Abstract
BackgroundTranscriptome map is a powerful tool for a variety of biological studies; transcriptome maps that include different organs, tissues, cells and stages of development are currently available for at least 30 plants. Some of them include samples treated by environmental or biotic stresses. However, most studies explore only limited set of organs and developmental stages (leaves or seedlings). In order to provide broader view of organ-specific strategies of cold stress response we studied expression changes that follow exposure to cold (+ 4 °C) in different aerial parts of plant: cotyledons, hypocotyl, leaves, young flowers, mature flowers and seeds using RNA-seq.ResultsThe results on differential expression in leaves are congruent with current knowledge on stress response pathways, in particular, the role of CBF genes. In other organs, both essence and dynamics of gene expression changes are different. We show the involvement of genes that are confined to narrow expression patterns in non-stress conditions into stress response. In particular, the genes that control cell wall modification in pollen, are activated in leaves. In seeds, predominant pattern is the change of lipid metabolism.ConclusionsStress response is highly organ-specific; different pathways are involved in this process in each type of organs. The results were integrated with previously published transcriptome map of Arabidopsis thaliana and used for an update of a public database TraVa: http://travadb.org/browse/Species=AthStress.
Highlights
Transcriptome map is a powerful tool for a variety of biological studies; transcriptome maps that include different organs, tissues, cells and stages of development are currently available for at least 30 plants
We have introduced a metric “differentially expressed (DE) Score” in A. thaliana transcriptome map, which corresponds to the number of pairwise comparisons where gene was DE and reflects both width of gene expression pattern and difference in the expression level
Genes that are annotated with the Gene Ontology (GO):0009631 and GO:0009409 categories have median DE Score 1326
Summary
Transcriptome map is a powerful tool for a variety of biological studies; transcriptome maps that include different organs, tissues, cells and stages of development are currently available for at least 30 plants. In order to provide broader view of organ-specific strategies of cold stress response we studied expression changes that follow exposure to cold (+ 4 °C) in different aerial parts of plant: cotyledons, hypocotyl, leaves, young flowers, mature flowers and seeds using RNA-seq. Transcriptome map, or gene expression atlas, is a collection of expression profiles of all genes in different organs, tissues or cells under various environmental conditions [1]. Despite of gene expression atlas definition, only few papers includes transcriptome profiles of samples under stress conditions as a part of main dataset [8, 11, 12] or for the verification of map completeness [5]. The main regulator genes in A. thaliana were discovered in cold response studies using classic genetics
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