Populus tremula x Populus alba
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA244820 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR1246865_1.fastq.gz | Fastqsanger.gz | |||
| SRR1246865_2.fastq.gz | Fastqsanger.gz | |||
| SRR1246866_1.fastq.gz | Fastqsanger.gz | |||
| SRR1246866_2.fastq.gz | Fastqsanger.gz | |||
| SRR1246867_1.fastq.gz | Fastqsanger.gz |
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Project description:To obtain genes expression in different parts of 84k poplar stems, transcriptome sequencing was performed using Illumina Novaseq 6000 second-generation sequencing platform from Shanghai BIOZERON Co. Ltd (www.biozeron.com). Selecte three stem segments of plants REPEAT 1, 2 and 3 with good and similar growth to use: 2nd-3rd internodes (poplar stem top: PST1, PST2, PST3); 9th-10th internodes (poplar stem middle: PSM1, PSM2, PSM3); 14th-15th internodes (poplar stem bottom: PSB1, PSB2, PSB3). [Or the three repeating organisms are also called poplar A, B, C. From top to bottom, the three parts of the stem are also called stem 1, 2, 3.]
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Project description:Here we applied a novel approach to isolate nuclei from complex plant tissues (https://doi.org/10.1371/journal.pone.0251149), to dissect the transcriptome profiling of the hybrid poplar (Populus tremula × alba) vegetative shoot apex at single-cell resolution.
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Project description:Effect of MiSSP7 overexpression on the Poplar root transcriptome
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Project description:Gene expression response of Populus cell cultures subjected to methyl jasmonate feeding was analyzed using the Affymetrix poplar genome microarrays. Keywords: Stress response
2009-12-01 | GSE16773 | GEO
Project description:Plants transition through juvenile and adult phases of vegetative development in a process known as vegetative phase change (VPC). In poplars (genus Populus) the differences between these stages are subtle, making it difficult to determine when this transition occurs. Previous studies of VPC in poplars have relied on plants propagated in vitro, leaving the natural progression of this process unknown. We examined developmental morphology of seed-grown and in vitro derived Populus tremula × alba (clone 717-1B4), and compared the phenotype of these to transgenics with manipulated miR156 expression, the master regulator of VPC. In seed-grown plants, most traits changed from node-to-node during the first 3 months of development but remained constant after node 25. Many traits remained unchanged in clones over-expressing miR156, or were enhanced when miR156 was lowered, demonstrating their natural progression is regulated by the miR156/SPL pathway. The characteristic leaf fluttering of Populus is one of these miR156-regulated traits. Vegetative development in plants grown from culture mirrored that of seed-grown plants, allowing direct comparison between plants often used in research and those found in nature. These results provide a foundation for further research on the role of VPC in the ecology and evolution of this economically important genus.
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Project description:Gene expression response of Populus cell cultures subjected to methyl jasmonate feeding was analyzed using the Affymetrix poplar genome microarrays. Experiment Overall Design: Populus tremuloides suspension cells were treated with methyl jasmonate (MJ) in DMSO or with DMSO alone (C). Cells were harvested after 48 hours. Two biological replicates were obtained for each condition.
2009-12-14 | E-GEOD-16773 | biostudies-arrayexpress
Project description:Poplar 84K (Populus alba x P. tremula var. glandulosa) is a fast-growing poplar hybrid. Originated in South Korea, this hybrid has been extensively cultivated in northern China. Due to the economic and ecological importance of this hybrid and high transformability, we now report the de novo sequencing and assembly of a male individual of poplar 84K using PacBio and Hi-C technologies. The final reference nuclear genome (747.5?Mb) has a contig N50 size of 1.99?Mb and a scaffold N50 size of 19.6?Mb. Complete chloroplast and mitochondrial genomes were also assembled from the sequencing data. Based on similarities to the genomes of P. alba var. pyramidalis and P. tremula, we were able to identify two subgenomes, representing 356?Mb from P. alba (subgenome A) and 354?Mb from P. tremula var. glandulosa (subgenome G). The phased assembly allowed us to detect the transcriptional bias between the two subgenomes, and we found that the subgenome from P. tremula displayed dominant expression in both 84K and another widely used hybrid, P. tremula x P. alba. This high-quality poplar 84K genome will be a valuable resource for poplar breeding and for molecular biology studies.
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Project description:Effect of hypoxia on gene expression in Grey poplar
| PRJNA109943 | ENA
Project description:Microarray technology was used to assess transcriptome changes in poplar (Populus alba L.) under a realistic simulation of increased UV-B radiation. Plants were UV-Bbe (UV-B biologically effective radiation) supplemented with a dose of 6 kJ/m2/day for 12 hours per day and allowed to recover during the night. Poplar plants were UV-B treated using a refined controlled environment able to guarantee a realistic simulation of natural conditions, especially for light parameters such as presence of background UV-B radiation for control plants and balanced PAR/UV-A/UV-B ratio. A time course experiment was planned to look both at the rapid and delayed response of poplar to UVB; two time points after 3 h (T3h) and 30 h (6th hour of the third day of treatment, T30h) were considered. 4 independent biological replicates were analysed for each time point. Competitive hybridisations were carried out using the PICME 28K microarray. Keywords: Time course experiment, stress response
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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.
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