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1,076 results for “Metabarcoding”
Figure 5 from: Ceballos-Escalera A, Richards J, Arias MB, Inward DJG, Vogler AP (2022) Metabarcoding of insect-associated fungal communities: a comparison of internal transcribed spacer (ITS) and large-subunit (LSU) rRNA markers. MycoKeys 88: 1-33. https://doi.org/10.3897/mycokeys.88.77106
Figure 5 ML tree of Sordariomycetes constructed from the reference sequence alignments and OTUs for both markers (clustering thresholds: 98% ITS2, 99% LSU D1-D2). Leotia lubrica (Leotiomycetes) was specified as the outgroup. The assignment of OTUs by each of the three classifiers (RDP, IDTAXA, Protax-fungi) is shown by coloured boxes. Terminals missing these boxes are the reference sequences. Coloured dots on the nodes of the tree indicate the hypothetical ancestor defining monophyletic groups corresponding to the various orders of Sordariomycetes. The extent of each order is indicated by the coloured inner ring. Note that the ancestor of an order is defined by the youngest node from which all reference sequences are descended; OTUs falling outside of the resulting clades appear as 'unassigned' by the phylogenetic analysis approach. The distribution of ITS2 (red squares) and LSU D1-D2 (blue bullets) relative to the reference set (yellow stars) on each of the tips of the tree. Note the limited presence of ITS sequences in the Ophiostomatales (in top right quadrant).
Figure 8 from: Ceballos-Escalera A, Richards J, Arias MB, Inward DJG, Vogler AP (2022) Metabarcoding of insect-associated fungal communities: a comparison of internal transcribed spacer (ITS) and large-subunit (LSU) rRNA markers. MycoKeys 88: 1-33. https://doi.org/10.3897/mycokeys.88.77106
Figure 8 Proportion of OTUs assigned to each Order from metabarcoding with LSU (left panel) and ITS (right panel) markers based on the RDP classifier and the phylogenetic tree, under increasing threshold values.
Elasmobranch diversity across a remote coral reef atoll revealed through environmental DNA metabarcoding
<p><span><span><span><span><span><span><span><span><span><span><span>As elasmobranchs are becoming increasingly threatened, efficient methods for monitoring the distribution and diversity of elasmobranch populations are required. Environmental DNA (eDNA) metabarcoding is an increasingly applied technique that enables mass identification of entire communities and is an effective method for the detection of rare and elusive species. We performed an eDNA metabarcoding survey for fish communities around a coral reef atoll in the Chagos Archipelago and assessed the diversity and distribution of elasmobranch species detected within these communities. Our eDNA survey detected 353 amplicon sequence variants (ASVs) attributed to fishes, 12 of which were elasmobranchs. There were no differences in fish communities based on the presence and absence of ASVs between sample depth (surface and 40m) or sampling habitat, but communities based on read abundance were significantly different between habitats. The dominant elasmobranch species were grey reef (<i>Carcharhinus amblyrhynchos</i>) and silvertip (<i>C. albimarginatus</i>) sharks, and elasmobranch communities were significantly different between sampling depth and habitat. Overall, we find that eDNA metabarcoding can be used to reveal the diversity of elasmobranchs within broader taxonomic assays, but further research and development of targeted metabarcoding primers may be required before it can be integrated into a toolkit for monitoring these species.</span></span></span></span></span></span></span></span></span></span></span></p>
Supplementary material 1 from: Biessy L, Pearman JK, Waters S, Vandergoes MJ, Wood SA (2022) Metagenomic insights to the functional potential of sediment microbial communities in freshwater lakes. Metabarcoding and Metagenomics 6: e79265. https://doi.org/10.3897/mbmg.6.79265
Figures S1–S6
Supplementary material 2 from: Biessy L, Pearman JK, Waters S, Vandergoes MJ, Wood SA (2022) Metagenomic insights to the functional potential of sediment microbial communities in freshwater lakes. Metabarcoding and Metagenomics 6: e79265. https://doi.org/10.3897/mbmg.6.79265
Tables S1, S2
Supplemental R code and csv files for statistical analysis on Doi et al. "Effects of species traits and ecosystem characteristics on species detection by eDNA metabarcoding in lake fish communities"
<p>Supplemental R code and csv files for statistical analysis on Doi et al. "Effects of species traits and ecosystem characteristics on species detection by eDNA metabarcoding in lake fish communities"</p>
Supplementary material 2 from: Keck F, Hürlemann S, Locher N, Stamm C, Deiner K, Altermatt F (2022) A triad of kicknet sampling, eDNA metabarcoding, and predictive modeling to assess richness of mayflies, stoneflies and caddisflies in rivers. Metabarcoding and Metagenomics 6: e79351. https://doi.org/10.3897/mbmg.6.79351
Tables S1–S4
Supplementary material 3 from: Miya M, Sado T, Oka S-i, Fukuchi T (2022) The use of citizen science in fish eDNA metabarcoding for evaluating regional biodiversity in a coastal marine region: A pilot study. Metabarcoding and Metagenomics 6: e80444. https://doi.org/10.3897/mbmg.6.80444
Table S3
Supplementary material 1 from: Miya M, Sado T, Oka S-i, Fukuchi T (2022) The use of citizen science in fish eDNA metabarcoding for evaluating regional biodiversity in a coastal marine region: A pilot study. Metabarcoding and Metagenomics 6: e80444. https://doi.org/10.3897/mbmg.6.80444
Table S1
Supplementary material 2 from: Miya M, Sado T, Oka S-i, Fukuchi T (2022) The use of citizen science in fish eDNA metabarcoding for evaluating regional biodiversity in a coastal marine region: A pilot study. Metabarcoding and Metagenomics 6: e80444. https://doi.org/10.3897/mbmg.6.80444
Table S2
Supplementary material 4 from: Miya M, Sado T, Oka S-i, Fukuchi T (2022) The use of citizen science in fish eDNA metabarcoding for evaluating regional biodiversity in a coastal marine region: A pilot study. Metabarcoding and Metagenomics 6: e80444. https://doi.org/10.3897/mbmg.6.80444
Table S4
Supplementary material 5 from: Miya M, Sado T, Oka S-i, Fukuchi T (2022) The use of citizen science in fish eDNA metabarcoding for evaluating regional biodiversity in a coastal marine region: A pilot study. Metabarcoding and Metagenomics 6: e80444. https://doi.org/10.3897/mbmg.6.80444
Supplementary methods
Supplementary material 4 from: Hintikka S, Carlsson JE, Carlsson J (2022) The bacterial hitchhiker's guide to COI: Universal primer-based COI capture probes fail to exclude bacterial DNA, but 16S capture leaves metazoa behind. Metabarcoding and Metagenomics 6: e80416. https://doi.org/10.3897/mbmg.6.80416
COI library ASV tax
Supplementary material 1 from: Hintikka S, Carlsson JE, Carlsson J (2022) The bacterial hitchhiker's guide to COI: Universal primer-based COI capture probes fail to exclude bacterial DNA, but 16S capture leaves metazoa behind. Metabarcoding and Metagenomics 6: e80416. https://doi.org/10.3897/mbmg.6.80416
File S1
Supplementary material 3 from: Hintikka S, Carlsson JE, Carlsson J (2022) The bacterial hitchhiker's guide to COI: Universal primer-based COI capture probes fail to exclude bacterial DNA, but 16S capture leaves metazoa behind. Metabarcoding and Metagenomics 6: e80416. https://doi.org/10.3897/mbmg.6.80416
16S library ASV tax
Supplementary material 5 from: Hintikka S, Carlsson JE, Carlsson J (2022) The bacterial hitchhiker's guide to COI: Universal primer-based COI capture probes fail to exclude bacterial DNA, but 16S capture leaves metazoa behind. Metabarcoding and Metagenomics 6: e80416. https://doi.org/10.3897/mbmg.6.80416
Unassigned COIASVs krona
Supplementary material 2 from: Hintikka S, Carlsson JE, Carlsson J (2022) The bacterial hitchhiker's guide to COI: Universal primer-based COI capture probes fail to exclude bacterial DNA, but 16S capture leaves metazoa behind. Metabarcoding and Metagenomics 6: e80416. https://doi.org/10.3897/mbmg.6.80416
Metadata all
Supplementary material 6 from: Jeunen G-J, Lipinskaya T, Gajduchenko H, Golovenchik V, Moroz M, Rizevsky V, Semenchenko V, Gemmell NJ (2022) Environmental DNA (eDNA) metabarcoding surveys show evidence of non-indigenous freshwater species invasion to new parts of Eastern Europe. Metabarcoding and Metagenomics 6: e68575. https://doi.org/10.3897/mbmg.6.e68575
Macro-invertebrate abundances as observed by the hydrobiological survey
Supplementary material 8 from: Jeunen G-J, Lipinskaya T, Gajduchenko H, Golovenchik V, Moroz M, Rizevsky V, Semenchenko V, Gemmell NJ (2022) Environmental DNA (eDNA) metabarcoding surveys show evidence of non-indigenous freshwater species invasion to new parts of Eastern Europe. Metabarcoding and Metagenomics 6: e68575. https://doi.org/10.3897/mbmg.6.e68575
Environmental DNA detections from the passive surveillance for both metabarcoding assays
Supplementary material 2 from: Jeunen G-J, Lipinskaya T, Gajduchenko H, Golovenchik V, Moroz M, Rizevsky V, Semenchenko V, Gemmell NJ (2022) Environmental DNA (eDNA) metabarcoding surveys show evidence of non-indigenous freshwater species invasion to new parts of Eastern Europe. Metabarcoding and Metagenomics 6: e68575. https://doi.org/10.3897/mbmg.6.e68575
Metabarcoding qPCR assays and the respective primer sets used for biodiversity detection
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