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Direct RNA ONT sequencing of pine roots under ammonium nutrition

ABSTRACT: Direct RNA ONT sequencing of pine roots under ammonium nutrition

PROVIDER: PRJNA731860 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR14613168_1.fastq.gz	Fastqsanger.gz
	SRR14613169_1.fastq.gz	Fastqsanger.gz
	SRR14613170_1.fastq.gz	Fastqsanger.gz
	SRR14613171_1.fastq.gz	Fastqsanger.gz
	SRR14613172_1.fastq.gz	Fastqsanger.gz

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Direct RNA ONT sequencing of pine roots under ammonium nutrition

Project description:Epitranscriptomics modifications constitute a gene expression checkpoint in all living organism including plants. Considering the relevance of nitrogen nutrition and metabolism for the correct plant growth and development, it can be hypothesized that epitranscriptome changes must regulate every biological process in plants including nitrogen nutrition. In the present work, the epritranscriptomics changes in maritime pine roots caused by ammonium nutrition have been monitored through direct RNA sequencing using Oxford Nanopore Technology. The main transcriptome responses to ammonium nutrition affected to transcripts involved in nitrogen and carbon metabolisms, defense response, hormone synthesis and signaling, and translation. Additionally to a global detection of epitranscriptomics marks, the m6A deposition and its dynamics have been identified, which seems to be important regulators of translation when compared with the proteomic profiles of the same samples. In this sense, the obtained results suggest that protein translation is finely regulated through the epitranscriptomics marks maybe through changes in mRNA polyA length, transcript amount and ribosome protein composition. The multiomics results in the present study suggest that the epitranscriptome must modulate the responses to development and environmental changes, including ammonium nutrition, through buffering, filtering and focusing the final products of the gene expression.

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miRNA expression of Pinus pinaster roots under ammonium nutrition

Project description:In the present study, the miRNA expression changes in the maritime pine roots from seedlings of one-month old under different levels of ammonium nutrition was analyzed.

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Proteomic profile of Pinus pinaster roots under ammonium nutrition

Project description:Ammonium nutrition was studied at short times (24 hours) in roots from one month-old seedlings of maritime pine. Control seedlings were irrigated with 80 mL of water (C) and the experimental seedlings with 80 mL of 3 mM NH4Cl. Root samples were collected at 24 hours post-irrigation and immediately frozen in liquid N. This experiment was carried out three independent times.

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miRNA expression of Pinus pinaster roots under ammonium nutrition

Project description:miRNA expression of Pinus pinaster roots under ammonium nutrition

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Project description:Epitranscriptomics modifications constitute a gene expression checkpoint in all living organism including plants. Considering the relevance of nitrogen nutrition and metabolism for the correct plant growth and development, it can be hypothesized that epitranscriptome changes must regulate every biological process in plants including nitrogen nutrition. In the present work, the epritranscriptomics changes in maritime pine roots caused by ammonium nutrition have been monitored through RIP-seq. The main transcriptome responses to ammonium nutrition affected to transcripts involved in nitrogen and carbon metabolisms, defense response, hormone synthesis and signaling, and translation. The m6A deposition and its dynamics have been identified, which seems to be important regulators of translation when compared with the proteomic profiles of the same samples. The present study suggest that the epitranscriptome must modulate the responses to development and environmental changes, including ammonium nutrition, through buffering, filtering and focusing the final products of the gene expression.

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Project description:The main objective of the present work is the transcriptomic analysis of the interaction between nitrogen nutrition and CO2 levels in maritime pine. For this purpose, seedlings were fertilized with nitrate or ammonium and grown in two different CO2 levels: normal (400 ppm) and high (720ppm).

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