• adaptation;
  • cis trans-regulation;
  • coffee (Coffea arabica);
  • homoeologous gene expression;
  • polyploidy;
  • RNA-sequencing;
  • transcriptome


  • Polyploidy has occurred throughout the evolutionary history of plants and led to diversification and plant ecological adaptation. Functional plasticity of duplicate genes is believed to play a major role in the environmental adaptation of polyploids. In this context, we characterized genome-wide homoeologous gene expression in Coffea arabica, a recent allopolyploid combining two subgenomes that derive from two closely related diploid species, and investigated its variation in response to changing environment.
  • The transcriptome of leaves of C. arabica cultivated at different growing temperatures suitable for one or the other parental species was examined using RNA-sequencing. The relative contribution of homoeologs to gene expression was estimated for 9959 and 10 628 genes in warm and cold conditions, respectively.
  • Whatever the growing conditions, 65% of the genes showed equivalent levels of homoeologous gene expression. In 92% of the genes, relative homoeologous gene expression varied < 10% between growing temperatures.
  • The subgenome contributions to the transcriptome appeared to be only marginally altered by the different conditions (involving intertwined regulations of homeologs) suggesting that Carabica's ability to tolerate a broader range of growing temperatures than its diploid parents does not result from differential use of homoeologs.