Polyploidy and genome evolution in plants, Current Opinion in Plant Biology, vol.8, issue.2, pp.135-141, 2005. ,
DOI : 10.1016/j.pbi.2005.01.001
Organ-Specific Silencing of Duplicated Genes in a Newly Synthesized Cotton Allotetraploid, Genetics, vol.168, issue.4, pp.2217-2226, 2004. ,
DOI : 10.1534/genetics.104.033522
Genes duplicated by polyploidy show unequal contributions to the transcriptome and organ-specific reciprocal silencing, Proceedings of the National Academy of Sciences, vol.100, issue.8, pp.4649-4654, 2003. ,
DOI : 10.1073/pnas.0630618100
Evolution of Duplicate Gene Expression in Polyploid and Hybrid Plants, Journal of Heredity, vol.98, issue.2, pp.136-137, 2007. ,
DOI : 10.1093/jhered/esl061
The origin of cultivated Coffea arabica L. varieties revealed by AFLP and SSR markers. Theoretical and Applied genetics, pp.894-900, 2002. ,
Adaptive radiation in Coffea subgenus Coffea L. (Rubiaceae) in Africa and Madagascar, Plant Systematics and Evolution, vol.49, issue.1-2, pp.51-64, 2010. ,
DOI : 10.1007/s00606-009-0255-8
Dosage balance in gene regulation: biological implications. Trends in Genetic, pp.219-226, 2005. ,
DOI : 10.1016/j.tig.2005.02.010
Widespread paleopolyploidy in model plant species inferred from age distributions of duplicate genes. The Plant Cell, pp.1667-1678, 2004. ,
Gametes with the somatic chromosome number: mechanisms of their formation and role in the evolution of autopolyploid plants, New Phytologist, vol.13, issue.1, pp.1-22, 1995. ,
DOI : 10.1007/BF00035336
Tissue-specific silencing of homoeologs in natural populations of the recent allopolyploid Tragopogon mirus, New Phytologist, vol.229, issue.1, pp.175-183, 2010. ,
DOI : 10.1111/j.1469-8137.2010.03205.x
Does hybridization between divergent progenitors drive whole-genome duplication? Molecular Ecology, pp.3334-3339, 2009. ,
Comparative sequence analyses indicate that Coffea (Asterids) and Vitis (Rosids) derive from the same paleo-hexaploid ancestral genome, Molecular Genetics and Genomics, vol.174, issue.5, pp.493-501, 2010. ,
DOI : 10.1007/s00438-010-0534-7
Les caféiers. L'amélioration des plantes tropicales. coédition Cirad-Orstom, pp.171-196, 1988. ,
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
RNAi of met1 Reduces DNA Methylation and Induces Genome-Specific Changes in Gene Expression and Centromeric Small RNA Accumulation in Arabidopsis Allopolyploids, Genetics, vol.178, issue.4, pp.1845-1858, 2008. ,
DOI : 10.1534/genetics.107.086272
Molecular mechanisms of polyploidy and hybrid vigor, Trends in Plant Science, vol.15, issue.2, pp.57-71, 2010. ,
DOI : 10.1016/j.tplants.2009.12.003
Genetic and Epigenetic Mechanisms for Gene Expression and Phenotypic Variation in Plant Polyploids. Annual review of plant biology, pp.377-406, 2007. ,
Mechanisms of genomic rearrangements and gene expression changes in plant polyploids, BioEssays, vol.434, issue.3, pp.240-252, 2006. ,
DOI : 10.1002/bies.20374
First intergeneric hybrids (Psilanthusebracteolatus Hiern´CoffeaHiern´Hiern´Coffea arabica L.)in coffee trees, Canadian Journal of Botany, vol.76, pp.542-546, 1998. ,
DOI : 10.1139/b98-017
Duplicated genes evolve independently after polyploid formation in cotton, Proceedings of the National Academy of Sciences, vol.96, issue.25, pp.14406-14411, 1999. ,
DOI : 10.1073/pnas.96.25.14406
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC24449
(Rubiaceae): inter- and intra-specific variation in African species, Canadian Journal of Botany, vol.73, issue.1, pp.14-20, 1995. ,
DOI : 10.1139/b95-002
Phylogenetic Analysis of Chloroplast DNA Variation inCoffeaL, Molecular Phylogenetics and Evolution, vol.9, issue.1, pp.109-117, 1998. ,
DOI : 10.1006/mpev.1997.0453
Impacts of drought and temperature stress on coffee physiology and production: a review, Brazilian Journal of Plant Physiology, vol.18, issue.1, pp.55-81, 2006. ,
DOI : 10.1590/S1677-04202006000100006
Differential contributions to the transcriptome of duplicated genes in response to abiotic stresses in natural and synthetic polyploids, New Phytologist, vol.5, issue.Suppl. 1, pp.1045-1057, 2011. ,
DOI : 10.1111/j.1469-8137.2011.03650.x
Evolutionary Genetics of Genome Merger and Doubling in Plants, Annual Review of Genetics, vol.42, issue.1, pp.443-461, 2008. ,
DOI : 10.1146/annurev.genet.42.110807.091524
Plants with double genomes might have had a better chance to survive the Cretaceous-Tertiary extinction event, Proceedings of the National Academy of Sciences, pp.5737-5742, 2009. ,
DOI : 10.1073/pnas.0900906106
Rapid Elimination of Low-Copy DNA Sequences in Polyploid Wheat: A Possible Mechanism for Differentiation of Homoeologous Chromosomes, Genetics, vol.147, issue.3, pp.1381-1387, 1997. ,
Coordinated and Fine-Scale Control of Homoeologous Gene Expression in Allotetraploid Cotton, Journal of Heredity, vol.100, issue.4, pp.487-490, 2009. ,
DOI : 10.1093/jhered/esp003
Gene duplication and evolutionary novelty in plants, New Phytologist, vol.18, issue.3, pp.557-564, 2009. ,
DOI : 10.1111/j.1469-8137.2009.02923.x
Duplicate gene expression in allopolyploid Gossypium reveals two temporally distinct phases of expression evolution, BMC Biology, vol.6, issue.1, pp.1-16, 2008. ,
DOI : 10.1186/1741-7007-6-16
Genomic Changes in Resynthesized Brassica napus and Their Effect on Gene Expression and Phenotype, THE PLANT CELL ONLINE, vol.19, issue.11, pp.3403-3417, 2007. ,
DOI : 10.1105/tpc.107.054346
External factors accelerate expression divergence between duplicate genes. Trends in Genetic, pp.162-166, 2007. ,
DOI : 10.1016/j.tig.2007.02.005
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2065749
Distinguishing Among Evolutionary Models for the Maintenance of Gene Duplicates, Journal of Heredity, vol.100, issue.5, pp.605-617, 2009. ,
DOI : 10.1093/jhered/esp047
BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95, NT. Nucleic Acids Symposium, vol.98, issue.41, pp.95-98, 1999. ,
Introgression into the allotetraploid coffee ( Coffea arabica L.): segregation and recombination of the C. canephora genome in the tetraploid interspecific hybrid ( C. arabica ?? C. canephora), TAG Theoretical and Applied Genetics, vol.104, issue.4, pp.661-668, 2002. ,
DOI : 10.1007/s001220100747
Polyploidy and genome restructuring: a variety of outcomes, Current Opinion in Genetics & Development, vol.19, issue.6, pp.600-606, 2009. ,
DOI : 10.1016/j.gde.2009.10.005
Genomic and expression plasticity of polyploidy, Current Opinion in Plant Biology, vol.13, issue.2, pp.153-159, 2010. ,
DOI : 10.1016/j.pbi.2009.11.004
Ancestral polyploidy in seed plants and angiosperms, Nature, vol.38, issue.7345, pp.473-97, 2011. ,
DOI : 10.1038/nature09916
Transcriptional activation of retrotransposons alters the expression of adjacent genes in wheat, Nature Genetics, vol.160, issue.1, pp.102-106, 2002. ,
DOI : 10.1007/s004380000390
Origin and genetic diversity of Coffea arabica L. based on DNA molecular markers, 16ème Colloque Scientifique International sur le Café, pp.9-14, 1995. ,
Brief communication. Single-locus inheritance in the allotetraploid Coffea arabica L. and interspecific Hybrid C. arabica X C. canephora, Journal of Heredity, vol.91, issue.1, pp.81-85, 2000. ,
DOI : 10.1093/jhered/91.1.81
Molecular analysis of introgressive breeding in coffee ( Coffea arabica L.), Theoretical and Applied Genetics, pp.139-146, 2000. ,
DOI : 10.1007/s001220050019
Molecular characterisation and origin of the Coffea arabica L. genome. Molecular and General Genetics, pp.259-266, 1999. ,
Phylogenetic relationships of coffee-tree species ( Coffea L.) as inferred from ITS sequences of nuclear ribosomal DNA, TAG Theoretical and Applied Genetics, vol.94, issue.6-7, pp.947-955, 1997. ,
DOI : 10.1007/s001220050500
Genetic and physical mapping of the SH3 region that confers resistance to leaf rust in coffee tree (Coffea arabica L.), Tree Genetics & Genomes, vol.153, issue.6, pp.973-980, 2010. ,
DOI : 10.1007/s11295-010-0306-x
The Impact of Polyploidy on Grass Genome Evolution, PLANT PHYSIOLOGY, vol.130, issue.4, pp.1587-1593, 2002. ,
DOI : 10.1104/pp.015727
Polyploid formation in cotton is not accompanied by rapid genomic changes, Genome, vol.44, issue.3, pp.321-330, 2001. ,
DOI : 10.1139/g01-011
URL : http://orbi.ulg.ac.be/jspui/handle/2268/119320
Expression Partitioning between Genes Duplicated by Polyploidy under Abiotic Stress and during Organ Development, Current Biology, vol.17, issue.19, pp.1669-1674, 2007. ,
DOI : 10.1016/j.cub.2007.08.030
URL : http://doi.org/10.1016/j.cub.2007.08.030
The probability of duplicate gene preservation by subfunctionalization, Genetics, vol.154, issue.1, pp.459-473, 2000. ,
Genomic changes in synthetic Arabidopsis polyploids, The Plant Journal, vol.167, issue.2, pp.221-230, 2004. ,
DOI : 10.1111/j.1365-313X.2004.02297.x
A matter of size: developmental control of organ size in plants, Current Opinion in Plant Biology, vol.4, issue.6, pp.533-539, 2001. ,
DOI : 10.1016/S1369-5266(00)00212-0
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, issue.5, pp.371-377, 2003. ,
DOI : 10.1007/s00438-003-0939-7
Detection and effects of a homeologous reciprocal transposition in Brassica napus, Genetics, vol.165, issue.3, pp.1569-1577, 2003. ,
Understanding mechanisms of novel gene expression in polyploids, Trends in Genetics, vol.19, issue.3, pp.141-147, 2003. ,
DOI : 10.1016/S0168-9525(03)00015-5
The Evolutionary Consequences of Polyploidy, Cell, vol.131, issue.3, pp.452-462, 2007. ,
DOI : 10.1016/j.cell.2007.10.022
Impact of transposable elements on the organization and function of allopolyploid genomes. The New Phytologist, pp.37-45, 2010. ,
URL : https://hal.archives-ouvertes.fr/hal-01203938
The ploidy effects in plant gene expression: Progress, problems and prospects, Science in China Series C: Life Sciences, vol.129, issue.4, pp.295-301, 2008. ,
DOI : 10.1007/s11427-008-0039-3
Parental squabbles and genome expression: lessons from the polyploids, Journal of Biology, vol.8, issue.4, p.43, 2009. ,
DOI : 10.1186/jbiol140
URL : http://doi.org/10.1186/jbiol140
AFLP analysis of introgression in coffee cultivars (Coffea arabica L.)derived from a natural interspecific hybrid, Euphytica, issue.124, pp.265-271, 2002. ,
The marks, mechanisms and memory of epigenetic states in mammals, Biochemical Journal, vol.356, issue.1, pp.1-10, 2001. ,
DOI : 10.1042/bj3560001
PATHWAYS, MECHANISMS, AND RATES OF POLYPLOID FORMATION IN FLOWERING PLANTS, Annual Review of Ecology and Systematics, vol.29, issue.1, pp.467-501, 1998. ,
DOI : 10.1146/annurev.ecolsys.29.1.467
Epigenetics and plant evolution. The New Phytologist, pp.81-91, 2005. ,
DOI : 10.1111/j.1469-8137.2005.01491.x
Internal transcribed spacer repeat-specific primers and the analysis of hybridization in the Glycine tomentella (Leguminosae) polyploid complex, Molecular Ecology, vol.120, issue.12, pp.2691-2702, 2002. ,
DOI : 10.1046/j.1365-294X.2002.01640.x
Effects of reunited diverged regulatory hierarchies in allopolyploids and species hybrids, Trends in Genetics, vol.19, issue.11, pp.597-600, 2003. ,
DOI : 10.1016/j.tig.2003.09.005
Primer 3 on the WWW for general users and for biologist programmers, Bioinformatics Methods and Protocols: Methods in Molecular Biology, pp.365-386, 2000. ,
Genetic and epigenetic consequences of recent hybridization and polyploidy in Spartina (Poaceae), Molecular Ecology, vol.93, issue.4, pp.1163-1175, 2005. ,
DOI : 10.1111/j.1365-294X.2005.02488.x
Identification and Characterization of Shared Duplications between Rice and Wheat Provide New Insight into Grass Genome Evolution, THE PLANT CELL ONLINE, vol.20, issue.1, pp.11-24, 2008. ,
DOI : 10.1105/tpc.107.056309
URL : https://hal.archives-ouvertes.fr/hal-00964148
Multiple rounds of speciation associated with reciprocal gene loss in polyploid yeasts, Nature, vol.102, issue.7082, pp.341-345, 2006. ,
DOI : 10.1038/nature04562
Polyploidy: recurrent formation and genome evolution, Trends in Ecology & Evolution, vol.14, issue.9, pp.348-352, 1999. ,
DOI : 10.1016/S0169-5347(99)01638-9
Polyploidy and angiosperm diversification, American Journal of Botany, vol.96, issue.1, pp.336-348, 2009. ,
DOI : 10.3732/ajb.0800079
A quantitative genomic imbalance gene expression assay in a hexaploid species: wheat (Triticum aestivum), Genome, vol.52, issue.1, pp.89-94, 2009. ,
Detection of Chromosomal Rearrangements Derived From Homeologous Recombination in Four Mapping Populations of Brassica napus L., Genetics, vol.169, issue.2, pp.967-979, 2005. ,
DOI : 10.1534/genetics.104.033209
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, issue.3, pp.1053-1066, 2010. ,
DOI : 10.1104/pp.110.162438
Stochastic and Epigenetic Changes of Gene Expression in Arabidopsis Polyploids, Genetics, vol.167, issue.4, pp.1961-1973, 2004. ,
DOI : 10.1534/genetics.104.027896
Evolutionary changes in cis and trans gene regulation, Nature, vol.69, issue.6995, pp.85-88, 2004. ,
DOI : 10.1002/1097-010X(20001015)288:3<205::AID-JEZ2>3.0.CO;2-S
The frequency of polyploid speciation in vascular plants, Proceedings of the national Academy of sciences, pp.13875-13879, 2009. ,
DOI : 10.1073/pnas.0811575106
Genomic aspects of research involving polyploid plants, Plant Cell, Tissue and Organ Culture (PCTOC), vol.105, issue.3, pp.387-397, 2010. ,
DOI : 10.1007/s11240-010-9826-1
Phylogenetic detection of numerous gene duplications shared by animals, fungi and plants. genome biology, p.38, 2010. ,