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4,144 results for “ITS barcode”
F I G U R E 2 in Assessing the diversity of Australian tarantulas (Araneae: Theraphosidae) using DNA barcoding and iterative species delimitation
F I G U R E 2 Histogram of HKY pairwise distance with bars increasing by 0.25 pairwise distance.
Figure 2 in DNA barcoding for the identification of Limonia crane flies (Diptera: Limoniidae) from China, including a new species and a newly recorded species
Figure 2. Barcoding gap of Limonia COI sequences.
Figure 1 in DNA barcoding, visual-guide resource, new localities and host associations of genus Periglischrus Oudemans, 1902 (Acari: Mesostigmata, Spinturnicidae) from Minas Gerais, Brazil
Figure 1 Geographical distribution of sampling localities ofPeriglischrus spp.
FIGURE 1 in Comparative performance of a multi-locus barcoding approach to enhance taxonomic resolution of New Zealand mosquitoes (Diptera: Culicidae)
FIGURE 1 (Continued)
Table 2. A in DNA barcoding of the genus Verbascum (Scrophulariaceae) in the Arabian Peninsula
<p><b>Table 2.</b> A comparison of the individual and combined datasets from parsimony analysis.</p><table><tbody><tr><th></th><th>ITS</th><th><i>matK</i></th><th><i>rbcL</i></th><th><i>trnL</i></th><th>Combined chloroplastic</th><th>Combined chloroplastic and ITS</th></tr></tbody><tbody><tr><th>No. of sequences</th><td>62</td><td>62</td><td>62</td><td>62</td><td>62</td><td>62</td></tr><tr><th>Alignment length (bp)</th><td>449</td><td>735</td><td>561</td><td>819</td><td>2115</td><td>2564</td></tr><tr><th>No. of variable characters (%)</th><td>239 (53.2)</td><td>16 (2.1)</td><td>7 (1.2)</td><td>16 (2.3)</td><td>39 (1.8)</td><td>375 (14.6)</td></tr><tr><th>No. of informative characters (%)</th><td>50 (11.1)</td><td>54 (7.3)</td><td>10 (1.7)</td><td>35 (4.2)</td><td>99 (4.6)</td><td>342 (13.3)</td></tr><tr><th>No. of most equally parsimonious trees</th><td>10,000</td><td>7</td><td>6</td><td>1455</td><td>390</td><td>10,000</td></tr><tr><th>Tree length</th><td>380</td><td>73</td><td>20</td><td>58</td><td>156</td><td>939</td></tr><tr><th>Consistency index</th><td>0.8763</td><td>0.9726</td><td>1.0000</td><td>0.9310</td><td>0.9295</td><td>0.8807</td></tr><tr><th>Retention index</th><td>0.8309</td><td>0.9835</td><td>1.0000</td><td>0.9728</td><td>0.9618</td><td>0.8724</td></tr><tr><th>Rescaled consistency index</th><td>0.7282</td><td>0.9565</td><td>1.0000</td><td>0.9057</td><td>0.8940</td><td>0.7684</td></tr></tbody></table>
Data from: Establishing community-wide DNA barcode references for conserving mangrove forests in China
<p><b>Background:</b> Mangrove ecosystems have been the focus of global attention for their crucial role in sheltering coastal communities and retarding global climate change by sequestering 'blue carbon'. China is relatively rich in mangrove diversity, with one-third of the ca. 70 true mangrove species and a number of mangrove associate species occurring naturally along the country's coasts. Mangrove ecosystems, however, are widely threatened by intensifying human disturbances and rising sea levels. The urgent need to protect mangrove ecosystems could be assisted by using barcoding technology, which provides rapid species identification. </p> <p><b>Results</b>: To investigate this potential, 898 plant specimens were collected from 33 of the major mangrove sites in China. Based on the morphologic diagnosis, the specimens were assigned to 72 species, including all 28 true mangrove species and all 12 mangrove associate species recorded in China. Three chloroplast DNA markers <i>rbcL</i>, <i>trnH-psbA</i>, <i>matK</i>, and one nuclear marker <i>ITS2</i> were chosen to investigate the utility of using barcoding to identify these species. According to the criteria of barcoding gaps in genetic distance, sequence similarity and phylogenetic monophyly, we propose that a single marker, <i>ITS2</i>, is sufficient to barcode the species of mangroves and their associates in China. Furthermore, <i>rbcL</i> or <i>trnH-psbA</i> can also be used to gather supplement confirming data. In using these barcodes, we revealed a very low level of genetic variation among geographic locations in the mangrove species, which is an alert to their vulnerability to climate and anthropogenic disturbances. </p> <p><strong>Conclusion:</strong> We suggest to use <em>ITS2</em> to barcode mangrove species and terrestrial coastal plants in South China. The DNA barcode sequences we obtained would be valuable in monitoring biodiversity and the restoration of ecosystems, which are essential for mangrove conservation.</p>
Dataset: DNA barcodes and microsatellites: how they complement for species identification in the complex genus Tamarix (Tamaricaceae)
<p class="CuerpoA">DNA barcoding allows the identification of an organism by comparing the sequence of selected DNA regions (barcodes) with a previously compiled database, and it can be useful for taxonomic identification of species in complex genera, such as <i>Tamarix</i>. Many species of this genus show convergent morphology, which leads to frequent errors in their identification. Highly variable genetic markers, such as microsatellites or short sequence repeats (SSR), could be used to differentiate species where DNA barcodes fail. Here, we tested the ability of both, five different marker regions (<i>rbcL</i>, <i>matK</i>, ITS, <i>trnH</i>-<i>psbA</i>, and <i>ycf1</i>), and 14 microsatellites, to properly identify <i>Tamarix</i> species, especially those from the Mediterranean Basin, and compared the pros and cons of the different analytical methods for species identification. DNA barcoding allows the genetic identification of certain species in <i>Tamarix</i>. The two-locus barcodes <i>matK</i>+ITS and ITS+<i>ycf1</i> were the best-performing combinations, allowing up to 69% and 70%, respectively, correct identification. However, DNA barcoding failed in phylogenetically close groups, such as many Mediterranean species. The use of SSR can aid the identification of species, and the combination of both types of data (DNA barcoding and SSR) improved the success. The combination of data was especially relevant in detecting the presence of hybridization processes, which are common in the genus. However, caution must be exercised when choosing the clustering methods for the SSR data, since different methods can lead to very different results.</p>
Sequencing of individual barcoded cDNAs on Pacific Biosciences and Oxford Nanopore technologies reveals platform-specific error patterns (repository for Genome Research paper, 2022)
<p>Simulated ONT and PacBio RNA-Seq data for "Sequencing of individual barcoded cDNAs on Pacific Biosciences and Oxford Nanopore technologies reveals platform-specific error patterns" paper (Mikheenko et al., Genome Research, 2022). All details can be found in the Methods section of the paper.</p> <p><strong>PacBio.simulated_uniform_coverage.fasta.gz</strong> and <strong>ONT.simulated_uniform_coverage.fasta.gz files</strong> were used in Supplemental Note “Benchmarking of the read-to-isoform assignment algorithm”.</p> <p><strong>ONT.simulated_real_expression.fasta.gz</strong> file and all GTF files were used in the Section "Splice site correction improves transcript discovery precision". <strong>mouse.gencode.M26.spatial.15percent.reduced.gtf</strong> was used as the annotation file for all tools. <strong>mouse.gencode.M26.spatial.15percent.expressed.gtf </strong>contains the set of all expressed isoforms. <strong>mouse.gencode.M26.spatial.15percent.expressed_kept.gtf</strong> contains those of the isoforms that are in presented in the annotation file ("known" transcripts), <strong>mouse.gencode.M26.spatial.15percent.reduced.gtf</strong> contains expressed isoforms that were removed from the annotation ("novel" transcripts).</p>
DoTA-seq processed datasets (barcode: read mappings)
<p>Processed DoTA-seq sequencing reads to generate barcode: read mapping tables. This data is further processed to generate figures 1-3.</p>
Data and processing scripts for PRISM barcode sequencing data used in "Massively parallel pooled screening reveals genomic determinants of nanoparticle-cell interactions"
<p>Sequencing data for the PRISM barcodes generated after nano-particle treatment is presented in this repository alongside the code to process the sequencing counts to generate the binning probabilities and weighted scores. <br> <br> For the details please see the original publication or the bioarxiv preprint: https://doi.org/10.1101/2021.04.05.438521<br> <br> The raw data is provided in PILOT_DATA_COUNTS.csv and EXPERIMENT_DATA_COUNTS.csv files, for the pilot and the actual experiment. <br> <br> For each of these files an R script is provided to process them, along with the output of the scripts (PILOT_DATA_PROBABILITIES.csv and EXPERIMENT_DATA_PROBABILITIES.csv)</p>
Origin, diversity, and biogeography of Antarctic scale worms (Polychaeta: Polynoidae): a wide-scale barcoding approach
<p>Aim: The Antarctic marine environment hosts diversified and highly endemic benthos owing to its unique geologic and climatic history. Current warming trends have increased the urgency of understanding Antarctic species history to predict how environmental changes will impact ecosystem functioning. Antarctic benthic lineages have traditionally been examined under three hypotheses: 1) high endemism and local radiation, 2) emergence of deep-sea taxa through thermohaline circulation, 3) species migrations across the Polar Front. In this study, we investigated which hypotheses best describe benthic invertebrate origins by examining Antarctic scale worms.</p> <p>Location: Southern Ocean, Kerguelen archipelago, South American peninsula, Indian Ocean, New Zealand.</p> <p>Taxon: Scale worm polychaetes (Polynoidae).</p> <p>Methods: We amassed 670 polynoids from the Southern Ocean and neighbouring areas and performed phylogenetic reconstructions to identify lineages across geographic regions, aided by mitochondrial markers Cytochrome c oxidase subunit I (Cox1) and 16S ribosomal RNA (16S). Additionally, we produced haplotype networks at the species scale to examine genetic diversity, biogeographic separations, and past demography.</p> <p>Results: The Cox1 dataset provided the most illuminating insights into the evolution of polynoids. Eunoe sp. was present at South America and Kerguelen, in favour of the latter acting as a migration crossroads. Harmothoe fuligineum, widespread around the Antarctic continent, was also present but isolated at Kerguelen, possibly resulting from historical freeze-thaw cycles. The genus Polyeunoa appears to have diversified prior to colonizing the continent, leading to the cooccurrence of at least three cryptic species around the Southern and Indian Oceans. Analyses identified that nearly all populations are presently expanding following a bottleneck event, possibly caused by habitat reduction from the last glacial episodes.</p> <p>Main Conclusions: This study details the largest phylogenetic dataset assembled to date for Antarctic polynoids. These findings provide insight into past demographic events experienced by Antarctic marine benthos and identify multiple origin scenarios for contemporary polynoids. </p>
A new taxonomist-curated reference library of DNA barcodes for Neotropical electric fishes (Teleostei: Gymnotiformes)
<p>DNA barcoding is a useful tool for identifying species; however, successful barcode-based identification requires a reference library of barcode sequences from accurately identified specimens. Here we present a reference library of <em>co1</em> barcode sequences for the Neotropical electric knifefish order Gymnotiformes (Teleostei: Ostariophysi), a model taxon for studies of tropical diversification and biogeography, genomics, behaviour, and neurobiology. Our library contains barcodes for 167 of the ca. 270 valid species of gymnotiforms derived from geo-referenced museum voucher specimens, and includes sequences from 26 type specimens and 21 specimens from type localities, most of which we collected. To assess the state of gymnotiform barcodes in two main public barcode repositories, GenBank and BOLD, we compared the barcodes in these databases to our reference library. Our analysis shows that a considerable proportion of gymnotiform barcodes in GenBank and BOLD are mis- or unidentified. We encourage taxonomists to develop and publish barcode reference libraries composed of carefully curated barcode sequences.</p>
Data from: Evaluating species richness using proteomic fingerprinting and DNA-barcoding – a case study on meiobenthic copepods from the Clarion Clipperton Fracture Zone
<p><span>The Clarion Clipperton Fracture Zone (CCZ) is a vast deep-sea region harboring a highly diverse benthic fauna, which will be affected by potential future deep-sea mining of metal-rich polymetallic nodules. Despite the need for conservation plans and monitoring strategies in this context, the majority of taxonomic groups remains scientifically undescribed. However, molecular rapid assessment methods such as DNA-barcoding and Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) provide the potential to accelerate specimen identification and biodiversity assessment significantly in the deep-sea areas. In this study, we successfully applied both methods to investigate the diversity of meiobenthic copepods in the eastern CCZ, including the first application of MALDI-TOF MS for the identification of these deep-sea organisms. Comparing several different species delimitation tools for both datasets, we found that biodiversity values were very similar, with Pielou's Evenness varying between 0.97 and 0.99 in all datasets. Still, direct comparisons of species clusters revealed differences between all techniques and methods, which are likely caused by the high number of rare species being represented by only one specimen, despite our extensive dataset of more than 2000 specimens. Hence, we regard our study as a first approach toward setting up a reference library for mass spectrometry data of the CCZ in combination with DNA-barcodes. We conclude that proteome fingerprinting, as well as the more established DNA-barcoding, can be seen as a valuable tool for rapid biodiversity assessments in the future, even when no reference information is available.</span></p>
Data and Files for Zito, Rigon and Dunson (2022): "Inferring taxonomic affiliation from DNA barcoding aiding in discovery of new taxa"
<p>This folder contains the data and the R code to reproduce the figures and tables in the paper Zito, Rigon and Dunson (2022) - "Inferring Taxonomic placement from DNA barcoding aiding in discovery of new taxa", accepted as open access publication in Methods in Ecology and Evolution.</p> <p>The file "main_FinBOL.R" reproduces the tables in the main document and in the Supporting information available online for the analysis of the FinBOL data, while "main_Simulation_Section4_SI.R" reproduces the simulation in Section 4 of the Supporting information. </p> <p>All data are saved in the folder "data". For replicability purposes, we added version 2.13 of the RDP classifier to the repository, in the folder "RDP/java". This has been downloaded from https://sourceforge.net/projects/rdp-classifier/. </p> <p>For questions, contact the author at alessandro.zito@duke.edu<br> </p>
Figure 3 in Hydrodroma angelieri (Acari, Hydrachnidia: Hydrodromidae) a new water mite species from Corsica based on morphological and DNA barcode evidence
Figure 3 Neighbor-joining tree based on studiedHydrodroma COI sequences.
Figs 1–3 in Morphological redescription and DNA barcoding of Kaluginia lebetiformis Makarchenko, 1987 (Diptera: Chironomidae, Diamesinae) from South Korea
Figs 1–3. Adult male of Kaluginia lebetiformis Makarchenko from South Korea. 1 – total
Figs 4–10 in Morphological redescription and DNA barcoding of Kaluginia lebetiformis Makarchenko, 1987 (Diptera: Chironomidae, Diamesinae) from South Korea
Figs 4–10. Hypopygium of Kaluginia lebetiformis Makarchenko from South Sakhalin (4)
Figs 3–5 in Morphological redescription and DNA barcoding of Monodiamesa kamora Makarchenko et Yavorskaya (Diptera: Chironomidae) from the Amur River basin (Russian Far East)
Figs 3–5. Hypopygium of Monodiamesa kamora (holotype). 3 – total view, from above;
Figs 1–2 in Morphological redescription and DNA barcoding of Monodiamesa kamora Makarchenko et Yavorskaya (Diptera: Chironomidae) from the Amur River basin (Russian Far East)
Figs 1–2. Hypopygium of Monodiamesa kamora (paratype). 1 – total view, from above;
A specimen-level dataset of functional traits and DNA barcodes for Chinese bees
<p>The full potential for using DNA barcodes for profiling functional trait diversity has yet to be determined in plants and animals, thus we outline a general framework for quantifying functional trait diversity of insect community DNA and propose and assess the accuracy of three methods for achieving this. </p> <p>We built a novel dataset of traits and DNA barcodes for wild bees in China. An informatics framework was developed for phylogeny-based integration of these data and prediction of traits for any subject barcodes, and compared to two Blast-based methods of trait assignment. </p> <p>Under the specimen-level dataset, rate and accuracy of trait assigned dropped with an increase in distance between the query and its nearest reference member, though phylogenetic assignment was found to perform best under several criteria. For a wider range of compiled traits, conservative life-history traits showing the highest rates of assignment, for example sociality was predicted with confidence at 53%, parasitism at 44%, and nest location at 33%. </p> <p>Bayesian phylogenetic assignment of traits showed particular advantage over distance-based methods in the much lower rate that it would return incorrect state predictions when the query lacked relatives in the reference data. Automated, taxon-independent trait assignment might be applied at scale to either barcodes or metabarcodes in any invertebrates. With the further generation of integrated barcode and trait data, the assignment accuracy of the method is likely to increase. </p>
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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)
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DANDI Archive for NWB datasets
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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.