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Cork and holm oak associated oomycete communities

ABSTRACT: Metabarcoding of oomycetes associated with Quercus suber and Q. ilex using cox2 for metabarcoding

PROVIDER: PRJEB27803 | ENA |

REPOSITORIES: ENA

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Dataset's files

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			Action	DRS
	ERR2714300_1.fastq.gz	Fastqsanger.gz
	ERR2714300_2.fastq.gz	Fastqsanger.gz
	ERR2714310_1.fastq.gz	Fastqsanger.gz
	ERR2714310_2.fastq.gz	Fastqsanger.gz
	ERR2714301_1.fastq.gz	Fastqsanger.gz

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Decoding drought tolerance mechanisms in Holm oak (Quercus ilex) throught a combined transcriptomics and proteomics analysis

Project description:Transcript profiling of leaves from Quercus ilex seedlings subjected to well-watering and drought-stress (irrigation withdrawal) conditions

2020-04-03 | GSE145009 | GEO

The impact of drought on phellem development: morpho-physiological adaptations and gene expression dynamics in cork oak stems

Project description:This work aimed to characterize the molecular adaptations occurring in cork oak (Quercus suber) stems in adaptation to drought, and identify key genetic pathways regulating phellem development. One-year-old cork oak plants were grown for additional 6 months under well-watered (WW) or water-deficit (WD) conditions and main stems were targeted for transcriptomic analysis. WD had a negative impact on secondary growth, decreasing the activity of the vascular cambium and phellogen. Following a tissue-specific approach, we analyzed the transcriptional changes imposed by WD in phellem (outer bark), inner bark, and xylem, and found a global downregulation of genes related to cell division, cell wall biogenesis, lignin and/or suberin biosynthesis. Phellem and phloem showed a concerted upregulation of photosynthesis-related genes, suggesting a determinant role of stem photosynthesis in the adaptation of young plants to long-term drought. The data gathered will be important to further harness the diverse genetic background of this species for the development of optimized management practices.

2024-04-29 | E-MTAB-13376 | biostudies-arrayexpress

Quercus

Project description:Quercus ilex, Quercus suber, Quercus ilex x suber Raw sequence reads RADS

| PRJNA505763 | ENA

Decoding drought tolerance mechanisms in Holm oak (Quercus ilex) throught a combined transcriptomics and proteomics analysis

Project description:Drought is considered as a threat to the sustainability of Mediterranean forests and, of the agro-silvo-pastoral “dehesa” system. Holm oak (Quercus ilex L.) is one of the most representative species of these ecosystems and this abiotic stress causes a high tree mortality rate, being more accused at the seedling stage. In this study, an integrative analysis of transcriptome and proteome in leaves of Q. ilex seedlings under drought conditions was carried out to identify gene products involved in the metabolic pathways related to drought tolerant mechanisms.

2022-11-11 | PXD017493 | Pride

Rhytidome- and cork- type barks of holm oak, cork oak and their hybrids highlight processes leading to cork formation

Project description:The periderm is basic for land plants due to its protective role during radial growth, which is achieved by the polymers deposited in the cell walls. Despite the research on the topic has unravelled the role of several enzymes and transcription factors, many questions remain open, especially those regarding cell development. Here we use the outer bark of cork oak (cork), holm oak (rhytidome), and their natural hybrids’ to further understand the mechanisms underlying periderm development. Cork is an outstanding model as it consists of a thick and very homogeneous periderm produced by a permanent mother-cell layer (phellogen). Conversely, holm oak contains a more heterogeneous bark including several thin periderms mixed with phloem, also known as a rhytidome. The inclusion of hybrid samples showing rhytidome-type and cork-type barks is valuable to approach cork development, allowing an accurate identification of candidate genes and processes. The present study underscores that biotic stress and cell death signalling are enhanced in rhytidome-type barks while lipid metabolism and cell cycle are enriched in cork-type barks. Based on the DEGs most expressed related to development, we highlight that cell division, cell expansion, and cell differentiation could account for the differences found between cork and rhytidome-type barks.

2024-06-12 | GSE227020 | GEO

The transcriptome of Oak roots associated with truffles

Project description:Illumina HiSeq technology was used to generate mRNA profiles from mycorrhizal Quercus robur roots. Tuber melanosporum, T. aestivum and T.magnatum mycorrhizal root tips were harvested and used for RNA extraction. Paired-end reads of 100 bp were generated and aligned to Quercus robur CDS using CLC Genomics Workbench 9.

2018-07-01 | GSE97122 | GEO

Quercus suber

Project description:Quercus suber

| PRJNA218877 | ENA

2-DE proteomics analysis of drought treated seedlings of Quercus ilex

Project description:Applying a gel-based proteomic approach, the dynamic changes in root proteins of drought treated Quercus ilex subsp. Ballota [Desf.] Samp. seedlings were followed. Water stress was applied on 20 day-old holm oak plantlets by water limitation for a period of 10 and 20 days, each followed by 10 days of recovery. Root proteins were extracted using trichloroacetate/acetone/phenol protocol and subjected to two-dimensional electrophoresis. Coomassie colloidal stained gel images were analysed and spot intensity data subjected to multivariate statistical analysis. Selected consistent spots in the three biological replicas, presenting significant changes under stress, were subjected to MALDI-TOF mass spectrometry (peptide mass fingerprinting and MS/MS). For protein identification, combined search was performed with MASCOT search engine over NCBInr Viridiplantae and Uniprot databases. Taxonomy Holm oak (Quercus ilex subsp. Ballota [Desf.] Samp.). Dentro de Q. ilex hay dos subespecies, ilex ilex e ilex Ballota.

2015-09-09 | PXD002484 | Pride

Cork oak and climate change: Disentangling drought effects on cork chemical composition.

Project description:Climate change induces in the Mediterranean region more frequent and extreme events, namely, heat waves and droughts, disturbing forest species and affecting their productivity and product quality. The cork oak (Quercus suber) is present along the western Mediterranean basin and its outer bark (cork) is sustainably collected and used for several products, mainly wine bottle stoppers. Since most cork properties arise from its chemical composition, this research studies the effect of drought on cork chemical composition (suberin, lignin, polysaccharides and extractives) and on polysaccharide and suberin monomeric composition. Three sets of cork samples, from the same site, were examined: in one set the cork grew without drought; in another two drought events occurred during cork growth and in the third one drought event happened. The results show that, in general, drought does not affect the proportion of the main components of cork, the monomers of suberin or of polysaccharides, with few exceptions e.g. drought increased ethanol extractives and xylose in polysaccharides and decreased arabinose in polysaccharides. The variability associated to the tree is much more relevant than the effect of drought conditions and affects all the parameters analyzed. Therefore, our research suggests that the tree genetic information, or its expression, plays a much more important role on the chemical composition of cork than the drought conditions occurring during cork growth. In practical terms, the potential increased occurrence of droughts arising from climatic changes will not compromise the performance of cork as a sealant for wine bottles.

| S-EPMC7210947 | biostudies-literature

Quercus suber

Project description:Quercus suber overview

| PRJNA232788 | ENA