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7 results for “taxonomic coverage”
DNA sequence and taxonomic gap analyses to quantify the coverage of aquatic cyanobacteria and eukaryotic microalgae in reference databases: Results of a survey in the Alpine region
<p>This dataset has been prepared as part of the Interreg Alpine Space project Eco-AlpsWater (ASP569) - <em>Innovative Ecological Assessment and Water Management Strategy for the Protection of Ecosystem Services in Alpine Lakes and Rivers</em>, <a href="https://www.alpine-space.eu/projects/eco-alpswater/en/home">https://www.alpine-space.eu/projects/eco-alpswater/en/home</a></p> <p>Individual archives include 16S rRNA (cyanobacteria) and 18S rRNA (microalgae) FASTA sequences and associated blastn results obtained from the high throughput sequencing of plankton and biofilm bulk/eDNA samples collected in 2019 in 37 lakes and 22 rivers across the Alpine region. These are supporting files for the paper by Salmaso et al., 2022. DNA sequence and taxonomic gap analyses to quantify the coverage of aquatic cyanobacteria and eukaryotic microalgae in reference databases: Results of a survey in the Alpine region. Science of the Total Environment, in press.</p>
One‐locus‐several‐primers: A strategy to improve the taxonomic and haplotypic coverage in diet metabarcoding studies
In diet metabarcoding analyses, insufficient taxonomic coverage of PCR primer sets generates false negatives that may dramatically distort biodiversity estimates. In this paper, we investigated the taxonomic coverage and complementarity of three cytochrome c oxidase subunit I gene (COI) primer sets based on in silico analyses and we conducted an in vivo evaluation using fecal and spider web samples from different invertivores, environments, and geographic locations. Our results underline the lack of predictability of both the coverage and complementarity of individual primer sets: (a) sharp discrepancies exist observed between in silico and in vivo analyses (to the detriment of in silico analyses); (b) both coverage and complementarity depend greatly on the predator and on the taxonomic level at which preys are considered; (c) primer sets' complementarity is the greatest at fine taxonomic levels (molecular operational taxonomic units [MOTUs] and variants). We then formalized the "one‐locus‐several‐primer‐sets" (OLSP) strategy, that is, the use of several primer sets that target the same locus (here the first part of the COI gene) and the same group of taxa (here invertebrates). The proximal aim of the OLSP strategy is to minimize false negatives by increasing total coverage through multiple primer sets. We illustrate that the OLSP strategy is especially relevant from this perspective since distinct variants within the same MOTUs were not equally detected across all primer sets. Furthermore, the OLSP strategy produces largely overlapping and comparable sequences, which cannot be achieved when targeting different loci. This facilitates the use of haplotypic diversity information contained within metabarcoding datasets, for example, for phylogeography and finer analyses of prey–predator interactions.
One‐locus‐several‐primers: A strategy to improve the taxonomic and haplotypic coverage in diet metabarcoding studies
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Appendix. The status of global taxonomic checklist preparation for flowering plant families (based on Angiosperm Phylogeny Group II but modified to reflect circumscriptions of existing checklists). If a checklist is complete and available on the Internet then the URL is also given. The species numbers (sp. no.) given are either based on actual working lists (WL) where they exist or are based on Stevens (2006) if no WL is available. Five categories are used to describe the status of a particular working list: 1, checklist complete and accessible via the Internet now; 2, checklist available on Internet by end of 2007 (Asteraceae 2010); 3, checklist complete but not online; 4, some online lists giving partial coverage may be available; 5, no global checklist being compiled so far as known. in Towards Target 1 of the Global Strategy for Plant Conservation: A working list of all known plant species - Progress and prospects
Appendix. The status of global taxonomic checklist preparation for flowering plant families (based on Angiosperm Phylogeny Group II but modified to reflect circumscriptions of existing checklists). If a checklist is complete and available on the Internet then the URL is also given. The species numbers (sp. no.) given are either based on actual working lists (WL) where they exist or are based on Stevens (2006) if no WL is available. Five categories are used to describe the status of a particular working list: 1, checklist complete and accessible via the Internet now; 2, checklist available on Internet by end of 2007 (Asteraceae 2010); 3, checklist complete but not online; 4, some online lists giving partial coverage may be available; 5, no global checklist being compiled so far as known.
Data from: Revisiting the ichthyodiversity of Java and Bali through DNA barcodes: taxonomic coverage, identification accuracy, cryptic diversity and identification of exotic species
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Supplementary material 2 from: Ahmed M, Back MA, Prior T, Karssen G, Lawson R, Adams I, Sapp M (2019) Metabarcoding of soil nematodes: the importance of taxonomic coverage and availability of reference sequences in choosing suitable marker(s). Metabarcoding and Metagenomics 3: e36408. https://doi.org/10.3897/mbmg.3.36408
: Data type: source code
Supplementary material 1 from: Ahmed M, Back MA, Prior T, Karssen G, Lawson R, Adams I, Sapp M (2019) Metabarcoding of soil nematodes: the importance of taxonomic coverage and availability of reference sequences in choosing suitable marker(s). Metabarcoding and Metagenomics 3: e36408. https://doi.org/10.3897/mbmg.3.36408
: Data type: species data
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.