Changes in the sap proteome of Eucalyptus grandis and Eucalyptus urophylla plants grown at elevated CO2 atmosphere
Ontology highlight
ABSTRACT:
INSTRUMENT(S):
ORGANISM(S): Eucalyptus Urophylla Eucalyptus Grandis
TISSUE(S): Vascular Cambium
SUBMITTER: 
Felipe Silva
LAB HEAD: Tiago Santana Balbuena
PROVIDER: PXD050082 | Pride | 2025-05-30
REPOSITORIES: Pride
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| GRA1680.raw | Raw | |||
| GRA1C.raw | Raw | |||
| GRA2680.raw | Raw | |||
| GRA2C.raw | Raw | |||
| GRA3680.raw | Raw |
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Project description:We present a label free proteome dataset of the vascular sap proteome of three commercially important Eucalyptus species (Eucalyptus camaldulensis, Eucalyptus grandis and Eucalyptus urophylla). Protein extraction from the vascular system was carried out using a pressure bomb, in solution digested and peptides were analyzed using a Q-Exactive instrument. Protein identification was carried out using stringent database searches and only in silico predicted extracellular proteins were considered as part of the sap proteome. The results here described can be used as a reference for the proteome sap analysis of Eucalyptus plants grown under different conditions.
2025-05-30 | PXD037915 | Pride
Project description:Background: Eucalyptus species and interspecific hybrids exhibit valuable growth and wood properties that make them a highly desirable commodity. However, these trees are challenged by a wide array of biotic stresses during their lifetimes. The Eucalyptus grandis reference genome sequence provides a resource to study pest and pathogen defence mechanisms in long-lived woody plants. E. grandis trees are generally susceptible to Chrysoporthe austroafricana, a causal agent of stem cankers on eucalypts. The aim of this study was to characterize the defence response of E. grandis against C. austroafricana. Results: Hormone profiling of susceptible and moderately resistant clonal E. grandis genotypes indicated a reduction in salicylic acid and gibberellic acid levels at 3 days post inoculation. We hypothesized that these signaling pathways may facilitate resistance. To further investigate other defence mechanisms at this time point, transcriptome profiling was performed. This revealed that cell wall modifications and response to oxidative stress form part of the defence responses common to both genotypes, whilst changes in the hormone signaling pathways may contribute to resistance. Additionally the expression of selected candidate defence response genes was induced earlier in moderately resistant trees than in susceptible trees, supporting the hypothesis that a delayed defence response may occur in the susceptible interaction. Conclusion: The ability of a host to fine-tune its defence responses is crucial and the responses identified in this study extends our understanding of plant defence, gained from model systems, to woody perennials. E. grandis trees were stem inoculated with C. austroafricana. RNA was extracted from stem material harvested 3 days post inoculation for transcriptome profiling. Three biological replicates of harvested material was sent for RNA-sequencing
2015-04-03 | E-GEOD-67554 | biostudies-arrayexpress
Project description:Eucalyptus grandis e Eucalyptus globulus are among the most widely cultivated trees, differing in lignin composition and plantation areas. As temperature is a key modulator in plant metabolism, a large-scale proteome analysis was carried out to investigate changes induced in plantlets grown at different temperatures.
2017-09-25 | PXD005743 | Pride
Project description:Histone modifications play an integral role in plant development, but have been poorly studied in woody plants. Investigating chromatin organization in wood-forming tissue and its role in regulating gene expression allows us to understand the mechanisms underlying cellular differentiation during xylogenesis (wood formation) and identify novel functional regions in plant genomes. However, woody tissue poses unique challenges for using high-throughput chromatin immunoprecipitation (ChIP) techniques for studying genome-wide histone modifications in vivo. We investigated the role of the modified histone H3K4me3 (trimethylated lysine 4 of histone H3) in gene expression during the early stages of wood formation using ChIP-seq in Eucalyptus grandis, a woody biomass model. Plant chromatin fixation and isolation protocols were optimized for developing xylem tissue collected from field-grown E. grandis trees. A “nano-ChIP-seq” procedure was employed for ChIP DNA amplification. Over 9 million H3K4me3 ChIP-seq and 18 million control paired-end reads were mapped to the E. grandis reference genome for peak-calling using Model-based Analysis of ChIP-Seq. The 12,177 significant H3K4me3 peaks identified covered ~1.5% of the genome and overlapped some 9,623 protein-coding genes and 38 noncoding RNAs. H3K4me3 library coverage, peaking ~600 - 700 bp downstream of the transcription start site, was highly correlated with gene expression levels measured with RNA-seq. Overall, H3K4me3-enriched genes tended to be less tissue-specific than unenriched genes and were overrepresented for general cellular metabolism and development gene ontology terms. Relative expression of H3K4me3-enriched genes in developing secondary xylem was higher than unenriched genes, however, and highly expressed secondary cell wall-related genes were enriched for H3K4me3 as validated using ChIP-qPCR. In this first genome-wide analysis of a modified histone in a woody tissue, we developed optimized a ChIP-seq procedure suitable for field-collected samples. In developing E. grandis xylem, H3K4me3 enrichment is an indicator of active transcription, consistent with its known role in sustaining pre-initiation complex formation in yeast. The H3K4me3 ChIP-seq data from this study paves the way to understanding the chromatin landscape and epigenomic architecture of xylogenesis in plants, and complements RNA-seq evidence of gene expression for the future improvement of the E. grandis genome annotation. Examination of H3K4me3 in developing secondary xylem tissue from two clonal individuals of E. grandis growing in the field
2015-04-15 | E-GEOD-67873 | biostudies-arrayexpress
Project description:Chloroplast is a subcellular compartment in which solar radiation is used to generate simple sugar compounds in a complex process named photosynthesis. It is very sensitive to environmental fluctuations and your development is intimately related with the development of the whole plant at different stages. Seasonal climate variations can also drive plant growth and development, favoring a metabolic adaptation of the life cycle with changes in the environment. The characterization of chloroplast proteome dynamics can contribute to a better understanding about the mechanisms involved in leaf development process and seasonal variations in this compartment. Therefore, the goal of this studied was to carried out an exploratory analysis of chloroplast alterations during leaf development and seasonal variations in Eucalyptus grandis chloroplast proteome.
2022-10-28 | PXD029004 | Pride
Project description:Purpose: Water stress limits plant survival and production in many parts of the world. Identification of genes and alleles responding to water stress conditions is important in breeding plants better adapted to drought. Currently there are no studies examining the transcriptome wide gene and allelic expression patterns under water stress conditions. We used RNA sequencing (RNA-seq) to identify the candidate genes and alleles and to explore the evolutionary signatures of selection Methods: We studied the effect of water stress on gene expression in Eucalyptus camaldulensis seedlings derived from three natural populations. We used reference-guided transcriptome mapping to study gene expression. Reads mapping to predicted transcripts were analysed with edgeR pacakge to study differntial expression of genes under control and water-stress conditions. SNPs within the genes were obtained using pileup file generated with samtools and the SNP frequencies were analysed with VarScan package. SNPs were further characterised as sysnonymous and non-synonymous using popoolation2 pacakge. Results: Several genes showed differential expression between control and stress conditions. Gene ontology (GO) enrichment tests revealed up-regulation of 140 stress-related gene categories and down-regulation of 35 metabolic and cell wall organisation gene categories. More than 190,000 single nucleotide polymorphisms (SNPs) were detected and 2737 of these showed differential allelic expression. Allelic expression of 52% of these variants was correlated with total gene expression. Signatures of selection patterns were studied by estimating the proportion of nonsynonymous to synonymous substitution rates (Ka/Ks). The average Ka/Ks ratio among the 13,719 genes was 0.39 indicating that most of the genes are under purifying selection. Among the positively selected genes (Ka/Ks > 1.5) apoptosis and cell death categories were enriched. Of the positively selected genes, ninety genes showed differential expression and 27 SNPs from 17 positively selected genes showed differential allelic expression between treatments. Conclusions: Correlation of allelic expression of several SNPs with total gene expression indicates that these variants may be the cis-acting variants or in linkage disequilibrium with such variants. Enrichment of apoptosis and cell death gene categories among the positively selected genes reveals the past selection pressures experienced by the populations used in this study. Leaf mRNA of 12 samples were used to study the gene expression under control and water-stress conditions. Three samples under water-stress conditions and three samples under control conditions were used as biological replicates for differenctial gene expression between the treatments. High-throughput sequence reads from mRNA samples were generated by deep sequencing with Illumina GAIIx.
2012-07-17 | E-GEOD-39369 | biostudies-arrayexpress
Project description:Over recent decades the progression of natural autumnal senescence has been increasingly delayed across wide areas of the Northern Hemisphere and is thought to be caused by rising temperature. Recently this delay has been shown to be partly attributable to rising atmospheric carbon dioxide concentrations [CO2]. Here, for the first time, we present a possible mechanistic explanation for this phenomenon. Using a plantation of Populus x euramericana grown at elevated [CO2] (e[CO2]) using Free-Air CO2 Enrichment (FACE) technology, we investigated the molecular and biochemical basis underlying this response. Using a poplar cDNA microarray where late growing season and senescing leaves from ambient [CO2] (a[CO2]) and e[CO2] were compared, revealed unique increases and decreases in transcript abundance in the e[CO2] treatment. Growth at e[CO2]caused the greatest increase in the abundance of transcripts catalysing steps in the anthocyanin biosynthetic pathway and an increase in leaf anthocyanin content. Leaf sucrose and starch content were also increased during senescence in e[CO2] and associated with a higher abundance of transcripts in the sucrose and starch biosynthetic pathways. We propose that in e[CO2], autumnal photosynthesis and sugar accumulation results in changes in genes expression that include further investment in secondary carbon metabolism leading to anthocyanin production. This enables prolonged leaf longevity during natural autumnal senescence through increased availability of carbon and improved stress tolerance while in contrast this may also have a negative effect on the control of dormancy. Samples GSM398292..GSM398314 (late senescence samples only): Six replicate trees were labelled in the unfertilised sub-plots of plots 1-4 in the POP/EUROFACE site (http://www.unitus.it/euroface/) and the 10th leaf down from the closed apical bud of the dominant branch were labelled. Leaves were sampled to liquid nitrogen (18th October 2004) and stored at -80 oC. Extracted RNA was tested for quality and quantity and of that passing the test equal quantities of RNA from each replicate were taken and each sample from the control plots (plots 2 and 3) were randomly paired with a sample from and elevated CO2 plot (plots 1 and 4). From the resulting 9 dual channel hybridisations 6 had the control sample in the Cy3 channel and 3 had the elevated CO2 sample in the Cy3 channel. The 6 samples with Cydye orientation as Cy3=control (ambient CO2) and Cy5 = treated (elevated CO2) are as follows: GSM398296, GSM398301, GSM398303, GSM398304, GSM398305 and GSM398306. The 3 samples with dye swap i.e Cy3 = treated (elevated CO2) are as follows and Cy5 = control (ambient CO2) are as follows: GSM398292, GSM398313 and GSM398314. Samples GSM398426..GSM398474: Four replicate leaves per sub-plot were sampled and flash frozen into liquid nitrogen, on 31 August 2004, and prior to visible senescence but around the time of bud-set as given by Calfapietra et al., (2003) [1]. The tenth leaf down the dominant stem (which represented the first fully expanded mature leaf of maximum size) from a reference leaf of 30 mm in length (leaf one) were selected. On the 14th September twenty trees from within each experimental plot were taken. The tenth leaf down the dominant stem (which represented the first fully expanded mature leaf of maximum size) from a reference leaf of 30 mm in length (leaf one) were labelled on the main-stem above the petiole. All labelled leaves were a uniform height (approx 0.3 m) from the canopy top across all treatments and not shaded by the canopy. Four replicate leaves from within each sub-plot were sampled during each harvest (except on 18th October when six replicate leaves were sampled). Each sampling time was restricted to two hours within the same day and across sampling day’s uniform cloud free skies were chosen. September samplings took place between 15.00 and 17.00 when climatic variables were generally consistent; later in the season time of sampling was adjusted to an earlier two hour period after mid-day when climatic variables were generally consistent. A chlorotic canopy was evident in plots five and six, as described by Liberloo et al. (2007) therefore any subsequent analysis was for plots one to four only. Six replicate labelled leaves were sampled (as above) from each sub-plot on 18th October 2004
2010-01-31 | E-GEOD-15874 | biostudies-arrayexpress
Project description:Adventitious rooting (AR) is an obligatory step for vegetative propagation of commercial woody species. Paper industries have interest in Eucalyptus globulus Labill and its hybrids due to low lignin and lipid contents, which facilitate cellulose extraction. However, this species and some of its hybrids are recalcitrant to rooting, often requiring exogenous auxin supply. Here we performed a comparative analysis of proteome changes during AR of E. globulus and the easy-to-root species Eucalyptus grandis W. Hill and the effects of exogenous auxin in different phases of the process (induction and formation), using a label-free quantification method. We identified 398 differentially abundant proteins, which were predicted to be involved in different biological pathways, mainly oxidative stress, energy metabolism and photosynthesis. Notable differences between species included proteins involved in oxidative stress, carbon and secondary metabolism. Exogenous auxin appeared to affect the availability of carbon sources and other phytohormones, besides cell cycle and microtubule- related proteins. Important players were also identified in each phase of AR. This is the first in depth analysis of protein changes during AR in Eucalyptus. The findings can be used in future studies to evaluate rooting competence in different genotypes and provide leads for AR improvement.
2019-08-19 | PXD013924 | Pride
Project description:Adventitious rooting (AR) is an obligatory step for vegetative propagation of commercial woody species. Paper industries have interest in Eucalyptus globulus Labill and its hybrids due to low lignin and lipid contents, which facilitate cellulose extraction. However, this species and some of its hybrids are recalcitrant to rooting, often requiring exogenous auxin supply. Here we performed a comparative analysis of proteome changes during AR of E. globulus and the easy-to-root species Eucalyptus grandis W. Hill and the effects of exogenous auxin in different phases of the process (induction and formation), using a label-free quantification method. We identified 398 differentially abundant proteins, which were predicted to be involved in different biological pathways, mainly oxidative stress, energy metabolism and photosynthesis. Notable differences between species included proteins involved in oxidative stress, carbon and secondary metabolism. Exogenous auxin appeared to affect the availability of carbon sources and other phytohormones, besides cell cycle and microtubule- related proteins. Important players were also identified in each phase of AR. This is the first in depth analysis of protein changes during AR in Eucalyptus. The findings can be used in future studies to evaluate rooting competence in different genotypes and provide leads for AR improvement.
2019-08-19 | PXD013925 | Pride
Project description:Eucalyptus rust is caused by the biotrophic fungus, Austropuccinia psidii, which affects commercial plantations of Eucalyptus, a major raw material for the pulp and paper industry in Brazil. Aiming to uncover the molecular mechanisms involved in rust resistance and susceptibility in Eucalyptus grandis, we used epifluorescence microscopy to follow the fungus development inside the leaves of two contrasting half-sibling genotypes (rust-resistance and rust-susceptible), to determine the time-course for comparative metabolomic and proteomic analyses in plantlets artificially inoculated with rust. Within 24 hours of complete fungal invasion, a total of 709 plant metabolites showed that the rust-resistant genotype suppressed many metabolites 6 hours after inoculation (hai), with responses being progressively induced after 12 hai. In contrast, the rust-susceptible genotype displayed an alternated metabolite response to infection, which culminated in a strong suppression at 24 hai. Multivariate analyses of genotypes and time points were used to select 16 differential metabolites chemically classified as flavonoids, benzenoids and other compounds. Applying the Weighted Gene Co-Expression Network Analysis (WGCNA), rust-resistant and rust-susceptible genotypes had, respectively, 871 and 852 proteins grouped into 14 and 13 modules, of which 10 and 7 protein modules were significantly correlated to the selected metabolites. Functional analyses revealed roles for oxidative-dependent responses leading to temporal activity of metabolites and proteins after 12 hai in rust-resistance, while the initial over-accumulation of metabolites and correlated proteins caused a lack of progressive response after 12 hai in rust-susceptible genotype. This study provides a brief understand on the temporal divergences of resistant and susceptible molecular responses of E. grandis plants to rust.
2021-09-09 | PXD021280 | Pride