@article {3301,
	title = {Contribution of subgenomes to the transcriptome and their intertwined regulation in the allopolyploid Coffea arabica grown at contrasted temperatures.},
	journal = {The New phytologist},
	volume = {200},
	year = {2013},
	month = {2013 Oct},
	pages = {251-60},
	abstract = {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{\textquoteright}s ability to tolerate a broader range of growing temperatures than its diploid parents does not result from differential use of homoeologs.},
	issn = {1469-8137},
	doi = {10.1111/nph.12371},
	author = {Combes, Marie-Christine and Dereeper, Alexis and Severac, Dany and Bertrand, Beno{\^\i}t and Lashermes, Philippe}
}
