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44 results for “Chaetoceros”
Chaetoceros decipiens (UNC1416) reference transcriptome
<p>Reference transcriptome and associated annotations for <em>Chaetoceros decipiens </em>(UNC1416). </p> <p>A culture was grown into late exponential phase for filtration. Total RNA was extracted using the RNAqueous-4PCR Total RNA Isolation Kit (Ambion, Foster City, CA, USA) according to the manufacturer’s protocol with an initial bead beating step to disrupt cells. RNA libraries were created with either the Illumina TruSeq Stranded mRNA Library Preparation Kit. The library was sequenced on an Illumina MiSeq (300 bp, paired-end reads) and an Illumina HiSeq 2500 with one lane in high output mode (100 bp, paired-end reads) and another lane in rapid run mode (150 bp, paired-end reads).</p> <p>Raw reads were trimmed for quality with Trimmomatic v0.36 then assembled <em>de novo </em>with Trinity v2.5.1 with the default parameters for paired-reads and a minimum contig length of 90 bp. Contigs were clustered based on 99% similarity using CD-HIT-EST v4.7 and then protein sequences were predicted with GeneMark S-T. Protein sequences were annotated by best-homology (lowest E-value) with the KEGG (Release 86.0), UniProt (Release 2018_03), and PhyloDB (v1.076) databases via BLASTP v2.7.1 (E-value ≤ 10<sup>-5</sup>) and with Pfam 31.0 via HMMER v3.1b2 (Dataset S2). KEGG Ortholog (KO) annotations were assigned from the top hit with a KO annotation from the top 10 hits (<a href="https://github.com/ctberthiaume/keggannot">https://github.com/ctberthiaume/keggannot</a>).</p> <p>Provided here are predicted proteins as nucleotides and peptides. Raw reads are deposited in SRA (SRP234548).</p>
FIGURES 1-4 in Morphology and taxonomy of Chaetoceros heterovalvatus, a rare marine diatom
FIGURES 1-4. Chaetoceros heterovalvatus. LM fresh preparation, complete cell (1), LM fresh preparation, vaulted valve with curved setae (2), SEM vaulted valve with curved setae (3), SEM valve with divergent setae and rimoportula (arrow) (4), Scale bar 10 µm (1,2), 2 µm (3,4).
Chain length, growth rate and clearance rate of Thalassiosira Rotula, Chaetoceros Curvisetus, and Chaetoceros Affinis when exposed to copepodamides.
<p>Colony formation is common feature among non-motile marine phytoplankton. Several theories exist around the potential benefits of larger colonies. Here we test the hypothesis that predation is one of the drivers behind colony formation and chain length plasticity. We exposed cultures of Thalassiosira rotula, Chaetoceros curvisetus and Chaetoceros affinis to copepodamides, a chemical alarm cue released by copepods and perceived as an indicator of predation threat by their prey. This was coupled with a grazing experiment which compared copepod grazing rates on different chain lengths. Our results show that T. rotula and C. curvisetus decreased their chain lengths by 79% and 49%, respectively, in response to copepodamides. Single cells and short chains were grazed at lower rates compared to long chains and the copepodamide driven size shift led to 30% and 12% lower grazing in T. rotula and C. curvisetus respectively. In contrast, C. affinis showed a slight increased chain length in response to copepodamides although non-significant. We found that 2 of 3 studied species reduce their chain length in response to the presence copepod grazers. Altered size structure has implications for the route of carbon in the marine food webs and carbon export to deeper strata.</p>
Fig 20 in Diversity in the Globally Distributed Diatom Genus Chaetoceros (Bacillariophyceae): Three New Species from Warm-Temperate Waters
Fig 20. The original drawings of species of the C. lorenzianus complex. A: Resting spore of C. mitra by Bailey [17]. B and C: C. mitra by Cleve [18]. Vegetative chain, intercalary valve, terminal seta and apical view of seta positions (C), and chain with resting spores (B, lectotype). D: Vegetative chain of C. lorenzianus by Grunow [8]. E and F: Chaetoceros decipiens by Cleve [7]. G and H: Resting spores of C. lorenzianus by Okamura [39]. doi:10.1371/journal.pone.0168887.g020
Fig 5 in Diversity in the Globally Distributed Diatom Genus Chaetoceros (Bacillariophyceae): Three New Species from Warm-Temperate Waters
Fig 5. Chaetoceros elegans sp. nov. SEM (A–E) and TEM (F and G). A: Terminal valve view with external process of rimoportula and poroids on valve face; strain MC1048. B and C: Intercalary cells demonstrating large apertures and valve faces; strain M1 (B), strain MC1048 (C). D and E: Terminal valves with central processes (arrowheads) and silica ear-like structures (arrows in D) in strain YL7. F: Annulus, costae and poroid pattern near intercalary valve centre; strain YL7. G: Parallel rows of poroids on the mantle; arrowhead indicates ring-shaped constriction; strain YL7. A–E scale bars, 5 μm. F and G scale bars, 2 μm. doi:10.1371/journal.pone.0168887.g005
Fig 19 in Diversity in the Globally Distributed Diatom Genus Chaetoceros (Bacillariophyceae): Three New Species from Warm-Temperate Waters
Fig 19. Molecular phylogenetic tree. Based on analyses of the D1-D3 region of the LSU rDNA sequences. Numbers indicated on the branches are posterior probability of Bayesian analyses (MrB) and boot strap support of neighbor joining (NJ), maximum parsimony (MP) and maximum likelihood (ML) analyses. doi:10.1371/journal.pone.0168887.g019
Fig 1 in Diversity in the Globally Distributed Diatom Genus Chaetoceros (Bacillariophyceae): Three New Species from Warm-Temperate Waters
Fig 1. LM of Chaetoceros decipiens. A, C, E, F: Chain views of lectotype material MIC5366 (A) and strains P10E5 (C), P14B3B (E), D12 (F). B and D: Detail of chains showing constrictions (arrows) between the mantle and the girdle bands, and the fused extensions of sibling setae, which are short, longer or even absent (arrowheads); lectotype material MIC5366 (B) and strain P10E5 (D). G: Chain view of strain D10, note the V-shaped protrusion located centrally on the terminal valve (arrowhead). A and C: scale bars, 50 μm. B, D, E, F: scale bars, 20 μm. G: scale bar, 10 μm. doi:10.1371/journal.pone.0168887.g001
Fig 4 in Diversity in the Globally Distributed Diatom Genus Chaetoceros (Bacillariophyceae): Three New Species from Warm-Temperate Waters
Fig 4. LM of Chaetoceros elegans sp. nov. Strain YL7. A: Chain view displaying seta divergence in the apical plane. B: Solitary cell. C: Chain view demonstrating large apertures and chloroplasts. D: End of chain showing constrictions (arrows) between the mantle and the girdle, and V-shaped protrusion (arrowhead) located centrally on terminal valve. A and B scale bars, 50 μm. C and D scale bars, 20 μm. doi:10.1371/journal.pone.0168887.g004
Fig 13 in Diversity in the Globally Distributed Diatom Genus Chaetoceros (Bacillariophyceae): Three New Species from Warm-Temperate Waters
Fig 13. LM of Chaetoceros mitra. Strain P10A1. A: Straight chain showing seta divergence and apertures. B: Detail of chain showing constrictions (arrows) between mantle and girdle. C: Valve structure of terminal valve. A and B scale bars, 20 μm. C scale bar, 10 μm. doi:10.1371/journal.pone.0168887.g013
Fig 12 in Diversity in the Globally Distributed Diatom Genus Chaetoceros (Bacillariophyceae): Three New Species from Warm-Temperate Waters
Fig 12. Chaetoceros mannaii sp. nov. LM (A), SEM (B) and TEM (C–F); strain N1. A and B: Setae with oval poroids. C: Terminal valve showing valve structure and rimoportula with external projection. D: Poroids and costae on the mantle. E and F: Girdle bands with poroids. A scale bar, 10 μm. B scale bar, 5 μm. C–F scale bars, 2 μm. doi:10.1371/journal.pone.0168887.g012
Fig 8 in Diversity in the Globally Distributed Diatom Genus Chaetoceros (Bacillariophyceae): Three New Species from Warm-Temperate Waters
Fig 8. Chaetoceros laevisporus sp. nov. LM (A–C), SEM (D and E) and TEM (F). Fig A: Part of a chain showing constrictions (arrows) between mantle and girdle, and V- shaped protrusion (arrowhead) located centrally on the terminal valve; strain N7. B: Dividing chain showing seta divergence; strain DY1. C: Structure of terminal seta; strain DY1. D: Chain in girdle view showing cells and apertures; strain N7. E: Terminal valve with rimoportula without external process (arrowhead); strain N7. F: Valve views of intercalary (upper) and terminal valves (below); strain N7. A, C, D scale bars, 20 μm. B scale bar, 100 μm. E and F scale bars, 5 μm. doi:10.1371/journal.pone.0168887.g008
Fig 18 in Diversity in the Globally Distributed Diatom Genus Chaetoceros (Bacillariophyceae): Three New Species from Warm-Temperate Waters
Fig 18. Comparison of setae poroid densities. Small letters on the x-axis indicate statistically significant differences among taxa. doi:10.1371/journal.pone.0168887.g018
Fig 7 in Diversity in the Globally Distributed Diatom Genus Chaetoceros (Bacillariophyceae): Three New Species from Warm-Temperate Waters
Fig 7. Resting spores of Chaetoceros elegans sp. nov. LM (A and B) and SEM (C–F). A and B: Resting spores within mother cells in a chain; strain MC785. C and D: Released resting spores, showing two elongated elevations with dichotomous branching processes distally on the primary valve face and one (C) or two bulges (Fg D) on the secondary valve face; strain Ch12A1. E: Internal view of secondary valve with a ring of marginal punctae; strain Ch12A1. F: Hooks on the distal tips; strain MC785. A and B scale bars, 20 μm. C–E scale bars, 5 μm. F scale bar, 1 μm. doi:10.1371/journal.pone.0168887.g007
Fig 6 in Diversity in the Globally Distributed Diatom Genus Chaetoceros (Bacillariophyceae): Three New Species from Warm-Temperate Waters
Fig 6. Chaetoceros elegans sp. nov. LM (C), TEM (A, B, H) and SEM (D–G). A and B: Overlapping ear-like structures (arrows) and small gap between the crossing bases of sibling setae in strain YL7. C: Terminal seta with partly visible poroids in LM; strain YL7. D and E: Seta structure showing elongated poroids (D, strain Ch12A1) and tear-shaped poroids (E, strain M1) and F and G: Detail of setae poroids; strain Ch12A1 (F) and strains MC785 (G). H: Girdle band; strain YL7. All scale bars are 2μm, except 10 μm in C. doi:10.1371/journal.pone.0168887.g006
Fig 3. Chaetoceros decipiens. Strain D10 in Diversity in the Globally Distributed Diatom Genus Chaetoceros (Bacillariophyceae): Three New Species from Warm-Temperate Waters
Fig 3. Chaetoceros decipiens. Strain D10, SEM (A–C) and TEM (D). A: Solitary cell with silica fringes. B: Intercalary cells with overlapping silica membrane (arrow). C: Detail of fused seta bases, silica membrane and fringes on the mantle (arrowhead). D: Rows of poroids on the mantle. A and B scale bars, 10 μm. C and D scale bars, 2 μm. doi:10.1371/journal.pone.0168887.g003
Fig 17 in Diversity in the Globally Distributed Diatom Genus Chaetoceros (Bacillariophyceae): Three New Species from Warm-Temperate Waters
Fig 17. Comparison of setae poroid sizes. Small letters on the x-axis indicate statistically significant differences among taxa. doi:10.1371/journal.pone.0168887.g017
Fig 2 in Diversity in the Globally Distributed Diatom Genus Chaetoceros (Bacillariophyceae): Three New Species from Warm-Temperate Waters
Fig 2. Chaetoceros decipiens. LM (A and B), TEM (C, D, H-J) and SEM (E-G). A-E: Seta structure of lectotype MIC5366 (A), strains P14B3B (B) and D10 (C–E), showing the 4–6 sided seta with poroids and small spines. F: Terminal valve with fringes (arrowheads); strain D10. G: Silica warts on the basal ring of the mantle; strain D10. H: Annulus, costae and poroid pattern on intercalary valve; strain P10E5. I: Terminal valve showing rimoportula without external process (arrowhead); strain D10. J: Girdle bands; strain D10. A and B scale bars, 10 μm. C–J scale bars, 2 μm. doi:10.1371/journal.pone.0168887.g002
Fig 15 in Diversity in the Globally Distributed Diatom Genus Chaetoceros (Bacillariophyceae): Three New Species from Warm-Temperate Waters
Fig 15. Chaetoceros mitra resting spores. LM (A–C), TEM (D) and SEM (E–G); strain P10A1. A: Early stage of resting spore formation. B and C: Mature resting spores within mother cells. D: Two elongated processes with dichotomous branches distally. E–G: Resting spores in different views, showing a row of silica warts along the secondary valve edge (arrowheads in E) and a ring of puncta at the secondary valve mantle (arrowheads in G). A–C scale bars, 10 μm. D–G scale bars, 5 μm. doi:10.1371/journal.pone.0168887.g015
Fig 11 in Diversity in the Globally Distributed Diatom Genus Chaetoceros (Bacillariophyceae): Three New Species from Warm-Temperate Waters
Fig 11. Chaetoceros mannaii sp. nov. LM (A and B), SEM (C and E) and TEM (D and F); strain N1. A: Straight chain showing seta divergence and constrictions (arrows) between the mantle and the girdle. B: Oval valve face. C and D: Intercalary cells, with ear-like structures (arrowheads in D) at the bases of setae in heavily silicified frustule. E and F: Terminal valves, with ear-like structures at the seta bases (arrowheads in E) and distinct constriction above the ring (arrowheads in F). A scale bar, 20 μm. B–F scale bars, 5 μm. doi:10.1371/journal.pone.0168887.g011
Fig 14 in Diversity in the Globally Distributed Diatom Genus Chaetoceros (Bacillariophyceae): Three New Species from Warm-Temperate Waters
Fig 14. Chaetoceros mitra. LM (A), SEM (B, C, F, G) and TEM (D, E, H–J); strain P10A1. A–E: Setae showing round-oval poroids and spines, using different microscopy techniques. F: Intercalary valves showing wing-like structures (arrowhead), and furrows above the basal ring of mantle (arrows). G: Terminal valve showing rimoportula without external tube (arrowhead), furrow above the basal ring of mantle (arrows) and fringe (curved arrow). H: Intercalary valve face. I and J: Girdle bands. A scale bar, 10 μm. B, C, F–H scale bars, 5 μm. D, E, I, J scale bars, 2 μm. doi:10.1371/journal.pone.0168887.g014
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