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.
DOI : 10.1371/journal.pgen.1004180
URL : https://journals.plos.org/plosgenetics/article/file?id=10.1371/journal.pgen.1004180&type=printable

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, 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.
DOI : 10.1111/j.1469-8137.2012.04365.x
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.
DOI : 10.1038/sj.hdy.6801045
URL : https://www.nature.com/articles/6801045.pdf

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 BurrowsWheeler 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.
DOI : 10.1111/evo.12157
URL : http://onlinelibrary.wiley.com/doi/10.1111/evo.12157/pdf

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.
DOI : 10.1186/1741-7007-10-3
URL : https://bmcbiol.biomedcentral.com/track/pdf/10.1186/1741-7007-10-3?site=bmcbiol.biomedcentral.com

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.
DOI : 10.1038/ncomms1954
URL : http://www.nature.com/articles/ncomms1954.pdf

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. , and L. W. , RSeQC: quality control of RNA-seq experiments, Bioinformatics, vol.28, pp.2184-2185, 2012.
DOI : 10.1093/bioinformatics/bts356
URL : https://academic.oup.com/bioinformatics/article-pdf/28/16/2184/16905998/bts356.pdf

J. Wang, Genomewide nonadditive gene regulation in Arabidopsis allotetraploids, Genetics, vol.172, pp.507-517, 2006.
DOI : 10.1534/genetics.105.047894
URL : http://www.genetics.org/content/genetics/172/1/507.full.pdf

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.
DOI : 10.1038/nature02698

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.
DOI : 10.1098/rstb.2010.0023
URL : http://rstb.royalsocietypublishing.org/content/royptb/365/1547/1717.full.pdf

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.
DOI : 10.1038/hdy.2012.94
URL : https://hal.archives-ouvertes.fr/hal-01515003

, Associate editor: Patricia Wittkopp Regulatory Divergence between Parental Alleles GBE

, Advance Access publication March, vol.7, pp.1110-1121, 2015.

R. Adams and K. L. , Evolution of duplicate gene expression in polyploid and hybrid plants, J Hered, vol.98, issue.2, pp.136-141, 2007.

K. L. Adams, R. Cronn, R. Percifield, and J. F. Wendel, Genes duplicated by polyploidy show unequal contributions to the transcriptome and organspecific reciprocal silencing, Proc Natl Acad Sci U S A, vol.100, issue.8, pp.4649-4654, 2003.

K. L. Adams, R. Percifield, and J. F. Wendel, Organ-specific silencing of duplicated genes in a newly synthesized cotton allotetraploid, Genetics, vol.168, issue.4, pp.2217-2226, 2004.

K. L. Adams and J. F. Wendel, Polyploidy and genome evolution in plants, Curr Opin Plant Biol, vol.8, issue.2, pp.135-141, 2005.

F. Anthony, L. Diniz, M. C. Combes, and P. Lashermes, Adaptive radiation in Coffea subgenus Coffea L. (Rubiaceae) in Africa and Madagascar, Plant Syst Evol, vol.285, issue.1-2, pp.51-64, 2010.

A. Bardil, J. Dantas-de-almeida, M. C. Combes, P. Lashermes, and B. Bertrand, Genomic expression dominance in the natural allopolyploid Coffea arabica is massively affected by growth temperature, New Phytol, 2011.
DOI : 10.1111/j.1469-8137.2011.03833.x
URL : https://nph.onlinelibrary.wiley.com/doi/pdf/10.1111/j.1469-8137.2011.03833.x

R. Buggs, N. M. Elliott, L. Zhang, J. Koh, L. F. Viccini et al., Tissue-specific silencing of homoeologs in natural populations of the recent allopolyploid Tragopogon mirus, New Phytol, vol.186, issue.1, pp.175-183, 2010.

R. Buggs, L. Zhang, N. Miles, J. A. Tate, L. Gao et al., Transcriptomic shock generates evolutionary novelty in a newly formed natural allopolyploid plant, Curr Biol, vol.21, pp.551-556, 2011.
DOI : 10.1016/j.cub.2011.02.016
URL : https://doi.org/10.1016/j.cub.2011.02.016

A. Cenci, M. C. Combes, and P. Lashermes, Comparative sequence analyses indicate that Coffea (Asterids) and Vitis (Rosids) derive from the same paleohexaploid ancestral genome, Mol Genet Genomics, vol.283, issue.5, pp.493-501, 2010.
DOI : 10.1007/s00438-010-0534-7

A. Cenci, M. C. Combes, and L. P. Forthcoming, Genome evolution in diploid and tetraploid Coffea species as revealed by comparative analysis of orthologous genome segments, Plant Mol Biol. Mol Genet Genomics, 2011.

B. Chaudhary, L. Flagel, R. M. Stupar, J. A. Udall, N. Verma et al., Reciprocal silencing, transcriptional bias and functional divergence of homeologs in polyploid cotton (Gossypium), Genetics, vol.182, issue.2, pp.503-517, 2009.
DOI : 10.1534/genetics.109.102608
URL : http://www.genetics.org/content/genetics/182/2/503.full.pdf

Z. F. Chen, Genetic and epigenetic mechanisms for gene expression and phenotypic variation in plant polyploids, Annu Rev Plant Biol, vol.58, pp.377-406, 2007.
DOI : 10.1146/annurev.arplant.58.032806.103835
URL : http://europepmc.org/articles/pmc1949485?pdf=render

Z. F. Chen and Z. Ni, Mechanisms of genomic rearrangements and gene expression changes in plant polyploids, Bioessays, vol.28, issue.3, pp.240-252, 2006.

L. Comai, The advantages and disadvantages of being polyploid, Nat Rev Genet, vol.6, issue.11, pp.836-846, 2005.

F. M. Damatta, C. Ramalho, and J. D. , Impacts of drought and temperature stress on Coffea physiology and production: a review, Braz J Plant Physiol, vol.18, issue.1, pp.55-81, 2006.

A. P. Davis, R. Govaerts, D. M. Bridson, and P. Stoffelen, An annotated taxonomic conspectus of the genus Coffea (Rubiaceae), Bot J Linn Soc, vol.152, pp.465-512, 2006.

S. Dong and K. L. Adams, Differential contributions to the transcriptome of duplicated genes in response to abiotic stresses in natural and synthetic polyploids, New Phytol, vol.190, issue.4, pp.1045-1057, 2011.

L. Flagel, J. Udall, D. Nettleton, and J. Wendel, Duplicate gene expression in allopolyploid Gossypium reveals two temporally distinct phases of expression evolution, BMC Biol, vol.6, pp.1-16, 2008.
DOI : 10.1186/1741-7007-6-16
URL : https://bmcbiol.biomedcentral.com/track/pdf/10.1186/1741-7007-6-16?site=bmcbiol.biomedcentral.com

L. E. Flagel, L. Chen, B. Chaudhary, and J. F. Wendel, Coordinated and finescale control of homoeologous gene expression in allotetraploid cotton, J Hered, vol.100, issue.4, pp.487-490, 2009.

T. A. Hall, BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT, Nucleic Acids Symp, vol.41, pp.95-98, 1999.

M. J. Hegarty and S. J. Hiscock, The complex nature of allopolyploid plant genomes, Heredity, vol.103, issue.2, pp.100-101, 2009.
DOI : 10.1038/hdy.2009.61
URL : http://www.nature.com/hdy/journal/v103/n2/pdf/hdy200961a.pdf

R. Hovav, J. Udall, B. Chaudhary, R. Rapp, L. Flagel et al., Partitioned expression of duplicated genes during development and evolution of a single cell in a polyploid plant, Proc Natl Acad Sci U S A, vol.105, issue.16, pp.6191-6195, 2008.

A. L. Hufton and G. Panopoulou, Polyploidy and genome restructuring: a variety of outcomes, Curr Opin Genet Dev, vol.19, issue.6, pp.600-606, 2009.

S. Jackson and Z. J. Chen, Genomic and expression plasticity of polyploidy, Curr Opin Plant Biol, vol.13, issue.2, pp.153-159, 2010.
DOI : 10.1016/j.pbi.2009.11.004
URL : http://europepmc.org/articles/pmc2880571?pdf=render

P. Lashermes, Single-locus inheritance in the allotetraploid Coffea arabica L. and interspecific Hybrid C. arabica x C. canephora, J Hered, vol.91, issue.1, pp.81-85, 2000.

P. Lashermes, M. C. Combes, A. Ribas, A. Cenci, L. Mahé et al., Genetic and physical mapping of the S H 3 region that confers resistance to leaf rust in coffee tree (Coffea arabica L.), Tree Genet Genomes, vol.6, issue.6, pp.973-980, 2010.

P. Lashermes, M. C. Combes, J. Robert, P. Trouslot, D. 'hont et al., Molecular characterisation and origin of the Coffea arabica L. genome, Mol Gen Genet, vol.261, issue.2, pp.259-266, 1999.
DOI : 10.1007/s004380050965

A. R. Leitch and I. J. Leitch, Genomic plasticity and the diversity of polyploid plants, Science, vol.320, issue.5875, pp.481-483, 2008.
DOI : 10.1126/science.1153585

J. Y. Lin, R. M. Stupar, C. Hans, D. L. Hyten, and S. A. Jackson, Structural and functional divergence of a 1-Mb duplicated region in the soybean (Glycine max) genome and comparison to an orthologous region from Phaseolus vulgaris, Plant Cell, vol.22, pp.2545-2561, 2010.

Z. Liu and K. L. Adams, Expression partitioning between genes duplicated by polyploidy under abiotic stress and during organ development, Curr Biol, vol.17, pp.1669-1674, 2007.
DOI : 10.1016/j.cub.2007.08.030
URL : https://doi.org/10.1016/j.cub.2007.08.030

S. Anders and W. Huber, Differential expression analysis for sequence count data, Genome Biology, vol.11, p.106, 2010.
DOI : 10.1038/npre.2010.4282.1
URL : http://precedings.nature.com/documents/4282/version/1/files/npre20104282-1.pdf

F. Anthony, L. Diniz, M. C. Combes, and P. Lashermes, Adaptive radiation in Coffea subgenus Coffea L. (Rubiaceae) in Africa and Madagascar, Plant Systematics and Evolution, vol.285, pp.51-64, 2010.
DOI : 10.1007/s00606-009-0255-8
URL : http://doi.org/10.1007/s00606-009-0255-8

M. Barrier, R. H. Robichaux, and M. D. Purugganan, Accelerated regulatory gene evolution in an adaptive radiation, Proceedings of the National Academy of Sciences, vol.98, pp.208-218, 2001.
DOI : 10.1073/pnas.181257698
URL : http://www.pnas.org/content/98/18/10208.full.pdf

J. A. Birchler, N. C. Riddle, D. L. Auger, and R. A. Veitia, Dosage balance in gene regulation: biological implications, Trends in Genetics, vol.21, pp.219-226, 2005.
DOI : 10.1016/j.tig.2005.02.010

J. A. Birchler and R. A. Veitia, The gene balance hypothesis: from classical genetics to modern genomics, Plant Cell, vol.19, pp.395-402, 2007.
DOI : 10.1105/tpc.106.049338
URL : http://www.plantcell.org/content/plantcell/19/2/395.full.pdf

G. Blanc and K. H. Wolfe, Widespread paleopolyploidy in model plant species inferred from age distributions of duplicate genes, Plant Cell, vol.16, pp.1667-1678, 2004.

A. Bombarely, K. D. Edwards, J. Sanchez-tamburino, and L. A. Mueller, Deciphering the complex leaf transcriptome of the allotetraploid species Nicotiana tabacum: a phylogenomic perspective, BMC Genomics, vol.13, p.406, 2012.

R. Buggs, S. Chamala, W. Wu, L. Gao, G. D. May et al., Characterization of duplicate gene evolution in the recent natural allopolyploid Tragopogon miscellus by next-generation sequencing and Sequenom iPLEX MassARRAY genotyping, Molecular Ecology, vol.19, pp.132-146, 2010.

R. Buggs, S. Renny-byfield, M. Chester, I. E. Jordon-thaden, F. Viccini et al., Next-generation sequencing and genome evolution in allopolyploids, American Journal of Botany, vol.99, pp.372-382, 2012.
DOI : 10.3732/ajb.1100395
URL : http://www.amjbot.org/content/99/2/372.full.pdf

R. Buggs, L. Zhang, N. Miles, J. A. Tate, L. Gao et al., Transcriptomic shock generates evolutionary novelty in a newly formed, natural allopolyploid plant, Current Biology, vol.21, pp.551-556, 2011.
DOI : 10.1016/j.cub.2011.02.016
URL : https://doi.org/10.1016/j.cub.2011.02.016

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 Molecular Biology, vol.78, pp.135-145, 2012.

B. Chaudhary, L. Flagel, R. M. Stupar, J. A. Udall, N. Verma et al., Reciprocal silencing, transcriptional bias and functional divergence of homeologs in polyploid cotton (Gossypium), Genetics, vol.182, pp.503-517, 2009.
DOI : 10.1534/genetics.109.102608
URL : http://www.genetics.org/content/genetics/182/2/503.full.pdf

Z. J. Chen, Genetic and epigenetic mechanisms for gene expression and phenotypic variation in plant polyploids, Annual Review of Plant Biology, vol.58, pp.377-406, 2007.
DOI : 10.1146/annurev.arplant.58.032806.103835
URL : http://europepmc.org/articles/pmc1949485?pdf=render

Z. J. Chen and Z. Ni, Mechanisms of genomic rearrangements and gene expression changes in plant polyploids, BioEssays, vol.28, pp.240-252, 2006.

L. Comai, The advantages and disadvantages of being polyploid, Nature Reviews Genetics, vol.6, pp.836-846, 2005.
DOI : 10.1038/nrg1711

M. C. Combes, A. Cenci, H. Baraille, B. Bertrand, and P. Lashermes, Homeologous gene expression in response to growing temperature in a recent allopolyploid, Coffea arabica L.). Journal of Heredity, vol.103, pp.36-46, 2012.
DOI : 10.1093/jhered/esr120
URL : https://academic.oup.com/jhered/article-pdf/103/1/36/2687445/esr120.pdf

A. Conesa and S. , Blast2GO: a comprehensive suite for functional analysis in plant genomics, International Journal of Plant Genomics, pp.1-13, 2008.
DOI : 10.1155/2008/619832
URL : http://downloads.hindawi.com/archive/2008/619832.pdf

A. Conesa, S. Garcia-gomez, J. M. Terol, J. Talon, M. Robles et al., Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research, Bioinformatics, vol.21, pp.3674-3676, 2005.
DOI : 10.1093/bioinformatics/bti610
URL : https://academic.oup.com/bioinformatics/article-pdf/21/18/3674/521920/bti610.pdf

J. Cros, M. C. Combes, P. Trouslot, F. Anthony, S. Hamon et al., Phylogenetic analysis of chloroplast DNA variation in Coffea L, Molecular Phylogenetics and Evolution, vol.9, pp.109-117, 1998.
DOI : 10.1006/mpev.1997.0453

F. M. Damatta and J. Ramalho, Impacts of drought and temperature stress on coffee physiology and production: a review, Brazilian Journal of Plant Physiology, vol.18, pp.55-81, 2006.

A. P. Davis, R. Govaerts, D. M. Bridson, and P. Stoffelen, An annotated taxonomic conspectus of the genus Coffea (Rubiaceae), Botanical Journal of the Linnean Society, vol.152, pp.465-512, 2006.

S. Dong and K. L. Adams, Differential contributions to the transcriptome of duplicated genes in response to abiotic stresses in natural and synthetic polyploids, New Phytologist, vol.190, pp.1045-1057, 2011.

L. Flagel, J. Udall, D. Nettleton, and J. F. Wendel, Duplicate gene expression in allopolyploid Gossypium reveals two temporally distinct phases of expression evolution, BMC Biology, vol.6, p.16, 2008.
DOI : 10.1186/1741-7007-6-16
URL : https://bmcbiol.biomedcentral.com/track/pdf/10.1186/1741-7007-6-16?site=bmcbiol.biomedcentral.com

L. E. Flagel, L. Chen, B. Chaudhary, and J. F. Wendel, Coordinated and fine-scale control of homoeologous gene expression in allotetraploid cotton, Journal of Heredity, vol.100, pp.487-490, 2009.

L. E. Flagel and J. F. Wendel, Evolutionary rate variation, genomic dominance and duplicate gene expression evolution during allotetraploid cotton speciation, New Phytologist, vol.186, pp.184-193, 2010.
DOI : 10.1111/j.1469-8137.2009.03107.x
URL : http://onlinelibrary.wiley.com/doi/10.1111/j.1469-8137.2009.03107.x/pdf

M. Freeling and B. C. Thomas, Gene-balanced duplication, like tetraploidy, provide predictable drive to increase morphological complexity, Genome Research, vol.16, pp.805-814, 2006.
DOI : 10.1101/gr.3681406
URL : http://genome.cshlp.org/content/16/7/805.full.pdf

C. E. Grover, J. P. Gallagher, E. P. Szadkowski, M. J. Yoo, L. E. Flagel et al., Homoeolog expression bias and expression level dominance in allopolyploids, New Phytologist, vol.196, pp.966-971, 2012.
DOI : 10.1111/j.1469-8137.2012.04365.x
URL : https://hal.archives-ouvertes.fr/hal-01515008

M. J. Hegarty, Hybridization: expressing yourself in a crowd, Current Biology, vol.21, pp.254-255, 2011.
DOI : 10.1016/j.cub.2011.02.035
URL : https://doi.org/10.1016/j.cub.2011.02.035

M. J. Hegarty, G. L. Barker, A. C. Brennan, K. J. Edwards, R. J. Abbott et al., Changes to gene expression associated with hybrid speciation in plants: further insights from transcriptomic studies in Senecio, Philosophical Transactions of the Royal Society B, vol.363, pp.3055-3069, 2008.
DOI : 10.1098/rstb.2008.0080
URL : http://rstb.royalsocietypublishing.org/content/royptb/363/1506/3055.full.pdf

M. J. Hegarty, L. Barker, I. D. Wilson, R. J. Abbott, K. J. Edwards et al., Transcriptome shock after interspecific hybridization in Senecio is ameliorated by genome duplication, Current Biology, vol.16, pp.1652-1659, 2006.
DOI : 10.1016/j.cub.2006.06.071
URL : https://doi.org/10.1016/j.cub.2006.06.071

M. J. Hegarty and S. J. Hiscock, The complex nature of allopolyploid plant genomes, Heredity, vol.103, pp.100-101, 2009.
DOI : 10.1038/hdy.2009.61
URL : http://www.nature.com/hdy/journal/v103/n2/pdf/hdy200961a.pdf

J. Higgins, A. Magusin, M. Trick, F. Fraser, and B. I. , Use of mRNA-seq to discriminate contributions to the transcriptome from the constituent genomes of the polyploid crop species Brassica napus, BMC Genomics, vol.13, p.247, 2012.

R. Hovav, J. Udall, B. Chaudhary, R. Rapp, L. Flagel et al., Partitioned expression of duplicated genes during development and evolution of a single cell in a polyploid plant, Proceedings of the National Academy of Sciences, vol.105, pp.6191-6195, 2008.

D. C. Ilut, J. E. Coate, A. K. Luciano, T. G. Owens, G. D. May et al., A comparative transcriptomic study of an allotetraploid and its diploid progenitors illustrates the unique advantages and challenges of RNA-seq in plant species, American Journal of Botany, vol.99, pp.383-396, 2012.

S. Jackson and Z. J. Chen, Genomic and expression plasticity of polyploidy, Current Opinion in Plant Biology, vol.13, pp.153-159, 2010.
DOI : 10.1016/j.pbi.2009.11.004
URL : http://europepmc.org/articles/pmc2880571?pdf=render

Y. Jiao, N. J. Wickett, S. Ayyampalayam, A. S. Chanderbali, L. Landherr et al., Ancestral polyploidy in seed plants and angiosperms, Nature, vol.473, pp.97-100, 2011.
DOI : 10.1038/nature09916

S. Kaur, M. G. Francki, and J. W. Forster, Identification, characterization and interpretation of single-nucleotide sequence variation in allopolyploid crop species, Plant Biotechnology Journal, vol.10, pp.125-138, 2012.

E. Kim and Z. J. Chen, Unstable transcripts in Arabidopsis allotetraploids are associated with nonadditive gene expression in response to abiotic and biotic stresses, PLoS ONE, vol.6, p.24251, 2011.
DOI : 10.1371/journal.pone.0024251
URL : https://doi.org/10.1371/journal.pone.0024251

P. Lashermes, Single-locus inheritance in the allotetraploid Coffea arabica L. and interspecific hybrid C. arabica 9 C. canephora, Journal of Heredity, vol.91, pp.81-85, 2000.

P. Lashermes, M. C. Combes, A. Ribas, A. Cenci, and E. H. Mah-e-l, Genetic and physical mapping of the SH3 region that confers resistance to leaf rust in coffee tree, Coffea arabica L.). Tree Genetics & Genomes, vol.6, pp.973-980, 2010.

P. Lashermes, M. C. Combes, J. Robert, P. Trouslot, D. 'hont et al., Molecular characterisation and origin of the Coffea arabica L. genome, Molecular and General Genetics, vol.261, pp.259-266, 1999.

P. Lashermes, M. C. Combes, P. Trouslot, and A. Charrier, Phylogenetic relationships of coffee-tree species (Coffea L.) as inferred from ITS sequences of nuclear ribosomal DNA, Theoretical and Applied Genetics, vol.94, pp.947-955, 1997.
DOI : 10.1007/s001220050500

A. R. Leitch and I. J. Leitch, Genomic plasticity and the diversity of polyploid plants, Science, vol.320, pp.481-483, 2008.

H. Li and R. Durbin, Fast and accurate short read alignment with BurrowsWheeler transform, Bioinformatics, vol.25, pp.1754-1760, 2009.
DOI : 10.1093/bioinformatics/btp324
URL : https://academic.oup.com/bioinformatics/article-pdf/25/14/1754/605544/btp324.pdf

Z. Liu and K. L. Adams, Expression partitioning between genes duplicated by polyploidy under abiotic stress and during organ development, Current Biology, vol.17, pp.1669-1674, 2007.
DOI : 10.1016/j.cub.2007.08.030
URL : https://doi.org/10.1016/j.cub.2007.08.030

M. Lynch and J. Conery, The evolutionary fate and consequences of duplicate genes, Science, vol.290, pp.1151-1155, 2000.
DOI : 10.1126/science.290.5494.1151

A. Madlung, Polyploidy and its effects on evolutionary success: old questions revisited with new tools, Heredity, vol.110, pp.99-104, 2013.
DOI : 10.1038/hdy.2012.79
URL : https://www.nature.com/articles/hdy201279.pdf

A. Mckenna, M. Hanna, E. Banks, A. Sivachenko, K. Cibulskis et al., The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data, Genome Research, vol.20, pp.1297-1303, 2010.

K. Mochida, Y. Yamazaki, and Y. Ogihara, Discrimination of homoeologous gene expression in hexaploid wheat by SNP analysis of contigs grouped from a large number of expressed sequence tags, Molecular Genetics and Genomics, vol.270, pp.371-377, 2003.

A. Mortazavi, B. A. Williams, K. Mccue, L. Schaeffer, and B. Wold, Mapping and quantifying mammalian transcriptomes by RNA-Seq, Nature Methods, vol.5, pp.621-628, 2008.
DOI : 10.1038/nmeth.1226

T. Nomura, A. Ishihara, R. C. Yanagita, T. R. Endo, and H. Iwamura, Three genomes differentially contribute to the biosynthesis of benzoxazinones in hexaploid wheat, Proceedings of the National Academy of Sciences, vol.102, pp.490-506, 2005.

T. C. Osborn, J. C. Pires, J. A. Birchler, D. L. Auger, Z. J. Chen et al., Understanding mechanisms of novel gene expression in polyploids, Trends in Genetics, vol.19, pp.141-147, 2003.
DOI : 10.1016/s0168-9525(03)00015-5

S. P. Otto and J. Whitton, Polyploid incidence and evolution, Annual Review of Genetics, vol.34, pp.401-437, 2000.
DOI : 10.1146/annurev.genet.34.1.401
URL : http://www.zoology.ubc.ca/~otto/Reprints/OttoWhitton2000.pdf

D. Pignatta and L. Comai, Parental squabbles and genome expression: lessons from the polyploids, Journal of Biology, vol.8, p.43, 2009.
DOI : 10.1186/jbiol140
URL : https://jbiol.biomedcentral.com/track/pdf/10.1186/jbiol140?site=jbiol.biomedcentral.com

R. A. Rapp, J. A. Udall, and J. F. Wendel, Genomic expression dominance in allopolyploids, BMC Biology, vol.7, p.18, 2009.
DOI : 10.1186/1741-7007-7-18
URL : https://bmcbiol.biomedcentral.com/track/pdf/10.1186/1741-7007-7-18?site=bmcbiol.biomedcentral.com

N. C. Riddle and J. A. Birchler, Effects of reunited diverged regulatory hierarchies in allopolyploids and species hybrids, Trends in Genetics, vol.19, pp.597-600, 2003.

X. Shi, D. Ng, C. Zhang, L. Comai, W. Ye et al., Cis-and trans-regulatory divergence between progenitor species determines gene-expression novelty in Arabidopsis allopolyploids, Nature Communications, vol.3, p.950, 2012.
DOI : 10.1038/ncomms1954
URL : http://www.nature.com/articles/ncomms1954.pdf

K. Stamati, I. Mackay, and W. Powell, A quantitative genomic imbalance gene expression assay in a hexaploid species: wheat (Triticum aestivum), 2009.
DOI : 10.1139/g08-096

, Genome/ National Research Council Canada, vol.52, pp.89-94

R. A. Veitia, S. Bottani, and J. A. Birchler, Cellular reaction to gene dosage imbalance: genomic, transcriptomic and proteomic effects, Trends in Genetics, vol.24, pp.390-397, 2008.

R. O. Vidal, J. Mondego, D. Pot, A. B. Ambrosio, A. C. Andrade et al., A high-throughput data mining of single nucleotide polymorphisms in Coffea species expressed sequence tags suggests differential homeologous gene expression in the allotetraploid Coffea arabica, Plant Physiology, vol.154, pp.1053-1066, 2010.

J. Wang, L. Tian, H. S. Lee, N. E. Wei, H. Jiang et al., Genomewide nonadditive gene regulation in Arabidopsis allotetraploids, Genetics, vol.172, pp.507-517, 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.

M. J. Yoo, E. Szadkowski, and J. F. Wendel, Homeolog expression bias and expression level dominance in allopolyploid cotton, Heredity, vol.110, pp.171-180, 2012.

Q. Yu, R. Guyot, A. De-kochko, A. Byers, R. Navajas-p-erez et al., Micro-collinearity and genome evolution in the vicinity of an ethylene receptor gene of cultivated diploid and allopolyploid coffee species (Coffea), Plant Journal, vol.67, pp.305-317, 2011.

, Selon les phénomènes étudiés, les résultats de ces études révèlent des variations plus

K. L. Adams, R. Cronn, R. Percifield, and J. F. Wendel, Genes duplicated by polyploidy show unequal contributions to the transcriptome and organ-specific reciprocal silencing, Proc. Natl. Acad. Sci. U.S.A, vol.100, pp.4649-4654, 2003.

K. L. Adams, R. Percifield, and J. F. Wendel, Organ-specific silencing of duplicated genes in a newly synthesized cotton allotetraploid, Genetics, vol.168, pp.2217-2226, 2004.

M. L. Ainouche, P. M. Fortune, A. Salmon, C. Parisod, M. Grandbastien et al.,

M. , Hybridization, polyploidy and invasion: lessons from Spartina (Poaceae), Biol. Invasions, vol.11, pp.1159-1173, 2009.

M. Ainouche, H. Chelaifa, J. Ferreira, S. Bellot, A. Ainouche et al., Polyploid evolution in Spartina : dealing with highly redundant hybride genomes. in Polyploidy and genome evolution. Soltis PS and Soltis DE, 2012.

S. Akama, R. Shimizu-inatsugi, K. K. Shimizu, and J. Sese, Genome-wide quantification of homeolog expression ratio revealed nonstochastic gene regulation in synthetic allopolyploid Arabidopsis, Nucleic Acids Res, vol.42, p.46, 2014.

W. Albertin, A. K. Balliau, T. Brabant, P. Davanture, M. Malosse et al., Differential regulation of gene products in newly synthesized Brassica napus allotetraploids is not related to protein function nor subcellular localization, BMC Genomics, vol.8, p.56, 2007.

W. Albertin, T. Balliau, P. Brabant, A. Chèvre, F. Eber et al., Numerous and rapid nonstochastic modifications of gene products in newly synthesized Brassica napus allotetraploids, Genetics, vol.173, pp.1101-1113, 2006.
DOI : 10.1534/genetics.106.057554
URL : http://www.genetics.org/content/genetics/173/2/1101.full.pdf

W. Albertin and P. Marullo, Polyploidy in fungi: evolution after whole-genome duplication, Proc. R. Soc, vol.279, pp.2497-2509, 2012.
DOI : 10.1098/rspb.2012.0434
URL : http://rspb.royalsocietypublishing.org/content/royprsb/279/1738/2497.full.pdf

K. Alix, J. Joets, C. D. Ryder, J. Moore, G. C. Barker et al., The CACTA transposon Bot1 played a major role in Brassica genome divergence and gene proliferation, 2008.

, Plant J. Cell Mol. Biol, vol.56, pp.1030-1044

S. Anders and W. Huber, Differential expression analysis for sequence count data, Genome Biol, vol.11, p.106, 2010.
DOI : 10.1038/npre.2010.4282.1
URL : http://precedings.nature.com/documents/4282/version/1/files/npre20104282-1.pdf

F. Anthony, C. Combes, C. Astorga, B. Bertrand, G. Graziosi et al., The origin of cultivated Coffea arabica L. varieties revealed by AFLP and SSR markers, TAG Theor. Appl. Genet. Theor. Angew. Genet, vol.104, pp.894-900, 2002.

F. Anthony and P. Lashermes, Origin, evolution, and diversity of the Coffee (Coffea arabica L, 2005.

, genome in Plant Genome: Biodiversity and Evolution, vol.1

A. K. Sharma and A. Sharma,

F. Anthony, L. Diniz, M. Combes, and P. Lashermes, Adaptive radiation in Coffea subgenus, 2010.

L. Coffea, Rubiaceae) in Africa and Madagascar, Plant Syst. Evol, vol.285, pp.51-64

N. Arrigo and M. S. Barker, Rarely successful polyploids and their legacy in plant genomes, Curr. Opin. Plant Biol, vol.15, pp.140-146, 2012.

M. J. Axtell, Classification and comparison of small RNAs from plants, Annu. Rev. Plant Biol, vol.64, pp.137-159, 2013.

S. J. Baldwin and B. C. Husband, Genome duplication and the evolution of conspecific pollen precedence, Proc. R. Soc. Lond. B Biol. Sci, vol.278, pp.2011-2017, 2011.

A. Bardil, J. D. De-almeida, M. C. Combes, P. Lashermes, and B. Bertrand, Genomic expression dominance in the natural allopolyploid Coffea arabica is massively affected by growth temperature, New Phytol, vol.192, pp.760-774, 2011.

F. S. Barreto, R. J. Pereira, and R. S. Burton, Hybrid dysfunction and physiological compensation in gene expression, Mol. Biol. Evol, vol.32, pp.613-622, 2015.

G. 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, Genome Biol. Evol, vol.5, pp.1309-1323, 2013.

F. Berthou, C. Mathieu, and F. Vedel, Chloroplast and mitochondrial DNA variation as indicator of phylogenetic relationships in the genus Coffea L, Theor. Appl. Genet, vol.65, pp.77-84, 1983.

J. A. Birchler, H. Yao, S. Chudalayandi, D. Vaiman, and R. A. Veitia, Heterosis. Plant Cell Online, vol.22, pp.2105-2112, 2010.

A. Blum, Heterosis, stress, and the environment: a possible road map towards the general improvement of crop yield, J. Exp. Bot, 2013.

A. Bombarely, K. D. Edwards, J. Sanchez-tamburrino, and L. A. Mueller, Deciphering the complex leaf transcriptome of the allotetraploid species Nicotiana tabacum: A phylogenomic perspective, BMC Genomics, vol.13, p.406, 2012.

F. Bretagnolle and J. D. Thompson, Gametes with the somatic chromosome number: mechanisms of their formation and role in the evolution of autopolyploid plants, New Phytol, vol.129, pp.1-22, 1995.

R. Buggs, S. Chamala, W. Wu, L. Gao, G. D. May et al.,

, Characterization of duplicate gene evolution in the recent natural allopolyploid Tragopogon miscellus by next-generation sequencing and Sequenom iPLEX MassARRAY genotyping, Mol. Ecol, vol.19, pp.132-146

R. Buggs, S. Chamala, W. Wu, J. A. Tate, P. S. Schnable et al., Rapid, repeated, and clustered loss of duplicate genes in allopolyploid plant populations of independent origin, Curr. Biol. CB, vol.22, pp.248-252, 2012.

R. Buggs, P. S. Soltis, and D. E. Soltis, Does hybridization between divergent progenitors drive wholegenome duplication?, Mol. Ecol, vol.18, pp.3334-3339, 2009.

R. Buggs, J. F. Wendel, J. J. Doyle, D. E. Soltis, P. S. Soltis et al., The legacy of diploid progenitors in allopolyploid gene expression patterns, Philos. Trans. R. Soc. B Biol. Sci, vol.369, 2014.

R. Buggs, L. Zhang, N. Miles, J. A. Tate, L. Gao et al., Transcriptomic shock generates evolutionary novelty in a newly formed, natural allopolyploid plant, Curr. Biol. CB, vol.21, pp.551-556, 2011.

A. Carvalho and C. A. Krug, Genética de Coffea XIII-Hereditariedade da característica erecta em Coffea arabica L, Bragantia, vol.10, pp.321-328, 1950.

A. Cenci, M. Combes, and P. Lashermes, Comparative sequence analyses indicate that Coffea (Asterids) and Vitis (Rosids) derive from the same paleo-hexaploid ancestral genome, Mol. Genet. Genomics, vol.283, pp.493-501, 2010.

A. Cenci, M. 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.

B. Chalhoub, F. Denoeud, S. Liu, I. Parkin, H. Tang et al.,

B. , Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome, Science, vol.345, pp.950-953, 2014.

P. L. Chang, B. P. Dilkes, M. Mcmahon, L. Comai, and S. V. Nuzhdin, Homoeolog-specific retention and use in allotetraploid Arabidopsis suecica depends on parent of origin and network partners, Genome Biol, vol.11, p.125, 2010.

H. Chelaifa, A. Monnier, and M. Ainouche, Transcriptomic changes following recent natural hybridization and allopolyploidy in the salt marsh species Spartina x townsendii and Spartina anglica (Poaceae), New Phytol, vol.186, pp.161-174, 2010.
URL : https://hal.archives-ouvertes.fr/hal-01117096

J. Chen, V. Nolte, and C. Schlötterer, Temperature stress mediates decanalization and dominance of gene expression in Drosophila melanogaster, PLoS Genet, vol.11, p.1004883, 2015.

Z. J. Chen, Genetic and epigenetic mechanisms for gene expression and phenotypic variation in Ppant polyploids, Annu. Rev. Plant Biol, vol.58, pp.377-406, 2007.

Z. J. Chen, Molecular mechanisms of polyploidy and hybrid vigor, Trends Plant Sci, vol.15, pp.57-71, 2010.

Z. J. Chen and Z. Ni, Mechanisms of genomic rearrangements and gene expression changes in plant polyploids, BioEssays, vol.28, pp.240-252, 2006.

M. Chester, J. P. Gallagher, V. V. Symonds, A. Silva, . Da et al.,

, Extensive chromosomal variation in a recently formed natural allopolyploid species, Tragopogon miscellus (Asteraceae), Proc. Natl. Acad. Sci, vol.109, pp.1176-1181

R. K. Chodavarapu, S. Feng, B. Ding, S. A. Simon, D. Lopez et al., Transcriptome and methylome interactions in rice hybrids, Proc. Natl. Acad. Sci. U.S.A, vol.109, pp.12040-12045, 2012.

J. E. Coate, H. Bar, and J. J. Doyle, Extensive translational regulation of gene expression in an allopolyploid (Glycine dolichocarpa), Plant Cell, vol.26, pp.136-150, 2014.

M. Combes, A. Cenci, H. Baraille, B. Bertrand, and P. Lashermes, Homeologous gene expression in response to growing temperature in a recent Allopolyploid (Coffea arabica L.), J. Hered, vol.103, pp.36-46, 2012.

M. Combes, Y. Hueber, A. Dereeper, S. Rialle, J. C. Herrera et al., Regulatory divergence between parental alleles determines gene expression patterns in hybrids, Genome Biology Evolution, vol.7, pp.1110-1121, 2015.

G. C. Conant, J. A. Birchler, and J. C. Pires, Dosage, duplication, and diploidization: clarifying the interplay of multiple models for duplicate gene evolution over time, Curr. Opin. Plant Biol, vol.19, pp.91-98, 2014.

G. C. Conant and K. H. Wolfe, Turning a hobby into a job: How duplicated genes find new functions, Nat. Rev. Genet, vol.9, pp.938-950, 2008.

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.

J. D. Coolon and P. J. Wittkopp, Cis-and trans-Regulation in Drosophila Interspecific Hybrids, Polyploid and Hybrid Genomics, 2013.

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.

D. J. Crawford, J. J. Doyle, D. E. Soltis, P. S. Soltis, and J. F. Wendel, Contemporary and future studies in plant speciation, morphological/floral evolution and polyploidy: honouring the scientific contributions of, 2014.

D. Leslie, Gottlieb to plant evolutionary biology, Philos. Trans. R. Soc. B Biol. Sci, vol.369, 20130341.

J. Cros, M. C. Combes, N. Chabrillange, and C. Duperray, Monnot des Angles A, Hamon S. 1995. Nuclear DNA content in the subgenus Coffea (Rubiaceae): inter-and intra-specif ic variation in African species, Can. J. Bot, pp.14-20

J. Cros, M. C. Combes, P. Trouslot, F. Anthony, S. Hamon et al., Phylogenetic analysis of chloroplast DNA variation in Coffea L, Mol. Phylogenet. Evol, vol.9, pp.109-117, 1998.

L. Cui, P. K. Wall, J. H. Leebens-mack, B. G. Lindsay, D. E. Soltis et al., Widespread genome duplications throughout the history of flowering plants, Genome Res, vol.16, pp.738-749, 2006.

F. M. Damatta and J. Ramalho, Impacts of drought and temperature stress on coffee physiology and production: a review, Braz. J. Plant Physiol, vol.18, pp.55-81, 2006.

F. M. Damatta, C. P. Ronchi, M. Maestri, and R. S. Barros, Ecophysiology of coffee growth and production, Braz. J. Plant Physiol, vol.19, pp.485-510, 2007.

A. P. Davis, R. Govaerts, D. M. Bridson, and P. Stoffelen, An annotated taxonomic conspectus of the genus Coffea (Rubiaceae), Bot. J. Linn. Soc, vol.152, pp.465-512, 2006.

A. P. Davis, J. Tosh, N. Ruch, and M. F. Fay, Growing coffee: Psilanthus (Rubiaceae) subsumed on the basis of molecular and morphological data; implications for the size, morphology, distribution and evolutionary history of Coffea, Bot. J. Linn. Soc, vol.167, pp.357-377, 2011.

R. B. Deal and S. Henikoff, Histone variants and modifications in plant gene regulation, Curr. Opin. Plant Biol, vol.14, pp.116-122, 2011.
DOI : 10.1016/j.pbi.2010.11.005
URL : http://europepmc.org/articles/pmc3093162?pdf=render

F. Denoeud, L. Carretero-paulet, A. Dereeper, G. Droc, R. Guyot et al., The coffee genome provides insight into the convergent evolution of caffeine biosynthesis, Science, vol.345, pp.1181-1184, 2014.

T. Eilam, Y. Anikster, E. Millet, J. Manisterski, and M. Feldman, Nuclear DNA amount and genome downsizing in natural and synthetic allopolyploids of the genera Aegilops and Triticum, Genome, vol.51, issue.8, pp.616-643, 2008.

T. Eilam, Y. Anikster, E. Millet, J. Manisterski, and M. Feldman, Genome Size in Diploids, Allopolyploids, and Autopolyploids of Mediterranean Triticeae, J. Bot, p.341380, 2010.
DOI : 10.1155/2010/341380
URL : http://downloads.hindawi.com/journals/jb/2010/341380.pdf

J. J. Emerson and W. 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.

B. J. Evans, A. R. Pyron, and J. J. Wiens, Polyploidization and Sex Chromosome Evolution in Amphibians in Polyploidy and genome evolution. Soltis PS and Soltis DE, 2012.
DOI : 10.1007/978-3-642-31442-1_18

D. '-erfurth, I. Jolivet, S. Froger, N. , C. O. Novatchkova et al., Turning meiosis into mitosis, PLoS Biol, vol.7, p.1000124, 2009.

D. '-erfurth, I. Jolivet, S. Froger, N. , C. O. Novatchkova et al., Mutations in AtPS1 (Arabidopsis thaliana parallel spindle 1) lead to the production of diploid pollen grains, PLoS Genet, vol.4, p.1000274, 2008.

M. C. Estep, M. R. Mckain, D. V. Diaz, J. Zhong, J. G. Hodge et al., Allopolyploidy, diversification, and the Miocene grassland expansion, Proc. Natl. Acad. Sci, vol.111, pp.15149-15154, 2014.
DOI : 10.1073/pnas.1404177111
URL : http://www.pnas.org/content/111/42/15149.full.pdf

J. A. Fawcett, S. Maere, and Y. Van-de-peer, Plants with double genomes might have had a better chance to survive the Cretaceous-Tertiary extinction event, Proc. Natl. Acad. Sci, vol.106, pp.5737-5742, 2009.
DOI : 10.1073/pnas.0900906106
URL : http://www.pnas.org/content/106/14/5737.full.pdf

M. Feldman and A. A. Levy, Genome evolution due to allopolyploidization in wheat, Genetics, vol.192, pp.763-774, 2012.
DOI : 10.1534/genetics.112.146316
URL : http://www.genetics.org/content/genetics/192/3/763.full.pdf

M. Feldman, B. Liu, G. Segal, S. Abbo, A. A. Levy et al., Rapid elimination of low-copy DNA sequences in polyploid wheat: a possible mechanism for differentiation of homoeologous chromosomes, Genetics, vol.147, pp.1381-1387, 1997.

L. E. Flagel, L. Chen, B. Chaudhary, and J. F. Wendel, Coordinated and fine-scale control of homoeologous gene expression in allotetraploid cotton, J. Hered, vol.100, pp.487-490, 2009.
DOI : 10.1093/jhered/esp003

L. E. Flagel and J. F. Wendel, Gene duplication and evolutionary novelty in plants, New Phytol, vol.183, pp.557-564, 2009.
DOI : 10.1111/j.1469-8137.2009.02923.x
URL : http://onlinelibrary.wiley.com/doi/10.1111/j.1469-8137.2009.02923.x/pdf

L. E. Flagel and J. F. Wendel, Evolutionary rate variation, genomic dominance and duplicate gene expression evolution during allotetraploid cotton speciation, New Phytol, vol.186, pp.184-193, 2010.
DOI : 10.1111/j.1469-8137.2009.03107.x
URL : http://onlinelibrary.wiley.com/doi/10.1111/j.1469-8137.2009.03107.x/pdf

L. Flagel, J. Udall, D. Nettleton, and J. Wendel, Duplicate gene expression in allopolyploid Gossypium reveals two temporally distinct phases of expression evolution, BMC Biol, vol.6, p.16, 2008.

A. Force, M. Lynch, F. B. Pickett, A. Amores, Y. L. Yan et al., Preservation of duplicate genes by complementary, degenerative mutations, Genetics, vol.151, pp.1531-1545, 1999.

R. T. Gaeta, C. Pires, and J. , Homoeologous recombination in allopolyploids: the polyploid ratchet, New Phytol, vol.186, pp.18-28, 2010.

R. T. Gaeta, J. C. Pires, F. Iniguez-luy, L. E. Osborn, and T. C. , Genomic changes in resynthesized Brassica napus and their effect on gene expression and phenotype, Plant Cell, vol.19, pp.3403-3417, 2007.

O. Garsmeur, J. C. Schnable, A. Almeida, C. Jourda, D. 'hont et al., Two evolutionarily distinct classes of paleopolyploidy, Mol. Biol. Evol, vol.31, pp.448-454, 2014.

M. A. Gehan, K. Greenham, T. C. Mockler, and C. R. Mcclung, Transcriptional networks-crops, clocks, and abiotic stress, Curr. Opin. Plant Biol, vol.24, pp.39-46, 2015.

M. Grassias and P. Kammacher, Observations sur la conjugaison chromosomique de Coffea arabica L, 1975.

T. Café-cacao, , vol.19, pp.177-190

R. M. Graze, L. M. Mcintyre, B. J. Main, M. L. Wayne, and S. V. Nuzhdin, , 2009.

, Drosophila melanogaster and Drosophila simulans, a genomewide analysis of Allele-Specific Expression, Genetics, vol.183, pp.547-561

R. M. Graze, L. L. Novelo, V. Amin, J. M. Fear, G. Casella et al., Allelic imbalance in Drosophila hybrid heads: exons, isoforms, and evolution, Mol. Biol. Evol, vol.29, pp.1521-1532, 2012.

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, 2014.

I. K. Greaves, M. Groszmann, H. Ying, J. M. Taylor, W. J. Peacock et al., Trans Chromosomal Methylation in Arabidopsis hybrids, Proc. Natl. Acad. Sci, vol.109, pp.3570-3575, 2012.

M. Groszmann, I. K. Greaves, Z. I. Albertyn, G. N. Scofield, W. J. Peacock et al., 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, J. P. Gallagher, E. P. Szadkowski, M. J. Yoo, L. E. Flagel et al., 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

C. E. Grover, Y. Yu, R. A. Wing, A. H. Paterson, and J. F. Wendel, A phylogenetic analysis of indel dynamics in the cotton genus, Mol. Biol. Evol, vol.25, pp.1415-1428, 2008.

M. W. Hahn, Distinguishing among evolutionary models for the maintenance of gene duplicates, J. Hered, vol.100, pp.605-617, 2009.

M. Ha, Understanding the chromatin remodeling code, Plant Sci, vol.211, pp.137-145, 2013.

M. Ha, J. Lu, L. Tian, V. Ramachandran, K. D. Kasschau et al.,

Z. J. Chen, Small RNAs serve as a genetic buffer against genomic shock in Arabidopsis interspecific hybrids and allopolyploids, Proc. Natl. Acad. Sci, vol.106, pp.17835-17840, 2009.

P. Hamon, P. Duroy, C. Dubreuil-tranchant, D. Mafra, P. Costa et al., Two novel Ty1-copia retrotransposons isolated from coffee trees can effectively reveal evolutionary relationships in the Coffea genus (Rubiaceae), Mol. Genet. Genomics, vol.285, pp.447-460, 2011.

M. Hao, J. Luo, D. Zeng, L. Zhang, S. Ning et al., QTug.sau-3B Is a Major Quantitative Trait Locus for Wheat Hexaploidization, Genes Genomes Genetics, vol.4, pp.1943-1953, 2014.

F. He, X. Zhang, J. Hu, F. Turck, X. Dong et al., 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, G. L. Barker, I. D. Wilson, R. J. Abbott, K. J. Edwards et al., Transcriptome shock after interspecific hybridization in Senecio is ameliorated by genome duplication, Curr. Biol, vol.16, pp.1652-1659, 2006.

J. Heslop-harrison, Genome evolution: extinction, continuation or explosion?, Curr. Opin. Plant Biol, vol.15, pp.115-121, 2012.
DOI : 10.1016/j.pbi.2012.03.006

H. E. Hoekstra and J. A. Coyne, The locus of evolution: evo devo and the genetics of adaptation, Evol. Int. J. Org. Evol, vol.61, pp.995-1016, 2007.

R. Hovav, J. A. Udall, B. Chaudhary, R. Rapp, L. Flagel et al., Partitioned expression of duplicated genes during development and evolution of a single cell in a polyploid plant, Proc. Natl. Acad. Sci, vol.105, pp.6191-6195, 2008.

A. L. Hughes, The evolution of functionally novel proteins after gene duplication, Proc. Biol. Sci, vol.256, pp.119-124, 1994.

G. Hu, J. Koh, M. Yoo, S. Chen, and J. F. Wendel, Gene-expression novelty in allopolyploid cotton: a proteomic perspective, Genetics, vol.200, pp.91-104, 2015.

H. Innan and F. Kondrashov, The evolution of gene duplications: classifying and distinguishing between models, Nat. Rev. Genet, vol.11, pp.97-108, 2010.

E. Jablonka and M. J. Lamb, The inheritance of acquired epigenetic variations, Int. J. Epidemiol, 2015.

O. Jaillon, J. Aury, B. Noel, A. Policriti, C. Clepet et al., The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla, Nature, vol.449, pp.463-467, 2007.
URL : https://hal.archives-ouvertes.fr/inria-00180136

A. B. James, N. H. Syed, S. Bordage, J. Marshall, G. A. Nimmo et al.,

H. G. , Alternative splicing mediates responses of the Arabidopsis circadian clock to temperature changes, Plant Cell, vol.24, pp.961-981, 2012.

E. Jenczewski and A. K. , From Diploids to Allopolyploids: The emergence of efficient pairing control genes in plants, Crit. Rev. Plant Sci, vol.23, pp.21-45, 2004.

Y. Jiao and A. H. Paterson, Polyploidy-associated genome modifications during land plant evolution, Philos. Trans. R. Soc. B Biol. Sci, vol.369, 2014.
DOI : 10.1098/rstb.2013.0355
URL : http://rstb.royalsocietypublishing.org/content/369/1648/20130355.full.pdf

Y. Jiao, N. J. Wickett, S. Ayyampalayam, A. S. Chanderbali, L. Landherr et al., Ancestral polyploidy in seed plants and angiosperms, Nature, vol.473, p.97, 2011.
DOI : 10.1038/nature09916

K. Kashkush, M. Feldman, and A. A. Levy, Transcriptional activation of retrotransposons alters the expression of adjacent genes in wheat, Nat. Genet, vol.33, pp.102-106, 2002.

M. Kellis, B. W. Birren, and E. S. Lander, Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces cerevisiae, Nature, vol.428, pp.617-624, 2004.

M. Kenan-eichler, D. Leshkowitz, L. Tal, E. Noor, C. Melamed-bessudo et al., Wheat hybridization and polyploidization results in deregulation of small RNAs, Genetics, vol.188, pp.263-272, 2011.

J. Koh, S. Chen, N. Zhu, F. Yu, P. S. Soltis et al., Comparative proteomics of the recently and recurrently formed natural allopolyploid Tragopogon mirus (Asteraceae) and its parents, New Phytol, vol.196, pp.292-305, 2012.

J. Koh, P. S. Soltis, and D. E. Soltis, Homeolog loss and expression changes in natural populations of the recently and repeatedly formed allotetraploid Tragopogon mirus (Asteraceae), BMC Genomics, vol.11, p.97, 2010.

C. A. Krug and A. Mendes, Cytological observations in Coffea. IV, J. Genet, vol.39, pp.189-203, 1940.

D. Kuo, K. Licon, S. Bandyopadhyay, R. Chuang, C. Luo et al., , 2010.

, Coevolution within a transcriptional network by compensatory trans and cis mutations, Genome Res, vol.20, pp.1672-1678

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, Single-locus inheritance in the allotetraploid Coffea arabica L. and interspecific Hybrid C. arabica x C. canephora, J. Hered, vol.91, pp.81-85, 2000.

P. Lashermes, M. Combes, Y. Hueber, D. Severac, and A. Dereeper, Genome rearrangements derived from homoeologous recombination following allopolyploidy speciation in coffee, Plant J, vol.78, pp.674-685, 2014.

P. Lashermes, M. Combes, J. Robert, P. Trouslot, D. 'hont et al., Molecular characterisation and origin of the Coffea arabica L. genome, Mol. Gen. Genet, vol.261, pp.259-266, 1999.

P. Lashermes, J. Cros, M. C. Combes, P. Trouslot, F. Anthony et al., Inheritance and restriction fragment length polymorphism of chloroplast DNA in the genus Coffea L, Theor. Appl. Genet, vol.93, pp.626-632, 1996.

P. Lashermes, J. Cros, P. Marmey, and A. Charrier, Use of random amplified DNA markers to analyse genetic variability and relationships of Coffea species, Genet. Resour. Crop Evol, vol.40, pp.91-99, 1993.

T. Lee, H. Kim, and I. Lee, Network-assisted crop systems genetics: network inference and integrative analysis, Curr. Opin. Plant Biol, vol.24, pp.61-70, 2015.

S. Liu, G. J. Baute, and K. L. Adams, Organ and cell type-specific complementary expression patterns and regulatory neofunctionalization between duplicated genes in Arabidopsis thaliana, Genome Biol. Evol, vol.3, pp.1419-1436, 2011.

Z. Liu and K. L. Adams, Expression Partitioning between Genes Duplicated by Polyploidy under Abiotic Stress and during Organ Development, Curr. Biol, vol.17, pp.1669-1674, 2007.

J. Louarn, Hybrides interspécifiques entre Coffea canephora Pierre et Coffea eugenioides Moore. Café-Cacao-Thé, vol.20, pp.433-452, 1976.

J. Louarn, J. C. Pires, L. E. Vogelzang, R. Oslach, L. Osborn et al., Patterns of sequence loss and cytosine methylation within a population of newly resynthesized Brassica napus allopolyploids, Structure génétique des caféiers africains diploïdes basée sur la fertilité des hybrides interspécifiques. Association Scientifique Internationale du Café, 15eme Colloque. Montpellier Lukens LN, vol.140, pp.336-348, 1993.

M. Lynch and A. Force, The probability of duplicate gene preservation by subfunctionalization, Genetics, vol.154, pp.459-473, 2000.

B. K. Mable, Why polyploidy is rarer in animals than in plants": myths and mechanisms, Biol. J. Linn. Soc, vol.82, pp.453-466, 2004.

B. K. Mable, M. A. Alexandrou, and M. I. Taylor, Genome duplication in amphibians and fish: an extended synthesis, J. Zool, vol.284, pp.151-182, 2011.

A. Madlung, Polyploidy and its effect on evolutionary success: old questions revisited with new tools, Heredity, vol.110, pp.99-104, 2012.

A. Madlung, R. W. Masuelli, B. Watson, S. H. Reynolds, J. Davison et al., Remodeling of DNA methylation and phenotypic and transcriptional changes in synthetic Arabidopsis allotetraploids, Plant Physiol, vol.129, pp.733-746, 2002.

A. Madlung, A. P. Tyagi, B. Watson, H. Jiang, T. Kagochi et al., Genomic changes in synthetic Arabidopsis polyploids, Plant J, vol.41, pp.221-230, 2004.

A. Madlung and J. F. Wendel, Genetic and epigenetic aspects of polyploid evolution in plants, Cytogenet. Genome Res, vol.140, pp.270-285, 2013.

H. Maherali, A. E. Walden, and B. C. Husband, Genome duplication and the evolution of physiological responses to water stress, New Phytol, vol.184, pp.721-731, 2009.

A. Marmagne, P. Brabant, H. Thiellement, and A. K. , Analysis of gene expression in resynthesized Brassica napus allotetraploids: transcriptional changes do not explain differential protein regulation, New Phytol, vol.186, pp.216-227, 2010.

P. Martinez-palacios, Réponse des composants non codants du génome-éléments transposables et petits

, ARNs-à un évènement allopolyploïde : le génome du colza (Brassica napus) comme modèle d'étude

O. Maurin, A. P. Davis, M. Chester, E. F. Mvungi, Y. Jaufeerally-fakim et al., Towards a Phylogeny for Coffea (Rubiaceae): identifying well-supported lineages based on nuclear and plastid DNA sequences, Ann. Bot, vol.100, pp.1565-1583, 2007.

I. Mayrose, S. H. Zhan, C. J. Rothfels, N. Arrigo, M. S. Barker et al., Methods for studying polyploid diversification and the dead end hypothesis: a reply to Soltis, New Phytol, vol.206, pp.27-35, 2014.

I. Mayrose, S. H. Zhan, C. J. Rothfels, K. Magnuson-ford, M. S. Barker et al., Recently formed polyploid plants diversify at lower rates, Science, vol.333, pp.1257-1257, 2011.

C. J. Mcmanus, J. D. Coolon, M. O. Duff, J. Eipper-mains, B. R. Graveley et al., Regulatory divergence in Drosophila revealed by mRNA-seq, Genome Res, vol.20, pp.816-825, 2010.

G. D. Moghe and S. Shiu, The causes and molecular consequences of polyploidy in flowering plants, Ann. N. Y. Acad. Sci, vol.1320, pp.16-34, 2014.

C. Montagnon, P. Cubry, and T. Leroy, Coffea canephora Pierre genetic improvement: Acquired knowledge, strategies and perspectives, Cah. Agric, vol.21, pp.143-153, 2006.

D. Ng, C. Zhang, M. Miller, Z. Shen, S. P. Briggs et al., Proteomic divergence in Arabidopsis autopolyploids and allopolyploids and their progenitors, Heredity, vol.108, pp.419-430, 2012.

Z. Ni, E. Kim, M. Ha, E. Lackey, J. Liu et al., Altered circadian rhythms regulate growth vigour in hybrids and allopolyploids, Nature, vol.457, pp.327-331, 2009.

T. Nomura, A. Ishihara, R. C. Yanagita, T. R. Endo, and H. Iwamura, Three genomes differentially contribute to the biosynthesis of benzoxazinones in hexaploid wheat, Proc. Natl. Acad. Sci. U. S. A, vol.102, pp.16490-16495, 2005.

K. Osabe, J. D. Clement, F. Bedon, F. A. Pettolino, L. Ziolkowski et al.,

, Genetic and DNA Methylation Changes in Cotton (Gossypium) Genotypes and Tissues, PLoS ONE, vol.9, p.86049

S. P. Otto, The Evolutionary Consequences of Polyploidy, Cell, vol.131, pp.452-462, 2007.

S. G. Palusa and A. Reddy, Differential recruitment of splice variants from SR pre-mRNAs to polysomes during development and in response to stresses, Plant Cell Physiol, vol.56, pp.421-427, 2015.

M. K. Pandit, M. Pocock, and W. E. Kunin, Ploidy influences rarity and invasiveness in plants, J. Ecol, vol.99, pp.1108-1115, 2011.
DOI : 10.1111/j.1365-2745.2011.01838.x
URL : https://besjournals.onlinelibrary.wiley.com/doi/pdf/10.1111/j.1365-2745.2011.01838.x

C. Parisod, Polyploids integrate genomic changes and ecological shifts, New Phytol, vol.193, pp.297-300, 2012.
DOI : 10.1111/j.1469-8137.2011.04008.x
URL : https://nph.onlinelibrary.wiley.com/doi/pdf/10.1111/j.1469-8137.2011.04008.x

C. Parisod, A. K. Just, J. Petit, M. Sarilar, V. Mhiri et al., Impact of transposable elements on the organization and function of allopolyploid genomes, New Phytol, vol.186, pp.37-45, 2010.
URL : https://hal.archives-ouvertes.fr/hal-01203938

C. Parisod, A. Salmon, T. Zerjal, M. Tenaillon, M. Grandbastien et al., Rapid structural and epigenetic reorganization near transposable elements in hybrid and allopolyploid genomes in Spartina, New Phytol, vol.184, pp.1003-1015, 2009.
DOI : 10.1111/j.1469-8137.2009.03029.x
URL : https://hal.archives-ouvertes.fr/hal-00448908

A. H. Paterson, J. E. Bowers, and B. A. Chapman, Ancient polyploidization predating divergence of the cereals, and its consequences for comparative genomics, Proc. Natl. Acad. Sci. U.S.A, vol.101, pp.9903-9908, 2004.

Y. Pécrix, G. Rallo, H. Folzer, M. Cigna, S. Gudin et al., Polyploidization mechanisms: temperature environment can induce diploid gamete formation in Rosa sp, J. Exp. Bot, vol.62, pp.3587-3597, 2011.

Y. Van-de-peer, J. A. Fawcett, S. Proost, L. Sterck, and K. Vandepoele, The flowering world: a tale of duplications, Trends Plant Sci, vol.14, pp.680-688, 2009.

M. Petit, C. Guidat, J. Daniel, E. Denis, E. Montoriol et al., Mobilization of retrotransposons in synthetic allotetraploid tobacco, New Phytol, vol.186, pp.135-147, 2010.
URL : https://hal.archives-ouvertes.fr/hal-01203912

I. Privat, A. Bardil, A. B. Gomez, D. Severac, C. Dantec et al., PUCE CAFE" Project: the first 15K coffee microarray, a new tool for discovering candidate genes correlated to agronomic and quality traits, BMC Genomics, vol.12, pp.5-5
URL : https://hal.archives-ouvertes.fr/hal-01788751

B. Prud'homme, N. Gompel, and S. B. Carroll, Emerging principles of regulatory evolution, Proc. Natl. Acad. Sci, vol.104, pp.8605-8612, 2007.

B. Qi, W. Huang, B. Zhu, X. Zhong, J. Guo et al., Global transgenerational gene expression dynamics in two newly synthesized allohexaploid wheat (Triticum aestivum) lines, BMC Biol, vol.10, p.3, 2012.
DOI : 10.1186/1741-7007-10-3
URL : https://bmcbiol.biomedcentral.com/track/pdf/10.1186/1741-7007-10-3

M. S. Ramanna and E. Jacobsen, Relevance of sexual polyploidization for crop improvement-A review, Euphytica, vol.133, pp.3-8, 2003.

J. Ramsey, Polyploidy and ecological adaptation in wild yarrow, Proc. Natl. Acad. Sci, vol.108, pp.7096-7101, 2011.
DOI : 10.1073/pnas.1016631108
URL : http://europepmc.org/articles/pmc3084070?pdf=render

J. Ramsey and D. W. Schemske, Pathways, mechanisms, and rates of polyploid formation in flowering plants, Annu. Rev. Ecol. Syst, vol.29, pp.467-501, 1998.

J. Ramsey and D. W. Schemske, Neopolyploidy in Flowering Plants, Annu. Rev. Ecol. Syst, vol.33, pp.589-639, 2002.
DOI : 10.1146/annurev.ecolsys.33.010802.150437

R. A. Rapp, J. A. Udall, and J. F. Wendel, Genomic expression dominance in allopolyploids, BMC Biol, vol.7, p.18, 2009.
DOI : 10.1186/1741-7007-7-18
URL : https://bmcbiol.biomedcentral.com/track/pdf/10.1186/1741-7007-7-18

R. A. Rapp and J. F. Wendel, Epigenetics and plant evolution, New Phytol, vol.168, pp.81-91, 2005.
DOI : 10.1111/j.1469-8137.2005.01491.x

A. Reddy, Y. Marquez, M. Kalyna, and A. Barta, Complexity of the alternative splicing landscape in plants, Plant Cell, vol.25, pp.3657-3683, 2013.

S. Renny-byfield, M. Chester, A. Kova?ík, S. Comber, M. Grandbastien et al., Next generation sequencing reveals genome downsizing in allotetraploid Nicotiana tabacum, predominantly through the elimination of paternally derived repetitive DNAs, Mol. Biol. Evol, vol.28, pp.2843-2854, 2011.

S. Renny-byfield, A. Kova?ík, M. Chester, R. A. Nichols, J. Macas et al., Independent, rapid and targeted loss of highly repetitive DNA in natural and synthetic allopolyploids of Nicotiana tabacum, PLoS ONE, vol.7, p.36963, 2012.

S. Renny-byfield, A. Kovarik, L. J. Kelly, J. Macas, P. Novak et al., Diploidization and genome size change in allopolyploids is associated with differential dynamics of low-and high-copy sequences, Plant J, vol.74, pp.829-839, 2013.
URL : https://hal.archives-ouvertes.fr/hal-01190554

S. Renny-byfield and J. F. Wendel, Doubling down on genomes: Polyploidy and crop plants, Am. J. Bot, vol.101, pp.1711-1725, 2014.

A. Salmon, M. L. Ainouche, and J. F. Wendel, Genetic and epigenetic consequences of recent hybridization and polyploidy in Spartina (Poaceae), Mol. Ecol, vol.14, pp.1163-1175, 2005.

A. Salmon, L. Flagel, Y. B. Udall, J. A. Wendel, and J. F. , Homoeologous nonreciprocal recombination in polyploid cotton, New Phytol, vol.186, pp.123-134, 2010.
URL : https://hal.archives-ouvertes.fr/hal-01097005

T. Saminathan, P. Nimmakayala, S. Manohar, S. Malkaram, A. Almeida et al., Differential gene expression and alternative splicing between diploid and tetraploid watermelon, J. Exp. Bot, vol.66, pp.1369-1385, 2015.

C. D. Schlichting and M. A. Wund, Phenotypic plasticity and epigenetic marking: an assessment of evidence for genetic accommodation, Evolution, vol.68, pp.656-672, 2014.

M. E. Schranz, S. Mohammadin, and P. P. Edger, Ancient whole genome duplications, novelty and diversification: the WGD Radiation Lag-Time Model, Curr. Opin. Plant Biol, vol.15, pp.147-153, 2012.

H. Shen, H. He, J. Li, W. Chen, X. Wang et al., Genomewide analysis of DNA methylation and gene expression changes in two Arabidopsis ecotypes and their reciprocal hybrids, Plant Cell, vol.24, pp.875-892, 2012.

Y. Shen, Y. Zhang, J. Zou, J. Meng, and J. Wang, Comparative proteomic study on Brassica hexaploid and its parents provides new insights into the effects of polyploidization, J. Proteomics, vol.112, pp.274-284, 2015.

Y. Shen, Z. Zhou, Z. Wang, W. Li, C. Fang et al., Global dissection of alternative splicing in paleopolyploid soybean, Plant Cell, vol.26, pp.996-1008, 2014.

D. Smet, R. Adams, K. L. Vandepoele, K. , V. Montagu et al., , 2013.

, Convergent gene loss following gene and genome duplications creates single-copy families in flowering plants, Proc. Natl. Acad. Sci. U.S.A, vol.110, pp.2898-2903

D. E. Soltis, V. A. Albert, J. Leebens-mack, C. D. Bell, A. H. Paterson et al., Polyploidy and angiosperm diversification, Am J Bot, vol.96, pp.336-348, 2009.

D. E. Soltis, R. Buggs, J. J. Doyle, and P. S. Soltis, What we still don't know about polyploidy, Taxon, vol.59, pp.1387-1403, 2010.

D. E. Soltis, R. Buggs, W. B. Barbazuk, S. Chamala, M. Chester et al.,

, The early stages of polyploidy : rapid and repeated evolution in Tragopogon. in Polyploidy and genome evolution. Soltis PS and Soltis DE

D. E. Soltis, M. C. Segovia-salcedo, I. Jordon-thaden, L. Majure, N. M. Miles et al., Are polyploids really evolutionary dead-ends (again)? A critical reappraisal of Mayrose, New Phytol, vol.202, pp.1105-1117, 2011.
DOI : 10.1111/nph.12756
URL : http://onlinelibrary.wiley.com/doi/10.1111/nph.12756/pdf

D. E. Soltis, C. J. Visger, and P. S. Soltis, The polyploidy revolution then?and now: Stebbins revisited, Am. J. Bot, vol.101, pp.1057-1078, 2014.
DOI : 10.3732/ajb.1400178
URL : http://www.amjbot.org/content/101/7/1057.full.pdf

K. Stamati, I. Mackay, and W. Powell, A quantitative genomic imbalance gene expression assay in a hexaploid species: wheat (Triticum aestivum), Genome, vol.52, pp.89-94, 2009.
DOI : 10.1139/g08-096

D. L. Stern and V. Orgogozo, The loci of evolution: how predictable is genetic evolution? Evolution, vol.62, pp.2155-2177, 2008.

N. H. Syed, M. Kalyna, Y. Marquez, A. Barta, and J. Brown, Alternative splicing in plants-coming of age, Trends Plant Sci, vol.17, pp.616-623, 2012.

E. Szadkowski, F. Eber, V. Huteau, M. Lodé, C. Huneau et al., The first meiosis of resynthesized Brassica napus, a genome blender, New Phytol, vol.186, pp.102-112, 2010.
URL : https://hal.archives-ouvertes.fr/hal-00729633

J. A. Tate, P. Joshi, K. A. Soltis, P. S. Soltis, and D. E. Soltis, On the road to diploidization? Homoeolog loss in independently formed populations of the allopolyploid Tragopogon miscellus (Asteraceae), BMC Plant Biol, vol.9, p.80, 2009.

J. A. Tate, Z. Ni, A. Scheen, J. Koh, C. A. Gilbert et al., Evolution and expression of homeologous loci in Tragopogon miscellus (Asteraceae), a recent and reciprocally formed allopolyploid, Genetics, vol.173, pp.1599-1611, 2006.

A. S. Thomas, The wild coffees of Uganda, Empire journal of Experimental Agriculture, vol.12, issue.45, p.1, 1944.

B. C. Thomas, B. Pedersen, and M. Freeling, Following tetraploidy in an Arabidopsis ancestor, genes were removed preferentially from one homeolog leaving clusters enriched in dose-sensitive genes, 2006.
DOI : 10.1101/gr.4708406
URL : http://genome.cshlp.org/content/16/7/934.full.pdf

, Genome Res, vol.16, pp.934-946

K. A. Thompson, B. C. Husband, and H. Maherali, Climatic niche differences between diploid and tetraploid cytotypes of Chamerion angustifolium (Onagraceae), Am. J. Bot, vol.101, pp.1868-1875, 2014.

I. Tirosh, N. Sigal, and N. Barkai, Divergence of nucleosome positioning between two closely related yeast species: genetic basis and functional consequences, Mol. Syst. Biol, vol.6, p.365, 2010.

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.

K. Vanneste, G. Baele, S. Maere, and Y. Van-de-peer, Analysis of 41 plant genomes supports a wave of successful genome duplications in association with the Cretaceous-Paleogene boundary, Genome. Research, 2014.

K. Vanneste, S. Maere, and Y. Van-de-peer, Tangled up in two: a burst of genome duplications at the end of the Cretaceous and the consequences for plant evolution, Philos. Trans. R. Soc. Lond. B. Biol. Sci, vol.369, 1648.

B. Wang and V. Brendel, Genomewide comparative analysis of alternative splicing in plants, Proc. Natl. Acad. Sci. U.S.A, vol.103, pp.7175-7180, 2006.

J. Wang, L. Tian, H. Lee, and Z. J. Chen, Nonadditive regulation of FRI and FLC loci mediates flowering-time variation in Arabidopsis allopolyploids, Genetics, vol.173, pp.965-974, 2006.

J. Wang, L. Tian, H. Lee, N. E. Wei, H. Jiang et al., Genomewide Nonadditive Gene Regulation in Arabidopsis Allotetraploids, Genetics, vol.172, pp.507-517, 2006.

J. Wang, L. Tian, A. Madlung, H. Lee, M. Chen et al.,

, Stochastic and epigenetic changes of gene expression in Arabidopsis polyploids, Genetics, vol.167, pp.1961-1973

Y. Wang, X. Wang, and A. H. Paterson, Genome and gene duplications and gene expression divergence: a view from plants, Ann. N. Y. Acad. Sci, vol.1256, pp.1-14, 2012.

Z. Wang, X. Sun, Y. Zhao, X. Guo, H. Jiang et al., Evolution of gene regulation during transcription and translation, Genome Biol. Evol, vol.7, pp.1155-1167, 2015.

H. Weiss-schneeweiss, K. Emadzade, T. Jang, and G. M. Schneeweiss, Evolutionary consequences, constraints and potential of polyploidy in plants, Cytogenet. Genome Res, vol.140, pp.137-150, 2013.

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.

P. J. Wittkopp and G. Kalay, Cis-regulatory elements: molecular mechanisms and evolutionary processes underlying divergence, Nat. Rev. Genet, vol.13, pp.59-69, 2012.

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

M. R. Woodhouse, J. C. Schnable, B. S. Pedersen, E. Lyons, D. Lisch et al., Following tetraploidy in maize, a short deletion mechanism removed genes preferentially from one of the two homeologs, PLoS Biol, vol.8, p.1000409, 2010.

T. E. Wood, N. Takebayashi, M. S. Barker, I. Mayrose, P. B. Greenspoon et al., The frequency of polyploid speciation in vascular plants, Proc Natl Acad Sci U.S.A, vol.106, pp.13875-13879, 2009.

W. Xiong, X. Li, D. Fu, J. Mei, Q. Li et al., DNA methylation alterations at 5?-CCGG sites in the interspecific and intraspecific hybridizations derived from Brassica rapa and Brassica napus, PLoS ONE, vol.8, p.65946, 2013.

Z. Xiong, R. T. Gaeta, and J. C. Pires, Homoeologous shuffling and chromosome compensation maintain genome balance in resynthesized allopolyploid Brassica napus, Proc. Natl. Acad. Sci. U.S.A, vol.108, p.7908, 2011.

C. Xu, Y. Bai, X. Lin, N. Zhao, L. Hu et al., Genome-wide disruption of gene expression in allopolyploids but not hybrids of rice subspecies, Mol. Biol. Evol, vol.31, pp.1066-1076, 2014.

Y. Xu, L. Zhong, X. Wu, X. Fang, and J. Wang, Rapid alterations of gene expression and cytosine methylation in newly synthesized Brassica napus allopolyploids, Planta, vol.229, pp.471-483, 2009.

C. Yang, L. Zhao, H. Zhang, Z. Yang, H. Wang et al., Evolution of physiological responses to salt stress in hexaploid wheat, Proc. Natl. Acad. Sci, vol.111, pp.11882-11887, 2014.

X. Yang, C. Ye, Z. Cheng, T. J. Tschaplinski, S. D. Wullschleger et al., Genomic aspects of research involving polyploid plants, Plant Cell Tissue Organ Cult, vol.104, pp.387-397, 2010.

M. Yoo, E. Szadkowski, and J. F. Wendel, Homoeolog expression bias and expression level dominance in allopolyploid cotton, Heredity, vol.110, pp.171-180, 2012.
URL : https://hal.archives-ouvertes.fr/hal-01515003

P. G. Zhang, S. Z. Huang, A. Pin, and K. L. Adams, Extensive divergence in alternative splicing patterns after gene and genome duplication during the evolutionary history of Arabidopsis, Mol. Biol. Evol, vol.27, pp.1686-1697, 2010.

N. Zhao, B. Zhu, M. Li, L. Wang, L. Xu et al., Extensive and heritable epigenetic remodeling and genetic stability accompany allohexaploidization of wheat, Genetics, vol.188, pp.499-510, 2011.

R. Zhou, N. Moshgabadi, and K. L. Adams, Extensive changes to alternative splicing patterns following allopolyploidy in natural and resynthesized polyploids, Proc. Natl. Acad. Sci, vol.108, pp.16122-16127, 2011.

X. Zhou, L. Z. Ma, and H. , Phylogenetic detection of numerous gene duplications shared by animals, fungi and plants, Genome Biol, vol.11, issue.4, 2010.