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Fig. 1 in Constraints on Phylogenetic Interrelationships among Four Free-living Litostomatean Lineages Inferred from 18S rRNA gene-ITS Region sequences and Secondary Structure of the ITS2 molecule

Fig. 1. Phylogeny based on the 18S rRNA gene of 64 free-living litostomatean taxa (alignment 18S-A). Posterior probabilities for Bayesian inference and bootstrap values for maximum likelihood were mapped onto the 50% majority rule Bayesian consensus tree. Dashes indicate ML bootstrap values below 50%. Sequences in bold were obtained during this study. The scale bar indicates two substitutions per one hundred nucleotide positions. For details on taxa, evolutionary model used, and characteristics of the 18S-A alignment, see Supplementary Table S1 and S2.

Fig. 8 in Constraints on Phylogenetic Interrelationships among Four Free-living Litostomatean Lineages Inferred from 18S rRNA gene-ITS Region sequences and Secondary Structure of the ITS2 molecule

Fig. 8. Structure logo of ITS2 helices II and III in various higher litostomatean taxa. The height of a base is proportional to its frequency in multiple sequence alignments.

Fig. 2 in Constraints on Phylogenetic Interrelationships among Four Free-living Litostomatean Lineages Inferred from 18S rRNA gene-ITS Region sequences and Secondary Structure of the ITS2 molecule

Fig. 2. Phylogeny based on the ITS1-5.8S-ITS2 region of 60 free-living litostomatean taxa (alignment ITSR-A). Posterior probabilities for Bayesian inference and bootstrap values for maximum likelihood were mapped onto the best ML tree. Dashes indicate posterior probabilities below 0.50 and ML bootstrap values below 50%. Sequences in bold were obtained during this study. The scale bar indicates nine substitutions per one hundred nucleotide positions. For details on taxa, evolutionary model used, and characteristics of the ITSR-A alignment, see Supplementary Table S1 and S2.

Fig. 7 in Constraints on Phylogenetic Interrelationships among Four Free-living Litostomatean Lineages Inferred from 18S rRNA gene-ITS Region sequences and Secondary Structure of the ITS2 molecule

Fig. 7. Consensus secondary structure of ITS2 helices II and III in various higher litostomatean taxa.

opencc-by-4.0Jun 2024View details →

RDP Classifier training files for 16S rRNA sequences from GTDB

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: <ul> <li><code>genus.zip</code> - Genus level</li> <li><code>species.zip</code> - Species level</li> </ul> The code in <code>prepare_files.R</code> was used to prepare the GTDB sequence and taxonomy files for retraining the RDP Classifier. Notes: <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).

opencc-by-4.0Jan 2024View details →

◂Fig. 6 A molecular phylogeny of 56 systematically representative Peridiniaceae, including 42 accessions assignable to P. cinctum from various geographic regions. Maximum likelihood tree (– ln = 21,884.93), as inferred from a rRNA nucleotide alignment (1137 parsimony-informative sites) and with strain number information. Numbers on branches are ML bootstrap (above) and Bayesian support values (below) for the clusters (asterisks indicate maximal support values, values under 50 and 0.90, respectively, are not shown). Clades are indicated (CZE Czech Republic, E East, GER Germany, HET Heterocapsaceae, N North, PPE Protoperidiniaceae, POL Poland, rbn ribotype n, S South, SWE Sweden, UKR Ukraine, W West) in Bumps on the back: An unusual morphology in phylogenetically distinct Peridinium aff. cinctum (= Peridinium tuberosum; Peridiniales, Dinophyceae)

◂Fig. 6 A molecular phylogeny of 56 systematically representative Peridiniaceae, including 42 accessions assignable to P. cinctum from various geographic regions. Maximum likelihood tree (– ln = 21,884.93), as inferred from a rRNA nucleotide alignment (1137 parsimony-informative sites) and with strain number information. Numbers on branches are ML bootstrap (above) and Bayesian support values (below) for the clusters (asterisks indicate maximal support values, values under 50 and 0.90, respectively, are not shown). Clades are indicated (CZE Czech Republic, E East, GER Germany, HET Heterocapsaceae, N North, PPE Protoperidiniaceae, POL Poland, rbn ribotype n, S South, SWE Sweden, UKR Ukraine, W West)

opencc-by-4.0Oct 2021View details →

◂Fig. 4 A molecular tree of 51 systematically representative Peridiniaceae, including all 28 accessions assignable to P. volzii. Maximum Likelihood tree (–ln = 22,017.62), as inferred from a rRNA nucleotide alignment (1,129 parsimony-informative sites) and with strain number information. Numbers on branches are ML bootstrap (above) and Bayesian support values (below) for the clusters (asterisks indicate maximal support values, values under 50 and 0.90, respectively, are not shown). Clades are indicated (abbreviations: HET, Heterocapsaceae; PPE, Protoperidiniaceae) in Morphological and molecular variability of Peridinium volzii Lemmerm. (Peridiniaceae, Dinophyceae) and its relevance for infraspecific taxonomy

◂Fig. 4 A molecular tree of 51 systematically representative Peridiniaceae, including all 28 accessions assignable to P. volzii. Maximum Likelihood tree (–ln = 22,017.62), as inferred from a rRNA nucleotide alignment (1,129 parsimony-informative sites) and with strain number information. Numbers on branches are ML bootstrap (above) and Bayesian support values (below) for the clusters (asterisks indicate maximal support values, values under 50 and 0.90, respectively, are not shown). Clades are indicated (abbreviations: HET, Heterocapsaceae; PPE, Protoperidiniaceae)

opencc-by-4.0Dec 2015View details →

Fig. 3. Phylogenetic trees from reported 18S in Molecular systematics analysis of Lymantria dispar based on 18S rRNA and cox1 mtDNA sequence data

Fig. 3. Phylogenetic trees from reported 18S rRNA genes of insects according to NJ. A. Based on sequences of full-length. B. Based on second conserved region.

opencc-by-4.0Dec 2015View details →

Fig. 4 in Molecular systematics analysis of Lymantria dispar based on 18S rRNA and cox1 mtDNA sequence data

Fig. 4. Phylogenetic trees based on partial sequences from reported cox1 genes of insects according to NJ.

opencc-by-4.0Dec 2015View details →

Fig.1 in Molecular systematics analysis of Lymantria dispar based on 18S rRNA and cox1 mtDNA sequence data

Fig.1. PCR result of 18S rRNA of Lymantria dispar. Separated bands (from left to right). 18S1, 18S2, 18S rRNA, DL2000 marker.

Fig. 4 in Molecular profiling of 18S rRNA reveals seasonal variation and diversity of diatoms community in the Han River, South Korea

Fig. 4. Principal component analysis (PCA) biplot showing the seasonal variation of (A) all the diatom OTU reads, (B) most frequent diatom OTU detected, sampled in March (spring), June (summer), September (autumn), and December (winter). Calculated based on the number of OTU reads in each sample. Each dot represents diatom OTU recovered in this study.

Fig. 2 in Molecular profiling of 18S rRNA reveals seasonal variation and diversity of diatoms community in the Han River, South Korea

Fig. 2. Rarefaction curves representing the numbers of Operational Taxonomic Units (OTUs) of diatoms vs. the number of tags sampled from pyrosequencing data.

Fig. 1 in Molecular profiling of 18S rRNA reveals seasonal variation and diversity of diatoms community in the Han River, South Korea

Fig. 1. Seasonal variation in water temperature and DO (A), pH and conductivity (B) and TN and TP (C), and cell counts and Chla (D) at the Seongsan Bridge of Han River, Korea.

Fig. 3 in Molecular profiling of 18S rRNA reveals seasonal variation and diversity of diatoms community in the Han River, South Korea

Fig. 3. (A) Proportion of each eukaryotic taxon (eukaryote, phytoplankton, and diatom), (B) relative abundance of phytoplankton, and (C) relative abundance of diatom taxa. These data were calculated by using 18S rRNA pyrosequencing reads. Taxonomic identity of "others" represents taxa with less than 1% composition of total reads.

opencc-by-4.0Apr 2019View details →

A Comprehensive Assessment of Demographic, Environmental and Host Genetic Associations with Gut Microbiome Diversity in Healthy Individuals (16S rRNA gene sequencing data)

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.