Ontology highlight
ABSTRACT:
PROVIDER: PRJNA565538 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR10120332_1.fastq.gz | Fastqsanger.gz | |||
| SRR10120332_2.fastq.gz | Fastqsanger.gz | |||
| SRR10120333_1.fastq.gz | Fastqsanger.gz | |||
| SRR10120333_2.fastq.gz | Fastqsanger.gz | |||
| SRR10120334_1.fastq.gz | Fastqsanger.gz |
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Project description:Ectomycorrhizal fungi are dependent on host trees for carbon supply. In return ectomycorrhizal fungi supply trees with water and nutrients. It is known that when ectomycorrhizal fungi have exploited a nutrient rich patch in soil, the carbon allocation to mycelia in that patch is reduced, with the consequence of mycelia dying, but less is known of the dynamics of this senescence. We cultivated the ectomycorrhizal fungus Paxillus involutus in an axenic system. We collected growth and transcriptome data at different stages of carbon starvation during fungal growth. Carbon starvation induced a decrease in fungal biomass, which coincided with the release of NH4+ and the expression of genes connected with autophagy as well as protease and chitinase activity. Monoaromatic compounds, chitin and protease activity was detected in the liquid growth media during carbon starvation. The exudation of NH4+ and increase of monoaromatic compound during C starvation suggests senescence and autolysis of P. involutus. Together with the upregulation of genes involved in autophagy, chitinase and endopeptidase activity this points towards a controlled senescence including recycling of compounds originating from the fungi. Reduced C allocation to ectomycorrhizal mycelia in recently depleted nutrient patches in forest soils must be of ubiquitous nature. Understanding the mechanisms during exploitation of nutrients by ectomycorrhizal fungi is of great importance for understanding carbon and nutrient dynamics in forest soils. This is to our knowledge the first study describing the carbon starvation response in an ectomycorrhizal fungus.
2014-04-01 | GSE54940 | GEO
Project description:Ectomycorrhizal fungi are dependent on host trees for carbon supply. In return ectomycorrhizal fungi supply trees with water and nutrients. It is known that when ectomycorrhizal fungi have exploited a nutrient rich patch in soil, the carbon allocation to mycelia in that patch is reduced, with the consequence of mycelia dying, but less is known of the dynamics of this senescence. We cultivated the ectomycorrhizal fungus Paxillus involutus in an axenic system. We collected growth and transcriptome data at different stages of carbon starvation during fungal growth. Carbon starvation induced a decrease in fungal biomass, which coincided with the release of NH4+ and the expression of genes connected with autophagy as well as protease and chitinase activity. Monoaromatic compounds, chitin and protease activity was detected in the liquid growth media during carbon starvation. The exudation of NH4+ and increase of monoaromatic compound during C starvation suggests senescence and autolysis of P. involutus. Together with the upregulation of genes involved in autophagy, chitinase and endopeptidase activity this points towards a controlled senescence including recycling of compounds originating from the fungi. Reduced C allocation to ectomycorrhizal mycelia in recently depleted nutrient patches in forest soils must be of ubiquitous nature. Understanding the mechanisms during exploitation of nutrients by ectomycorrhizal fungi is of great importance for understanding carbon and nutrient dynamics in forest soils. This is to our knowledge the first study describing the carbon starvation response in an ectomycorrhizal fungus. A one-chip study (data from 12 subarrays collected from a 12-plex Nimblegen microarray (ID 527890) using total RNA recovered from three separate glass-bead cultures of Paxillus involutus (ATCC200175) grown on Minimum Melin Norkrans medium (MMN) amended with ammonium (C/N ratio 3) and harvested at different times of carbon starvation.)
2014-04-01 | E-GEOD-54940 | biostudies-arrayexpress
Project description:Young Fagus sylvatica trees (approximately 7 to 8 years) were collected from a natural regeneration beech forest. The trees were excavated with intact soil cores, roots and top organic layer. The trees were then kept outdoors at the Department of Forest Botany, Georg-August-Universität Göttingen. Plants were protected from rain, and light conditions were matched to those of the natural stand using a shading net; otherwise, plants were exposed to natural climatic conditions. The soil moisture was regularly measured; plants were watered with deionized water as needed to keep soil moisture close to the original conditions. Trees was randomly relocated on a weekly basis throughout the experiment to avoid biasses caused by location or light effects. After 21 weeks, a treatment was applied to understand the physiological mechanisms of inorganic nitrogen uptake and assimilation under conditions of an inorganic nitrogen saturated forest simulation: Plants were fertilized with either a 20 mM solution of KNO3, a 20 mM solution of NH4Cl, or demineralized water (control) for 2 days. On the third day, the trees were harvested. Root tips were immediately shock-frozen in liquid nitrogen and used for RNA extraction.
2020-12-14 | E-MTAB-8931 | biostudies-arrayexpress
Project description:Wood stiffness is the most important wood quality trait of forest trees for structural timber production. We investigated genes differentially transcribed in radiate pine trees with distinct wood stiffness using bulked segregant analysis (BSA) and cDNA microarrays. Transcript accumulation in earlywood (EW) and latewood (LW) of high (HS) and low stiffness (LS) trees in two progeny trials was compared.
2011-06-01 | GSE23020 | GEO
Project description:ARDS-mediated lung transcriptome alterations were identified in forest musk deer. Moreover, multiple transcripts/genes involved in lung development and lung defense responses to bacteria/viruses/fungi in ARDS were filtered out in forest musk deer.
2022-10-19 | GSE191259 | GEO
Project description:Many trees form ectomycorrhizal symbiosis with fungi. During symbiosis, the tree roots supply sugar to the fungi in exchange for nitrogen, and this process is critical for the nitrogen and carbon cycles in forest ecosystems. However, the extents to which ectomycorrhizal fungi can liberate nitrogen and modify the soil organic matter and the mechanisms by which they do so remain unclear since they have lost many enzymes for litter decomposition that were present in their free-living, saprotrophic ancestors. Using time-series spectroscopy and transcriptomics, we examined the ability of two ectomycorrhizal fungi from two independently evolved ectomycorrhizal lineages to mobilize soil organic nitrogen. Both species oxidized the organic matter and accessed the organic nitrogen. The expression of those events was controlled by the availability of glucose and inorganic nitrogen. Despite those similarities, the decomposition mechanisms, including the type of genes involved as well as the patterns of their expression, differed markedly between the two species. Our results suggest that in agreement with their diverse evolutionary origins, ectomycorrhizal fungi use different decomposition mechanisms to access organic nitrogen entrapped in soil organic matter. The timing and magnitude of the expression of the decomposition activity can be controlled by the below-ground nitrogen quality and the above-ground carbon supply.
2018-11-30 | GSE110485 | GEO
Project description:An attractive objective in the breeding of forest trees is to reduce the content of lignin or alter the lignin composition. However, for long-lived forest trees, such as conifers, it is time consuming and expensive to wait until mature wood is formed for estimating how different ligninfication genes affect cell wall differentiation. The aim of this work was to examine the possibility of detecting changes in global gene expression and of genes involved in lignin biosynthesis already in embryogenic cultures carrying the native Norway spruce cinnamoyl CoA reductase (CCR) gene in antisense orientation. Several genes, including genes regulating phenylalanine ammonia-lyase and peroxidase, regulating different pathways associated with lignin biosynthesis were affected but the transcript abundances of genes regulating lignin biosynthesis were not affected. Functional assignment defined by Gene Ontology terms, which provide functional classification for genes and gene products representing their corresponding biological process, cellular component and molecular function showed that transformation with asCCR affects a broad spectrum of functional categories, especially processes taking place in the cell wall. Furthermore, many changes in genes related to chromatin, DNA and chromosome take place. Keywords: transgenic Norway spruce, embryogenic culture
2006-12-27 | GSE6524 | GEO
Project description:Climate change forecasts increase the susceptibility of forest due to longer drier seasons. The adaptive management protocols have highlighted the reduction of the forest densification to improve their vulnerability to extreme climate events (i.g. drought). One of this sensitive woody species to climate change is the Abies pinsapo, a relic conifer tree endemic from the southern Spain. Previous works have shown changes in their trends because of the climate change action, being carried out experimental thinning management in their lowest distribution limit, in Sierra de las Nieves Natural Park (Malaga). Our objective is to evaluate the water improvements of thinned trees in terms of light availability by means of a shading treatment in those thinned trees. To do that we have evaluated the synergic effect of ecophysiology, metabolomics and transcriptomics in control, thinning and thinning+shading plots in wet and dry seasons for two years. The results showed strong differences between summer and spring seasons at the three studied levels. The water deficit shows a greater influence than light exposure in the ecophysiology and metabolomics tree response. And the transcriptomics suggested an improvement of thinned trees when light exposure was reduced. Our results support the necessity of adaptive forest management in order to improve the conservation status of A. pinsapo forest. The combination of different levels of tree response is paramount to understand and predict the tree physiology under water and light stress conditions.
2022-07-17 | GSE208073 | GEO
Project description:Understanding of mechanisms of resistance of forest trees against microbial pathogens is an essential prerequisite for the development of sustainable forestry practices and for the improvement of commercially-grown trees via either conventional breeding or rational genetic engineering. We have studied the transcriptional response of Scots pine trees to Heterobasidion annosum infection under field conditions. By comparing responses of trees to wounding and to fungal inoculation we could identify a set of genes that were specifically responding to fungal infection. We have also investigated a contribution of Scots pine antimicrobial protein Sp-AMP2 to the host antimicrobial defense to evaluate the potential of Sp-AMP genes as molecular markers for resistance breeding.
2017-12-31 | GSE87881 | GEO