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1,076 results for “Metabarcoding”
Supplementary material 1 from: Parisy B, Schmidt NM, Wirta H, Stewart L, Pellissier L, Holben WE, Pannoni S, Somervuo P, Jones MM, Siren J, Vesterinen E, Ovaskainen O, Roslin T (2023) Ecological signals of arctic plant-microbe associations are consistent across eDNA and vegetation surveys. Metabarcoding and Metagenomics 7: e99979. https://doi.org/10.3897/mbmg.7.99979
Complementary figures and details about the article
Supplementary material 8 from: Macher T-H, Schütz R, Yildiz A, Beermann AJ, Leese F (2023) Evaluating five primer pairs for environmental DNA metabarcoding of Central European fish species based on mock communities. Metabarcoding and Metagenomics 7: e103856. https://doi.org/10.3897/mbmg.7.103856
Unmodified TaXon tables of each primer pair
Supplementary material 7 from: Macher T-H, Schütz R, Yildiz A, Beermann AJ, Leese F (2023) Evaluating five primer pairs for environmental DNA metabarcoding of Central European fish species based on mock communities. Metabarcoding and Metagenomics 7: e103856. https://doi.org/10.3897/mbmg.7.103856
Protocol for the adapted NucleoMag Tissue Kit
Supplementary material 5 from: Macher T-H, Schütz R, Yildiz A, Beermann AJ, Leese F (2023) Evaluating five primer pairs for environmental DNA metabarcoding of Central European fish species based on mock communities. Metabarcoding and Metagenomics 7: e103856. https://doi.org/10.3897/mbmg.7.103856
List of all ambiguous assignments
Supplementary material 11 from: Macher T-H, Schütz R, Yildiz A, Beermann AJ, Leese F (2023) Evaluating five primer pairs for environmental DNA metabarcoding of Central European fish species based on mock communities. Metabarcoding and Metagenomics 7: e103856. https://doi.org/10.3897/mbmg.7.103856
Python scripts used in this study
Supplementary material 6 from: Macher T-H, Schütz R, Yildiz A, Beermann AJ, Leese F (2023) Evaluating five primer pairs for environmental DNA metabarcoding of Central European fish species based on mock communities. Metabarcoding and Metagenomics 7: e103856. https://doi.org/10.3897/mbmg.7.103856
List of over splitting rates per primer pair for each detected species
Supplementary material 10 from: Macher T-H, Schütz R, Yildiz A, Beermann AJ, Leese F (2023) Evaluating five primer pairs for environmental DNA metabarcoding of Central European fish species based on mock communities. Metabarcoding and Metagenomics 7: e103856. https://doi.org/10.3897/mbmg.7.103856
Processed and manually curated TaXon tables of each primer pair
Data from: Home is where the hollow is: Revealing vertebrate tree hollow user biodiversity with eDNA metabarcoding
<p>Tree hollows are essential for many vertebrate species, providing both nesting sites and shelter. Globally, old hollow-bearing trees are in decline resulting in many dependent species being under threat. It is therefore imperative that vital hollow-bearing trees are preserved, but it is logistically difficult to rapidly determine which hollows are being used and by which taxa. Here, we investigate the efficacy of eDNA metabarcoding as a survey tool for vertebrate hollow users. We compared the identity and richness of hollow-inhabiting vertebrate taxa using eDNA metabarcoding of both sediment from the tree hollows, and material collected using roller swabs. Samples (n = 138) were collected from hollow-bearing tuart trees (<em>Eucalyptus</em> <em>gomphocephala</em>; N = 28), within both an urban remnant and a relatively undisturbed forested area of South-West Western Australia. We detected a wide range of vertebrate taxa, including cryptic species such as the brush-tailed phascogale (<em>Phascogale</em> <em>tapoatafa</em>), while also providing ecologically informative data, such as hollow use by invasive Rainbow Lorikeet (<em>Trichoglossus</em> <em>moluccanus</em>) within the study areas. Our results showed variation in the species detected between methods, with the roller swab method detecting a greater number of species and a higher mean species richness per sample than hollow sediment did. The species detected from both methods did not perfectly overlap, highlighting the value of using multiple methods or substrates to detect a greater number of taxa. Our results suggest eDNA metabarcoding from tree hollow samples offers a sensitive and resource-efficient method of monitoring vertebrate hollow users, if enough hollows are sampled. This provides not only a broad biodiversity assessment tool but also an effective method for detecting taxa that may be elusive using other methods.</p>
DNA metabarcoding assessment of Neotropical ichthyoplankton communities is marker-dependent
<p>Raw sequencing file of the arcticle "<strong>DNA metabarcoding assessment of Neotropical ichthyoplankton communities is marker-dependent</strong>", by Daniel Fonseca Teixeira<sup>1, 2</sup>, Heron Oliveira Hilário<sup>1</sup>, Gilmar Bastos Santos<sup>1</sup>, Daniel Cardoso Carvalho<sup>1*</sup></p> <p>1- Post-Graduate Program in Vertebrate Biology, Pontifical Catholic University of Minas Gerais, PUC Minas, Belo Horizonte 30535-610, Brazil;</p> <p>2- Post-Graduate Program in Genetics, Federal University of Minas Gerais, Belo Horizonte 31270-901, Brazil;</p> <p>The study of ichthyoplankton is paramount to understanding fish assemblages’ reproductive dynamics. DNA metabarcoding has been applied as a rapid, cost-effective, and accurate taxonomy tool, allowing the identification of multiple individuals simultaneously. However, there remain significant challenges when using DNA metabarcoding, such as molecular marker choice according to the taxonomic resolution and length of the fragment to be sequenced, primer bias, incomplete reference databases, and qualitative inferences incongruences. Here, 30 ichthyoplankton pools collected from a Neotropical river were identified at a molecular level using DNA metabarcoding to compare the resolution, sensibility, specificity and relative read abundance (RRA) recovery of three molecular markers: the standard COI fragment (650pb, with each strand analyzed individually) and two short 12S rRNA genes markers (@ 200bp - NeoFish and MiFish markers). The combined use of the three markers increased the genera detection rates by 25% to 87.5%, allowing an increased taxonomic coverage and robust taxonomic identification of complex Neotropical ichthyoplankton communities. RRA is marker-dependent, indicating caution is still needed whilst inferring species abundance based on DNA metabarcoding data when using PCR-dependent protocols.</p>
Chisholm Lake sedimentary unprocessed fish metabarcoding DNA sequences
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Reference sequence database for eDNA metabarcoding of San Francisco estuary fishes and invertebrates
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Data from: Metabarcoding of freshwater invertebrates to detect the effects of a pesticide spill
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Data from: Towards accurate species-level metabarcoding of arthropod communities from the tropical forest canopy
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metabarcoding data for: Benchmark of bioinformatics tools for fast and accurate species identification from environmental DNA metabarcoding
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Network analysis with either Illumina or MinION reveals that detecting vertebrate species requires metabarcoding of iDNA from a diverse fly community
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Data from: Universal and blocking primer mismatches limit the use of high-throughput DNA sequencing for the quantitative metabarcoding of arthropods
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DNA metabarcoding data characterizing insectivorous diet of purple martins (Progne subis subis) using two COI primer sets (ANML and ZBJ)
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Food from faeces: evaluating the efficacy of scat DNA metabarcoding in dietary analyses
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Data from: Comparative authentication of Hypericum perforatum herbal products using DNA metabarcoding, TLC and HPLC-MS
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Data from: Not all are free-living: high-throughput DNA metabarcoding reveals a diverse community of protists parasitizing soil metazoa
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International Brain Laboratory public data
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OpenNeuro
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