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Marine metagenome

ABSTRACT: Metagenomics of diazotrophic community associated with Phaeodactylum tricornutum

PROVIDER: PRJNA923279 | ENA |

REPOSITORIES: ENA

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Dataset's files

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			Action	DRS
	SRR24446623_subreads.fastq.gz	Fastqsanger.gz
	SRR24446624_1.fastq.gz	Fastqsanger.gz
	SRR24446624_2.fastq.gz	Fastqsanger.gz
	SRR27010089_1.fastq.gz	Fastqsanger.gz
	SRR27010089_2.fastq.gz	Fastqsanger.gz

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Mapping of H3K4me3 in the model diatom Phaeodactylum tricornutum

Project description:Chromatin organization in Phaeodactylum tricornutum

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Transcriptional response of the marine pennate diatom Phaeodactylum tricornutum to Fe limitation

Project description:Diatoms, which are responsible for up to 40% of the 45 to 50 billion metric tons of organic carbon production each year in the sea, are particularly sensitive to Fe stress. Here we describe the transcriptional response of the pennate diatom Phaeodactylum tricornutum to Fe limitation using a partial genome microarray based on EST and genome sequence data. Processes carried out by components rich in Fe, such as photosynthesis, mitochondrial electron transport and nitrate assimilation are down-regulated to cope with the reduced cellular iron quota. This retrenchment is compensated by nitrogen (N) and carbon (C) reallocation from protein and storage carbohydrate degradation, adaptations to chlorophyll biosynthesis and pigment metabolism, removal of excess electron s by mitochondrial alternative oxidase (AOX), augmented Fe-independent oxidative stress responses, and sensitized iron capture mechanisms. Keywords: Marine phytoplankton, pinnate diatom Wild-type Phaeodactylum tricornutum was grown under Fe replete (10,000 nM) and Fe limiting (5nM) conditions. Partial genome gene expression analysis of iron-inducible genes was conducted using a two-color competitive hybridization microarray.

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Evolutionary and functional analysis of DNA methyltransferases in micro-eukaryotes: Insights from the model diatom Phaeodactylum tricornutum [RNA-seq]

Project description:Loss of DNA methylation is traditionally associated with transcriptional up-regulation of transposable elements. Here we describe for the first time expression changes upon loss of DNA methylation in diatoms using Phaeodactylum tricornutum as a model species. The loss of DNA methylation was obtained by generation of DNMT5 KOs, a divergent DNMT with SNF-like domains. Expression analysis confirm the loss of DNA methylation is associated with de-repression of transposable elements in Phaeodactylum tricornutum with indirect effects on protein coding genes.

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Analysis of the α-1,3 fucosyltransferase gene funtion in diatom Phaeodactylum tricornutum

Project description:Anylasis of the α-1,3 fucosyltransferase gene function in diatom Phaeodactylum tricornutum

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Anylasis of the diatom Phaeodactylum tricornutum under 64-75-5,Tetracycline hydrochloride stress

Project description:Anylasis of the diatom Phaeodactylum tricornutum under 64-75-5,Tetracycline hydrochloride stress

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Next generation sequencing of Phaeodactylum tricornutum grown with and without nitrogen

Project description:We have done next generation sequencing of optically thin, exponentialy growing Phaeodactylum tricornutum cultures grown with and without nitrogen source to improve our undestanding of the pathways regulation under conditions that promote lipid accumulation (N-starvation). 3 biologically independent exponentially growing culture of Phaeodactylum tricornutum were pelleted and washed several times with N-free media. Each culture was devided to 2 replicates with initial cell concentration of 2X105 cells/mL, one with NaNO3 as nitrogen source and the other without any nitrogen source. The cuture were bubbled foro 48 hours and sampled for transcriptome together with other physiological parameters and lipid analysis.

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The unusual properties of the photosynthetic cytochrome c550 from the red algal lineage evidence additional biological roles

Project description:Cytochrome c550 is an extrinsic component in the luminal side of photosystem II in cyanobacteria, as well as in eukaryotic algae from the red photosynthetic lineage including, among others, diatoms. By using strong and specific protease inhibitors we have confirmed that cytochrome c550 from the diatom Phaeodactylum tricornutum is expressed as a truncated form lacking the last hydrophobic residues at the C-terminal.. Phaeodactylum tricornutum cytochrome c550 seems to be modified at a post-translational level as the gene is appropriately transcribed. In addition, co-immunoprecipitation and mass spectrometry experiments have allowed the identification of novel interactions of Phaeodactylum tricornutum cytochrome c550 with proteins related to the CO2 concentrating mechanism and assimilation located in the chloroplast pyrenoid. Furthermore, immunoelectron microscopy analysis indicates that although cytochrome c550 is mainly located in the thylakoid domain of the chloroplast, it can also be found in the pyrenoid. The results are interpreted in terms of a specific protein modification associated to a higher PSII turnover or to new alternative functions of the heme protein, maybe related to carbon fixation.

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Evolutionary and functional analysis of DNA methyltransferases in micro-eukaryotes: Insights from the model diatom Phaeodactylum tricornutum [Bisulfite-Seq]

Project description:DNA methylation has been associated with transcriptional repression of transposable elements. Here we describe the first DNA methylation deficient cell line of a diatom by generating DNMT5:KOs in Phaeodactylum tricornutum. These data show the extend of the loss of DNA methylation in DNMT5:KOs compared to the reference strain. All DNA methylation is lost in DNMT5:KOs.

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Transcriptional response of the marine pennate diatom Phaeodactylum tricornutum to Fe limitation

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