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33 results for “primer evaluation”
In silico and empirical evaluation of twelve metabarcoding primer sets for insectivorous diet analyses
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Data from: Primer sets evaluation and sampling method assessment for the monitoring of fish communities in the North-western part of the Mediterranean Sea through eDNA metabarcoding
<p>Environmental DNA (eDNA) metabarcoding appears to be a promising tool for surveying fish communities. However, the effectiveness of this method relies on primer set performance and on a robust sampling strategy. While some studies have evaluated the efficiency of several primers for fish detection, it has not yet been assessed <em>in situ </em>for the Mediterranean Sea. In addition, mainly surface waters were sampled and no filter porosity testing was performed. In this pilot study, our aim was to evaluate the ability of six primer sets, targeting 12S rRNA (AcMDB07; MiFish; Tele04) or 16S rRNA (Fish16S; Fish16SFD; Vert16S) loci, to detect fish species in the Mediterranean Sea using a metabarcoding approach. We also assessed the influence of sampling depth and filter pore size (0.45 µm <em>versus</em> 5 µm filters). To achieve this, we developed a novel sampling strategy allowing simultaneous surface and bottom filtration of large water volumes along on-site the same transect. We found that 16S rRNA primer sets enabled more fish taxa to be detected across each taxonomic level. The best combination was Fish16S/Vert16S/AcMDB07, which recovered 95% of the 97 fish species detected in our study. There were highly significant differences in species composition between surface and bottom samples. Filters of 0.45 µm led to the detection of significantly more fish species. Therefore, to maximize fish detection in the studied area, we recommend to filter both surface and bottom waters through 0.45 µm filters and to use a combination of these three primer sets.</p>
Data from: Evaluation of primer pairs for eDNA‐based assessment of Ephemeroptera, Plecoptera, and Trichoptera across a biogeographically diverse region
<p><span>Macroinvertebrates serve as key indicators in ecological assessments of aquatic ecosystems, where the composition and richness of their communities is indicative of environmental and anthropogenic drivers. Established monitoring of macroinvertebrates is expensive, time-consuming, and relies on expert taxonomic knowledge. In contrast, biomonitoring based on molecular tools can support faster characterization of aquatic communities but needs validation for the target taxonomic groups and the study region. Here, we used data from a biomonitoring program covering a large biogeographic gradient to compare the routine kick-net method with eDNA metabarcoding. We used two primer pairs targeting COI, one targeting a broad metazoan spectrum (miCOIintF/jgHCO2198) and another more recently developed primer pair optimized for the detection of freshwater invertebrates (fwhF2/EPTDr2n). We used the data of the macroinvertebrate monitoring with a focus on the orders of Ephemeroptera, Plecoptera, and Trichoptera across 92 rivers in Switzerland, covering four continental drainage basins and an elevational range from 198 to 1650 m a.s.l. Across all sampled sites, the kick-net detected more distinct taxa than either of the metabarcoding approaches. At a site level, however, both primer pairs detected on average more species. Comparing both primer pairs, the fwhF2/EPTDr2n primer pair captured more species assigned to the indicator groups Ephemeroptera, Plecoptera, and Trichoptera, and showed a significantly larger overlap with the kick-net method. However, the community composition still varied significantly among the different approaches. Fewer Trichopterans were recovered by eDNA metabarcoding, whereas the fwhF2/EPTDr2n primer pair detected more Plecopterans than the other two approaches. This study highlights the importance of optimization and validation of novel molecular approaches under consideration of the target organismal group and the study area.</span></p>
Data from: Primer sets evaluation and sampling method assessment for the monitoring of fish communities in the North-western part of the Mediterranean Sea through eDNA metabarcoding
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Data from: Evaluation of primer pairs for eDNA‐based assessment of Ephemeroptera, Plecoptera, and Trichoptera across a biogeographically diverse region
Open the record for dataset details and reuse information.
Fig. 2 in Barcoding diatoms: evaluation of the V4 subregion on the 18S rRNA gene, including new primers and protocols
Fig. 2 Box-and-whisker plot of intraspecific and intrageneric (x-axis) genetic distances measured in uncorrected p-distances (y-axis). Thick black lines indicate median values, boxes represent upper and lower quartiles, whiskers indicate value ranges, circles represent outliers
Fig. 1 in Barcoding diatoms: evaluation of the V4 subregion on the 18S rRNA gene, including new primers and protocols
Fig. 1 Consensus secondary structure of the 18S locus (SSU rRNA gene) in diatoms (181 sequences), based on the Toxarium undulatum 18S secondary structure model as reference sequence. Upper-case letters indicate that nucleotides at corresponding positions are conserved in 98– 100% of sequences, lower-case letters indicate 90–98% conservation, dots 80–90% conservation, circles indicate greater than 20% variability.
Supplementary material 9 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 TaXon tables of each primer pair (subtracted negative controls and filtered for fish and lamprey taxa OTUs)
Supplementary material 1 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
Pairwise comparison of the log-transformed reads of the non-normalized mock community (MC1) compared to the DNA concentration (ng/ul) of each species
Supplementary material 3 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
Sampled specimens and their respective species assignment collected for the fish mock community, extraction date, collection site, and concentration after DNA extraction
Supplementary material 4 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 species reported from Germany, their occurrence status, and their presence in the mock community (data from fishbase.org)
Supplementary material 2 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
Pairwise comparison of the log-transformed reads of the non-normalized mock community (MC1) compared to log-transformed reads of the normalized mock community (MC2) of each species
Data from: Evaluating the performance of targeted sequence capture, RNA-Seq, and degenerate-primer PCR cloning for sequencing the largest mammalian multigene family
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Supplementary material 1 from: Sakata MK, Kawata MU, Kurabayashi A, Kurita T, Nakamura M, Shirako T, Kakehashi R, Nishikawa K, Hossman MY, Nishijima T, Kabamoto J, Miya M, Minamoto T (2022) Development and evaluation of PCR primers for environmental DNA (eDNA) metabarcoding of Amphibia. Metabarcoding and Metagenomics 6: e76534. https://doi.org/10.3897/mbmg.6.76534
Supporting Information
Supplementary material 9 from: Weigand AM, Macher J-N (2018) A DNA metabarcoding protocol for hyporheic freshwater meiofauna: Evaluating highly degenerate COI primers and replication strategy. Metabarcoding and Metagenomics 2: e26869. https://doi.org/10.3897/mbmg.2.26869
Table S6: Taxa identified based on morphology :
Supplementary material 8 from: Weigand AM, Macher J-N (2018) A DNA metabarcoding protocol for hyporheic freshwater meiofauna: Evaluating highly degenerate COI primers and replication strategy. Metabarcoding and Metagenomics 2: e26869. https://doi.org/10.3897/mbmg.2.26869
Table S5: MetazoaMOTU list with 2-out-of-3 replicate strategy and excluding site 61 :
Supplementary material 7 from: Weigand AM, Macher J-N (2018) A DNA metabarcoding protocol for hyporheic freshwater meiofauna: Evaluating highly degenerate COI primers and replication strategy. Metabarcoding and Metagenomics 2: e26869. https://doi.org/10.3897/mbmg.2.26869
Table S4: MetazoaMOTU list with all replicates and including site 61 :
Supplementary material 6 from: Weigand AM, Macher J-N (2018) A DNA metabarcoding protocol for hyporheic freshwater meiofauna: Evaluating highly degenerate COI primers and replication strategy. Metabarcoding and Metagenomics 2: e26869. https://doi.org/10.3897/mbmg.2.26869
Table S3: Overview of raw reads and quality filtered reads :
Supplementary material 3 from: Weigand AM, Macher J-N (2018) A DNA metabarcoding protocol for hyporheic freshwater meiofauna: Evaluating highly degenerate COI primers and replication strategy. Metabarcoding and Metagenomics 2: e26869. https://doi.org/10.3897/mbmg.2.26869
Figure S2: Taxonomic composition of hyporheic community with all metazoan MOTUs :
Supplementary material 5 from: Weigand AM, Macher J-N (2018) A DNA metabarcoding protocol for hyporheic freshwater meiofauna: Evaluating highly degenerate COI primers and replication strategy. Metabarcoding and Metagenomics 2: e26869. https://doi.org/10.3897/mbmg.2.26869
Table S2: Primer combinations :
ScienceDex guides
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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.