Hybrid aspen (Populus tremula x tremuloides) cambial zone RNA-sequencing with 35um wide fraction scheme
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ABSTRACT:
PROVIDER: PRJEB13583 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR1361000.fastq.gz | Fastqsanger.gz | |||
| ERR1361010.fastq.gz | Fastqsanger.gz | |||
| ERR1361020.fastq.gz | Fastqsanger.gz | |||
| ERR1361030.fastq.gz | Fastqsanger.gz | |||
| ERR1361040.fastq.gz | Fastqsanger.gz |
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Project description:Aim of the project: Genome wide gene expression profiles across the cambial zone are analyzed in 35um resolution from wild type hybrid aspen (Populus tremula x tremuloides) and two independent LMX5::AtIPT7 over expressor transgenic Populus tree lines.
2016-07-14 | E-MTAB-4631 | biostudies-arrayexpress
Project description:The expression of stress-related genes induced by feeding of chestnut moth larvae (Conistra vaccinii L.) was studied with Vitreoscilla hemoglobin-expressing (VHb) and non-transgenic hybrid aspen lines (Populus tremula x P. tremuloides). Besides the herbivore-injured leaves (L1), cDNA microarray analyses were conducted using uninjured leaves of hybrid aspen lines positioned above (A) and below (B) the herbivory exposed leaves.
2013-04-24 | GSE46331 | GEO
Project description:Aim of the project: Genome wide gene expression analysis for cytokinin (100nM 2ip, 20nM NaPi buffer) fast (1h) response genes from 3 months old Hybrid aspen(Populus tremula x tremuloides)apical part (30 cm from tip; diameter:4-5mm) of stem. Stems of two individuals (trees 15 and 16) was cut into 50-100um thick (free hand)cross sections randomly selected stem discs are set to two pools: cytokinin treatment and control treatment. Samples are collected noon time (11:00-11:30). Cytokinin treatment: stem discs (several hundred) are submerged with 100nM 2ip, 20nM NaPi buffer, with modest shaking for 60 min +/- 2 min (time to collect about 30mg stem discs (several dozens) for RNA sample. Control treatment: identical to cytokinin treatment, only without 100nM 2ip.
2016-07-14 | E-MTAB-4635 | biostudies-arrayexpress
Project description:In this study we report on transgenic hybrid aspen (Populus tremula x P. tremuloides) lines that showed potential to increase biomass production both in the greenhouse and after five years of growth in the field. The transgenic lines carried an overexpression construct for Populus tremula x tremuloides vesicle-associated membrane protein (VAMP)-associated protein PttVAP27-17 (Potri.019G116400) that was selected from a gene-mining program for novel regulators of wood formation. A proteomic analysis was performed to characterize the overall effect of the overexpression of PttVAP27-17 on plant metabolic pathways. 20 mg of xylem sample for the selected wild type (WT) and three transgenic lines (lines 1,2 and 3) was collected in the following manner from two-months-old, greenhouse grown trees: The frozen bottom-part of the stem (10-17 cm portion from the base of the stem) was peeled, and the surface of the secondary xylem consisting of living vessels and fibers (into the depth of approximately one mm from the surface) was scraped. The xylem scrapings were ground to fine powder in liquid nitrogen and stored at -80oC. The analyses included 3-5 biological replicates for each of the transgenic lines, and seven replicates for the wild type.
2021-09-10 | PXD023826 | Pride
Project description:The expression of stress-related genes induced by feeding of chestnut moth larvae (Conistra vaccinii L.) was studied with Vitreoscilla hemoglobin-expressing (VHb) and non-transgenic hybrid aspen lines (Populus tremula x P. tremuloides). Besides the herbivore-injured leaves (L1), cDNA microarray analyses were conducted using uninjured leaves of hybrid aspen lines positioned above (A) and below (B) the herbivory exposed leaves. Two-condition experiment, control vs. herbivory exposure. Two hybrid aspen lines: non-transgenic V617 and VHb expressing V617 /45. Of each plant, three leaf types were analysed: the injured/uninjured leaf (L1) and nonorthostichous leaf positioned above (A) and below (B). Biological replicates: 3. On each array, two samples representing L1, A or B leaf type of control and herbivory treatment of either V617 or V617/45 line. line V617: wt_A_rep1-3, wt_B_rep1-3, wt_L1_rep1-3 line V617/45: VHb_A_rep1-3, VHb_B_rep1-3, VHb_L1_rep1-3 leaf type A: wt_A_rep1-3, VHb_A_rep1-3 leaf type B: wt_B_rep1-3, VHb_B_rep1-4 leaf type L1: wt_L1_rep1-3, VHb_L1_rep1-5
2013-04-24 | E-GEOD-46331 | biostudies-arrayexpress
Project description:Background Ionic aluminum (mainly Al3+) is rhizotoxic and can be present in acid soils at concentrations high enough to inhibit root growth. Many forest tree species grow naturally in acid soils and often tolerate high concentrations of Al. Previously, we have shown that aspen (Populus tremula) releases citrate and oxalate from roots in response to Al exposure. To obtain further insights into the root responses of aspen to Al, we investigated root gene expression at Al conditions that inhibit root growth. Results Treatment of the aspen roots with 500 µM Al induced a strong inhibition of root growth within 6 h of exposure time. The root growth subsequently recovered, reaching growth rates comparable to that of control plants. Changes in gene expression were determined after 6 h, 2 d, and 10 d of Al exposure. Replicated transcriptome analyses using the Affymetrix poplar genome array revealed a total of 175 significantly up-regulated and 69 down-regulated genes, of which 70% could be annotated based on Arabidopsis genome resources. Between 6 h and 2 d, the number of responsive genes strongly decreased from 202 to 26, and then the number of changes remained low. The responses after 6 h were characterized by genes involved in cell wall modification, ion transport, and oxidative stress. Two genes with prolonged induction were closely related to the Arabidopsis Al tolerance genes ALS3 (for Al sensitive 3) and MATE (for multidrug and toxin efflux protein, mediating citrate efflux). Patterns of expression in different plant organs and in response to Al indicated that the two aspen genes are homologs of the Arabidopsis ALS3 and MATE. Conclusion Exposure of aspen roots to Al results in a rapid inhibition of root growth and a large change in root gene expression. The subsequent root growth recovery and the concomitant reduction in the number of responsive genes presumably reflect the success of the roots in activating Al tolerance mechanisms. The aspen genes ALS3 and MATE may be important components of these mechanisms.
2010-08-24 | GSE19297 | GEO
Project description:BACKGROUND:The genus Populus is accepted as a model system for molecular tree biology. To investigate gene functions in Populus spp. trees, generating stable transgenic lines is the common technique for functional genetic studies. However, a limited number of genes have been targeted due to the lengthy transgenic process. Transient transformation assays complementing stable transformation have significant advantages for rapid in vivo assessment of gene function. The aim of this study is to develop a simple and efficient transient transformation for hybrid aspen and to provide its potential applications for functional genomic approaches. RESULTS:We developed an in planta transient transformation assay for young hybrid aspen cuttings using Agrobacterium-mediated vacuum infiltration. The transformation conditions such as the infiltration medium, the presence of a surfactant, the phase of bacterial growth and bacterial density were optimized to achieve a higher transformation efficiency in young aspen leaves. The Agrobacterium infiltration assay successfully transformed various cell types in leaf tissues. Intracellular localization of four aspen genes was confirmed in homologous Populus spp. using fusion constructs with the green fluorescent protein. Protein-protein interaction was detected in transiently co-transformed cells with bimolecular fluorescence complementation technique. In vivo promoter activity was monitored over a few days in aspen cuttings that were transformed with luciferase reporter gene driven by a circadian clock promoter. CONCLUSIONS:The Agrobacterium infiltration assay developed here is a simple and enhanced throughput method that requires minimum handling and short transgenic process. This method will facilitate functional analyses of Populus genes in a homologous plant system.
| S-EPMC3476444 | biostudies-literature
Project description:Hybrid aspen (Populus tremula x tremuloides)1h cytokinin induction and 1h control treatment data.
| PRJEB13390 | ENA
Project description:Background: Solubilized aluminum (Al) is rhizotoxic and can be present in acid soils at levels that inhibit root growth. Acid soils are found throughout the world and often support forests. However, unlike in herbaceous plants, little is known about the mechanisms by which forest trees respond to and tolerate Al. To begin to elucidate these mechanisms, we characterized transcriptomic changes in response to Al in roots of aspen (Populus tremula L.). Results: Aspen roots were treated with Al in solution culture for 6 h, 54 h, and 246 h. Transcriptomic changes were assessed by the Affymetrix GeneChip Poplar Genome Array. The analysis revealed 176 induced and 66 suppressed genes. The majority of these genes were regulated at 6 h, presumably reflecting root growth, which was strongly inhibited at 6 h and partially was recovered at 2 d and 10 d. Enrichment analysis identified sets of functionally related genes whose members were statistically over-represented compared to the genes on the microarray. These sets included genes related to cell wall modification, oxidative stress, cell death, and transport processes. Two of the genes involved in transport were related to the Arabidopsis Al tolerance genes AtALS3 (aluminum sensitive 3), possibly mediating redistribution of Al, and AtMATE (multi-drug and toxin extrusion), facilitating exudation of citrate. Expression patterns in response to Al in different plant tissues indicated that the two aspen genes are homologs of AtALS3 and AtMATE, suggesting that aspen and Arabidopsis share common mechanisms to cope with Al. Conclusion: This is the first survey of transcriptomic changes in response to Al in a forest tree. The results of our study provide a valuable set of data, which will help to further our understanding of the mechanisms and their regulation that enable aspen to grow in environments with toxic levels of Al. Aspen roots were treated with Al in solution culture for 6 h, 54 h, 246 h to cover a broad range of exposure times. Transcriptomic changes were assessed by the Affymetrix GeneChip Poplar Genome Array. For each time point, root tips of three independant plants were analyzed.
2010-08-24 | E-GEOD-19297 | biostudies-arrayexpress
Project description:To evaluate the efficacy of the gene-deletor system in aspen, we evaluated the system for foreign gene removal in a hybrid aspen clone, INRA 353-53 (Populus tremula × P. tremuloides). The recombinase flipping DNA (FLP) gene was under the control of the heat-inducible promoter of Gmhsp17.6-L, and the β-glucuronidase (gusA) gene which was under the control of the 35S promoter and were constructed using the gene-deletor system in the pCaLFGmFNLFG vector. Six transgenic plants and their sublines were heated at 42 °C for 8 h and gene deletion was verified by polymerase chain reaction (PCR). Three lines exhibited partial transgene deletion while the remaining three lines did not delete. Transgenic lines were evaluated by Southern-blot analyses, verifying that the six transgenic plant lines all had a single copy of transfer DNA (t-DNA). Two partial-deletion lines and two non-deletion lines were analysed for methylation and expression of promoter and recombinase. Hardly any methylation was detected in the Gmhsp17.6-L promoter or recombinase FLP gene sequences, however, the expression of the promoter and recombinase was increased significantly in the partial-deletion compared with the non-deletion line after heat-shock treatment. These results suggest that the excision efficiency had no direct relationship with methylation status of the Gmhsp17.6-L promoter and FLP recombinase, yet was affected by the expression of the Gmhsp17.6-L and FLP after heat-shock treatment.
| S-EPMC6210648 | biostudies-literature