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196 results for “16S rRNA”
Tara Pacific 16S rRNA ASV table for bacterial communities of crustose coralline algae from the Tuamotu archipelago (French Polynesia)
<p>This data is the result of the primary analysis of the 16S rRNA gene sequencing data collected from the CCA samples collected during the Tara Pacific expedition. The analysis was conducted using cutadapt/snakemake/dada2 and usearch. A full README is contained within the parent data upload (<a href="https://doi.org/10.5281/zenodo.4451892">https://doi.org/10.5281/zenodo.4451892</a>).</p>
Fig. 4 in MITOCHONDRIAL 16S AND 12S rRNA SEQUENCE ANALYSIS IN FOUR SALMONID SPECIES FROM ROMANIA
Fig. 4. Majority with bootstrap support consensus trees for combined data (16S rRNA and 12S rRNA). (a) Combined data Neighbor Joining tree, distance model Kimura 2 Parameters, transition/transversion ratio 2.3; (b) combined data Maximum Parsimony tree; (c) combined data Maxi-
Fig. 3. Majority with bootstrap support consensus trees for 12S in MITOCHONDRIAL 16S AND 12S rRNA SEQUENCE ANALYSIS IN FOUR SALMONID SPECIES FROM ROMANIA
Fig. 3. Majority with bootstrap support consensus trees for 12S rRNA. (a) 12S rRNA Maximum Parsimony tree; (b) 12S rRNA Neighbor Joining tree, distance model Kimura 2 Parameters, transi-
Fig. 2. Majority with bootstrap support consensus trees for 16S in MITOCHONDRIAL 16S AND 12S rRNA SEQUENCE ANALYSIS IN FOUR SALMONID SPECIES FROM ROMANIA
Fig. 2. Majority with bootstrap support consensus trees for 16S rRNA. (a) 16S rRNA Neighbor Joining tree, distance model Kimura 2 Parameters, transition/transversion ratio 2.3; (b) 16S rRNA Maximum Parsimony tree; (c) 16S rRNA Maximum Likelihood tree
RDP Classifier training files for 16S rRNA sequences from GTDB
<p>16S rRNA gene sequences from the <a href="https://gtdb.ecogenomic.org/">Genome Taxonomy Database</a> (GTDB release 220) were used to retrain the <a href="https://github.com/rdpstaff/classifier">RDP Classifier</a> (version 2.13). Two sets of training files are provided:</p> <ul> <li><code>genus.zip</code> - Genus level</li> <li><code>species.zip</code> - Species level</li> </ul> <p>The code in <code>prepare_files.R</code> was used to prepare the GTDB sequence and taxonomy files for retraining the RDP Classifier. Notes:</p> <ul> <li>Steps to retrain the RDP Classifier are adapted from <a href="https://john-quensen.com/tutorials/training-the-rdp-classifier/">https://john-quensen.com/tutorials/training-the-rdp-classifier/</a></li> <li>Python scripts (lineage2taxTrain.py and addFullLineage.py) are available at <a href="https://github.com/rdpstaff/classifier/issues/18">https://github.com/rdpstaff/classifier/issues/18</a></li> <li>The first 1000 training sequences (<code>train_nodups_1000.fasta</code>) are used for benchmarking the classification accuracy (see results at end of <code>prepare_files.R</code>).</li> </ul>
FIG. 4 in A journey through Cyanobacteria in Brazil: a review of novel genera and 16S rRNA sequences
FIG. 4. — Phylogenetic analysis of Brasilonema Fiore, Sant'Anna, de Paiva Azevedo, Komarek, Kaštovský, Sulek & Lorenzi and other Cyanobacteria reference strains. Brazilian strains are in bold.
FIG. 5 in A journey through Cyanobacteria in Brazil: a review of novel genera and 16S rRNA sequences
FIG. 5. — Phylogenetic analysis of Capilliphycus T.A.Caires, Sant'Anna & J.M.Nunes and other Cyanobacteria reference strains. Brazilian strains are in bold.
FIG. 3 in A journey through Cyanobacteria in Brazil: a review of novel genera and 16S rRNA sequences
FIG. 3. — Phylogenetic reconstruction of 16S rDNA of Brazilian strains and reference strains of Cyanobacteria. The strains marked in green are Brazilian genera. The stripe colors represent taxonomical orders.
FIG. 2 in A journey through Cyanobacteria in Brazil: a review of novel genera and 16S rRNA sequences
FIG. 2. — Flowchart of search methods for identification and selection of Brazilian 16S rDNA sequences from GenBank (NCBI).
A Comprehensive Assessment of Demographic, Environmental and Host Genetic Associations with Gut Microbiome Diversity in Healthy Individuals (16S rRNA gene sequencing data)
<p>Microbiome data accompanying manuscript "A Comprehensive Assessment of Demographic, Environmental and Host Genetic Associations with Gut Microbiome Diversity in Healthy Individuals". Data is available for alpha- and beta- diversity, as well as for individual taxa both in binary and quantitative phenotypic representation. Data is available for 827 individuals that gave consent for their data to be shared outside of the Milieu intérieur consortium. </p>
Figure 2. Maximum likelihood tree from 16S rRNA data under the best-fitting model T92 in Notes on the distribution and biology of northern brown shrimp Farfantepenaeus aztecus (Ives, 1891) in the eastern Mediterranean
Figure 2. Maximum likelihood tree from 16S rRNA data under the best-fitting model T92 + G. Numbers above branches indicate bootstrap values among 1000 replicates. Branches without bootstrap numbers mean that the bootstrap values are below 50%.
Figure. Phylogram showing phylogenetic relationships estimated using maximum likelihood analysis of 16S rRNA and COXI gene revealed the grouping of Orthochirus iranus, O. farzanpay, O. stockwelli, O. zagrosensis, O. innesi (JQ514244.1 Morocco), and O. bicolor (KT716038.1 India), with the outgroup species Androctonus crassicauda (FJ217732). in A study of genetic diversity among different population of Orthochirus sp. based on cytochrome C oxidase subunit I and 16srRNA sequencing
Figure. Phylogram showing phylogenetic relationships estimated using maximum likelihood analysis of 16S rRNA and COXI gene revealed the grouping of Orthochirus iranus, O. farzanpay, O. stockwelli, O. zagrosensis, O. innesi (JQ514244.1 Morocco), and O. bicolor (KT716038.1 India), with the outgroup species Androctonus crassicauda (FJ217732).
Fig. 4. Phylogenetic relationships generated from the 16S rRNA gene for 16 in A survey of auchenorrhynchan insects for identification of potential vectors of the 16SrIV-D phytoplasma in Florida
Fig. 4. Phylogenetic relationships generated from the 16S rRNA gene for 16SrIV phytoplasmas by using maximum likelihood (1,000 replicates) methods in MEGA. The 16S partial sequence amplified from Haplaxius crudus (indicated by the black triangle) and unidentified Cicadellidae specimen (indicated by the white triangle) from this study were included in the analysis.
Microbial 16S rRNA gene (DNA) and transcripts (cDNA) along a boreal soil-freshwater-estuary continuum
<p>This repository stores the processed files of the 16S rRNA sequencing reads (DNA and cDNA) of the La Romaine project, which were processed through the DADA2 pipeline. Files are '.rds' files and/or '.csv' files readable by the open statistical software R. The project is part of the Industrial Research Chair in Carbon Biogeochemistry in Boreal Aquatic systems (CarBBAS Chair) led by Paul A. del Giorgio.</p> <p>Samples were pooled by plate ID and season to be processed by DADA2. The number before each '*_seqtab.rds' file corresponds to a pool. ID details are in "splitdf_new.rds".</p> <p>Raw sequences can be found on SRA under the Bioproject number: PRJNA693020. Intermediate processing files are stored here. And scripts are available on <a href="https://github.com/CarBBAS/Paper_Stadler-delGiorgio_ISMEJ_2021">Github</a>.</p> <p>Files are being uploaded as manuscripts are published.</p> <p>Currently available files:</p> <ul> <li>2015-2017: 16S rRNA gene and transcripts (DNA and cDNA) in spring, summer, autumn (shallow sequencing) <ul> <li>Part of the manuscript: "Terrestrial connectivity, upstream aquatic history and seasonality shape bacterial community assembly within a large boreal aquatic network". The ISME Journal. 2021.</li> </ul> </li> </ul>
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>
Comparing bacterial microbiome composition of Xylocopa species across populations using PacBio 16S rRNA gene sequencing
Open the record for dataset details and reuse information.
A novel method to assess the integrity of frozen archival DNA samples: Alpha-diversity ratios of short and long-read 16S rRNA gene sequences
Open the record for dataset details and reuse information.
Raw Fast5 data for "Microbiota profiling with long amplicons using Nanopore sequencing: full-length 16S rRNA gene and the 16S-ITS-23S of the rrn operon" - PART I
<p>Raw Fast5 data for "Microbiota profiling with long amplicons using Nanopore sequencing: full-length 16S rRNA gene and the 16S-ITS-23S of the rrn operon". See Supplementary Table 2 for associating each sample to its barcode.</p> <p>- FC1_1 includes data for the HM mock community from BEI resources and skin microbiome of the chin in dogs.</p> <p>- FC1_2 includes data for the dorsal skin samples</p> <p>- FC2 includes data for the Zymobiomics mock community and Staphylococcus pseudintermedius isolate</p> <p> </p> <p> </p>
16S rRNA sequences from Mediterranean Sparidae gut microbiome
<p><span>Animals have been developing key associations with micro-organisms through evolutionary processes and ecological diversification. Hence, in some host clades, phylogenetic distance between hosts is correlated to dissimilarity in microbiomes, a pattern called phylosymbiosis. Teleost fishes, despite being the most diverse and ancient group of vertebrate, have received little attention from the microbiome perspective and our understanding of its determinants is currently limited. In this study, we assessed the gut microbiome of 12 co-occurring species of teleost representing a large breadth of ecological diversity and originating from a single family (<i>i.e.</i> the Sparidae). We tested how host evolutionary history, diet composition and morphological traits are related to fish gut microbiome. Despite fish species having different microbiomes, there is no phylosymbiosis signal in this fish family, but gut length and diet had a strong influence on the microbiome. We revealed that the only species with a specialized herbivorous diet, <i>Sarpa salpa</i> had a 3.3 times longer gut than carnivorous species and such a long gut favor the presence of anaerobic bacteria typical of herbivorous gut microbiomes. Hence, dietary uniqueness is paired with both unique gut anatomy and unique microbiome.</span></p>
16S rRNA Sequence Data, Brazilian Coffee Soils
<p>16S sequencing data for DNA extracted from soils from Brazillian coffee farms. Sequenced on Illumina MiSeq with primers from Caporaso (2011, 2012).</p>
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