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ABSTRACT: Phaeodactylum tricornutum transcriptome

PROVIDER: PRJNA554372 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR9677670.fastq.gz	Fastqsanger.gz
	SRR9677680.fastq.gz	Fastqsanger.gz
	SRR9677690.fastq.gz	Fastqsanger.gz
	SRR9677700.fastq.gz	Fastqsanger.gz
	SRR9677671.fastq.gz	Fastqsanger.gz

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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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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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Identification and Characterization of MicroRNAs from Phaeodactylum tricornutum by High-throughput Sequencing and Bioinformatics Analysis

Project description:Diatoms, which are important planktons widespread in various aquatic environments, are believed to play a vital role in primary production as well as silica cycling. The genomes of the pennate diatom Phaeodactylum tricornutum and the centric diatom Thalassiosira pseudonana have been sequenced, revealing some characteristics of the diatomsâ mosaic genome as well as some features of their fatty acid metabolism and urea cycle, and indicating their unusual properties. To identify microRNAs (miRNAs) from P. tricornutum and to study their probable roles in nitrogen and silicon metabolism, we constructed and sequenced small RNA (sRNA) libraries from P. tricornutum under normal (PT1), nitrogen-limited (PT2) and silicon-limited (PT3) conditions. A total of 13 miRNAs were identified. They were probable P. tricornutum-specific novel miRNAs. These miRNAs were differentially expressed in PT1, PT2 and PT3, and their potential targets were involved in various processes. Our results indicated that P. tricornutum contained novel miRNAs that differed from miRNAs of other organisms and that they might play important regulator roles in P. tricornutum metabolism.

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Project description:An experiment was performed to determine the similarities on the RNA level between different conditions where cell division stops in the diatom Phaeodactylum tricornutum. Many of these conditions also increase the accumulation of lipids within the cell or impair photosynthesis. The different metabolic responses were evaluated and the dataset was mined for potential transcriptional regulators of these changes. The experimental setup was as follows: Cells from the pennate diatom Phaeodactylum tricornutum were grown in ESAW medium under continous fluorescent light at 21C in baffled shakeflasks. Exponentially growing cells were harvested by centrifugation and washed twice in 21gr/L NaCL to remove nutrients. Cells were subsequently resuspended in the five different media/conditions (control, darkness, no nitrate, no phosphate, nocodazole).

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