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4,144 results for “ITS barcode”
Fig. 14. Leuckartiara longicalcar, n in DNA barcoding of some Pandeidae species (Cnidaria, Hydrozoa, Anthoathecata)
Fig. 14. Leuckartiara longicalcar, n. spec., living animal (paratype), total height about 15 mm.
Fig. 1 in DNA barcoding of some Pandeidae species (Cnidaria, Hydrozoa, Anthoathecata)
Fig. 1. Neoturris abyssi, original illustration of Sars (1874).
Dataset from: A curated DNA barcode reference library for parasitoids of northern European cyclically outbreaking geometrid moths
<p><span>Large areas of forests are annually damaged or destroyed by outbreaking insect pests. Understanding the factors that trigger and terminate such population eruptions has become crucially important, as plants, plant-feeding insects, and their natural enemies may respond differentially to the ongoing changes in the global climate. In northernmost Europe, climate-driven range expansions of the geometrid moths <em>Epirrita autumnata</em> and <em>Operophtera brumata</em> have resulted in overlapping and increasingly severe outbreaks. Delayed density-dependent responses of parasitoids are a plausible explanation for the ten-year population cycles of these moth species, but the impact of parasitoids on geometrid outbreak dynamics is unclear due to a lack of knowledge on the host ranges and prevalences of parasitoids attacking the moths in nature. To overcome these problems, we reviewed the literature on parasitism in the focal geometrid species in their outbreak range, and then constructed a DNA barcode reference library for all relevant parasitoid species based on reared specimens and sequences obtained from public databases. The combined parasitoid community of<em> E. autumnata</em> and <em>O. brumata</em> consists of 32 hymenopteran species, all of which can be reliably identified based on their barcode sequences. The curated barcode library presented here opens up new opportunities for estimating the abundance and community composition of parasitoids across populations and ecosystems based on mass barcoding and metabarcoding approaches. Such information can be used for elucidating the role of parasitoids in moth population control, possibly also for devising methods for reducing the extent, intensity, and duration of outbreaks.</span></p>
Data from: Delineating seagrass species in the genera Halodule and Halophila from Tanzanian coastal waters using ITS and rbcL DNA barcoding
<p>The seagrass species in <em>Halodule</em> and <em>Halophila</em> may for several reasons be considered as taxonomic complexes. They show close evolutionary relationships, morphological plasticity, and share similar features making misidentifications likely when morphological identification is applied. In Tanzanian coastal waters, there is some uncertainty about the identity of members of <em>Halodule</em>, particularly the existence of <em>Halodule wrightii</em> and the species composition of the <em>Halophila ovalis</em> complex. This study used morphology as well as internal transcribed spacer (ITS1 and ITS2) and ribulose-bisphosphate carboxylase (rbcL) DNA barcoding to identify species of <em>Halodule</em> and <em>Halophila</em>. Seagrass samples were collected during low spring tides, from Tanzania's coastal waters of Tanga, Dar es Salaam, Mtwara, Mafia Island, and Unguja Island, from August 2020 to February 2022. Morphological diagnosis, phylogenetic analysis, and evolutionary divergences inferred from the ITS gene supported the identification of five species, namely <em>Halophila ovalis</em>, <em>H. minor,</em> and <em>H. stipulacea</em>, with the first two forming the <em>H. ovalis</em> complex; as well as <em>Halodule uninervis</em> and <em>H. pinifolia</em>. It is the first time that <em>H. pinifolia</em> is reported in Tanzania. This is the first study reporting the delineation of seagrass species in East African coastal waters using DNA barcoding coupled with morphology.</p>
Efficient isolation of rare B cells using next-generation antigen barcoding
<p><strong>ABSTRACT:</strong> The ability to efficiently isolate antigen-specific B cells in high throughput will greatly accelerate the discovery of therapeutic monoclonal antibodies (<strong>mAbs</strong>) and catalyze rational vaccine development. Traditional mAb discovery is a costly and labor-intensive process, although recent advances in single-cell genomics using emulsion microfluidics allow simultaneous processing of thousands of individual cells. Here we present a streamlined method for isolation and analysis of large numbers of antigen-specific B cells, including next generation antigen barcoding and an integrated computational framework for B cell multi-omics. We demonstrate the power of this approach by recovering thousands of antigen-specific mAbs, including the efficient isolation of extremely rare precursors of VRC01-class and IOMA-class broadly neutralizing HIV mAbs.</p> <p> </p>
The Dung Beetle Oxyomus of Taiwan (Coleoptera: Scarabaeidae): Review of the Fauna, a New Species and its Larva Associated by DNA Barcoding
<p>Complete photo documentation and DNA barcodes datasets used for the paper</p>
Toward understanding insect species introduction and establishment: a community-level barcoding approach using island beetles
<p>Since Darwin put forward his opposing hypotheses to explain the successful establishment of species in areas outside their native ranges, the preadaptation and competition-relatedness hypotheses, known as Darwin's naturalisation conundrum, numerous studies have sought to understand the relative importance of each. Here we take advantage of well-characterised beetle communities across laurel forests of the Canary Islands for a first evaluation of the relative support for Darwin's two hypotheses within arthropods. We generated a mitogenome backbone tree comprising nearly half of the beetle genera recorded within the Canary Islands for the phylogenetic placement of native and introduced species sampled in laurel forests, using cytochrome c oxidase I (COI) sequences. For comparative purposes, we also assembled and phylogenetically placed a data set of COI sequences for introduced beetle species that were not sampled within laurel forests. Our results suggest a stronger effect of species preadaptation over resource competition, while also revealing an underappreciated shortfall in arthropod biodiversity data – knowledge of endemic species. We name this the Humboldtean shortfall, and suggest that similar studies using arthropods should incorporate DNA barcode sequencing to mitigate this problem.</p>
Fig. 4 in Combining morphology and DNA barcoding resolves the taxonomy of Western Malagasy Liotrigona Moure, 1961 (Hymenoptera: Apidae: Meliponini)
Fig. 4. Holotype worker of Liotrigona kinzelbachi sp. n., lateral view. Scale unit = 0.1 mm.
Obuasi case study data: Performance of neutral SNP barcodes to determine genetic diversity and structure of Plasmodium falciparum in Africa
<p>A small number of informative biallelic single nucleotide polymorphisms (SNPs) have been proposed to be an economical method to fast-track the genotyping and relatedness analysis of <em>Plasmodium</em> <em>falciparum</em> in malaria-endemic areas. Whilst used successfully in low-transmission areas where infections are monoclonal and highly related, we present the first study to evaluate the performance of these 24- and 96-SNP molecular barcodes in African countries characterised by moderate-to-high transmission. Using haplotypes generated from the MalariaGEN <em>P. falciparum</em> Community Project version 6 database, 52.3% of infections were multiclonal, generating high frequencies of mixed-allele calls (MACs) per isolate. Both multiclonality and low heterozygosity of SNPs impeded haplotype construction for analyses of relatedness. Although fewer SNPs provided usable data, these SNP barcodes weakly identified genetic differentiation across large geographic distances. However, both minor and major alleles' frequencies were temporally unstable. We conclude that these standardised SNP barcodes are vulnerable to ascertainment bias. While large numbers of SNPs acquired by whole-genome sequencing and computational methods to construct haplotypes present a way forward, these approaches may not be practical or cost-effective for surveillance on large scales in malaria-endemic areas. </p>
Figure 6 in New records of water mites from the Balkans revealed by DNA barcoding (Acari, Hydrachnidia)
Figure 6. Neighbour-joining tree based on studied Hygrobates trigonicus COI sequences.
DNA barcoding data for springsnails
<p class="MsoNormal">In desert environments, unique communities depend on groundwater at springs. There is a diverse radiation of small (<5 mm) snails found across the desert southwest in North America. Nearly all springsnail species are considered critically imperiled with their existence depending on maintenance of spring-flows in regions of declining water availability. Extant, endemic, springsnails in the Trans-Pecos region of Texas include one species of <em>Pseudotryonia </em>Hershler, 2001, five nominal <em>Tryonia</em> W. Stimpson, 1865 (Cochliopidae) and seven <em>Pyrgulopsis</em> Call & Pilsbry, 1886<em> </em>(Hydrobiidae). Four of these snails are classified as endangered under the US Endangered Species Act. Survey work was conducted at the type and previously reported localities of named springsnails and 116 previously unsampled spring sites to locate and identify additional populations. Sequences of the DNA barcoding region were used to establish a database of known sequences from the named species and confirm identifications of new populations encountered.</p>
DNA barcoding for the assessment of marine and coastal Fish Diversity from the Coast of Mozambique
<p><span>The ichthyological provinces of Mozambique are understudied hotspots of global fish diversity. In this study, we applied DNA barcoding to identify the composition of the fish fauna from the coast of Mozambique. A total of 143 species belonging to 104 genera, 59 families, and 30 orders were identified. The overall K2P distance of the COI sequences within species ranged from 0.00% to 1.51%, while interspecific distances ranged from 3.64% to 24.49%. Moreover, the study revealed 15 threatened species according to the IUCN Red List of Threatened Species, with elasmobranchs being the most represented group. Additionally, the study also uncovered four new species that were not previously recorded in this geographic area, including <em>Boleophthalmus dussumieri, Maculabatis gerrardi, Hippocampus kelloggi, and Lethrinus miniatus</em>. This study represents the first instance of utilizing molecular references to explore the fish fauna along the Mozambican coast. Our results indicate that DNA barcoding is a dependable technique for the identification and delineation of fish species in the waters of Mozambique. The DNA barcoding library established in this research will be an invaluable asset for advancing the understanding of fish diversity and guiding future conservation initiatives.</span></p>
COI Barcode sequences for arthropod species from the high Appalachian Mountains, USA
<p>Developing systematic conservation plans depends on a wealth of information on a region's biodiversity. For 'dark taxa' such as arthropods, such data is usually very incomplete and in most cases left out from assessments.</p> <p>Sky islands are important and often fragile biodiversity hotspots. Southern Appalachian high-elevation spruce-fir forests represent a particularly threatened sky-island ecosystem, hosting numerous endemic and threatened species, but their arthropods remain understudied.</p> <p>Here we use voucher-based megabarcoding to explore genetic differentiation among leaf-litter arthropod communities of these highlands, and to examine the extent to which they represent dispersed communities of more or less coherent species, manageable as a distributed unit. We assembled a dataset comprising >6000 COI sequences representing diverse arthropod groups to assess species richness and sharing across peaks and ranges. Comparisons were standardized across taxa using automated species delimitation, measuring endemism levels by putative species.</p> <p>Species-richness was high, with sites hosting from 86-199 litter arthropod species (not including mites or myriapods). Community profiles suggest that around one-fourth of these species are unique to single sky islands and more than one-third of all species are limited to a particular range. Across major taxa, endemicity was lowest in Araneae, and highest in neglected groups like Isopoda, Pseudoscorpionida, Protura, and Diplura.</p> <p>Southern Appalachian sky islands of spruce-fir habitat host significantly distinct leaf litter arthropod communities, with high levels of local endemicity. This is the first work to provide such a clear picture of peak and range uniqueness for a taxonomically broad sample. Ensuring the protection of a sizeable fraction of high-elevation litter species richness will therefore require attention at a relatively fine spatial scale.</p>
Field sampling and DNA-barcoding of fig pollinator wasps across host species and host developmental phase and on non-Ficus controls
<p><span>To better understand factors that might contribute to this observed range of specificity, we used sticky traps to capture fig-pollinating wasp individuals at 13 <em>Ficus</em> species, sampling at different stages of the reproductive cycle of the host figs (e.g. trees with receptive inflorescences, or vegetative trees, bearing only leaves). We also sampled at other tree species, using them as non-<em>Ficus</em> controls. DNA barcoding allowed us to identify the wasps to species, and therefore assign their presence and abundance to host fig species and the developmental stage of that individual tree. Here we upload the data and the R scripts used to analyze these data.</span></p>
Data for: Simultaneous subset tracing and miRNA profiling of tumor-derived exosomes via dual-surface-protein orthogonal barcoding
<p><span>The clinical potential of miRNA-based liquid biopsy has been largely limited by the heterogeneous sources in plasma and tedious assay processes. </span><span>Here we develop a precise and robust one-pot assay called dual-surface-protein</span><span>-guided</span><span> orthogonal recognition of tumor-derived exosomes and in-situ profiling of microRNAs (SORTER) to detect tumor-derived exosomal miRNAs and enhance the diagnostic accuracy of prostate cancer (PCa). The SORTER utilizes two allosteric aptamers against exosomal marker CD63 and tumor marker EpCAM to create an orthogonal labeling barcode and achieve selective sorting of tumor-specific exosome subtypes. Furthermore, the labeled barcode on tumor-derived exosomes initiated targeted membrane fusion with liposome probes to import miRNA detection reagents, enabling in-situ sensitive profiling of tumor-derived exosomal miRNAs. With a signature of six miRNAs, SORTER differentiated PCa and benign prostatic hyperplasia with an accuracy of 100%. Notably, the diagnostic accuracy reached 90.6% in the classification of metastatic and non-metastatic PCa. We envision that the SORTER will promote the clinical adaptability of miRNA-based liquid biopsy.</span></p>
Data for paper: Genomic data reveals new species and the limits of mtDNA barcode diagnostics to contain a global pest species complex (Diptera: Tephritidae: Dacinae)
<p>Files in this repository:</p><p>"COI_alignment.fas.zip" Zipped file of the FASTA alignment of the COI sequences.</p><p>"COI_IQtree.treefile" Newick treefile resulting from the IQ-tree analysis of the COI alignment.</p><p>"RAD-loci_alignment.nex.zip" Zipped file of the NEXUS alignment of RAD loci of 2295 samples.</p><p>"RAD-loci_IQtree.tre" Newick treefile resulting from the IQ-tree analysis of the RAD-loci alignment.</p><p>"RAD-SNP_alignment.usnps.nex" NEXUS alignment of the RAD-SNP data of 50 samples.</p><p>"RAD-SNP_SNAPP.trees" Set of Newick trees resulting from the BEAST SNAPP analysis.</p>
A barcode-based phylogenetic characterization of Phytophthora cactorum identifies two cosmopolitan lineages with distinct host affinities and the first report of Phytophthora pseudotsugae in California
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Longer is not always better: optimizing barcode length for large-scale species discovery and identification
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Expanded phylogeny of Nomadinae (Hymenoptera: Apidae) with integration of UCE and DNA barcode sequence data
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Data from: Barcoding 100K specimens in a single nanopore run
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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
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.