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ABSTRACT: Genetic Engineering of P. tricornutum

PROVIDER: PRJNA593624 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR10586392_1.fastq.gz	Fastqsanger.gz
	SRR10586393_1.fastq.gz	Fastqsanger.gz
	SRR10586394_1.fastq.gz	Fastqsanger.gz
	SRR10586395_1.fastq.gz	Fastqsanger.gz
	SRR10586396_1.fastq.gz	Fastqsanger.gz

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Project description:Shotgun Genetic Engineering

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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.

2011-08-08 | GSE29321 | GEO

Project description:Genome sequencing of Phaeodactylum tricornutum exposed to engineering nanomaterials

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Mapping of H3K4me3 in the model diatom Phaeodactylum tricornutum

Project description:Chromatin organization in Phaeodactylum tricornutum

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Levering2016 - Phaeodactylum tricornutum metabolic model

Project description:Diatoms are eukaryotic microalgae that contain genes from various sources, including bacteria and the secondary endosymbiotic host. Due to this unique combination of genes, diatoms are taxonomically and functionally distinct from other algae and vascular plants and confer novel metabolic capabilities. Based on the genome annotation, we performed a genome-scale metabolic network reconstruction for the marine diatom Phaeodactylum tricornutum. Due to their endosymbiotic origin, diatoms possess a complex chloroplast structure which complicates the prediction of subcellular protein localization. Based on previous work we implemented a pipeline that exploits a series of bioinformatics tools to predict protein localization. The manually curated reconstructed metabolic network iLB1027_lipid accounts for 1,027 genes associated with 4,456 reactions and 2,172 metabolites distributed across six compartments. To constrain the genome-scale model, we determined the organism specific biomass composition in terms of lipids, carbohydrates, and proteins using Fourier transform infrared spectrometry. Our simulations indicate the presence of a yet unknown glutamine-ornithine shunt that could be used to transfer reducing equivalents generated by photosynthesis to the mitochondria. The model reflects the known biochemical composition of P. tricornutum in defined culture conditions and enables metabolic engineering strategies to improve the use of P. tricornutum for biotechnological applications.

2023-03-10 | MODEL2204200002 | BioModels

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

2011-08-08 | E-GEOD-29321 | biostudies-arrayexpress

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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Transcriptome reponse of Phaeodactylum tricornutum to grazing effect

Project description:RNA-sequencing was used to evaluate the transcriptomic response to grazing stress for P. tricornutum strain CCAP 1055/1.

2017-01-10 | GSE93297 | GEO

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.

2023-03-15 | GSE186856 | GEO

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