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Analysis of gene-targeted DNA methylation patterns through the annual cycle in clonal epitypes of Norway spruce

ABSTRACT: Analysis of gene-targeted DNA methylation patterns through the annual cycle in clonal epitypes of Norway spruce

PROVIDER: PRJNA922200 | ENA |

REPOSITORIES: ENA

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Dataset's files

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			Action	DRS
	SRR23029319_1.fastq.gz	Fastqsanger.gz
	SRR23029319_2.fastq.gz	Fastqsanger.gz
	SRR23029320_1.fastq.gz	Fastqsanger.gz
	SRR23029320_2.fastq.gz	Fastqsanger.gz
	SRR23029321_1.fastq.gz	Fastqsanger.gz

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Analysis of gene-targeted DNA methylation patterns through the annual cycle in clonal epitypes of Norway spruce

Project description:Main goal of the study is to distinguish stable DNA methylation differences from dynamic changes during the annual cycle in different epitypes. We examined whether the extant epigenetic marks created during embryogenesis under EpI-temperature conditions are maintained in the resulting epitype trees. We used unique well-defined clonal epitypes with a stable epigenetic memory of the temperature sum experienced during embryogenesis impacting bud phenology. Due to the massive size of the Norway spruce genome (Nystedt et al., 2013), we used a targeted approach to address the DNA methylation status at a single-base resolution in specific target gene regions of selected genes involved in the epigenetic machinery and adaptive traits formation. From these we have characterized DNA methylation patterns in apical buds for 10 time points throughout the year to observe the differences between epitypes and its dynamics through the annual cycle of development.

2023-08-01 | GSE222491 | GEO

DNA methylome study of Norway spruce

Project description:Bisulfite treatment libraries were made to characterize DNA methylation of Norway spruce

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PARE libraries for the identification of miRNA target genes in Norway spruce

Project description:We constructed four PARE libraries for the identification of miRNA target genes in Norway spruce.

2015-09-02 | GSE65248 | GEO

Norway Spruce Cultured Cells Chitosan & C.polonica Stress

Project description:Conifer-specific responses to elicitation with the chemical elicitor chitosan have been investigated using a transcriptome analysis in Norway spruce using a cell suspension culture system that has been previously described (Phillips, Walter et al. 2007). This study has demonstrated that the early events following chitosan elicitation include calcium mediated signaling and an oxidative response that have not previously been described in intact trees. Keywords: stress response

2008-06-01 | GSE10771 | GEO

Fine root gene expression of Norway spruce cuttings

Project description:We investigated root associated fungi in young Norway spruce (Picea abies) cuttings rooted from slow- and fast-growing trees showing variable growth rate in long-term field experiments and compared their roots’ gene expression patterns five and 18 months after adventitious root initiation. Gene expression patterns of adventitious roots could not be systematically linked with the growth phenotype at the initiation of root formation, and thus fundamental differences in the receptiveness of fungal symbionts could not be assumed.

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Project description:Analysis of endophytic fungal communities of Norway spruce trees

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RNA-seq of Norway spruce seedlings exposed to gamma radiation

Project description:In order to test Norway spruce radiosensitivity to gamma radiation, 6 days old seedlings were exposed for 48 h to 60-Co source at dose rates 1, 10, 40 or 100 mGy/h.

2022-12-01 | E-MTAB-8081 | biostudies-arrayexpress

Unique organization of photosystem II supercomplexes and megacomplexes in Norway spruce.

Project description:Photosystem II (PSII) complexes are organized into large supercomplexes with variable amounts of light-harvesting proteins (Lhcb). A typical PSII supercomplex in plants is formed by four trimers of Lhcb proteins (LHCII trimers), which are bound to the PSII core dimer via monomeric antenna proteins. However, the architecture of PSII supercomplexes in Norway spruce (Picea abies (L.) Karst.) is different, most likely due to a lack of two Lhcb proteins, Lhcb6 and Lhcb3. Interestingly, the spruce PSII supercomplex shares similar structural features with its counterpart in the green alga Chlamydomonas reinhardtii (Kouřil et al.: New Phytol. 210, 808-814, 2016). Here we present a single-particle electron microscopy study of isolated PSII supercomplexes from Norway spruce that revealed binding of a variable amount of LHCII trimers to the PSII core dimer at positions that have never been observed in any other plant species so far. The largest spruce PSII supercomplex, which was found to bind 8 LHCII trimers, is even larger than the current largest known PSII supercomplex from Chlamydomonas reinhardtii. We have also shown that the spruce PSII supercomplexes can form various types of PSII megacomplexes, which were also identified in intact grana membranes. Some of these large PSII supercomplexes and megacomplexes were identified also in Pinus sylvestris, another representative of Pinaceae family. The structural variability and complexity of LHCII organization in Pinaceae seems to be related to the absence of Lhcb6 and Lhcb3 in this family and may be beneficial for the optimization of light-harvesting under varying environmental conditions.

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2015-09-02 | E-GEOD-65248 | biostudies-arrayexpress

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