Transcriptome response to embolism in stems of P. trichocarpa
Ontology highlight
ABSTRACT:
ORGANISM(S): Populus sp. Populus trichocarpa
PROVIDER: GSE32322 | GEO | 2011/09/23
SECONDARY ACCESSION(S): PRJNA147271
REPOSITORIES: GEO
Similar Datasets
Project description:Embolism and the refilling of xylem vessels are intrinsic to the ability of plants to handle the transport of water under tension. While the formation of an embolized vessel is an abiotic process, refilling against the pressure gradient requires biological activity to provide both the energy and the water needed to restore xylem transport capacity. We used microarrays to analyze the global transcriptome response of xylem parenchyma cells after embolism formation or infiltration of xylem tissue with sucrose solution. Plants subjected to artificial embolism treatment (ET), to sucrose infiltration treatment (ST), and controls (C) were selected for RNA extraction and hybridization on Affymetrix microarrays. Embolism was artificially induced through air-injection into the stems of the ET plants, while ST plants were exposed to osmotic stress by adding sucrose to the growing solution. Woody stems were respectively collected 90 minutes following the injection and after 90 minutes of exposure to sucrose.
2011-09-22 | E-GEOD-32322 | biostudies-arrayexpress
Project description:PtrHSFB3-1 and PtrMYB092 are xylem specific genes in xylem of P. trichocarpa, and their expression levels are down regulated most significantly in tension wood. These two transcription factors were transiently overexpressed in stem differentiating xylem (SDX) of P. trichocarpa , and transcriptomic sequencing was performed to identify the regulatory effects of the two transcription factors on wood formation related genes.
2020-07-11 | GSE154167 | GEO
Project description:To identify genes that are drought-responsive we conducted drought (soil water depletion) experiments on 3-month-old *P*. *trichocarpa *clonal plants. The plants undergo five different stages based on the appearance of their shoots and leaves during the drought experiments. Stage I: The shoot and leaves are green, and the leaves are well-spread. Stage II: The leaves are droopy. Stage III: The shoot is droopy, and the leaves are partially dry. Stage IV: The leaves are brown and totally dry. Stage V: The shoot is brown. With fully irrigation, the soil water content is 74% and the xylem water content is 80.6%. Plants in Stage III (Day 5) are under a mild drought state. The soil and xylem water content in Stage III dropped to 33% and 75.3%, respectively. Stage IV (Day 6-10) is a severe drought state where the soil and xylem water content continued decreasing to 29% and 74.3%, respectively in Day 7. The stressed plants from Stage I-IV could all recover in 3 days after rehydration, but the plants in Stage V could not recover after rehydration.
2018-12-27 | GSE79401 | GEO
Project description:We studied the changes that occur in gene transcription and the biosynthesis of cell-wall-related compounds during xylogenesis in Populus trichocarpa pioneer roots and stems. Transcriptional profiling was conducted with the use of microarrays to identify genes involved in xylem formation. Pioneer roots were examined in segments corresponding to their developmental stage: apical meristem (PR1), primary development (PR2), and secondary development (PR3). Comparative segments were used to analyze xylogenesis in stems: apical meristem with primary development (PS1), secondary development (PS2), and isolated secondary xylem (PS3). Results indicated that only approximately 10% of the genes that were identified to be differentially expressed during xylogenesis were common to both pioneer roots and stems. Despite the dissimilarity in gene expression, however, many fundamental mechanisms were similar, e.g. the pattern of expression of genes involved in the biosynthesis of cell wall proteins, polysaccharides and lignins. While hemicellulose degradation was typical for stems, possibly due to the intensive level of cell wall lignification. Our study is the first to conduct a comprehensive analysis, at the structural and molecular level, of xylogenesis, and clearly reveals the great complexity of molecular mechanisms underlying cell wall formation and modification during xylogenesis.
2019-10-14 | GSE126842 | GEO
Project description:affy_rewatering_poplar - rewatering - Biological question (15 lines max): Xylogenesis is a complex process and is highly influenced by environmental factors. Numerous studies have shown xylem structural acclimation to moderate and long-lasting water deficits. A decrease in cell lumen size and an increase in vessel density are generally observed. Other preliminary experiments in our laboratory focusing on a short and progressive drought-rewatering cycle in poplar show a gradual decrease in fibre size with decreasing water availability and an important rise in vessel number with irrigation recovery. This suggests a reorientation during the early stages of cambial derivatives differentiation towards vessel formation. The aim of this study is to characterize global gene expression in young differentiating xylem of poplar in response to a drought-rewatering cycle. Results should provide a comprehensive genomic basis for the xylem structural modifications observed.-The experimental design consisted in a differential water supply. Experiments were done on tilted trees to induce tension wood formation. Trees were regularly irrigated at full capacitance until July 18, 2007, the beginning of the experiment. Two sets of plants were designed. For each set, irrigation was withheld until July 25, 2007. At this time, one of the two sets (treated-sample) was re-irrigated at full capacitance during 14hrs (WDR) while the other one was maintained under water deficit (WD). Samples were collected after the 14hrs for all trees. Keywords: treated vs untreated comparison 6 arrays - poplar
2010-06-16 | E-GEOD-20061 | biostudies-arrayexpress
Project description:affy_rewatering_poplar - rewatering - Biological question (15 lines max): Xylogenesis is a complex process and is highly influenced by environmental factors. Numerous studies have shown xylem structural acclimation to moderate and long-lasting water deficits. A decrease in cell lumen size and an increase in vessel density are generally observed. Other preliminary experiments in our laboratory focusing on a short and progressive drought-rewatering cycle in poplar show a gradual decrease in fibre size with decreasing water availability and an important rise in vessel number with irrigation recovery. This suggests a reorientation during the early stages of cambial derivatives differentiation towards vessel formation. The aim of this study is to characterize global gene expression in young differentiating xylem of poplar in response to a drought-rewatering cycle. Results should provide a comprehensive genomic basis for the xylem structural modifications observed.-The experimental design consisted in a differential water supply. Experiments were done on tilted trees to induce tension wood formation. Trees were regularly irrigated at full capacitance until July 18, 2007, the beginning of the experiment. Two sets of plants were designed. For each set, irrigation was withheld until July 25, 2007. At this time, one of the two sets (treated-sample) was re-irrigated at full capacitance during 14hrs (WDR) while the other one was maintained under water deficit (WD). Samples were collected after the 14hrs for all trees. Keywords: treated vs untreated comparison
2010-06-03 | GSE20061 | GEO
Project description:Water transport is required for photosynthesis; thus plant vascular development must proceed such that water demands can be met during formation of new organs. Precise regulation of the balance between cell proliferation and differentiation in the cambial meristem defines formation of xylem and phloem, which constitute the vascular tissues. The TDIF-PXY/TDR signalling pathway is central to this process1. Peptide ligand, TDIF, encoded by CLE41 and CLE44 2, activates PXY/TDR receptors to maintain proliferative cambium. Cambium cells differentiate to xylem or phloem in the absence of active TDIF-PXY/TDR complexes. Vascular development is stimulated by light. After gemination, light induces the establishment of photoautotrophic growth via photosynthesis. Consequently, the differentiation of vascular cells must occur to favour the transport of water and minerals from the soil to the green tissues and newly developing organs. Plants perceive light through the action of photoreceptors, which modulate the activity of the transcription factors that orchestrate development. Despite the association between light signalling and vascular development, molecular mechanisms linking the two are unknown. Our work shows that vascular differentiation is inhibited in the dark by a mechanism that depends on PIF transcription factors. The dark accumulation of PIFs is necessary for CLE44 induction and thus maintenance of undifferentiated vasculature. In illuminated environments, PIF inactivation by photoreceptors causes a decrease in CLE44 expression. CLE44 reduction, in turn, leads to reduced PXY/TDR signalling which induces the xylem differentiation required to fulfil the water demands associated with photoautotrophic development.
2022-07-18 | GSE178268 | GEO
Project description:The plant xylem tissue is responsible for water transportation, mechanical support and lateral growth, and can be utilized as wood. The seed plant xylem has a radial system composed of ray parenchyma cells and an axial system of fusiform cells, including tracheids in gymnosperms and vessel elements and libriform fibers in angiosperms. Little is known about the developmental programs and evolutionary relationships of these xylem cell types. Here we show that the radial and axial systems of stem-differentiating xylem are differentially conserved across four divergent woody angiosperms. Through transcriptomic profiling of single cells and cell-type regions isolated by laser capture microdissection, we identified cell types corresponding to single-cell clusters in Populus trichocarpa. Cross-species analyses of single-cell trajectories demonstrated highly conserved development in ray lineages across angiosperms. While the core eudicots P. trichocarpa and Eucalyptus grandis share nearly identical fusiform cell lineages, the tracheids in the basal eudicot Trochodendron aralioides, an evolutionarily reversed character, exhibited an expression pattern highly similar to that of vessel elements. It suggests that water transportation, instead of mechanical support, is the dominant feature of tracheary elements. Furthermore, we found that the more basal angiosperm Liriodendron chinense has a distinct fusiform lineage. This evo-developmental framework of xylem cell lineages provides a comprehensive understanding of the formation of the most abundant tissue on Earth.
2022-12-25 | GSE180121 | GEO
Project description:affy_popsec_orleans_poplar - xyleme - This project aims to identify candidate genes for water deficit acclimation and/or adaptation in a tree species: poplar. Due to compelling evidence that transcriptional regulation plays a major role in regulating many biological processes, we will look for genes and gene expression networks related to drought stress. We intend to analyse the transcriptome in two poplar genotypes of contrasted tolerance to water deficit, at various stages and intensities of stress and simultaneously in whole xylem and cambial zone from young trees. The co-analysis of two genotypes of contrasted tolerance to water deficit should allow to better discriminating genes presenting a potential adaptative character from genes responding passively to the constraint. The consideration of both whole xylem and cambial zone will enable us to discriminate between regulations events originating from very young xylem cells undergoing their first steps of xylem differentiation (cambial zone) compared to whole xylem sample enriched in more differentiated xylem cells and parenchyma ray cells.-Two poplar clones, named Soligo (S) and Carpaccio (C) were submitted to 4 treatments: non-stressed control, severe-drought stress, mild-drought stress and early-drought stress. Two pools of 2 or 3 trees were considered as biological replicates. Two different samples were collected on each individual tree: whole stem xylem (X) and cambial zone plus very young expanding xylem (Y). Total RNAs were extracted from each tree and assemble in pool of 3 or 2 individuals using equimolar ratio for each X and for Y. One affymetrix slide corresponds to one pooled RNA sample (X or Y). A total number of slides : 4 treatments x 2 clones x 2 tissues x 2 biological replicates (pool) = 32 slides, will be done. Keywords: genotype and ecotype comparison,organ comparison,treated vs untreated comparison
2012-12-15 | GSE17220 | GEO
Project description:affy_popsec_orleans_poplar - xyleme - This project aims to identify candidate genes for water deficit acclimation and/or adaptation in a tree species: poplar. Due to compelling evidence that transcriptional regulation plays a major role in regulating many biological processes, we will look for genes and gene expression networks related to drought stress. We intend to analyse the transcriptome in two poplar genotypes of contrasted tolerance to water deficit, at various stages and intensities of stress and simultaneously in whole xylem and cambial zone from young trees. The co-analysis of two genotypes of contrasted tolerance to water deficit should allow to better discriminating genes presenting a potential adaptative character from genes responding passively to the constraint. The consideration of both whole xylem and cambial zone will enable us to discriminate between regulations events originating from very young xylem cells undergoing their first steps of xylem differentiation (cambial zone) compared to whole xylem sample enriched in more differentiated xylem cells and parenchyma ray cells.-Two poplar clones, named Soligo (S) and Carpaccio (C) were submitted to 4 treatments: non-stressed control, severe-drought stress, mild-drought stress and early-drought stress. Two pools of 2 or 3 trees were considered as biological replicates. Two different samples were collected on each individual tree: whole stem xylem (X) and cambial zone plus very young expanding xylem (Y). Total RNAs were extracted from each tree and assemble in pool of 3 or 2 individuals using equimolar ratio for each X and for Y. One affymetrix slide corresponds to one pooled RNA sample (X or Y). A total number of slides : 4 treatments x 2 clones x 2 tissues x 2 biological replicates (pool) = 32 slides, will be done. Keywords: genotype and ecotype comparison,organ comparison,treated vs untreated comparison 32 arrays - poplar
2012-12-15 | E-GEOD-17220 | biostudies-arrayexpress