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74 results for “Nitzschia”
Pseudo-nitzschia multistriata gene models
<p>The resource contains fasta files with the <em>Pseudo-nitzschia multistriata</em> gene models and proteins, Pm-1.4_mRNA_v3.fa and Pm-1.4_peptide_v3.fa, a file with the annotation, psmu_mRNA_uniref_2015_06_filt_ann_out.txt, and a file with mapping information, genes_v3_WA.gff3.</p>
A phylogenomics resource for the marine diatom Pseudo-nitzschia multistriata
<p>The resource contains phylogenetic trees built from approximately 9000 <em>P. multistriata </em>genes, comparing them to their orthologs (over 2 million sequences) across major taxa of archaea, bacteria and eukaryotes (Basu et al., 2017). For each orthologous group a tree is built twice using two different substitution models. Each sequence within a tree is given a specific ID which is a combination of a unique number along with a taxonomy code, for example "alla_stramenopile|34" signifies </p> <p> </p> <p>1) alla: organism Albugo laibachii.</p> <p>2) stramenopile: broad taxonomic class.</p> <p>3) 34: protein ID for Albugo laibachii DNA topoisomerase 2.</p> <p> </p> <p>The mapping between <em>Pseudo-nitzschia multistriata</em> proteins and the phylogenetic trees is present in the file "p.multistriata_gene_tree.txt". The detailed description of each protein ID given in any phylogenetic tree is present in the file "geneDB.txt". The phylogenetic trees generated using JTT and WAG substitution models of the FastTree program as present in the folders "treeJTT", "treeWAG".</p>
Image-derived indicators of phytoplankton community responses to Pseudo-nitzschia blooms
<p>Data associated with the manuscript "Image-derived indicators of phytoplankton community responses to <em>Pseudo-nitzschia</em> blooms" submitted to the journal <em>Harmful Algae</em>. There is an additional R script that calculates an interaction metric as described in the paper. </p>
FIG. 4 in A new Nitzschia Hassall species (Bacillariaceae, Bacillariophyta) from saline ponds in Serbia
FIG. 4. — Nitzschia austriaca Hust. SEM and LM images taken from Bela Bara saline pond. A-C, SEM external valve views of a frustule; C, arrow indicates more widely spaced center fibulae; D-W, LM valve views of a population arranged in decreasing length. Scale bars: A-C, 5 µm; D-W, 10 µm.
FIG. 1 in A new Nitzschia Hassall species (Bacillariaceae, Bacillariophyta) from saline ponds in Serbia
FIG. 1. — Location of the four study saline ponds in the Vojvodina Region, Serbia. A, Bela Bara; B, Čoka Kopovo; C, Velika Rusanda; D, Slatina.
FIG. 3 in A new Nitzschia Hassall species (Bacillariaceae, Bacillariophyta) from saline ponds in Serbia
FIG. 3. — Nitzschia haloserbica Vidaković, Ector, C.E.Wetzel & Krizmanić, sp. nov., SEM images taken from the type material (Bela Bara saline pond): A, C, E, SEM views of a frustule in valve view; B, SEM internal view of two valves from the same frustule; D, SEM internal view of the center of the valve with fibulae regularly distributed; F, SEM internal view of valve apex with helictoglossa and raphe; G, SEM internal detail view of valve apex with helictoglossa. Scale bars: A-C, 5 µm; D, G, 1 µm; E, 3 µm; F, 2 µm.
Transcriptome assemblies of Thalassiosira hyalina and Nitzschia frigida
<p>Transcriptome assemblies of Thalassiosira hyalina and Nitzschia frigida originating from a time course experiment, in which these two species were exposed to high light stress and monitored over 120h under low and high pCO2. The corresponding Sequencing data is deposited at the EBI ArrayExpress database under accession number E-MTAB-6999. Contigs were created with Trinity Assembler.</p> <p>The according publication is currently in review (8/6/2019): Higher sensitivity towards light stress and ocean acidification in an Arctic sympagic compared to a pelagic diatom;</p> <p>Author team: Ane C. Kvernvik, Sebastian D. Rokitta, Eva Leu, Lars Harms, Tove M. Gabrielsen, Björn Rost and Clara J. M. Hoppe</p> <p>Do not hesitate to contact the authors if you like more information!</p>
Ecological data of Pseudo-nitzschia delicatissima in the Gulf of Naples
<p>We present ecological information regarding the diatom <em>Pseudo-nitzschia allochrona </em>and other <em>P. delicatissima</em>-like species, collected in surface waters at long term ecological research (LTER) site, LTER-MC, in the Gulf of NAples. Cell density data were obtained for the group including <em>P, allochrona</em>, <em>P. arenysensis</em>, <em>P. delicatissima </em>and <em>P. dolorosa</em>, which are not distinguishable in light microscopy, and are presented along with temperature, salinity and nutrient data collected simultaneously. Based on molecular data from isolated strain and metabarcoding, <em>Pseudo-nitzschia</em><em> allochrona </em>was shown to occur invariably only in summer and autumn, whereas the other three species were always detected in winter or spring. We arbitrarily attributed autumn-winter density data to P. allochrona and spring-summer ones to the other three species. This way we could investigate the ecological niche of <em>P. allochrona</em> compared to that of the closely related species.</p>
Nitzschia sp. Nitz4 variant calling
<p>BAM file of read alignments used to call variants in the Nitzschia sp. Nitz4 genome. The BAM file was processed to mark duplicates and add read group names.</p>
Diamond-BLASTx of transcriptome contigs of Thalassiosira hyalina and Nitzschia frigida
<p>This is an annotation file, delivering the Diamond-BLASTx results for the contigs of the transcriptome assemblies of Thalassiosira hyalina and Nitzschia frigida. Theswe originate from a time course experiment, in which these two species were exposed to high light stress and monitored over 120h under low and high pCO2. The corresponding Sequencing data is deposited at the EBI ArrayExpress database under accession number E-MTAB-6999. Contigs were created with Trinity Assembler and are available under DOI:10.5281/zenodo.3361258</p> <p>The according publication is currently in review (8/6/2019): Higher sensitivity towards light stress and ocean acidification in an Arctic sympagic compared to a pelagic diatom;</p> <p>Author team: Ane C. Kvernvik, Sebastian D. Rokitta, Eva Leu, Lars Harms, Tove M. Gabrielsen, Björn Rost and Clara J. M. Hoppe</p> <p>Do not hesitate to contact the authors if you like more information!</p>
Ecological data of Pseudo-nitzschia delicatissima in the Gulf of Naples
Open the record for dataset details and reuse information.
Supplementary material 8 from: Olszyński RM, Zakrzewski PK, Rimet F, Sulkowska J, Peszek Ł, Żelazna-Wieczorek J (2024) Morphology and phylogeny of Nitzschia nandorii sp. nov. (Bacillariophyceae), a new small-celled lanceolate species from a post-mining reservoir. PhytoKeys 241: 1-26. https://doi.org/10.3897/phytokeys.241.117406
Confocal Laser Scanning Microscopy projection of rotating chloroplast of Nitzschia nandorii sp. nov.
Inhibition of toxic Pseudo-nitzschia spp. by the kelp, Saccharina latissima, and other seaweeds
<p><span>This package contains the datasets and R code used to produce the article “Inhibition of toxic <em>Pseudo-nitzschia </em>spp. by the kelp, <em>Saccharina latissima</em>, and other seaweeds,” which is to appear in Limnology and Oceanography.</span></p>
Differential Gene Expression Dataset of Thalassiosira hyalina and Nitzschia frigida: Response to light stress under contemporary and elevated pCO2
<p>This is a time-course gene expression dataset on the transcriptomic responses of <em>Thalassiosira hyalina</em> and <em>Nitzschia frigida</em> to light stress under contemporary and elevated pCO2. The corresponding Sequencing data is deposited at the EBI ArrayExpress database under accession number E-MTAB-6999. Contigs were created with Trinity Assembler and are available under DOI:10.5281/zenodo.3361258</p> <p>The according publication is currently in review (8/6/2019): Higher sensitivity towards light stress and ocean acidification in an Arctic sympagic compared to a pelagic diatom;</p> <p>Author team: Ane C. Kvernvik, Sebastian D. Rokitta, Eva Leu, Lars Harms, Tove M. Gabrielsen, Björn Rost and Clara J. M. Hoppe</p> <p>Do not hesitate to contact the authors if you like more information!</p>
FIGURES 23–29 in Two new Nitzschia species (Bacillariophyceae) from China, possessing a canal-raphe-conopeum system
FIGURES 23–29. Nitzschia gaoi, sp. nov., LM. 23–25. Three valves showing a slightly eccentric raphe system. 24. Photograph of holotype. 26. One valve showing a centrally positioned raphe system. 27–29. Three valves showing a slightly eccentric raphe system. 27. Photograph of isotype specimen. Scale bar = 10 μm for all figures.
FIGURES 45–49 in Two new Nitzschia species (Bacillariophyceae) from China, possessing a canal-raphe-conopeum system
FIGURES 45–49. Nitzschia gaoi, sp. nov., girdle band views, SEM. 45. Internal view of a whole valve with one girdle band. 46–47. Apices, note that the girdle band is open at one apex (Fig. 46) but closed at the other (Fig. 47). 48. External view of the apex, note the girdle band (arrow). 49. Apex showing the areolae of the girdle band covered by hymenes and terminating near each apex (Figs 46, 49, arrows). Scale bars = 10 μm (Fig. 45), 1 μm (Figs 46–49).
FIGURES 17–22 in Two new Nitzschia species (Bacillariophyceae) from China, possessing a canal-raphe-conopeum system
FIGURES 17–22. Nitzschia arierae, sp. nov., canal-raphe-conopeum system, SEM. 17. External view of the apex, note that the conopea are fused into the valve (arrow). 18–19. External view of central area, note conopeal canal, raphe canal and supporting points. 20–22. Internal views, note keels and supporting marks. Abbreviations: c = conopeum, cc = conopeal canal, cv = zone of valve face subtended by conopeum, f = fibula, k = keel, r = raphe slit, rc = raphe canal, sm = supporting mark, v = uncovered zone of valve face. Scale bars = 1 μm (Figs 17–18, 20–22), 2 μm (Fig. 19).
FIGURES 12–16 in Two new Nitzschia species (Bacillariophyceae) from China, possessing a canal-raphe-conopeum system
FIGURES 12–16. Nitzschia arierae, sp. nov., internal views, SEM. 12. A whole valve, note the interspaces narrower towards the poles. 13. Apex, note the distinctive apical pore field and the poroids in the keel zone (two arrows). 14–16. Central areas, showing the subtended zone different from the uncovered zone (Fig. 14, double-head arrows), shortened striae (arrows), dichotomous striae (wavy arrows), and poroids present in the keel zone (Figs 14–15, arrowheads). Scale bars = 10 μm (Fig. 12), 1 μm (Figs 13–16).
FIGURES 8–11 in Two new Nitzschia species (Bacillariophyceae) from China, possessing a canal-raphe-conopeum system
FIGURES 8–11. Nitzschia arierae, sp. nov., external views, SEM. 8. A whole valve, note the constant width of conopeum. 9. Apex, showing the apical pore field (wavy arrows), the hooked terminal fissure towards the dorsal side (arrowhead), and the supporting points (arrows). 10. Central area, note the supporting points (arrows). 11. Another apex, note the hooked terminal fissure towards the dorsal side (arrowhead) and the supporting points (arrows). Scale bars = 10 μm (Fig. 8), 1 μm (Figs 9–11).
FIGURES 1–7 in Two new Nitzschia species (Bacillariophyceae) from China, possessing a canal-raphe-conopeum system
FIGURES 1–7. Nitzschia arierae, sp. nov., LM. 1–7. Seven valves showing size reduction. 1. Photograph of isotype specimen, note the two rows of dark spots (six arrows) and the two parallel lines on either side of the raphe. 3. Photograph of holotype, note the centrally positioned raphe system. Scale bar = 10 μm for all figures.
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