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9 results for “Prymnesium parvum”
Prymnesium parvum 12B1 polyketide synthase (PKS) domain and module analysis
<p>The .zip file contains source data and code for an analysis that determines the modular structure from the domain structure of type I modular polyketide synthases (PKSs) in the Prymnesium parvum strain 12B1 gene annotation. In brief, a regex is used against a string representation of the PKS domain structures to determine the module structure. Some manual modifications for calling modules were performed where they deviated. Resulting data is available in the .zip file as .bed, .FASTA, .xlsx files. See Manuscript for further details.</p> <p>For versions after v1.0.5, analyses of B-type PKZILLA-B1 (i.e. from strain RCC3426) are also included. </p>
Analysis of Metabolomics Data to Assess Interactions in Microalgal Co-culture of Skeletonema marinoi and Prymnesium parvum
<p>This dataset refers to the metabolomics results from Metabolome Annotation QWorkflow on a co-culture of two microalgae: <em>Skeletonema marinoi </em>and <em>Prymnesium parvum</em>. The metabolomics data was acquired from endometabolome and exometabolome in both positive and negative MS modes. These will be referred as conditions. The files ms2_spectra_condition.mzML files have the MS2 combined from different MS2 files found on Zenodo with DOI: 10.5281/zenodo.10143233. The MS1 files are available on Zenodo as well with the DOI: 10.5281/zenodo.10143127</p> <p>The first section is about the results from the MS1 analysis. For the code used to generate these files, please refer to the code: <a href="https://github.com/zmahnoor14/MAW/tree/main/co-culture">https://github.com/zmahnoor14/MAW/tree/main/co-culture</a> </p> <ol> <li>Feature_info_condition.csv refers to the list of features with IDS, m/z, rt and intensity values. <ul> <li>The feature list is used to link the MS1 features to the features extracted from MS2 spectra.</li> </ul> </li> <li>Feature_list_condition.csv refers to the list of mzML origin file (samples) and the intensity of the features in those samples.</li> </ol> <p>The second section relates to the MS2 results. For source code please refer to: <a href="https://github.com/zmahnoor14/MAW/tree/main/Docker">https://github.com/zmahnoor14/MAW/tree/main/Docker</a></p> <ol> <li>SL_MAW_Coculture.csv contains list of metabolic features that were annotated and found to be present in the suspect list of either of the two organisms or both. The suspect lists for Skeletonema marinoi can be found at 10.5281/zenodo.5772755, and for Prymnesium parvum can be found at 10.5281/zenodo.7864506. </li> <li>unique_MAW_SMILES_coculture.csv file contains all information on unique SMILES.</li> <li>onlyDAF.csv contains differentially abundant features in either of the conditions: <em>S. marinoi </em>co-culture, <em>S. marinoi</em> mono-culture and similar conditions for <em>P. parvum</em>.</li> <li>condition_mergedResults-with-one-Candidates_sig_feat_for_only_inclusion.csv files contain all MS2 features and annotations together with the information on whether these features were found in the inclusion list (List provided for generating MS2 spectra in orbitrap), and whether these features were differential.</li> </ol>
Tandem Mass Spectrometry Data (LCMS-2) from Microalgal Co-culture of Skeletonema marinoi and Prymnesium parvum
<p>The mzML files in this dataset are the Liquid Chromatography Tandem Mass Spectrometry (LCMS-2) data files, derived from the RAW MS-2 files using GNPS file convertor. These files contain unprocessed features fragmented features from the MS-1 data files available as <10.5281/zenodo.10143127> acquired from the monocultures (single species: <em>Skeletonema marinoi</em> and <em>Prymnesium parvum</em> separately) and co-culture conditions of (<em>Skeletonema marinoi</em> and <em>Prymnesium parvum</em>). These files are used for structure annotations. </p> <p>The results of metabolomics annotation are available on Zenodo with DOI: 10.5281/zenodo.10143554</p>
Suspect List of Prymnesium parvum
<p>This list contains metabolites identified in the haptophyte Prymnesium parvum, together with a classification sunburst plot, depciting chemical classification based on ChemONT ontology. The most prevalent superclasses in this suspect list are: Organic acids and derivatives (26.2%), Lipids and lipid-like molecules (23.8%), Organic oxygen compounds (20.3%), and Nucleosides, nucleotides, and analogues (19.8 %).</p>
Liquid Chromatography Mass Spectrometry Data (LCMS-1) from Microalgal Co-culture of Skeletonema marinoi and Prymnesium parvum
<p>The mzML files in this dataset are the Liquid Chromatography Mass Spectrometry Data (LCMS-1) data files, derived from the RAW MS files using GNPS file convertor. These files contain unprocessed features acquired from the monocultures (single species: <em>Skeletonema marinoi</em> and <em>Prymnesium parvum</em> separately) and co-culture conditions of (<em>Skeletonema marinoi</em> and <em>Prymnesium parvum</em>). The microalgae were grown in co-culture chambers, so the naming convention A, and B refer to the two sides of the chamber. So, 1a and 1b are <em>S. marinoi</em> monocultures, but 11a and 11b refer to s. marinoi and <em>P. parvum</em> respectively.</p> <p>The results of metabolomics data analysis are available on Zenodo with DOI: 10.5281/zenodo.10143554</p>
Transcriptome Analysis from a co-culture of Skeletonema marinoi and Prymnesium parvum
<p>This Zenodo entry refers to a study using metabolomics and transcriptomic data analysis to analyse chemical interactions between two microalgae: <em>Skeletonema marinoi</em> and <em>Prymnesium parvum</em></p> <p>p_parvum_Eukaryota_augustus_gene_prediction.faa file contains the predicted protein sequences from the transcriptome of <em>Prymnesium parvum</em> using Augustus. This list is generated from a non-restrictive Busco Analysis.</p> <p>s_costatum_Stramenopiles_augustus_gene_prediction.faa file contains the predicted protein sequences from the transcriptome of <em>Skeletonema marinoi </em>using Augustus. This list is generated from a restrictive Busco Analysis.</p> <p>The files p_parvum_deseq2_results_all.csv and s_marinoi_deseq2_results_all.csv contain differential gene expression analysis, while p_parvum_deseq2_result_sorted_regulated_with_proteins.csv and s_marinoi_deseq2_result_sorted_regulated_with_proteins.csv contain only upregulated protein sequences in co-culture conditions.</p> <p>The genes_read.R script is used to generate the p_parvum_deseq2_result_sorted_regulated_with_proteins.csv and s_marinoi_deseq2_result_sorted_regulated_with_proteins.csv. The code for analysis from RAW reads to differential gene expression analysis is available on: <a href="https://github.com/Bioinformatics-Core-Facility-Jena/SE20220705_97">https://github.com/Bioinformatics-Core-Facility-Jena/SE20220705_97</a>. The RAW files are available on BioProject: PRJNA1006530</p> <p> </p> <p> </p>
Data for: Behavioral differences underlie toxicity and predation variation in blooms of Prymnesium parvum
<p>Much of the evolutionary ecology of toxic algal blooms (TABs) remains unclear, including the role of algal toxins in the adaptive 'strategies' of TAB-forming species. Most eukaryotic TABs are caused by mixotrophs that augment autotrophy with organic nutrient sources, including competing algae (intraguild predation). We leverage the standing diversity of TABs formed by the toxic, invasive mixotroph Prymnesium parvum to identify cell-level behaviors involved in toxin-assisted predation using direct observations as well as comparisons between genetically distinct low- and high-toxicity isolates. Our results suggest that P. parvum toxins are primarily delivered at close range and promote subsequent prey capture/consumption. Surprisingly, we find opposite chemotactic preferences for organic (prey-derived) and inorganic nutrients between differentially toxic isolates, respectively, suggesting behavioral integration of toxicity and phagotrophy. Variation in toxicity may therefore reflect broader phenotypic integration of key traits that ultimately contribute to the remarkable flexibility, diversity, and success of invasive populations.</p>
Data for: Behavioral differences underlie toxicity and predation variation in blooms of Prymnesium parvum
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Data from: Allelopathy as an emergent, exploitable public good in the bloom-forming microalga Prymnesium parvum
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