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9 results for “taxonomy, 16S, ITS”
16S rRNA phylogeny and clustering is not a reliable proxy for genome-based taxonomy in Streptomyces
<p>This file is intended as supplementary information for a forthcoming publication: 16S rRNA phylogeny and clustering is not a reliable proxy for genome-based taxonomy in <em>Streptomyces</em>. </p>
16S V4-V4 taxonomy classifier
<p>16S metabarcoding databases and naive-bayes classifier specific to the V4-V5 region. Built from the <a href="https://www.arb-silva.de/documentation/release-138/">Silva 138.1 SSU Ref NR 99</a> database using Qiime2 (version 2021.2).</p> <p>Primers used:</p> <p>EMP 16S 515f: GTGYCAGCMGCCGCGGTAA</p> <p>EMP 16S 926r: CCGYCAATTYMTTTRAGTTT</p> <table> <caption>File description</caption> <thead> <tr> <th scope="col"> <table> <thead> <tr> <th>File</th> <th>Description</th> </tr> </thead> <tbody> <tr> <td>silva-138-99-seqs.qza</td> <td>Full length Silva 138.1 SSU 99 sequences</td> </tr> <tr> <td>silva-138-99-tax.qza</td> <td>Taxa for full length Silva 138.1 SSU 99 database</td> </tr> <tr> <td>refseqs_V4-V5.qza</td> <td>Sequences for 16S V4-V5 (primers 515f, 926r), extracted from Silva 138.1 SSU 99, generated by qiime2-2021.2 (forward compatible)</td> </tr> <tr> <td>classifier_V4-V5.qza</td> <td>Unweighted (uniform) naive-bayes classifier for 16S V4-V5 (primers 515f, 926r) extracted from Silva 138.1 SSU 99, generated by qiime2-2021.2 </td> </tr> </tbody> </table> </th> <th scope="col"> </th> </tr> </thead> </table>
Figure 1. Bayesian inference tree built using COI, 16S rDNA and ITS2 in Integrated taxonomy reveals multiple species in the Dendrobaena byblica (Rosa, 1893) complex (Oligochaeta: Lumbricidae)
Figure 1. Bayesian inference tree built using COI, 16S rDNA and ITS2 sequences. The numbers indicate the posterior probabilities. The colours show the two main clades.
FIGURE 21. Maximum parsimony 16S rRNA phylogram for the Boophis albipunctatus group. From 485 total characters, 391 were constant and 72 in Integrative taxonomy of Malagasy treefrogs: combination of molecular genetics, bioacoustics and comparative morphology reveals twelve additional species of Boophis 2383
FIGURE 21. Maximum parsimony 16S rRNA phylogram for the Boophis albipunctatus group. From 485 total characters, 391 were constant and 72 parsimony informative. MP searches retained 26 trees of which a strict consensus is shown. Consensus support values higher than 50, from 2000 bootstrap replicates, are shown; an asterisk indicates Bayesian posterior probabilities equal or higher than 95%. Species newly described herein are in bold.
FIGURE 7. Maximum parsimony 16S in Integrative taxonomy of Malagasy treefrogs: combination of molecular genetics, bioacoustics and comparative morphology reveals twelve additional species of Boophis 2383
FIGURE 7. Maximum parsimony 16S rRNA phylogram of species of the Boophis goudoti group. From 510 total characters, 340 were constant and 130 parsimony informative. MP searches retained 3681 trees of which a strict consensus is shown. Consensus support values higher than 50, from 2000 bootstrap replicates, are shown; an asterisk indicates Bayesian posterior probabilities equal or higher than 95%. Species newly described or resurrected herein are in bold.
FIGURE 1. Maximum parsimony 16S in Integrative taxonomy of Malagasy treefrogs: combination of molecular genetics, bioacoustics and comparative morphology reveals twelve additional species of Boophis 2383
FIGURE 1. Maximum parsimony 16S rRNA phylogram for species in the Boophis majori and B. microtympanum groups. From 480 total characters, 336 were constant and 129 parsimony informative. MP searches retained 39 trees of which a strict consensus is shown. Consensus support values higher than 50, from 2000 bootstrap replicates, are shown; an asterisk indicates Bayesian posterior probabilities equal or higher than 95%. Species newly described or resurrected herein are in bold.
FIGURE 18. Maximum parsimony 16S in Integrative taxonomy of Malagasy treefrogs: combination of molecular genetics, bioacoustics and comparative morphology reveals twelve additional species of Boophis 2383
FIGURE 18. Maximum parsimony 16S rRNA phylogram for species in the Boophis luteus group. From 470 total characters, 347 were constant and 111 parsimony informative. MP searches retained 60 trees of which a strict consensus is shown. Consensus support values higher than 50, from 2000 bootstrap replicates, are shown; an asterisk indicates Bayesian posterior probabilities equal or higher than 95%. The species newly described herein is in bold.
FIGURE 16. Maximum parsimony 16S in Integrative taxonomy of Malagasy treefrogs: combination of molecular genetics, bioacoustics and comparative morphology reveals twelve additional species of Boophis 2383
FIGURE 16. Maximum parsimony 16S rRNA phylogram for species in the Boophis albilabris group. From 535 total characters, 445 were constant and 35 parsimony informative. MP searches retained 6 trees of which a strict consensus is shown. Consensus support values higher than 50, from 2000 bootstrap replicates, are shown; an asterisk indicates Bayesian posterior probabilities equal or higher than 95%. The species newly described herein is in bold.
Supplementary data for PhD Thesis - Appendix D.i: 16S community abundance and taxonomy data
<p>Abundance and taxonomic assignments from 3 Pyrosequencing runs, and 1 MiSeq run for chapters 2-5 of PhD Thesis.</p> <p>Data provided in tab- separated text format.</p>
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Allen Brain Atlas
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DANDI Archive for NWB datasets
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International Brain Laboratory public data
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OpenNeuro
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