Project description:A major effort is underway to study the natural variation within the model plant species, Arabidopsis thaliana. Much of this effort is focused on genome resequencing, however the translation of genotype to phenotype will be largely effected through variations within the transcriptomes at the sequence and expression levels. To examine the cross-talk between natural variation in genomes and transcriptomes, we have examined the transcriptomes of three divergent A. thaliana accessions using tiling arrays. Combined with genome resequencing efforts, we were able to adjust the tiling array datasets to account for polymorphisms between the accessions and therefore gain a more accurate comparison of the transcriptomes. The corrected results for the transcriptomes allowed us to correlate higher gene polymorphism with greater variation in transcript level among the accessions. Our results demonstrate the utility of combining genomic data with tiling arrays to assay non-reference accession transcriptomes.
Project description:A major effort is underway to study the natural variation within the model plant species, Arabidopsis thaliana. Much of this effort is focused on genome resequencing, however the translation of genotype to phenotype will be largely effected through variations within the transcriptomes at the sequence and expression levels. To examine the cross-talk between natural variation in genomes and transcriptomes, we have examined the transcriptomes of three divergent A. thaliana accessions using tiling arrays. Combined with genome resequencing efforts, we were able to adjust the tiling array datasets to account for polymorphisms between the accessions and therefore gain a more accurate comparison of the transcriptomes. The corrected results for the transcriptomes allowed us to correlate higher gene polymorphism with greater variation in transcript level among the accessions. Our results demonstrate the utility of combining genomic data with tiling arrays to assay non-reference accession transcriptomes.
Project description:Untargeted metabolomic analyses were carried out on seed coat/endosperm and seed embryo (dry seeds) of Arabidopsis thaliana Columbia-0 genotype. Three biological replicates were analyzed for each sample.
Project description:Using next-generation sequencing, we sequenced transcriptomes of A. thaliana plants infected by the pathogenic and the symbiotic fungus and analyzed plant and fungal gene expression changes between pathogenic and symbiotic interactions. Infected plants were sampled at early infection stages, 12, 24, 48 and 96 HPI (hours post inoculation)
Project description:Untargeted metabolomic analyses were carried out on seed coat/endosperm and seed embryo (dry seeds) of Arabidopsis thaliana Columbia-0 genotype. Three biological replicates were analyzed for each sample.
Project description:A fundamental question in biology is how gene expression is regulated to give rise to a phenotype. However, transcriptional variability is rarely considered and could influence the relationship between genotype and phenotype. It is known in unicellular organisms that gene expression is often noisy rather than uniform and has been proposed to be beneficial when environmental conditions are unpredictable. However, little is known about transcriptional variability in multicellular organisms. Using transcriptomic approaches, we analysed gene expression variability over a 24 hours time-course between individual Arabidopsis thaliana plants growing in stable conditions. We identified hundreds of genes that exhibit high inter-individual variability and found that many are involved in environmental responses. We also identified factors that might facilitate gene expression variability, such as gene size, the number of transcription factors regulating a gene and the chromatin environment. These results will bring a new light into the impact of transcriptional variability in gene expression regulation in plants.
Project description:This study evaluated the transcriptomic profiles of Arabidopsis thaliana (Col-0) plants grown along bacterial isolates whose interactions induce root morhology changes in the plant
