Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1076591 | ENA |
REPOSITORIES: ENA
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Project description:White-rot basidiomycete fungi are potent degraders of plant biomass with the ability to mineralize all lignocellulose components. Recent comparative genomics studies showed that these fungi use a wide diversity of enzymes for wood degradation. Deeper functional analyses are however necessary to understand the enzymatic mechanisms leading to lignocellulose breakdown. The Polyporale fungus Pycnoporus coccineus CIRM-BRFM310 grows well on both coniferous and deciduous wood. In the present study we analyzed the early response of the fungus to softwood (pine) and hardwood (aspen) feedstocks.
2016-10-10 | GSE74234 | GEO
Project description:ISR is the initiation of a beneficial association by certain fungi in the rhizosphere followed by the establishment of belowground-aboveground signaling communication may result in the induction of heightened host resistance to foliar and stem pathogens, as well as insect pests.
2019-09-24 | GSE137826 | GEO
Project description:• Reference to published study making use of this data: • Cseke LJ, Tsai C-J, Rogers A, Nelsen MP, White HL, Karnosky DF, Podila GK. (2009) Transcriptomic comparison in the leaves of two aspen genotypes having similar carbon assimilation rates but different allocation patterns under elevated CO2. New Phytologist. submitted. • This study compared the leaf transcription profiles, physiological characteristics, and primary metabolites of two Populus tremuloides genotypes (clones 216 and 271) known to differ in their responses to long-term elevated [CO2] (e[CO2]) at the Aspen FACE site near Rhinelander, WI. • Physiological responses of these clones are similar in photosynthesis, stomatal conductance, and leaf area index under e[CO2] yet very different in growth enhancement (0-10% in clone 216; 40-50% in clone 271). While few genes responded to long-term exposure to e[CO2], the transcriptional activity of leaf e[CO2]-responsive genes was distinctly different between the clones, differentially impacting multiple pathways during both early and late growing seasons. • Analysis of transcript abundance and carbon/nitrogen biochemistry suggests that the CO2-responsive clone (271) partitions C into pathways associated with active defense/response to stress, carbohydrate/starch biosynthesis and subsequent growth. The CO2-unresponsive clone (216) partitions C into pathways associated with passive defense (e.g. lignin, phenylpropanoid) and cell wall thickening. • This study indicates that there is significant variation in expression patterns between different tree genotypes in response to long-term exposure to e[CO2]. Consequently, future efforts to improve productivity or other advantageous traits for carbon sequestration should include an examination of genetic variability in CO2 responsiveness. Keywords: Tree genotype comparison under elevated [CO2]
2009-03-31 | GSE14881 | GEO
Project description:• Reference to published study making use of this data: • Cseke LJ, Tsai C-J, Rogers A, Nelsen MP, White HL, Karnosky DF, Podila GK. (2009) Transcriptomic comparison in the leaves of two aspen genotypes having similar carbon assimilation rates but different allocation patterns under elevated CO2. New Phytologist. submitted. • This study compared the leaf transcription profiles, physiological characteristics, and primary metabolites of two Populus tremuloides genotypes (clones 216 and 271) known to differ in their responses to long-term elevated [CO2] (e[CO2]) at the Aspen FACE site near Rhinelander, WI. • Physiological responses of these clones are similar in photosynthesis, stomatal conductance, and leaf area index under e[CO2] yet very different in growth enhancement (0-10% in clone 216; 40-50% in clone 271). While few genes responded to long-term exposure to e[CO2], the transcriptional activity of leaf e[CO2]-responsive genes was distinctly different between the clones, differentially impacting multiple pathways during both early and late growing seasons. • Analysis of transcript abundance and carbon/nitrogen biochemistry suggests that the CO2-responsive clone (271) partitions C into pathways associated with active defense/response to stress, carbohydrate/starch biosynthesis and subsequent growth. The CO2-unresponsive clone (216) partitions C into pathways associated with passive defense (e.g. lignin, phenylpropanoid) and cell wall thickening. • This study indicates that there is significant variation in expression patterns between different tree genotypes in response to long-term exposure to e[CO2]. Consequently, future efforts to improve productivity or other advantageous traits for carbon sequestration should include an examination of genetic variability in CO2 responsiveness. Keywords: Tree genotype comparison under elevated [CO2] 24 two-channel arrays, directly comparing RNA from trees grown in the ambient (control) [CO2] to RNA derived from the same genotype grown under e[CO2]. For each of 4 experimental conditions (clone 216 early season; clone 271 early season; clone 216 late season; clone 271 late season), three independent biological replicates derived from trees grown in three independent replicate FACE rings were used. In addition, each clone and time point included dye swap reciprocal two-color experiments for each biological replicate. Thus, six data points per cDNA are included (three biological replicates with two technical replicates each).
2009-03-31 | E-GEOD-14881 | biostudies-arrayexpress
Project description:Certain wood decay basidiomycetes, collectively referred to as brown-rot fungi rapidly depolymerize cellulose while leaving behind the bulk of cell wall lignin as a modified residue. The mechanism(s) employed are unclear, but considerable evidence implicates the involvement of diffusible oxidants, particularly hydroxyl radical. Toward a better understanding of this process, we have examined the transcriptome and secretome of Wolfiporia cocos when cultivated on media containing glucose, purified crystalline cellulose, aspen (Populus grandidentata) or lodgepole pine (Pinus contorta) as sole carbon source. Compared to glucose, 39, 331 and 357 genes exhibited 4-fold increases in transcript levels in cellulose, aspen and lodgepole pine, respectively. Mass spectrometry identified peptides corresponding to 64 glycoside hydrolase (GH) proteins and, of these, 17 corresponded to transcripts upregulated on one or both woody substrates. Most of these genes were broadly categorized as hemicellulases or chitinases. Consistent with an important role for ·OH in cellulose depolymerization, high transcript levels and upregulation were observed for genes involved in iron homeostasis, iron reduction and extracellular peroxide generation. These patterns of regulation differ markedly from the closely related brown rot fungus, Postia placenta, and expand the number of enzymes potentially involved in the oxidative depolymerization of cellulose. Medium containing glucose, microcrystalline cellulose, ground aspen or ground lodgepole pine was inoculated with W. cocos. RNA was purified from cultures. Single read 100 bp Illumina runs were performed.
2016-04-13 | E-GEOD-78007 | biostudies-arrayexpress
Project description:Previous studies have shown that a considerable proportion of the Arabidopsis genome cycles under circadian and/or diurnal conditions (Edwards et al., 2006 PMID: 16473970, Blaesing et al., 2005 PMID 16299223). It is likely that the correct phasing of gene expression plays an important role in improving the growth of the model plant (Dodd et al., 2005 PMID: 16040710). A key question is whether similar regulation is occurring in other higher plant species. In this study we measure the diurnal expression pattern of genes in the T89 clone of the hybrid aspen (Populus tremula L. x P. tremuloides Michx.) using the Affymetrix Poplar array. Samples (leaf blades) were taken at 4h intervals over the course of 2 diurnal cycles (18h Light: 6h Dark). Time-points were labelled relative to dawn (time 0) on the first day of sampling. T89 was selected as it has routinely been used for genetic modification since 1992 (Nilsson et al.) and is the genetic background for a large number of transgenic trees created in order to investigate the function of aspen genes, providing potential for genetic manipulations during our further studies. We also measured the diurnal expression pattern of genes in trees with a compromised circadian clock. Trees with less expressed LATE ELONGATED HYPOCOTYL 1 (LHY1) and LHY2 by RNA interference (lhy) line that was created in T89 clone of the aspen hybrid (Populus tremula L. x P. tremuloides Michx.) using the Affymetrix Poplar array. Samples (leaf blades) were taken at 4h intervals over the course of 2 diurnal cycles (18h Light: 6h Dark) as described above. Thus, time-points are labelled relative to dawn (time 0) on the first day of sampling. The data obtained from using a RNAi line in central Clock components complements the study of wild type T89, since they were grown and sampled at the same time under the same conditions.
2018-03-13 | E-MTAB-4516 | biostudies-arrayexpress