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3,292 results for “DNA Barcode”
Data from: ITS1: a DNA barcode better than ITS2 in eukaryotes?
A DNA barcode is a short piece of DNA sequence used for species determination and discovery. The internal transcribed spacer (ITS/ITS2) region has been proposed as the standard DNA barcode for fungi and seed plants, and has been widely used in DNA barcoding analyses for other biological groups, e.g. algae, protists, and animals. The ITS region consists of both ITS1 and ITS2 regions. Here, a large scale meta-analysis was carried out to compare ITS1 and ITS2 from three aspects: PCR amplification, DNA sequencing and species discrimination, in terms of the presence of DNA barcoding gaps, species discrimination efficiency, sequence length distribution, GC content distribution and primer universality. In total, 85,345 sequence pairs in ten major groups of eukaryotes, including ascomycetes, basidiomycetes, liverworts, mosses, ferns, gymnosperms, monocotyledons, eudicotyledons, insects, and fishes, covering 611 families, 3,694 genera, and 19,060 species, were analyzed. Using similarity-based methods, we calculated species discrimination efficiencies for ITS1 and ITS2 in all major groups, families, and genera. Using Fisher's exact test, we found that ITS1 has significantly higher efficiencies than ITS2 in 17 of the 47 families and 20 of the 49 genera, which are sample-rich. By in silico PCR amplification evaluation, primer universality of the extensively applied ITS1 primers was found superior to that of ITS2 primers. Additionally, shorter length of amplification product and lower GC content were discovered to be two other advantages of ITS1 for sequencing. In summary, ITS1 represents a better DNA barcode than ITS2 for eukaryotic species.
Data from: DNA barcoding of invasive plants in China: a resource for identifying invasive plants
Invasive plants have aroused attention globally for causing ecological damage and having a negative impact on the economy and human health. However, it can be extremely challenging to rapidly and accurately identify invasive plants based on morphology because they are an assemblage of many different families and many plant materials lack sufficient diagnostic characteristics during border inspections. It is therefore urgent to evaluate candidate loci and build a reliable genetic library to prevent invasive plants from entering China. In this study, five common single markers (ITS, ITS2, matK, rbcL and trnH-psbA) were evaluated using 634 species (including 469 invasive plant species in China, 10 new records to China, 16 potentially invasive plant species around the world but not introduced into China yet and 139 plant species native to China) based on three different methods. Our results indicated that ITS2 displayed largest intra- and interspecific divergence (1.72% and 91.46%). Based on NJ tree method, ITS2, ITS, matK, rbcL and trnH-psbA provided 76.84%, 76.5%, 63.21%, 52.86% and 50.68% discrimination rates, respectively. The combination of ITS+matK performed best and provided 91.03% discriminatory power, followed by ITS2+matK (85.78%). For identifying unknown individuals, ITS+matK had 100% correct identification rate based on our database, followed by ITS/ITS2 (both 93.33%) and ITS2+matK (91.67%). Thus, we propose ITS/ITS2+matK as the most suitable barcode for invasive plants in China. This study also demonstrated that DNA barcoding is an efficient tool for identifying invasive species.
Data from: DNA barcoding gap: reliable species identification over morphological and geographical scales
The philosophical basis, and utility of DNA barcoding has been a subject of numerous debates. While most literature embraces it, some studies continue to question its use in dipterans, butterflies, and marine gastropods. Here, we explore the utility of DNA barcoding in identifying spider species that vary in taxonomic affiliation, morphological diagnosibility and geographic distribution. Our first test searched for a "barcoding gap" by comparing intra- and interspecific means, medians and overlap in more than 75,000 computed Kimura 2 parameter (K2P) genetic distances in three families. Our second test compared K2P distances of congeneric species with high versus low morphological distinctness in 20 genera of 11 families. Our third test explored the effect of enlarging geographical sampling area at a continental scale on genetic variability in DNA barcodes within 20 species of nine families. Our results generally point towards a high utility of DNA barcodes in identifying spider species. However, the size of the barcoding gap strongly depends on taxonomic groups and practices. It is becoming critical to define the barcoding gap statistically more consistently, and to document its variation over taxonomic scales. Our results support models of independent patterns of morphological and molecular evolution by showing that DNA barcodes are effective in species identification regardless of their morphological diagnosibility. We also show that DNA barcodes represent an effective tool for identifying spider species over geographic scales, yet their variation contains useful biogeographic information.
Figure 5 from: Spelda J, Reip H, Oliveira Biener U, Melzer R (2011) Barcoding Fauna Bavarica: Myriapoda – a contribution to DNA sequence-based identifications of centipedes and millipedes (Chilopoda, Diplopoda). ZooKeys 156: 123-139. https://doi.org/10.3897/zookeys.156.2176
Figure 5 - Intraspecific COI variability (K2P): maximum pairwise distances; Chilopoda
Figure 3 from: Spelda J, Reip H, Oliveira Biener U, Melzer R (2011) Barcoding Fauna Bavarica: Myriapoda – a contribution to DNA sequence-based identifications of centipedes and millipedes (Chilopoda, Diplopoda). ZooKeys 156: 123-139. https://doi.org/10.3897/zookeys.156.2176
Figure 3 - Interspecific COI variability (K2P): distance to nearest neighbour; Chilopoda
Figure 6 from: Spelda J, Reip H, Oliveira Biener U, Melzer R (2011) Barcoding Fauna Bavarica: Myriapoda – a contribution to DNA sequence-based identifications of centipedes and millipedes (Chilopoda, Diplopoda). ZooKeys 156: 123-139. https://doi.org/10.3897/zookeys.156.2176
Figure 6 - Intraspecific COI variability (K2P): maximum pairwise distances; Diplopoda
Figure 4 from: Spelda J, Reip H, Oliveira Biener U, Melzer R (2011) Barcoding Fauna Bavarica: Myriapoda – a contribution to DNA sequence-based identifications of centipedes and millipedes (Chilopoda, Diplopoda). ZooKeys 156: 123-139. https://doi.org/10.3897/zookeys.156.2176
Figure 4 - Interspecific COI variability (K2P): distance to nearest neighbour; Diplopoda
Figure 8 from: van Nieukerken E, Wagner D, Baldessari M, Mazzon L, Angeli G, Girolami V, Duso C, Doorenweerd C (2012) Antispila oinophylla new species (Lepidoptera, Heliozelidae), a new North American grapevine leafminer invading Italian vineyards: taxonomy, DNA barcodes and life cycle. ZooKeys 170: 29-77. https://doi.org/10.3897/zookeys.170.2617
Figure 8 - Holocacista rivillei, venation.Female, Italy, RMNH.INS.24259.
Figure 29 from: van Nieukerken E, Wagner D, Baldessari M, Mazzon L, Angeli G, Girolami V, Duso C, Doorenweerd C (2012) Antispila oinophylla new species (Lepidoptera, Heliozelidae), a new North American grapevine leafminer invading Italian vineyards: taxonomy, DNA barcodes and life cycle. ZooKeys 170: 29-77. https://doi.org/10.3897/zookeys.170.2617
Figure 29 - Antispila oinophylla, distribution in North America.
Figure 2 from: Veijalainen A, Broad G, Wahlberg N, Longino J, Sääksjärvi I (2011) DNA barcoding and morphology reveal two common species in one: Pimpla molesta stat. rev. separated from P. croceipes (Hymenoptera, Ichneumonidae). ZooKeys 124: 59-70. https://doi.org/10.3897/zookeys.124.1780
Figure 2 - Pimpla molesta female, lateral view.
Figure 1 from: Veijalainen A, Broad G, Wahlberg N, Longino J, Sääksjärvi I (2011) DNA barcoding and morphology reveal two common species in one: Pimpla molesta stat. rev. separated from P. croceipes (Hymenoptera, Ichneumonidae). ZooKeys 124: 59-70. https://doi.org/10.3897/zookeys.124.1780
Figure 1 - Pimpla croceipes female, lateral view.
Figures 7-8 from: Hosoishi S, Ogata K (2014) Description and DNA barcoding of Crematogaster fraxatrix Forel, 1911 and two new closely related species from Cambodia and Indonesia (Hymenoptera, Formicidae). ZooKeys 374: 57-68. https://doi.org/10.3897/zookeys.374.5874
Figures 7-8 - Crematogaster simboloni. 7 lateral view 8 dorsal view of mesosoma.
Figures 1-2 from: Hosoishi S, Ogata K (2014) Description and DNA barcoding of Crematogaster fraxatrix Forel, 1911 and two new closely related species from Cambodia and Indonesia (Hymenoptera, Formicidae). ZooKeys 374: 57-68. https://doi.org/10.3897/zookeys.374.5874
Figures 1-2 - Crematogaster chhangi. 1 lateral view 2 dorsal view of mesosoma.
Figure 1 from: Backeljau T, Breugelmans K, Jordaens K, Adriaens E, Remon J, Quintana Cardona J (2013) DNA barcodes and phylogenetic affinities of the terrestrial slugs Arion gilvus and A. ponsi (Gastropoda, Pulmonata, Arionidae). ZooKeys 365: 83-104. https://doi.org/10.3897/zookeys.365.6104
Figure 1 - Arion ponsi Quintana Cardona, 2007 from Menorca (Balearic Islands, Spain).
Figure 5 from: Gere J, Kowiyou Y, Daru B, Mankga L, Maurin O, van der Bank M (2013) Incorporating trnH-psbA to the core DNA barcodes improves significantly species discrimination within southern African Combretaceae. ZooKeys 365: 129-147. https://doi.org/10.3897/zookeys.365.5728
Figure 5 - PCR efficiency for the four candidate barcodes (rbcLa, matK, trnH-psbA, nrITS).
Figure 6 from: Stahls G, Laiho J (2013) DNA barcodes identify Central-Asian Colias butterflies (Lepidoptera, Pieridae). ZooKeys 365: 175-196. https://doi.org/10.3897/zookeys.365.5879
Figure 6 - Neighbour-Joining tree using the K2P-model of COI sequences for Palaearctc Colias taxa.
Figure 4 from: Stahls G, Laiho J (2013) DNA barcodes identify Central-Asian Colias butterflies (Lepidoptera, Pieridae). ZooKeys 365: 175-196. https://doi.org/10.3897/zookeys.365.5879
Figure 4 - Strict consensus cladogram of the concatenated data set of COI + RpS2.
Figure 5 from: Stahls G, Laiho J (2013) DNA barcodes identify Central-Asian Colias butterflies (Lepidoptera, Pieridae). ZooKeys 365: 175-196. https://doi.org/10.3897/zookeys.365.5879
Figure 5 - Strict consensus cladogram of COI sequences for Palaearctic Colias taxa.
Figure 2 from: Stahls G, Laiho J (2013) DNA barcodes identify Central-Asian Colias butterflies (Lepidoptera, Pieridae). ZooKeys 365: 175-196. https://doi.org/10.3897/zookeys.365.5879
Figure 2 - Neighbour-Joining tree using the K2P-model for the COI sequences obtained in this study.
Figure 1 from: Stahls G, Laiho J (2013) DNA barcodes identify Central-Asian Colias butterflies (Lepidoptera, Pieridae). ZooKeys 365: 175-196. https://doi.org/10.3897/zookeys.365.5879
Figure 1 - Strict consensus cladogram of Colias COI sequences obtained in this study.
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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.