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Background  Allopolyploids contain genomes composed of more than two complete sets of chromosomes that originate from at least two species. Allopolyploidy has been suggested as an important evolutionary mechanism that can lead to instant speciation.  Arabidopsis suecica  is a relatively recent allopolyploid species, suggesting that its natural accessions might be genetically very similar to each other. Nonetheless, subtle phenotypic differences have been described between different geographic accessions of  A. suecica  grown in a common garden .Results  To determine the degree of genomic similarity between different populations of  A. suecica,  we obtained transcriptomic sequence, quantified SNP variation within the gene space, and analyzed gene expression levels genome-wide from leaf material grown in controlled lab conditions. Despite their origin from the same progenitor species, the two accessions of  A. suecica  used in our study show genomic and transcriptomic variation. We report significant gene expression differences between the accessions, mostly in genes with stress-related functions. Among the differentially expressed genes, there are a surprising number of homoeologs coordinately regulated between sister accessions.    Conclusions  Many of these homoeologous genes and other differentially expressed genes affect transpiration and stomatal regulation, suggesting that they might be involved in the establishment of the phenotypic differences between the two accessions.    Electronic supplementary material  The online version of this article (doi:10.1186/s12864-017-4067-x) contains supplementary material, which is available to authorized users.

Natural variation in stress response gene activity in the allopolyploid Arabidopsis suecica