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Data and analysis code for a toxin induction study on two species of Dinophysis dinoflagellates
<h3>General description</h3> <p>This repository contains the datasets, analysis code and output generated and used in the manuscript "Effects of copepod chemical cues on intra- and extracellular toxins in two species of <em>Dinophysis</em>", which has been published as a research article in Harmful Algae (https://doi.org/10.1016/j.hal.2024.102793).</p> <h3>Files</h3> <p><strong>HRMS_data_Dinophysis_induction_experiment.zip </strong>contains the source high-resolution mass-spectroscopy endometabolomics data in open file formats.</p> <p><strong>Put_annot_sign_affect_feat_metabol_data.xlsx</strong> (corresponds to <strong>Supplementary spreadsheet 1</strong> in the main manuscript) contains putative annotations of significantly affected features from the metabolomics data, for each <em>Dinophysis </em>species (<em>D.</em> <em>sacculus </em>and <em>D. acuminata</em>) and each mode of ionization. Notably, results obtained from GNPS (Global Natural Products Social Molecular Networking, <a href="https://gnps.ucsd.edu/" target="_blank" rel="noopener noreferrer">https://gnps.ucsd.edu/</a>), and SIRIUS (<a href="https://bio.informatik.uni-jena.de/sirius/" target="_blank" rel="noopener noreferrer">https://bio.informatik.uni-jena.de/sirius/</a>) were mentionned. When available, MS/MS spectra were also provided. </p> <p><strong>Tabl_sign_affect_feat.xlsx</strong> (corresponds to <strong>Supplementary spreadsheet 3</strong> in the main manuscript) contains tables of significantly affected features (ANOVA, Tukey’s post hoc test, adjusted p-value cut-offs of 0.001 or 0.01) from the metabolomics data, for each <em>Dinophysis </em>species (<em>sacculus </em>and <em>acuminata</em>) and each mode of ionization. A visual representation (heatmaps) of these significant fetures are available as Figs S3-S6 in the supplementary information of the main mauscript. </p> <p><strong>Toxin_analysis_code_output.Rmd</strong> is the R-markdown file that produces the interactive analysis output output (<strong>Toxin_analysis_code_output.html</strong>, corresponds to <strong>Supplementary code & output </strong>in the main manuscript) of the toxin analysis, and uses the datasets <strong>Toxin_analysis_data.csv</strong>,<strong> pca_score_sacculus.csv</strong>,<strong> </strong>and<strong> pca_score_acuminata.csv</strong> source datasets to perform the statistical analyses and generate figures (details for each dataset below).</p> <p><strong>Toxin_analysis_data.csv</strong> (corresponds to <strong>Supplementary spreadsheet 2</strong> in the main manuscript) contains the main data used to statistically analyse the toxin and growth dynamics of both <em>Dinophysis</em> species in response to different grazer treatments, and to produce the majority of the figures in the main manuscript (Figs. 2-6) and supplementary information (Figs. S1-S2). </p> <p><strong>pca_score_sacculus.csv</strong> & <strong>pca_score_acuminata.csv</strong> contain the scores of the first two principal components of the PCA performed on LC-HRMS derived metabolomic profiles of <em>D. sacculus </em>and <em>D. acuminata</em> respectively, in both positive and negative ion mode. These are used to produce PCA score plots (Fig. 6 in the main manuscript and Fig. S2 in the supplementary information).</p> <p><strong>custom.css</strong> is a custom html style sheet file that formats the <strong>Toxin_analysis_code_output.html</strong> to display scrollable tables correctly. It is used by <strong>Toxin_analysis_code_output.Rmd </strong>and is necessary for true reproduction of the output (<strong>.html</strong>) file.</p>
NMNH Botany Elevation Data: Dinoflagellates
Elevation data from specimens in the collections of the Smithsonian National Museum of Natural History Botany Department.<p></p>
Identifying Harmful Marine Dinoflagellates: Harmful Dinoflags
Faust, Maria A. and Rose A. Gulledge. Identifying Harmful Marine Dinoflagellates. Smithsonian Contributions from the United States National Herbarium, volume 42: 1-144 (including 48 plates, 1 figure and 1 table).<p></p>Faust, Maria A. and Rose A. Gulledge. Identifying Harmful Marine Dinoflagellates. Smithsonian Contributions from the United States National Herbarium, volume 42: 1-144 (including 48 plates, 1 figure and 1 table).
Role of TRP channels in dinoflagellate mechanotransduction
<p>This repository contains several files associated with the publication:</p> <p><strong>Transcriptome:</strong> <em>Lingulodinium polyedra </em>transcriptome assembled from 100 bp paired-end Illumina RNA sequences available at http://www.ebi.ac.uk/ (run accession SRR1184657) using the assembly and annotation pipeline “MakeMyTranscriptome” (https://github.com/bluegenes/MakeMyTranscriptome), which leverages the Trinity <em>de novo</em> assembler (v2.1.1; Grabherr 2011). The transcriptome contains 183,451 transcripts, with an N50 of 1161, and 66.5% GC (guanine-cytosine) content. Annotation-based assessment using BUSCO showed that this transcriptome contained 62% of eukaryotic genes predicted to be present in all eukaryotic assemblies. Open reading frames (ORFs) predicted using transDecoder are also provided as a second file (ends with .pep).</p> <p><strong>TRP-like polypeptide sequences: </strong>Transient Potential Receptor (TRP)-like polypeptide sequences identified in transcriptomic data from the dinoflagellate <em>Lingulodinium polyedra</em>.</p> <p><strong>Video: </strong>Video of luminescence from the dinoflagellate <em>Lingulodinium polyedra</em> in response to capsaicin treatment. Samples consisted of 1 ml volumes of <em>L. polyedra</em> culture containing approximately 7000 cells, kept in two separate glass vials. The injection of 0.1 ml volumes of control solution (left vial) and capsaicin (30 µM final concentration, right vial) at a rate of 1ml min<sup>-1</sup> caused some light response due to stimulation of cells by the fluid addition. However, following fluid addition the capsaicin treatment clearly stimulated luminescence in the <em>L. polyedra</em> cells, seen as individual sources of light, while the cells in the control treatment produced essentially no light.</p>
Fig. 9. Dinoflagellates from USGS Paleobotan. loc. R6234 in Cephalopods From The Cretaceous/Tertiary Boundary Interval On The Atlantic Coastal Plain, With A Description Of The Highest Ammonite Zones In North America. Part 2. Northeastern Monmouth County, New Jersey
Fig. 9. Dinoflagellates from USGS Paleobotan. loc. R6234, lower part of the Hornerstown Formation, Parkers Creek, 0.3 km east of Rt. 35, northwest of Eatontown, northeastern Monmouth County,
Fig. 8. Dinoflagellates from USGS Paleobotan. loc. R6234 in Cephalopods From The Cretaceous/Tertiary Boundary Interval On The Atlantic Coastal Plain, With A Description Of The Highest Ammonite Zones In North America. Part 2. Northeastern Monmouth County, New Jersey
Fig. 8. Dinoflagellates from USGS Paleobotan. loc. R6234, upper part of the New Egypt Formation and lower part of the Hornerstown Formation, Parkers Creek, 0.3 km east of Rt. 35, northwest of
Fig. 7. Dinoflagellates from northeastern Monmouth County, New Jersey. A, B, H, I. USGS Paleobotan. loc. R6234E in Cephalopods From The Cretaceous/Tertiary Boundary Interval On The Atlantic Coastal Plain, With A Description Of The Highest Ammonite Zones In North America. Part 2. Northeastern Monmouth County, New Jersey
Fig. 7. Dinoflagellates from northeastern Monmouth County, New Jersey. A, B, H, I. USGS Paleobotan. loc. R6234E, New Egypt Formation, approximately 1.5–2.0 m below the base of the Hornerstown Formation, Parkers Creek, 0.1 km east of Rt. 35, northwest of Eatontown. C, F, G. USGS Paleobotan.
Fig. 6. Dinoflagellates from USGS Paleobotan. loc. R6234H in Cephalopods From The Cretaceous/Tertiary Boundary Interval On The Atlantic Coastal Plain, With A Description Of The Highest Ammonite Zones In North America. Part 2. Northeastern Monmouth County, New Jersey
Fig. 6. Dinoflagellates from USGS Paleobotan. loc. R6234H, Tinton Formation, Hochhockson Brook, 0.2 km north of the intersection of Water Street and Tinton Avenue, northeastern Monmouth County, New Jersey. A–E. Isabelidinium cooksoniae (Alberti, 1959) Lentin & Williams, 1977 sensu lato.
Fig. 1 in Problematic Biases in the Availability of Molecular Markers in Protists: The Example of the Dinoflagellates
Fig. 1. Number of species of the most speciose dinoflagellate genera (> 11 species per genus). The empty bars represented the number of described species based on Gómez (2012a). The black bars represent the number of species with, at least, one nucleotide sequence available in DDBJ/EMBL/GenBank in January 2013.
data for paper: Predator-induced defense decreases growth rate and photoprotective capacity in a nitrogen-limited dinoflagellate
<p>this is the data for paper "Predator-induced defense decreases growth rate and photoprotective capacity in a nitrogen-limited dinoflagellate" </p>
Dinoflagellate cyst assemblage data from core JM09-020
<p>Absolute abundances (cysts g<sup>-1</sup>) of dinoflagellate cysts (dinocysts) species, total dinocyst abundance (cysts g<sup>-1</sup>), relative abundance of dinocysts produced by auto- and heterotrophic dinoflagellate species (%), and dry bulk density (g cm<sup>-3</sup>) for flux calculation in core JM09-020.</p>
Fig. 2 in The Acquisition of Plastids/Phototrophy in Heterotrophic Dinoflagellates
Fig. 2. Variation in degree of reduction of the retained endosymbiont or organelles in dinoflagellates with acquired phototrophy. Black thick lines: plasma membrane; Blue circles: a single membrane of unknown origin that separates the cryptophyte cytoplasm from the dinoflagellate cytoplasm; Red circles: digestive vacuole (= food vacuole). A – green Noctiluca scintillans harboring an intact cell of the prasinophyte Pedinomonas noctilucae; B–D – the three cases where the mechanism for acquisition of organelles by dinoflagellates is known; B – Amphidinium poecilochroum. The ingested cryptophyte organelles are encircled by a single membrane of unknown origin, and then are actively transferred to and digested in a digestive vacuole in the order of the numbers indicated; C – Gymnodinium acidotum (= G. aeruginosum). In the dinoflagellate, the cryptophyte's Golgi body (indicated in grey color) was degenerated. The cryptophyte nucleus and nucleomorph (indicated by dotted lines) were present in some cells, but not in other cells. In the dinoflagellate, a peduncle has been identified (Wilcox and Wedemayer 1984, Farmer and Roberts 1990), but it is not clear whether the peduncle feeding is actually involved in the ingestion process (Fields and Rhodes 1991). As in A. poecilochroum, the ingested cryptophyte organelles are encircled by a single membrane; D – Dinophysis spp. The arrow means that the plastids escape from the food vacuole and move to the cytoplasm of the dinoflagellate; E–G – cases where the mechanism for acquisition of cryptophyte organelles remains unknown. The plastids and other organelles may originate from a series of events leading to acquisition and subsequent degeneration of a whole-cell endosymbiont (i.e., an intact cryptophyte symbiont – E, F or G), or may be acquired as organelles via predation (i.e., kleptoplastidy; an ingested cryptophyte partially digested to give states shown in E, F or G); E – Amphidinium latum and Gymnodinium myriopyrenoides; F – Amylax triacantha. According to Koike and Takishita (2008), a single Amylax cell had 14 cryptophyte vestiges, of which only one was found to contain a cryptophyte nucleus (indicated by dotted line). The presence of a Golgi body and exectosome was not confirmed (indicated by question marks); G – Amphidinium wigrense retaining only plastids of cryptophyte origin.
Fig. 1 in The Acquisition of Plastids/Phototrophy in Heterotrophic Dinoflagellates
Fig. 1. Light micrographs of some dinoflagellates with acquired phototrophy. A – Amphisolenia bidentata (micrograph provided by Niels Daugbjerg); B – green Noctiluca scintillans (micrograph provided by Ken Furuya); C – Amphidinium poecilochroum; D – Gymnodinium eucyaneum (micrograph provided by Guoxiang Liu); E – Cryptoperidiniopsis sp.; F – Gymnodinium myriopyrenoides; G – undescribed Antarctic dinoflagellate (micrograph provided by C. Grier Sellers); H – Dinophysis caudata; I – Amylax triacantha; J – Dinophysis acuminata; K – Dinophysis fortii.
Figs 1A–H. Achradina pulchra. A–B in Achradina pulchra, a Unique Dinoflagellate (Amphilothales, Dinophyceae) with a Radiolarian-like Endoskeleton of Celestite (Strontium Sulfate)
Figs 1A–H. Achradina pulchra. A–B – Light micrographs of the isolated cells of Achradina pulchra for PCR analysis from the SW Atlantic (São Sebastião Channel). C–D – Other cells from the same sample. Note that the skeleton is internal. E–G – Scanning electron micrographs of the skeleton from the NE Atlantic (Seine and Sedlo Seamounts). H – X-ray energy dispersive spectroscopy (EDS) spectrum of the endoskeleton. Scale bars: 5 µm.
Figures 44–52 in Diversity and distribution of species of the planktonic dinoflagellate genus Alexandrium (Dinophyta) from the tropical and subtropical Mexican Pacific Ocean
Figures 44–52: Alexandrium tamarense, LM and SEM. (44) Cell in ventral view, LM. (45) Empty cell in ventral view with plate tabulation, LM. (46) Detail of the epitheca with some plates and ventral pore (arrow), LM. (47) Apical view, with plate tabulation, LM. (48, 49) Hypotheca with plate tabulation, including the posterior sulcal plate (Sp) and its pore (arrow), LM. (50) Epitheca with plate tabulation and the ventral pore (arrow), SEM. (51) Epitheca with plate tabulation, SEM. (52) Po with some plates surrounding it, and the ventral pore (arrow), SEM.
Figures 28–37 in Diversity and distribution of species of the planktonic dinoflagellate genus Alexandrium (Dinophyta) from the tropical and subtropical Mexican Pacific Ocean
Figures 28–37: Alexandrium monilatum, LM and SEM.(28, 29) A long chain (8 cells) and detail of that chain, respectively, LM. (30) Pair of cells in ventral view, SEM. (31) General outline of a cell, LM. (32) Cell in ventral view showing Po and 1′, SEM. (33) Detail of the cingulum and sulcus, showing the first apical plate (1′), SEM. (34) Apical view with plate tabulation, SEM. (35) Hypotheca showing the posterior sulcal plate (Sp) and its connecting pore (arrow), SEM. (36) Po plate with the conjunction pore and foramen, SEM. (37) Posterior sulcal plate showing the connection pore, LM.
Figures 20–21 in Diversity and distribution of species of the planktonic dinoflagellate genus Alexandrium (Dinophyta) from the tropical and subtropical Mexican Pacific Ocean
Figures 20–21: Alexandrium leei, LM. (20) Recently fixed cell in ventral view. (21) An empty cell in ventral view showing plate tabulation, arrow indicates the ventral pore in the first apical plate (1′).
Figures 9–11 in Diversity and distribution of species of the planktonic dinoflagellate genus Alexandrium (Dinophyta) from the tropical and subtropical Mexican Pacific Ocean
Figures 9–11: Alexandrium gaarderae, LM. (9, 10) Two different focal planes of a solitary cell in ventral view, showing the cell outline, cingulum and sulcus. (11) A cell in dorsal view.
Figures 2–8 in Diversity and distribution of species of the planktonic dinoflagellate genus Alexandrium (Dinophyta) from the tropical and subtropical Mexican Pacific Ocean
Figures 2–8: Alexandrium affine, LM. (2, 3) Chains of 8 and 3 cells, respectively. (4) An empty cell showing only the theca in ventral view. (5) Epitheca in ventral view showing the ventral pore (arrow) in the first apical plate (1′). (6) Epitheca with Po and 1′ showing the ventral pore (arrow). (7, 8) Po and posterior sulcal plate (Sp) (with a connecting pore), respectively.
Figures 67–69 in Diversity and distribution of species of the planktonic dinoflagellate genus Alexandrium (Dinophyta) from the tropical and subtropical Mexican Pacific Ocean
Figures 67–69: Alexandrium tropicale, LM. (67) Pair of cells. (68, 69) Epitheca and hypotheca with plate tabulation.
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