R. M. Ames and S. C. Lovell, Diversification at transcription factor binding sites within a species and the implications for environmental adaptation, Mol Biol Evol, vol.28, pp.3331-3344, 2011.

S. Anders and W. Huber, Differential expression analysis for sequence count data, Genome Biol, vol.11, p.106, 2010.

F. Anthony, L. Diniz, M. Combes, and P. Lashermes, Adaptive radiation in Coffea subgenus Coffea L. (Rubiaceae) in Africa and Madagascar, Plant Syst Evol, vol.285, pp.51-64, 2010.

M. Barrier, R. H. Robichaux, and M. D. Purugganan, Accelerated regulatory gene evolution in an adaptive radiation, Proc Natl Acad Sci U S A, vol.98, pp.10208-10213, 2001.

G. D. Bell, N. C. Kane, L. H. Rieseberg, and K. L. Adams, RNA-seq analysis of allele-specific expression, hybrid effects, and regulatory divergence in hybrids compared with their parents from natural populations, 2013.

, Genome Biol Evol, vol.5, pp.1309-1323

R. J. Buggs, The legacy of diploid progenitors in allopolyploid gene expression patterns, Philos Trans R Soc Lond B Biol Sci, vol.369, 2014.

A. Cenci, M. C. Combes, and P. Lashermes, Genome evolution in diploid and tetraploid Coffea species as revealed by comparative analysis of orthologous genome segments, Plant Mol Biol, vol.78, pp.135-145, 2012.

A. Cenci, M. Combes, and P. Lashermes, Differences in evolution rates among eudicotyledon species observed by analysis of protein divergence, J Hered, vol.104, pp.459-464, 2013.

V. Chagué, Genome-wide gene expression changes in genetically stable synthetic and natural wheat allohexaploids, New Phytol, vol.187, pp.1181-1194, 2010.

M. A. Chapman, S. J. Hiscock, and D. A. Filatov, Genomic divergence during speciation driven by adaptation to altitude, Mol Biol Evol, vol.30, pp.2553-2567, 2013.

R. K. Chodavarapu, Transcriptome and methylome interactions in rice hybrids, Proc Natl Acad Sci U S A, vol.109, pp.12040-12045, 2012.

M. Combes, A. Dereeper, D. Severac, B. Bertrand, and P. Lashermes, Contribution of subgenomes to the transcriptome and their intertwined regulation in the allopolyploid Coffea arabica grown at contrasted temperatures, New Phytol, vol.200, pp.251-260, 2013.

A. Conesa and S. Gotz, Blast2GO: a comprehensive suite for functional analysis in plant genomics, Int J Plant Genomics, p.619832, 2008.

A. Conesa, Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research, Bioinformatics, vol.21, pp.3674-3676, 2005.

J. D. Coolon, C. J. Mcmanus, K. R. Stevenson, B. R. Graveley, and P. J. Wittkopp, Tempo and mode of regulatory evolution in Drosophila, Genome Res, vol.24, pp.797-808, 2014.

E. Couturon, P. Lashermes, and A. Charrier, First intergeneric hybrids (Psilanthus ebracteolatus Hiern Coffea arabica L.) in coffee trees, Can J Bot, vol.76, pp.542-546, 1998.

C. R. Cowles, J. N. Hirschhorn, D. Altshuler, and E. S. Lander, Detection of regulatory variation in mouse genes, Nat Genet, vol.32, pp.432-437, 2002.

M. P. Cox, An interspecific fungal hybrid reveals cross-kingdom rules for allopolyploid gene expression patterns, PLoS Genet, vol.10, p.1004180, 2014.

J. Cros, Phylogenetic analysis of chloroplast DNA variation in Coffea L, Mol Phylogenet Evol, vol.9, pp.109-117, 1998.

F. Denoeud, The coffee genome provides insight into the convergent evolution of caffeine biosynthesis, Science, vol.345, pp.1181-1184, 2014.

M. Donoghue, C(m)CGG methylation-independent parentof-origin effects on genome-wide transcript levels in isogenic reciprocal F1 triploid plants, DNA Res, vol.21, pp.141-151, 2014.

J. J. Emerson and W. H. Li, The genetic basis of evolutionary change in gene expression levels, Philos Trans R Soc Lond B Biol Sci, vol.365, pp.2581-2590, 2010.

J. J. Emerson, Natural selection on cis and trans regulation in yeasts, Genome Res, vol.20, pp.826-836, 2010.

I. K. Greaves, M. Groszmann, A. Wang, W. J. Peacock, and E. S. Dennis, Inheritance of trans chromosomal methylation patterns from Arabidopsis F1 hybrids, Proc Natl Acad Sci, pp.2017-2022, 2014.

M. Groszmann, Changes in 24-nt siRNA levels in Arabidopsis hybrids suggest an epigenetic contribution to hybrid vigor, Proc Natl Acad Sci U S A, vol.108, pp.2617-2622, 2011.

C. E. Grover, Homoeolog expression bias and expression level dominance in allopolyploids, New Phytol, vol.196, pp.966-971, 2012.
URL : https://hal.archives-ouvertes.fr/hal-01515008

F. He, Genome-wide analysis of cis-regulatory divergence between species in the Arabidopsis genus, Mol Biol Evol, vol.29, pp.3385-3395, 2012.

M. J. Hegarty and S. J. Hiscock, The complex nature of allopolyploid plant genomes, Heredity, vol.103, pp.100-101, 2009.

M. V. Kapralov, A. A. Votintseva, and D. A. Filatov, Molecular adaptation during a rapid adaptive radiation, Mol Biol Evol, vol.30, pp.1051-1059, 2013.

C. R. Landry, D. L. Hartl, and J. M. Ranz, Genome clashes in hybrids: insights from gene expression, Heredity, vol.99, pp.483-493, 2007.

P. Lashermes, Molecular characterisation and origin of the Coffea arabica L. genome, Mol Gen Genet, vol.261, pp.259-266, 1999.

H. Li and R. Durbin, Fast and accurate long-read alignment with Burrows-Wheeler transform, Bioinformatics, vol.26, pp.589-595, 2010.

J. Louarn, Hybrides interspé cifiques entre Coffea canephora pierre et C. eugenioides Moore. Café Cacao Thé, vol.20, pp.433-452, 1976.

J. C. Marioni, C. E. Mason, S. M. Mane, M. Stephens, and Y. Gilad, RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays, Genome Res, vol.18, pp.1509-1517, 2008.

C. J. Mcmanus, Regulatory divergence in Drosophila revealed by mRNA-seq, Genome Res, vol.20, pp.816-825, 2010.

G. Muir, O. G. Osborne, J. Sarasa, S. J. Hiscock, and D. A. Filatov, Recent ecological selection on regulatory divergence is shaping clinal variation in senecio on Mount Etna, Evol Int J Org Evol, vol.67, pp.3032-3042, 2013.

M. Noirot, Genome size variations in diploid African Coffea species, Ann Bot, vol.92, pp.709-714, 2003.

B. Qi, Global transgenerational gene expression dynamics in two newly synthesized allohexaploid wheat (Triticum aestivum) lines, BMC Biol, vol.10, p.3, 2012.

H. Shen, Genome-wide analysis of DNA methylation and gene expression changes in two Arabidopsis ecotypes and their reciprocal hybrids, Plant Cell, vol.24, pp.875-892, 2012.

X. Shi, Cis-and trans-regulatory divergence between progenitor species determines gene-expression novelty in Arabidopsis allopolyploids, Nat Commun, vol.3, p.950, 2012.

I. Tirosh, S. Reikhav, A. A. Levy, and N. Barkai, A yeast hybrid provides insight into the evolution of gene expression regulation, Science, vol.324, pp.659-662, 2009.

L. Wang, W. S. Li, and W. , RSeQC: quality control of RNA-seq experiments, Bioinformatics, vol.28, pp.2184-2185, 2012.

J. Wang, Genomewide nonadditive gene regulation in Arabidopsis allotetraploids, Genetics, vol.172, pp.507-517, 2006.

A. Whitehead and D. L. Crawford, Variation within and among species in gene expression: raw material for evolution, Mol Ecol, vol.15, pp.1197-1211, 2006.

P. J. Wittkopp, B. K. Haerum, and A. G. Clark, Evolutionary changes in cis and trans gene regulation, Nature, vol.430, pp.85-88, 2004.

J. Wolf, J. Lindell, B. , and N. , Speciation genetics: current status and evolving approaches, Philos Trans R Soc B Biol Sci, vol.365, pp.1717-1733, 2010.

C. Xu, Genome-wide disruption of gene expression in allopolyploids but not hybrids of rice subspecies, Mol Biol Evol, vol.31, pp.1066-1076, 2014.

M. Yoo, E. Szadkowski, and J. F. Wendel, Homoeolog expression bias and expression level dominance in allopolyploid cotton, Heredity, vol.110, pp.171-180, 2013.
URL : https://hal.archives-ouvertes.fr/hal-01515003

, Associate editor: Patricia Wittkopp