Ontology highlight
ABSTRACT:
PROVIDER: PRJNA993858 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR25242227_1.fastq.gz | Fastqsanger.gz | |||
| SRR25242227_2.fastq.gz | Fastqsanger.gz | |||
| SRR25242228_1.fastq.gz | Fastqsanger.gz | |||
| SRR25242228_2.fastq.gz | Fastqsanger.gz | |||
| SRR25242229_1.fastq.gz | Fastqsanger.gz |
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Project description:The aim of this study was to analyze the impact of autotetraploidy on gene expression in Arabidopsis thaliana by comparing diploid versus tetraploid transcriptomes. In particular, this included the comparison of the transcriptome of different tetraploid A. thaliana ecotypes (Col-0 vs. Ler-0). The study was extended to address further aspects. One was the comparison of the transcriptomes in subsequent generations. This intended to obtain information on the genome wide stability of autotetraploid gene expression. Another line of work compared the transcriptomes of different diploid vs. tetraploid tissues. This aimed to investigate whether particular gene groups are specifically affected during the development of A. thaliana autotetraploids. Samples 1-8: Arabidopsis thaliana Col-0 tetraploid transcriptome. Transcriptional profiling and comparison of diploid vs. tetraploid Col-0 seedlings. The experiment was carried out with pedigree of independently generated and assessed tetraploid Col-0 lines. Samples 9-12: Arabidopsis thaliana Ler-0 tetraploid transcriptome. Transcriptional profiling and comparison of diploid vs. tetraploid Ler-0 seedlings. The experiment was carried out with pedigree of independently generated and assessed tetraploid Ler-0 lines. Samples 13-24: Arabidopsis thaliana Col-0 tetraploid transcriptome. Transcriptional profiling and comparison of diploid vs. tetraploid Col-0 leaves (6th - 8th). The experiment was carried out with pedigree of independently generated and assessed tetraploid Col-0 lines. Samples 25-32: Arabidopsis thaliana Ler-0 tetraploid transcriptome. Transcriptional profiling and comparison of diploid vs. tetraploid Ler-0 leaves (6th - 8th). The experiment was carried out with pedigree of independently generated and assessed tetraploid Ler-0 lines. Samples 33-36: Arabidopsis thaliana Ler-0 tetraploid transcriptome. Transcriptional profiling and comparison of tetraploid vs. tetraploid Ler-0 seedlings from the second (F2) and third (F3) generation after induction, respectively. The experiment was carried out with pedigree of independently generated and assessed tetraploid Ler-0 lines. Samples 37-40: Arabidopsis thaliana Col-0 tetraploid transcriptome. Transcriptional profiling and comparison of tetraploid vs. tetraploid Col-0 seedlings from the second (F2) and third (F3) generation after induction, respectively. The experiment was carried out with pedigree of independently generated and assessed tetraploid Col-0 lines. Samples 41-44: Arabidopsis thaliana Col-0/Ler-0 diploid transcriptome. Transcriptional profiling and comparison of diploid Col-0 vs. diploid Ler-0 seedlings. The experiment was carried out with pedigree of esrablished lines. Samples 45-48: Arabidopsis thaliana Col-0/Ler-0 tetraploid transcriptome. Transcriptional profiling and comparison of tetraploid Col-0 vs tetraploid Ler-0 seedlings. The experiment was carried out with pedigree of independently generated and assessed tetraploid Col-0 and Ler-0 lines.
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Project description:We developed an artificial genome evolution system, which we termed ‘TAQing’, by introducing multiple genomic DNA double-strand breaks using a heat-activatable endonuclease in Arabidopsis plant. The heat-activated endonuclease, TaqI, induced random DSBs, which resulted in diverse types of chromosomal rearrangements including translocations. To evaluate the potential of TAQing in multicellular organisms, we tested it in diploid and tetraploid Arabidopsis plants. In 9 out of 96 TQ4 plants, we detected 22 large copy number variations (CNVs) events compared witn wild type plant genome, whereas no CNV was found in the 16 control tetraploid plants, and 12 TQ2 plants. The combination of artificially introduced DSBs with whole-genome duplication (WGD) in plants enabled more complex genome reorganization.
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Project description:Tetraploid cells are more resistant against genotoxic stress (irradiation, platinum compounds, topoisomerase inhibitors) than their diploid precursors. Here, we studied the effect of cisplatin and/or Chk1 inhibition on the transcriptome of diploid and tetraploid HCT116 cells
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Project description:Polyploidization as the consequence of 2n gamete formation is a prominent mechanism in plant evolution. Studying its effects on the genome and its expression has both basic and applied interest. We crossed two diploid (2n=2x=16) M. sativa plants, a subsp. falcata seed parent and a coerulea x falcata pollen parent that produce a mixture of n and 2n eggs and pollen, respectively. Such cross produced full-sib diploid and tetraploid (2n=4x=32) progenies, the latter being the result of bilateral sexual polyploidization (BSP). These unique materials allowed us to investigate the effects of BSP, and separating the effect of intraspecific hybridization from those of polyploidization by comparing 2x with 4x full sib progeny plants. SSR marker segregation demonstrated tetrasomic inheritance for all chromosomes but one, demonstrating that these neotetraploids are true autotetraploids. BSP brought about increased biomass, earlier flowering, higher seed set and weight, larger leaves with larger cells. Microarray analyses with M. truncatula gene chips showed that several hundred genes, related to diverse metabolic functions, changed their expression level as a consequence of polyploidization. In addition, cytosine methylation increased in 2x but not in 4x hybrids. Our results indicate that sexual polyploidization induce significant transcriptional novelty, possibly mediated in part by DNA methylation, and phenotypic novelty that can be at the base of improved adaptation and reproductive success of tetraploid M. sativa with respect to its diploid progenitor. These polyploidy-induced changes may have promoted the adoption of tetraploid alfalfa in agriculture. Gene expression analysis of leaves at the vegetative stage of two Medicago sativa genotypes (PG-F9 and 12P) compared with three F1 diploid lines and three F1 tetraploid lines originating from crossing PG-F9 x 12P. Three biological replicates were taken for each sample, resulting in a total of twenty-four samples.
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