Abstract
Polyploidy is a prominent mode of speciation and a recurrent process during plant evolution. Allopolyploidization, that involves inter-species hybridization and genome doubling, can induce an extensive array of genomic rearrangements and gene expression changes generating plants with new abilities to adaptation. The study of the merger of divergent gene expression regulatory networks seems fundamental to elucidate the role of conciliation processes in the gene expression variations.The genus Coffea that contains diploid species able to hybridize and C. arabica a recent allopolyploid between two low divergent diploid species C. eugenioides and C. canephora, represents an appropriate model for this study. Indeed C. arabica can be grown in regions with marked variations in thermal amplitude while the parental species are less adapted to temperature variations. The aims of the present work are, on one hand, the study of the effects of hybridization on the expression and regulation of genes and on the other hand, the analysis of homeologous gene expression variation in response to changing environment.To examine the immediate effects of hybridization, the expression and regulation of genes in F1 hybrids between C. canephora and C. eugenioides were analyzed by genome-wide RNA-seq technology. Parental species are distinguished by an important proportion of trans-regulatory divergences. In hybrids, among divergently expressed genes between parental species and hybrids, 77% are expressed like one parent (expression level dominance). Gene expression was shown to result from the expression of both alleles, with occasional bias toward one genome. The gene expression patterns appear determined by complex combinations of cis- and trans-regulatory divergences of parental species and by intertwined parental trans-regulatory factors. The gene expression level depends on the simultaneous up and down-regulation of both alleles and the observed biased expression level dominance seems to be derived from the asymmetric effects of trans-regulatory parental factors on regulation of alleles. In the allopolyploid, at the genomic scale, both homeologous genes are also inter-regulated and contribute to the transcriptome.The transcriptome of leaves from C. arabica cultivated at different growing temperatures suitable for one or the other parental species was examined to analyze the variation of homeologous gene expression in variable conditions. The relative subgenome contributions to the transcriptome appear to be only marginally altered by the growing conditions. C. arabica’s ability to tolerate a broader range of growing temperatures than its diploid parents does not result from differential use of homeologs. The transcriptional response after a recent or old hybridization event was characterized by these studies. The genetic bases of the variations in allelic expression after the merger of parental gene expression regulatory networks, were elucidated and a model of regulation of homeologous gene expression in C. arabica is proposed. Keywords : allopolyploidy, hybridization, homeolog, Allelic Specific Expression (ASE), cis- trans-regulation, transcriptome, RNA-seq, adaptation, coffee tree.