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3,292 results for “DNA Barcode”
Figure 43 from: Pentinsaari M, Anderson R, Borowiec L, Bouchard P, Brunke A, Douglas H, Smith A, Hebert P (2019) DNA barcodes reveal 63 overlooked species of Canadian beetles (Insecta, Coleoptera). ZooKeys 894: 53-150. https://doi.org/10.3897/zookeys.894.37862
Figure 43 Lythraria salicariae (Paykull), habitus, L. Borowiec A male B female. Scale bar: 1.0 mm.
DNA barcode trnH-psbA is a promising candidate for efficient identification of forage legumes and grasses
<p><strong>Objective</strong></p> <p>Grasslands are widespread ecosystems that fulfil many functions. Plant species richness (PSR) is known to have beneficial effects on such functions and monitoring PSR is crucial for tracking the effects of land use and agricultural management on these ecosystems. Unfortunately, traditional morphology-based methods are labor-intensive and cannot be adapted for high-throughput assessments.</p> <p>DNA barcoding could aid increasing the throughput of PSR assessments in grasslands. In this proof-of-concept work, we aimed at determining which of three plant DNA barcodes (<em>rbcLa</em>, <em>matK</em> and <em>trnH-psbA</em>) best discriminates 16 key grass and legume species common in temperate sub-alpine grasslands.</p> <p><strong>Results</strong></p> <p>Barcode <em>trnH-psbA</em> had a 100% correct assignment rate (CAR) in the five analyzed legumes, followed by <em>rbcLa </em>(93.3%) and <em>matK</em> (55.6%). Barcode <em>trnH-psbA</em> had a 100% CAR in the grasses <em>Cynosurus cristatus</em>, <em>Dactylis glomerata</em> and <em>Trisetum flavescens</em>. However, the closely related <em>Festuca, Lolium </em>and <em>Poa</em> species were not always correctly identified, which led to an overall CAR in grasses of 66.7 %, 50.0% and 46.4% for<em> trnH-psbA</em>, <em>matK</em> and <em>rbcLa</em>, respectively. Barcode <em>trnH-psbA</em> is thus the most promising candidate for PSR assessments in permanent grasslands and could greatly support plant biodiversity monitoring on a larger scale.</p> <p><strong>Content of data file</strong></p> <p>This data file contains all raw data obtained during the study. The full information on the project can be found on the BOLD database (<a href="http://www.boldsystems.org/index.php/Public_SearchTerms">http://www.boldsystems.org/index.php/Public_SearchTerms</a>) using the search term SWFRG</p>
Figure 1 from: Kodada J, Jäch MA, Freitag H, Čiamporová-Zaťovičová Z, Goffová K, Selnekovič D, Čiampor Jr F (2020) Ancyronyx clisteri, a new spider riffle beetle species from Borneo, redescription of A. sarawacensis Jäch including a description of the larva and new distribution data for A. procerus Jäch using DNA barcodes (Coleoptera, Elmidae). ZooKeys 912: 25-64. https://doi.org/10.3897/zookeys.912.47796
Figure 1 Results of DNA COI analyses, maximum likelihood tree.
Figure 16 from: Kodada J, Jäch MA, Freitag H, Čiamporová-Zaťovičová Z, Goffová K, Selnekovič D, Čiampor Jr F (2020) Ancyronyx clisteri, a new spider riffle beetle species from Borneo, redescription of A. sarawacensis Jäch including a description of the larva and new distribution data for A. procerus Jäch using DNA barcodes (Coleoptera, Elmidae). ZooKeys 912: 25-64. https://doi.org/10.3897/zookeys.912.47796
Figure 16 Ancyronyx sarawacensis, holotype: A aedeagus, ventral view B same, lateral view.
Figure 2 from: Espinoza-Donoso S, Bobadilla D, Huanca-Mamani W, Vargas-Ortiz M, Vargas HA (2020) A new species of Ithome Chambers (Lepidoptera, Cosmopterigidae, Chrysopeleiinae) from the Atacama Desert revealed by morphology and DNA barcodes. ZooKeys 912: 125-138. https://doi.org/10.3897/zookeys.912.47562
Figure 2 Holotype of Ithome tamarugensis Vargas sp. nov. in dorsal view. Scale bar: 1 mm.
Figure 3 from: Huemer P, Karsholt O, Aarvik L, Berggren K, Bidzilya O, Junnilainen J, Landry J-F, Mutanen M, Nupponen K, Segerer A, Šumpich J, Wieser C, Wiesmair B, Hebert PDN (2020) DNA barcode library for European Gelechiidae (Lepidoptera) suggests greatly underestimated species diversity. ZooKeys 921: 141-157. https://doi.org/10.3897/zookeys.921.49199
Figure 3 Periods of descriptions of European Gelechiidae.
Appendix 8 in Morphometry and DNA barcoding reveal cryptic diversity in the genus Enteromius (Cypriniformes: Cyprinidae) from the Congo basin, Africa
Appendix 8. PC loadings of the PCA in Fig. 9. Most important loadings indicated in bold.
Appendix 6 in Morphometry and DNA barcoding reveal cryptic diversity in the genus Enteromius (Cypriniformes: Cyprinidae) from the Congo basin, Africa
Appendix 6. PC loadings of the PCA in Fig. 7. Most important loadings indicated in bold.
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: 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.
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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.