropical and subtropical coastal waters. Analysis of the mitochondrial cytochrome c oxidase subunit I (COI) gene sequences among S. nudus from GenBank revealed high genetic variation (p-distance, 0.115–0.235; k2p, 0.128–0.297) and paraphyletic relationships. These indicated misidentification and/or cryptic diversity may be present in the genus Sipunculus. To understand the genetic diversity and to manage the recourse of S. nudus, we collected specimens from coastal waters of southern China and Taiwan. In the phylogenetic topology, specimens can be separated into four distinct clades; three of these clades (clade A, B and C) were only represented from this region (southern China and Taiwan), but the clade D grouped with individuals from Central America (Atlantic coast). Furthermore, individuals of clades A and D were collected at the same location, which does not support the hypothesis that this genetic break reflects contemporary geographical isolation. The four distinct clades observed among coastal waters of southern China and Taiwan indicated underestimated diversity. It is noteworthy that the cryptic diversity is vulnerable under high pressure of human activity.
iBOL DNA barcode data for fungi (ITS)
<p>International Barcode of Life project (iBOL) Data Package for fungi, release 3.0</p>
iBOL DNA barcode data for plants
<p>International Barcode of Life project (iBOL) Data Packages for Plants, releases 2.00-6.00</p>
iBOL DNA barcode data for animals (COI)
<p>International Barcode of Life project (iBOL) Data Packages for animals, releases 0.5-6.00.</p>
Figures 49- 50 from: Jing M-D, Ding Y-H, Ма Y-T (2023) Description of three new species of Callyntrura (Japonphysa) (Collembola, Entomobryidae) from China with the aid of DNA barcoding. ZooKeys 1187: 237-260. https://doi.org/10.3897/zookeys.1187.109608
Figures 49- 50 Habitus of Callyntrura tongguensis sp. nov. (lateral view). Scale bars: 50 μm.
Figure 1 from: Jing M-D, Ding Y-H, Ма Y-T (2023) Description of three new species of Callyntrura (Japonphysa) (Collembola, Entomobryidae) from China with the aid of DNA barcoding. ZooKeys 1187: 237-260. https://doi.org/10.3897/zookeys.1187.109608
Figure 1 Record locality of all Chinese species of Callyntrura(s.l.) in China. Scale bar: 1000 km.
Figure 1 from: Schmid-Egger C, Schmidt S, Bogusch P (2024) DNA Barcoding of Central European Gasteruptiidae and the rarely-collected families Evaniidae, Stephanidae, Trigonalidae, and Aulacidae (Hymenoptera, Apocrita). ZooKeys 1189: 275-286. https://doi.org/10.3897/zookeys.1189.114478
Figure 1 Male of Gasteruption assectator from Saxony (Germany). (Photo W.H. Liebig).
Figure 3 from: Schmid-Egger C, Schmidt S, Bogusch P (2024) DNA Barcoding of Central European Gasteruptiidae and the rarely-collected families Evaniidae, Stephanidae, Trigonalidae, and Aulacidae (Hymenoptera, Apocrita). ZooKeys 1189: 275-286. https://doi.org/10.3897/zookeys.1189.114478
Figure 3 Female of Gasteruption minutum from Saxony (Germany) (Photo W.H. Liebig).
Figure 21 from: Boucher S, Savage J (2022) DNA barcoding of the leaf-miner flies (Diptera, Agromyzidae) of Mitaraka, French Guiana. ZooKeys 1083: 147-168. https://doi.org/10.3897/zookeys.1083.76651
Figure 21 Map of Agromyzidae species occurrence on BOLD. Map generated by BOLD (September 2021).
Figure 22 from: Boucher S, Savage J (2022) DNA barcoding of the leaf-miner flies (Diptera, Agromyzidae) of Mitaraka, French Guiana. ZooKeys 1083: 147-168. https://doi.org/10.3897/zookeys.1083.76651
Figure 22 Map of Melanagromyza species occurrence on BOLD. Map generated by BOLD (September 2021).
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.