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84 results for “SSU”
Silva SSU taxonomic training data formatted for DADA2 (Silva version 138)
<p>These DADA2-formatted training fasta files were derived from the Silva Project's version 138 release. See https://www.arb-silva.de/documentation/release-138/ for database and citation information. The Silva 138 database is licensed under Creative Commons Attribution 4.0 (CC-BY 4.0); see file "SILVA_LICENSE.txt". The fasta files were generated and checked for consistency with version 132 using the R code in the R-markdown document "silva-v138.Rmd".</p> <p>Version 2 removes the dependence on preprocessed files from mothur, which results in a greater number of bacterial and archeal sequences. It also includes a new version of the assignTaxonomy training set that goes through the species level for use with longer amplicons obtained from long-read amplicon sequencing.</p> <p>If you use these files, please cite one or both of the Silva references below (or at the above link) and the DADA2 paper (reference below). I also recommend citing or linking to the Zenodo record for this specific version in your Methods or published source code to record the specific taxonomic database files used in your analysis.</p> <p><strong>NOTE:</strong><strong> </strong>These Version 2 files are intended for use in classifying prokaryotic 16S sequencing data and are not appropriate for classifying eukaryotic ASVs. The new method implemented within DADA2 for constructing these files only includes 100 eukaryotic sequences for use as an outgroup.</p> <p><strong>NOTE:</strong> These Version 2 files have a known problem in 10/883 families and 114/3838 genera. See https://github.com/mikemc/dada2-reference-databases/blob/main/silva-138/v2/bad-taxa.csv for a list of affected taxa and https://github.com/benjjneb/dada2/issues/1293 for more information.</p>
Supplementary data to accompany "phyloFlash: A pipeline for rapid SSU rRNA-targeted profiling of metagenomes"
<p>Usage examples of the phyloFlash pipeline applied to shotgun metagenomic data sets.</p> <p>The phyloFlash software is available from https://github.com/HRGV/phyloFlash. Examples were generated with phyloFlash v3.3b.</p>
PR2_V9, a SSU V9 rDNA reference database with functional annotations.
<p>The present data set provides a tab separated text file compressed in a gzip archive. The file includes 63,401 18S V9 rDNA reference sequences for 44,084 unique eukaryotic taxa and 9,759 16S V9 rDNA references sequences for 9,661 unique prokaryotic taxa. It includes the following fields : sequence = nucleic acid sequence of reference; lineage = taxonomic path of the reference sequence; refs = original accession numbers corresponding to the reference sequence; name = reference sequence identifier; taxogroup = high-taxonomic level assignation of the reference sequence. The file also includes six categories of functional annotations: (1) chloroplast: yes, presence of permanent chloroplast; no, absence of permanent chloroplast ; NA, undetermined. (2) symbiont (small partner): parasite, the species is a parasite; commensal, the species is a commensal; mutualist, the species is a mutualist symbiont, most often a microalgal taxon involved in photosymbiosis; no the species is not involved in a symbiosis as small partner; NA, undetermined. (3) symbiont (host): photo, the host species relies on a mutualistic microalgal photosymbiont to survive (obligatory photosymbiosis); photo_falc, same as photo, but facultative relationship; photo_klep, the host species maintains chloroplasts from microalgal prey(s) to survive; photo_klep_falc, same as photo_klep, but facultative; Nfix, the host species must interact with a mutualistic symbiont providing N2 fixation to survive; Nfix_falc, same as Nfix, but facultative; no, the species is not involved in any mutualistic symbioses; NA, undetermined. (4) silicification; yes, the species has a silicified skeleton; no, it does not; NA, undetermined. (5) calcification; yes, the species has a calcified skeleton; no, it does not; NA, undetermined. (6) strontification; yes, the species has a skeleton made of strontium; no, it does not; NA, undetermined.</p>
Fig. 5 in Morphological and Morphogenetic Redescriptions and SSU rRNA Gene-based Phylogeny of the Poorly-known Species Euplotes amieti Dragesco, 1970 (Ciliophora, Euplotida)
Fig. 5. Phylogenetic tree based on SSU rRNA gene sequences, showing the position of Euplotes amieti (arrow) by Maximum Likelihood (ML) and Bayesian inference (BI). Numbers near branches denote ML bootstrap value/BI posterior probability value. '–' indicates topologies that differ between the ML and BI phylogenies. Fully supported (100%/1.00) branches are marked with solid circles. All branches are drawn to scale. The scale bar corresponds to 5 substitutions per 100 nucleotide positions. GenBank accession numbers are given for each species. Systematic classification is mainly according to Lynn (2008). Euplotid clades I–VI were designated according to Yi et al. (2009).
Fig. 1. Euplotes amieti Dragesco, 1970 in Morphological and Morphogenetic Redescriptions and SSU rRNA Gene-based Phylogeny of the Poorly-known Species Euplotes amieti Dragesco, 1970 (Ciliophora, Euplotida)
Fig. 1. Euplotes amieti Dragesco, 1970 in vivo (A), after protargol (B–D) and silver nitrate (E, F) impregnation. (A) Ventral view of a representative cell. Arrows indicate caudal cirri. (B) Different shapes of macronucleus. (C, D) Ventral (C) and dorsal (D) view, showing the infraciliature and nuclear apparatus. Arrow shows the sigmoidal adoral zone. (E, F) Silverline system on ventral (E) and dorsal side (F). Arrow shows the sigmoidal adoral zone. AZM, adoral zone of membranelles; CC, caudal cirri; CVP, contractile vacuole pore; FVC, frontoventral cirri; MC, marginal cirri; PM, paroral membrane; TC, transverse cirri. Scale bars: 100 μm.
Fig. 4 in Morphological and Morphogenetic Redescriptions and SSU rRNA Gene-based Phylogeny of the Poorly-known Species Euplotes amieti Dragesco, 1970 (Ciliophora, Euplotida)
Fig. 4. Photomicrographs of Euplotes amieti during morphogenesis after protargol impregnation. (A) Ventral view of a middle divider showing the migration of cirri and the division of the macronucleus. (B, C) Ventral view of an early divider demonstrating two sets of frontal-ventral-transverse cirral streaks (arrowheads) and the oral primordium in opisthe (arrow). (D) To show new cirri derived from the frontal-ventral-transverse cirral anlagen. (E) Ventral view, arrows point to the paroral membrane (PM) in the proter and the development of the PM-anlage in the opisthe; arrowhead indicates the frontal cirrus I/1 in the opisthe formed de novo. (F) Ventral view, indicating the marginal anlagen of the proter (arrow) and the opisthe (arrowhead). (G) Arrowheads showing the dorsal kinety anlage of an early divider. (H) Portion of the ventral view, showing the marginal cirri in the proter (arrow) and the opisthe (arrowhead). (I) Dorsal view, arrowheads indicating the development of the dorsal kinety anlage. (J) Portion of the dorsal view, to show the newly formed caudal cirri in the proter (arrowheads). Scale bars: 100 μm.
Fig. 3 in Morphological and Morphogenetic Redescriptions and SSU rRNA Gene-based Phylogeny of the Poorly-known Species Euplotes amieti Dragesco, 1970 (Ciliophora, Euplotida)
Fig. 3. Morphogenesis of Euplotes amieti after protargol impregnation. (A, B) Ventral (A) and dorsal (B) view of the same specimen at an early stage to show the five frontal-ventral-transverse cirral streaks and oral primordium within which membranelles are forming (arrow). (C, D) Ventral (C) and dorsal (D) view of the same specimen at a middle stage to show the completion of the cirral formation, the differen- tiation of caudal cirri at posterior ends of the two rightmost dorsal anlagen (arrowheads), the de novo formation of the new marginal cirri and the frontal cirrus I/1 in both proter and opisthe (arrows). (E, F) Ventral (E) and dorsal (F) view, showing the migration of newly formed cirri and the development of dorsal kineties, arrowheads show the marginal cirri. (G, H) Ventral (G) and dorsal (H) side of the same divider at a late stage showing infraciliature and nuclear apparatus. Scale bars: A–D = 100 μm; E–H = 150 μm.
Linked collectors and determiners for: Fungal 18S Ribosomal RNA (SSU) RefSeq Targeted Loci Project.
Natural history specimen data linked to collectors and determiners held within, "Fungal 18S Ribosomal RNA (SSU) RefSeq Targeted Loci Project". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/3bfbda20-1a91-4cf9-992f-bc1e9e5b7dad">https://bionomia.net/dataset/3bfbda20-1a91-4cf9-992f-bc1e9e5b7dad</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/3bfbda20-1a91-4cf9-992f-bc1e9e5b7dad">https://gbif.org/dataset/3bfbda20-1a91-4cf9-992f-bc1e9e5b7dad</a>. Formatted as a Frictionless Data package.
UMI SSU rRNA amplicon datasets
<p>Analysis of 721 SSU rRNA amplicon data from 58 stations in the Pacific Ocean. This item contains following files.</p> <p>abundance.csv</p> <p>- Read count of 155906 OTUs in UMI dataset</p> <p>centroid_seqs.fa</p> <p>- Centroid sequence of each OTU</p> <p>OTU_module_taxon.csv</p> <p>- Results of clustering by WGCNA analysis and assigned taxonomy using the SILVA database</p> <p>Thaumarchaeota.fasta</p> <p>- Sequenced used for phylogenetic analysis of Thaumarchaeota OTUs</p>
Fig. 5 in Morphological Redescription and SSU rDNA-based Phylogeny of Two Freshwater Ciliates, Uronema nigricans and Lembadion lucens (Ciliophora, Oligohymenophorea), with Discussion on the Taxonomic Status of Uronemita sinensis
Fig. 5. Maximum likelihood (ML) tree inferred from SSU rDNA sequences, showing the position of Uronema nigricans and Lembadion lucens (red arrows). Numbers near branches denote ML bootstrap value/BI posterior probability. Asterisks (*) indicate topologies that differ between the ML and BI analyses. Fully supported (100%/1.00) branches are marked with solid circles. Question marks (?) in red color indicate that the two sequences are possibly misidentified. The scale bar corresponds to 5 substitutions per 100 nucleotide positions. All branches are drawn to scale. Systematic classification mainly follows Lynn (2008).
Fig. 4 in Morphological Redescription and SSU rDNA-based Phylogeny of Two Freshwater Ciliates, Uronema nigricans and Lembadion lucens (Ciliophora, Oligohymenophorea), with Discussion on the Taxonomic Status of Uronemita sinensis
Fig. 4. Photomicrographs of Lembadion lucens from life (A–D, with A in bright field illumination and others in DIC microscopy) and after protargol staining (E–K). (A, B) Ventral views of representative individuals, cell in B was slightly depressed. Arrow shows caudal cilia. (C) Dorsal view, arrowhead points to the contractile vacuole. (D) Apical view, revealing the shape of cross section. Arrow shows oral cilia. (E) Ventral view of a stained cell, showing the silverline system. (F, G) Ventral (F) and dorsal (G) view of a representative individual, to show the ciliature and nuclear apparatus. (H) Micronucleus (arrow) and macronucleus. (I) Ventral view of posterior portion. Arrows depict two basal body rows of caudal cilia. (J) Mid portion of dorsal view, illustrating the monokinetids and dikinetids. (K) Detailed view, arrows show the two separated pairs of basal bodies and arrowheads indicate the posterior ends of four gradually shortened outer rows of adoral membranelle. Scale bars: 30 μm.
Fig. 6 in Morphological Redescription and SSU rDNA-based Phylogeny of Two Freshwater Ciliates, Uronema nigricans and Lembadion lucens (Ciliophora, Oligohymenophorea), with Discussion on the Taxonomic Status of Uronemita sinensis
Fig. 6. Sequence comparison of the small subunit ribosomal RNA gene determined by BioEdit 7.0.5.2 (Hall 1999), showing the unmatched nucleotides of Uronema nigricans MF072399 and Lembadion lucens MF072398 with their sister sequences in the same clades, respectively (see Fig. 5). Nucleotide positions are given at the top of each column. Insertions and deletions are compensated by introducing alignment gaps (–). Numbers of unmatched sites (n) and sequence similarity percentages (%) compared with Uronema nigricans MF072399 and Lembadion lucens MF072398 are also supplied. The two sequences with question marks (?) are possibly misidentified. ID, identical; n, numbers of unmatched sites; %, sequence similarity percentages.
Fig. 3 in Morphological Redescription and SSU rDNA-based Phylogeny of Two Freshwater Ciliates, Uronema nigricans and Lembadion lucens (Ciliophora, Oligohymenophorea), with Discussion on the Taxonomic Status of Uronemita sinensis
Fig. 3. Photomicrographs of Uronema nigricans from life (A–E, in bright field illumination) and after protargol (F–M) staining. (A–C) Right ventrolateral views of representative individuals, with cell in C slightly depressed. Arrow in A shows contractile vacuole, while in C indicates macronucleus. (D) View of caudal portion of another cell, arrow points to caudal cilium. (E) Different body sizes, showing conspicuous apical plate. (F, G) Ventral views of stained individuals, indicating the structure of scutica. (H, I) Portion views of oral apparatus, revealing the number of kinety rows in M2 (two rows in H and three rows in I). (J, K) Ventral (J) and dorsal (K) view of a representative individual to show the ciliature and nuclear apparatus. Arrow in J points to basal body of caudal cilium, arrow in K indicating the apical plate. (L, M) Left ventrolateral (L) and right dorsolateral (M) view of another stained individual to show the ciliature and oral apparatus. Scale bars: 15 μm (A, B); 30 μm (E).
Fig. 1 in Morphological Redescription and SSU rDNA-based Phylogeny of Two Freshwater Ciliates, Uronema nigricans and Lembadion lucens (Ciliophora, Oligohymenophorea), with Discussion on the Taxonomic Status of Uronemita sinensis
Fig. 1. Map and sampling site. The yellow dots on the map and two corresponding photographs (A, B) show the collecting sites. (A) Fresh- water river in Shenzhen, southern China (22°32'19"N; 114°06'45"E). (B) Huguangyan Lake, an oligotrophic lake in Zhanjiang, southern China (21°08'38"N; 110°16'20"E).
Supplementary data (simulated metagenome set 2) to accompany "phyloFlash – Rapid SSU rRNA profiling and targeted assembly from metagenomes"
<p>Comparison of SSU rRNA read extraction and targeted assembly from simulated shotgun metagenome of closely related Bacteorides strains.</p> <p>The phyloFlash software is available from https://github.com/HRGV/phyloFlash. Examples were generated with phyloFlash v3.3b.</p>
Supplementary data (simulated metagenome set 3) to accompany "phyloFlash – Rapid SSU rRNA profiling and targeted assembly from metagenomes"
<p>Comparison of SSU rRNA read extraction and targeted assembly from simulated shotgun metagenome of closely related Bacteorides strains.</p> <p>The phyloFlash software is available from https://github.com/HRGV/phyloFlash. Examples were generated with phyloFlash v3.3b.</p>
SSU rRNA Gene Analysis of the Environmental and Biological Influences on Carbonate Precipitation within Hot Spring Microbial Mats in Little Hot Creek, CA
<p>R Markdown notebook and all data required to recreate the 16S rRNA Gene analysis figures found in Wilmeth et. al (In Submission), including mapping files, BIOM files, and R markdown notebook. </p>
DADA2 formatted Silva SSU taxonomic training data (Silva version 138.1) with emended description of the genus Lactobacillus Beijerinck 1901
<p>These training fasta files are derived from the Silva 138.1 prokaryotic SSU taxonomic training data formatted for DADA2 (from <a href="https://zenodo.org/record/4587955">https://zenodo.org/record/4587955</a>). The species assignment file contains changes in species names according to <a href="https://doi.org/10.1099/ijsem.0.004107">Zheng et al. 2020</a> based on data from <a href="https://github.com/swuyts/lactotax/tree/master">Lactotax</a> (file <a href="https://github.com/swuyts/lactotax/raw/master/data/2023_05_30.xlsx">2023_05_30.xlsx</a>). The script in R for making changes in species names is in the silva.R file.</p> <p><br> Please cite one or both of the Silva references, the DADA2 paper (reference below), and the Zenodo record for this specific version in your Methods or published source code to record the specific taxonomic database files used in your analysis.</p>
FIGURE 1. Bayesian tree inferred from SSU gene DNA sequences. Posterior probabilities exceeding 50 in A review of the genus Tripylina Brzeski, 1963 (Nematoda: Triplonchida), with descriptions of five new species from New Zealand
FIGURE 1. Bayesian tree inferred from SSU gene DNA sequences. Posterior probabilities exceeding 50% are given on appropriate clades. Nematode species, GenBank numbers, locations are listed for each taxon if known.
FIGURE 5 Bayesian phylogenetic tree inferred from SSU gene DNA sequences. Posterior probabilities great than 50 in New Zealand species of the genus Tripyla Bastian, 1865 (Nematoda: Triplonchida: Tripylidae). I: A new species, a new record and key to long-tailed species
FIGURE 5 Bayesian phylogenetic tree inferred from SSU gene DNA sequences. Posterior probabilities great than 50% are given on appropriate clades. Nematode species, GenBank numbers, locations are listed for each taxon if known.
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
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
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.