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IlTisEkeb

ABSTRACT: Tischeria ekebladella (oak carl)

PROVIDER: PRJEB83503 | ENA |

REPOSITORIES: ENA

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			Action	DRS
		Other
	ERR14075546_1.fastq.gz	Fastqsanger.gz
	ERR14075546_2.fastq.gz	Fastqsanger.gz
	ERR14106124.fastq.gz	Fastqsanger.gz

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ilTisEkeb

Project description:Tischeria ekebladella (oak carl), genomic and transcriptomic data

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Extraction and high-throughput sequencing of oak heartwood DNA: assessing the feasibility of genome-wide DNA methylation profiling

Project description:Tree ring features are affected by environmental factors and therefore are the basis for dendrochronological studies to reconstruct past environmental conditions. Oak wood often provides the data for these studies because of the durability particularly of oak heartwood and, hence the availability of samples spanning long time periods of the distant past. Wood formation is regulated in part by epigenetic mechanisms such as DNA methylation. Studies in the methylation state of DNA preserved in oak heartwood thus could identify epigenetic tree ring features informing on past environmental conditions. We investigated the feasibility of such studies using heartwood samples core-drilled from the trunks of standing oak trees spanning the AD 1776-2014. Heartwood contains little DNA, and large amounts of phenolic compounds known to hinder the preparation of high-throughput sequencing libraries. We sequenced whole-genome and DNA methylome libraries for oak heartwood up to 100 and 50 years of age, respectively. However, only 56 genomic regions with sufficient coverage for quantitative methylation analysis were identified, suggesting that the high-throughput sequencing of DNA will be in principal feasible for wood formed <100 years ago is impeded by the reduction in library complexity caused by the bisulfite treatment used to generate the oak methylome.

2020-01-07 | GSE143201 | GEO

Analysis of oak stem lesions in Acute Oak Decline using shotgun proteomics

Project description:Acute Oak Decline (AOD) is a decline-disease currently spreading in Britain, threatening oak trees. Here, we analyze and compare the proteomes of inner bark tissue sampled from oak stems of trees symptomatic with AOD and non-symptomatic trees.

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Whole genome bisulfite sequencing for bud, catkin and leaf of California Valley Oak, Quercus lobata (SW786)

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ilTisDodo

Project description:Tischeria dodonaea, genomic and transcriptomic data

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Transcriptomic analysis of Phanerochaete chrysosporium mycelium in presence of oak acetonic extractives

Project description:The transcriptome of Phanerochaete chrysosporium control mycelium was compared to the transcriptome of mycelium grown on oak acetonic extractives containing medium. The array probes were designed from gene models taken from the Joint Genome Institute (JGI, Department of Energy) Phanerochaete chrysosporium genome sequence version 1. The aim of this study was to determine gene expression changes in Phanerochaete chrysosporium grown on oak extract with a special focus on detoxification systems.

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Elicitor specific mechanisms of defense priming in oak seedlings against powdery mildew

Project description:Defense priming sensitises plant defenses to enable a faster and stronger response to subsequent stress. Various chemicals can trigger priming, however the response remains unexplored in oak. Following treatment with salicylic acid (SA), jasmonic acid (JA), or β-aminobutyric acid (BABA), oak (Quercus robur) seedlings were infected with oak powdery mildew (Erysiphe alphitoides, PM). Whilst JA increased susceptibility to PM, BABA and SA enhanced resistance by priming callose deposition and SA-dependent gene expression, respectively. All three treatments had no impact on growth. To characterise molecular markers of priming, untargeted transcriptome and metabolome analyses were performed using RNAseq and LC-MS/MS. Differential gene expression analysis revealed around 2900, 1600, and 900 genes uniquely primed by each treatment BABA, SA, and JA, respectively. A limited number of enriched GO terms differentiated the three treatments. Meanwhile, metabolome analysis found roughly 340, 220, and 40 accumulated masses uniquely primed by BABA, SA, and JA, respectively. Pathway enrichment analysis linked BABA priming to alkaloids biosynthesis, whereas no specific pathways were identified for SA and JA priming. Our results confirm the existence of chemical-induced priming in oak and putatively identify associated molecular markers.

2025-02-28 | GSE277279 | GEO

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