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Pseudotsuga menziesii

ABSTRACT: SeqDepth Douglas-fir needle

PROVIDER: PRJNA205561 | ENA |

REPOSITORIES: ENA

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Dataset's files

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			Action	DRS
	SRR868709.fastq.gz	Fastqsanger.gz
	SRR908307.fastq.gz	Fastqsanger.gz
	SRR908308.fastq.gz	Fastqsanger.gz
	SRR908309.fastq.gz	Fastqsanger.gz

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Transcriptome responses to natural environments in Pseudotsuga menziesii (Douglas-fir)

Project description:Local adaptation and phenotypic plasticity are important components of plant responses to variations in environmental conditions. While local adaptation has been widely studied in trees, little is known about plasticity of gene expression in adult trees in response to ever-changing environmental conditions in natural habitats. Here we investigate plasticity of gene expression in needle tissue between two douglas-fir provenances represented by 25 adult trees using deep RNA sequencing (RNA-Seq). Using linear mixed models, we investigated the effect of temperature, soil water availability and photoperiod on the abundance of 59189 detected transcripts. Expression of more than 80% of all identified transcripts revealed a response to variations in environmental conditions in the field. GO term overrepresentation analysis revealed gene expression responses to temperature, soil water availability and photoperiod that are highly conserved among many plant taxa. However, expression differences between the two Douglas-fir provenances were rather small compared to the expression differences observed between individual trees. Although the effect of environment on global transcript expression was high, the observed genotype by environment (GxE) interaction of gene expression was surprisingly low, since only 21 of all detected transcripts showed a GxE interaction.

2016-09-20 | GSE73420 | GEO

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Project description:A long-read and short-read transcriptomics approach provides the first high-quality reference transcriptome and genome annotation for Pseudotsuga menziesii (Douglas-fir)

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Repetitive somatic embryogenesis induced cytological and proteomic changes in propagated embryogenic lines of Pseudotsuga menziesii [Mirb.]

Project description:Objectives: to characterize and to better understand changes at the cellular and molecular levels, in embryogenic lines in Douglas-fir obtained after repetitive somatic embryogenesis, that could explain improvement of their embryogenic potential : to primary lines, secondary ones showed an increase of their embryogenic potential; then tertiary lines showed again an improved embryogenic potential compared to second lines. Interestingly, the proteomic analysis further revealed different sets of significant proteins suggesting that each cycle of repetitive somatic embryogenesis is promoting substantial genome-wide rearrangement of the gene expression pattern.

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Proteome of Douglas-fir: a resource for genomic research

Project description:First Douglas fir proteomes by nLC-MS/MS from 12 different organs : root, stem, xylem, needle, bud, female and male flowers, immature and mature seed, immature and mature somatic embryos and callus.

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