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50 results for “18s rDNA”
Plankton Planet Pilot Project rDNA 18S V9 OTU tables
<p>This repository contains the rDNA 18S V9 OTU table, its rarefied version, and the related contextual data from Plankton Planet Pilot Project.</p> <p>In the file <strong>P2_TO_18SV9_otu_table.tsv.gz</strong>, each OTU, one per row, is described by the following fields: <strong>amplicon</strong> = identifier of the representative (most abundant) sequence of the swarm; <strong>total</strong> = total number of reads in the entire dataset; <strong>cloud</strong> = number of unique sequences constituting the OTU; <strong>length</strong> = length of the representative sequence; <strong>spread</strong> = number of samples in which the OTU has been found; <strong>quality</strong> = minimum expected error observed for the representative sequence, divided by sequence length; <strong>sequence</strong> = nucleic acid sequence of the representative sequence; <strong>identity</strong> = percentage of identity of the representative sequence to the closest reference sequence from PR2_V9 (https://doi.org/10.5281/zenodo.3768951); <strong>references</strong> = best hit reference sequence(s); <strong>taxonomy</strong> = taxonomic path assigned to the representative sequence; <strong>taxogroup</strong> = high-taxonomic level assignation of the representative barcode; <strong>chloroplast</strong> = <em>yes</em>: presence of permanent chloroplast / <em>no</em>: absence of permanent chloroplast / <em>NA</em>: undetermined; <strong>symb_small</strong> = <em>parasite</em>: the species is a parasite / <em>commensal</em>: the species is a commensal / <em>mutualist</em>: the species is a mutualist symbiont, most often a microalgal taxa involved in photosymbiosis / <em>no</em>: the species is not involved in a symbiosis as small partner / <em>NA</em>: undetermined; <strong>symbiont_host</strong> = <em>photo</em>: the host species relies on a mutualistic microalgal photosymbiont to survive (obligatory photosymbiosis) / <em>photo_falc</em>: same as photo, but facultative relationship / <em>photo_klep</em>: the host species maintains chloroplasts from microalgal prey(s) to survive / <em>photo_klep_falc</em>: same as <em>photo_klep</em>, but facultative / <em>Nfix</em> = the host species must interact with a mutualistic symbiont providing N2 fixation to survive / <em>Nfix_falc</em> = same as Nfix, but facultative / <em>no</em>: the species is not involved in any mutualistic symbioses; <em>NA</em>: undetermined; <strong>silicification</strong> = <em>yes</em>: the species has a silicified skeleton / <em>no</em>: it does not / <em>NA</em>: undetermined; <strong>calcification</strong> = <em>yes</em>: the species has a calcified skeleton / <em>no</em>: it does not / <em>NA</em>: undetermined; <strong>strontification</strong> = <em>yes</em>: the species has a skeleton made of strontium / <em>no</em>: it does not / <em>NA</em>: undetermined; <strong>PPXXX</strong> = number of reads in each of the 214 Plankton Planet samples; <strong>TARA_XXXXXXXXXX</strong> = number of reads in each of the 386 <em>Tara</em> Oceans samples.</p> <p>The file <strong>P2_TO_18SV9_otu_table_raref_313539.tsv.gz</strong> contains the same fields but with number of reads (total and per sample) obtained after random subsampling (313,539 reads per sample).</p> <p>In the file <strong>P2_TO_18SV9_context.tsv.gz</strong>, each sample is described by the following fields: <strong>sample</strong> = identifier of the sample; <strong>lower_size_fraction</strong> = lower limit of the size fraction in µm; <strong>upper_size_fraction</strong> = lower limit of the size fraction in µm; <strong>event_date</strong> = date (year-month-day); <strong>event_latitude</strong> = geographic position (latitude in DD); <strong>event_longitude</strong> = geographic position (longitude in DD); <strong>depth</strong> = depth in meters; <strong>temperature</strong> = sea water temperature in °C</p>
rDNA 18S V4 metabarcoding tables (Swarm) for Tara Oceans Expedition (2009-2013), including Tara Polar Circle Expedition (2013)
<p>Reads were grouped into OTUs using the following swarm-based pipeline: paired-end reads were merged with vsearch’s --fastq_mergepairs command (version 2.15.1, allowing for staggered reads; Rognes et al., 2016), and trimmed with cutadapt (version 3.0; Martin, 2011), keeping only reads containing both forward and reverse primers. After trimming, the expected error per read was estimated with vsearch’s command --fastq_filter and the option --eeout. Each sample was then de-replicated, i.e. strictly identical reads were merged, using vsearch’s command --derep_fulllength, and converted into fasta format. Clustering was performed at the sample level with swarm 3.0 using default parameters (Mahé et al., 2015). Prior to global clustering, individual fasta files (one per sample) were pooled and further dereplicated with vsearch. Files containing per-read expected error values were also dereplicated to retain only the lowest expected error for each unique sequence. Global clustering was performed with swarm (using the fastidious option). Cluster representative sequences were then searched for chimeras with vsearch’s command --uchime_denovo using default parameters (Edgar et al., 2011).<br> Clustering results, expected error values, taxonomic assignments, and chimera detection results were used to build a “raw” occurrence table. Reads without primers, reads shorter than 32 nucleotides and reads with uncalled bases (“N”) were discarded. For a “filtered” occurrence table, non-chimeric sequences, sequences with an expected error per nucleotide below 0.0002, and clusters containing at least 2 reads were retained. Since primer trimming is not perfect, some sequences can still contain primer fragments or be excessively trimmed. These sub- or super-sequences were identified using vsearch and merged with their closest, most abundant perfectly trimmed sequence. Finally, occurrence patterns throughout our sample collection were used to further refine the occurrence table. Clusters that contain sub-clusters with only a single-nucleotide difference but with different ecological patterns (defined here as uncorrelated abundance values in at least 5% of the samples) were turned into distinct clusters (https://github.com/frederic-mahe/fred-metabarcoding-pipeline). On the other hand, clusters with similar sequences that had correlated abundance values in at least 95% of the samples, were merged using a re-implementation of lulu's method (Frøslev et al. 2017; https://github.com/frederic-mahe/mumu).</p>
18S rDNA OTU table of fungal community in a tropical forest
<p>This study aims to elucidate how fungal community responses to N deposition</p>
SOMLIT-Astan time-series (2009-2016) rDNA 18S V4 ASV table (dada2)
<p>This repository contains a rDNA 18S V4 ASV table (astan-18sv4_dada2_v1.0.filtered.table.with.taxo.lulu.tsv.gz) for SOMLIT-Astan time-series (2009-2016). Each ASV, one per row, is described by the following fields: <strong>amplicon</strong> = ASV identifier; <strong>taxonomy</strong> = taxonomic path assigned to the ASV using IDTAXA; <strong>confidence</strong> = IDTAXA confidence scores for each taxonomic rank; <strong>sequence</strong> = ASV nucleic acid sequence; <strong>total</strong> = total number of reads for the entire dataset; <strong>spread</strong> = number of samples in which the ASV is detected; <strong>RAXXXXXX-X</strong> = number of reads in each of the 375 SOMLIT-Astan time-series samples. Sample ids contain information about the sampling date and the size fraction. The six digits after RA indicate the date (year, month and day), and the value after - indicate the size fraction, 02 for 0.2 to 3 µm and 3 for superior to 3 µm.</p> <p>How this table has been generated:</p> <p>The procedures used for DNA extraction and amplification of the 18S V4 region of the ribosomal operon are described in <a href="https://doi.org/10.1111/mec.16539">https://doi.org/10.1111/mec.16539</a>. The eukaryote-specific primers used were TAReuk454FWD1 (5’-CCAGCASCYGCGGTAATTCC-3’, Saccharomyces cerevisiae position 565‐584) and TAReukREV3 (5’-ACTTTCGTTCTTGATYRA-3’, Saccharomyces cerevisiae position 964‐981) (Stoeck et al., 2010). Raw sequences are available at the European Nucleotide Archive (ENA) under the project id PRJEB48571.</p> <p>The paired-end fastq files obtained from sequencing were demultiplexed and primers were removed using Cutadapt v2.8, filtering out untrimmed reads. Then, forward and reverse reads were trimmed at position 210 and reads with ambiguous nucleotides or with a maximum number of expected errors (maxEE) superior to 2 were filtered out using the function filterAndTrim() from the R package dada2 version 1.22 with R version 4.1.1 . For each run, error rates were defined using the function learnErrors(), reads were dereplicated using the function derepFastq() function and denoised using the dada() function with default options before being merged. Remaining chimaeras were removed using the function removeBimeraDenovo(). Only amplicon sequence variants (ASVs) with at least three reads in two samples were retained. ASVs were taxonomically assigned using IDTAXA with default parameters with the PR2 database version 4.14. Finally, the LULU curation approach was applied to the ASV table to remove remaining erroneous amplicons. For more details relative to the bioinformatic pipeline used to generate the ASV tables, see <a href="https://gitlab.sb-roscoff.fr/nhenry/rosko-naples-bioinfo">https://gitlab.sb-roscoff.fr/nhenry/rosko-naples-bioinfo</a>.</p>
Supplementary material 2 from: Šťáhlavský F, Opatova V, Just P, Lotz LN, Haddad CR (2018) Molecular technique reveals high variability of 18S rDNA distribution in harvestmen (Opiliones, Phalangiidae) from South Africa. Comparative Cytogenetics 12(1): 41-59. https://doi.org/10.3897/CompCytogen.v12i1.21744
Table S2 : Explanation note: Numbers of nuclei with different numbers of chiasmata in diplotene of Rhampsinitus leighi (2n = 26) from Vernon Crookes (cytotype I) and Silaka (cytotype II).
Supplementary material 1 from: Šťáhlavský F, Opatova V, Just P, Lotz LN, Haddad CR (2018) Molecular technique reveals high variability of 18S rDNA distribution in harvestmen (Opiliones, Phalangiidae) from South Africa. Comparative Cytogenetics 12(1): 41-59. https://doi.org/10.3897/CompCytogen.v12i1.21744
Table S1 : Explanation note: Measurements of the relative chromosome length (% RCL) and arm ratio of South African harvestmen from family Phalangiidae (± standard deviation). Numbers of measured metaphases are given in brackets following the species names.
Fig. 1 in Ultrastructural and immunocytochemical investigation of paramylon combined with new 18S rDNA-based secondary structure analysis clarifies phylogenetic affiliation of Entosiphon sulcatum (Euglenida: Euglenozoa)
Fig. 1 Phylograms obtained from maximum likelihood (ML) analyses of 182 euglenozoan taxa with new 18S rDNA sequences boxed and most ingroup taxa pruned to major groupings, sequences of Heterolobosea and Jakobida were used as outgroup. Congruent Bayesian inference (BI) posterior probability values>0.50 were mapped onto both ML trees and are
Fig. 4 in Ultrastructural and immunocytochemical investigation of paramylon combined with new 18S rDNA-based secondary structure analysis clarifies phylogenetic affiliation of Entosiphon sulcatum (Euglenida: Euglenozoa)
Fig. 4 Schematic phylogram combining molecular and morphological findings corroborating phylogenetic position of Entosiphon as sister group of Helicales within Euglenida. States of key characters are illustrated tabularly: black squares code presence and blanks absence, e.g., paramylon is present only in Entosiphon and Helicales. Unpaired base in 18S rDNA helix 44 is present in primordial petalomonads and kinetoplastids, but absent in more derived taxa within respective groups. White Roman numerals depict heterogeneous dispersal of different types of feeding apparatuses (FA) according to Triemer and Farmer (1991), white Arabic numerals count for number of rods in FA. Heterolobosea and Jakobida represent outgroup taxa
Figure 2 from: Sousa FB, Milanin T, Morandini AC, Espinoza LL, Flores-Gonzales A, Gomes AL.S, Matoso DA, Mathews PD (2021) Molecular diagnostic based on 18S rDNA and supplemental taxonomic data of the cnidarian coelozoic Ceratomyxa (Cnidaria, Myxosporea) and comments on the intraspecific morphological variation. Zoosystematics and Evolution 97(2): 307-314. https://doi.org/10.3897/zse.97.64769
Figure 2 Transmission electron microscopy images of Ceratomyxa amazonensis isolated of Symphysodon discus from the Unini River, Amazonas State, Brazil. a. Myxospore showing two sub-spherical polar capsules and sporoplasm (sp) occupying most of the myxospore volume; b. Detail of the apical suture (black arrow) and sporoplasmosomes (arrowheads); c. Detail of lateral suture (black arrow); d. Polar capsule displaying still uncoiled internal polar tubule (black arrow). Scale bars: 2 µm (a); 1 µm (c); 500 nm (b, d).
Figure 1 from: Sousa FB, Milanin T, Morandini AC, Espinoza LL, Flores-Gonzales A, Gomes AL.S, Matoso DA, Mathews PD (2021) Molecular diagnostic based on 18S rDNA and supplemental taxonomic data of the cnidarian coelozoic Ceratomyxa (Cnidaria, Myxosporea) and comments on the intraspecific morphological variation. Zoosystematics and Evolution 97(2): 307-314. https://doi.org/10.3897/zse.97.64769
Figure 1 Light photomicrographs of Ceratomyxa amazonensis plasmodia. a, b. Slightly elongated plasmodia showing mature myxospores (white asterisks) and few early sporogonic stages (arrows); c. Spherical plasmodium with two slightly crescent-shaped mature myxospores (ms) and containing early sporogonic stages (arrows); d. Differential interference contrast microscopy snapshot of a slightly crescent-shaped mature myxospore. Scale bars: 10 µm.
Data from: Secondary structure models of 18S and 28S rRNAs of the true bugs based on complete rDNA sequences of Eurydema maracandica Oshanin, 1871 (Heteroptera: Pentatomidae)
The sequences of 18S and 28S rDNAs have been used as molecular markers to resolve phylogenetic relationships of Heteroptera for two decades. The complete sequences of 18S rDNAs have been used in many studies, while in most studies only partial sequences of 28S rDNAs have been used due to technical difficulties of amplifying the complete lengths. In this study, we amplified the complete 18S and 28S rDNA sequences of Eurydema maracandica Oshanin, 1871, and reconstructed the secondary structure models of the corresponding rRNAs. In addition, and more importantly, all of the length variable regions of 18S rRNA were compared among 37 families of Heteroptera based on 140 sequences, and the D3 region of 28S rRNA was compared among 51 families based on 84 sequences. It was found that 8 length variable regions could potentially serve as molecular synapomorphies for some monophyletic groups. Therefore discoveries of more molecular synapomorphies for specific clades can be anticipated from amplification of complete 18S and 28S rDNAs of more representatives of Heteroptera.
Supplementary material 2 from: Reid BN, Servis JA, Timmers M, Rohwer F, Naro-Maciel E (2022) 18S rDNA amplicon sequence data (V1–V3) of the Palmyra Atoll National Wildlife Refuge, Central Pacific. Metabarcoding and Metagenomics 6: e78762. https://doi.org/10.3897/mbmg.6.78762
Figure S2
Supplementary material 5 from: Reid BN, Servis JA, Timmers M, Rohwer F, Naro-Maciel E (2022) 18S rDNA amplicon sequence data (V1–V3) of the Palmyra Atoll National Wildlife Refuge, Central Pacific. Metabarcoding and Metagenomics 6: e78762. https://doi.org/10.3897/mbmg.6.78762
Table S3
Supplementary material 6 from: Reid BN, Servis JA, Timmers M, Rohwer F, Naro-Maciel E (2022) 18S rDNA amplicon sequence data (V1–V3) of the Palmyra Atoll National Wildlife Refuge, Central Pacific. Metabarcoding and Metagenomics 6: e78762. https://doi.org/10.3897/mbmg.6.78762
Table S4
Supplementary material 1 from: Reid BN, Servis JA, Timmers M, Rohwer F, Naro-Maciel E (2022) 18S rDNA amplicon sequence data (V1–V3) of the Palmyra Atoll National Wildlife Refuge, Central Pacific. Metabarcoding and Metagenomics 6: e78762. https://doi.org/10.3897/mbmg.6.78762
Figure S1
Supplementary material 4 from: Reid BN, Servis JA, Timmers M, Rohwer F, Naro-Maciel E (2022) 18S rDNA amplicon sequence data (V1–V3) of the Palmyra Atoll National Wildlife Refuge, Central Pacific. Metabarcoding and Metagenomics 6: e78762. https://doi.org/10.3897/mbmg.6.78762
Table S2
Supplementary material 3 from: Reid BN, Servis JA, Timmers M, Rohwer F, Naro-Maciel E (2022) 18S rDNA amplicon sequence data (V1–V3) of the Palmyra Atoll National Wildlife Refuge, Central Pacific. Metabarcoding and Metagenomics 6: e78762. https://doi.org/10.3897/mbmg.6.78762
Table S1
Fig. 3 in Description of Sarcocystis scandentiborneensis sp. nov. from treeshrews (Tupaia minor, T. tana) in northern Borneo with annotations on the utility of COI and 18S rDNA sequences for species delineation
Fig. 3. Phylogenetic tree of nuclear 18S rDNA sequences of the Sarcocystidae, including the new Sarcocystis sp. from treeshrews (black symbols). Taxa of the Eimeriidae served as outgroup. Bayesian Inference was used for phylogeny reconstruction, whereby the general time-reversible substitution model (GTR + G + I) combined with an assumed among-site variation ('covariotide' model) was applied. Values for posterior probability are indicated behind nodes. Note that the new species is part of a monophyletic subclade previously tagged S1 (Wassermann et al., 2017), which includes taxa known to prefer snakes as definitive and rodents as intermediate hosts. Sequences E357-13 and E364-13 are available at GenBank under MN733816 and MN733817, respectively.
Data from: ALG11 – a new variable DNA marker for sponge phylogeny: comparison of phylogenetic performances with the 18S rDNA and the COI gene
Phylogenetic relationships within sponge classes are highly debated. The low phylogenetic signal observed with some current molecular data can be attributed to the use of few markers, usually slowly-evolving, such as the nuclear rDNA genes and the mitochondrial COI gene. In this study, we conducted a bioinformatics search for a new molecular marker. We sought a marker that (1) is likely to have no paralogs; (2) evolves under a fast evolutionary rate; (3) is part of a continuous exonic region; and (4) is flanked by conserved regions. Our search suggested the nuclear ALG11 as a potential suitable marker. We next demonstrated that this marker can indeed be used for solving phylogenetic relationships within sponges. Specifically, we successfully amplified the ALG11 gene from DNA samples of representatives from all four sponge classes as well as from several cnidarian classes. We also amplified the 18S rDNA and the COI gene for these species. Finally, we analyzed the phylogenetic performance of ALG11 to solve sponge relationships compared to and in combination with the nuclear 18S rDNA and the COI mtDNA genes. Interestingly, the ALG11 marker seems to be superior to the widely-used COI marker. Our work thus indicates that the ALG11 marker is a relevant marker which can complement and corroborate the phylogenetic inferences observed with nuclear ribosomal genes. This marker is also expected to contribute to resolving evolutionary relationships of other apparently slow-evolving animal phyla, such as cnidarians.
Figure 3. Phylogenetic trees obtained from morphological data. A in Combined-data phylogenetics and character evolution of Clitellata (Annelida) using 18S rDNA and morphology
Figure 3. Phylogenetic trees obtained from morphological data. A, phylogenetic tree obtained from one of the three replicate Bayesian inference runs of the somatic data set. Posterior probabilities of ± 0.85 are indicated in front of the nodes. B, phylogenetic tree obtained from one of the three replicate Bayesian inference runs of the spermatozoal data set. Posterior probabilities ± 0.85 are indicated in front of the nodes.
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