Contribution of subgenomes to the transcriptome and their intertwined regulation in the allopolyploid Coffea arabica grown at contrasted temperatures
Article first published online: 24 JUN 2013
© 2013 The Authors. New Phytologist © 2013 New Phytologist Trust
Volume 200, Issue 1, pages 251–260, October 2013
How to Cite
Combes, M.-C., Dereeper, A., Severac, D., Bertrand, B. and Lashermes, P. (2013), Contribution of subgenomes to the transcriptome and their intertwined regulation in the allopolyploid Coffea arabica grown at contrasted temperatures. New Phytologist, 200: 251–260. doi: 10.1111/nph.12371
- Issue published online: 26 AUG 2013
- Article first published online: 24 JUN 2013
- Manuscript Accepted: 14 MAY 2013
- Manuscript Received: 5 APR 2013
- cis trans-regulation;
- coffee (Coffea arabica);
- homoeologous gene expression;
- 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 C. arabica's ability to tolerate a broader range of growing temperatures than its diploid parents does not result from differential use of homoeologs.