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O. Couronne, Alexander Poliakov, Nicolas Bray, T. Ishkhanov, D. Ryaboy, E. Rubin, L. Pachter, I. Dubchak (2003)
Strategies and tools for whole-genome alignments.Genome research, 13 1
J. Heslop-Harrison, A. Brandes, S. Taketa, T. Schmidt, A. Vershinin, E. Alkhimova, A. Kamm, R. Doudrick, T. Schwarzacher, A. Katsiotis, S. Kubis, Amar Kumar, S. Pearce, A. Flavell, G. Harrison (2004)
The chromosomal distributions of Ty1-copia group retrotransposable elements in higher plants and their implications for genome evolutionGenetica, 100
Qingyi Yu, R. Guyot, A. Kochko, A. Byers, R. Navajas-Pérez, B. Langston, Christine Dubreuil-Tranchant, A. Paterson, V. Poncet, C. Nagai, R. Ming (2011)
Micro-collinearity and genome evolution in the vicinity of an ethylene receptor gene of cultivated diploid and allotetraploid coffee species (Coffea).The Plant journal : for cell and molecular biology, 67 2
Perla Hamon, M. Séguin, X. Perrier, Jean-Christophe Glaszmann (1999)
Diversité génétique des plantes tropicales cultivées
S. Dussert, Philippe Lashermes, F. Anthony, C. Montagnon, Pierre Trouslot, M. Combes, J. Berthaud, M. Noirot, S. Hamon (1999)
Le caféier, Coffea canephora
W. Oa, Jetty Ammiraju, Fei Lu, Abhijit Sanyal, Yeisoo Yu, Xiang Song, Ning Jiang, A. Pontaroli, T. Rambo, J. Currie, K. Collura, J. Talag, Chuanzhu Fan, J. Goicoechea, A. Zuccolo, Jinfeng Chen, J. Bennetzen, Mingsheng Chen, Scott Jackson, R. Wing
Dynamic Evolution of Oryza Genomes Is Revealed by Comparative Genomic Analysis of a Genus-wide Vertical Data Set
(2010)
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
P. Lashermes, M. Combes, J. Robert, P. Trouslot, A. D'Hont, F. Anthony, A. Charrier (1999)
Molecular characterisation and origin of the Coffea arabica L. genomeMolecular and General Genetics MGG, 261
S. Noir, S. Patheyron, M. Combes, P. Lashermes, B. Chalhoub (2004)
Construction and characterisation of a BAC library for genome analysis of the allotetraploid coffee species (Coffea arabica L.)Theoretical and Applied Genetics, 109
F. Anthony, L. Diniz, M. Combes, P. Lashermes (2010)
Adaptive radiation in Coffea subgenus Coffea L. (Rubiaceae) in Africa and MadagascarPlant Systematics and Evolution, 285
J. Salse, S. Bolot, Michaël Throude, Vincent Jouffe, B. Piégu, U. Quraishi, Thomas Calcagno, R. Cooke, M. Delseny, Catherine Feuilleta (2008)
Identification and Characterization of Shared Duplications between Rice and Wheat Provide New Insight into Grass Genome Evolution
Robert Gaeta, J. Pires (2010)
Homoeologous recombination in allopolyploids: the polyploid ratchet.The New phytologist, 186 1
E. Paux, D. Roger, E. Badaeva, G. Gay, M. Bernard, P. Sourdille, C. Feuillet (2006)
Characterizing the composition and evolution of homoeologous genomes in hexaploid wheat through BAC-end sequencing on chromosome 3B.The Plant journal : for cell and molecular biology, 48 3
N. Chantret, J. Salse, F. Sabot, S. Rahman, A. Bellec, B. Laubin, Ivan Dubois, C. Dossat, P. Sourdille, P. Joudrier, M. Gautier, L. Cattolico, M. Beckert, S. Aubourg, J. Weissenbach, M. Caboche, M. Bernard, P. Leroy, B. Chalhoub (2005)
Molecular Basis of Evolutionary Events That Shaped the Hardness Locus in Diploid and Polyploid Wheat Species (Triticum and Aegilops)w⃞The Plant Cell Online, 17
J. Ramsey, D. Schemske (2002)
NEOPOLYPLOIDY IN FLOWERING PLANTSAnnual Review of Ecology, Evolution, and Systematics, 33
K. Wolfe (2001)
Yesterday's polyploids and the mystery of diploidizationNature Reviews Genetics, 2
T. Wicker, F. Sabot, A. Hua-Van, J. Bennetzen, P. Capy, B. Chalhoub, A. Flavell, P. Leroy, M. Morgante, O. Panaud, E. Paux, P. SanMiguel, A. Schulman (2007)
A unified classification system for eukaryotic transposable elementsNature Reviews Genetics, 8
A. Ribas, A. Cenci, M. Combes, H. Etienne, P. Lashermes (2011)
Organization and molecular evolution of a disease-resistance gene cluster in coffee treesBMC Genomics, 12
J. Udall, P. Quijada, T. Osborn (2005)
Detection of Chromosomal Rearrangements Derived From Homeologous Recombination in Four Mapping Populations of Brassica napus L.Genetics, 169
A. Cenci, M. Combes, P. Lashermes (2010)
Comparative sequence analyses indicate that Coffea (Asterids) and Vitis (Rosids) derive from the same paleo-hexaploid ancestral genomeMolecular Genetics and Genomics, 283
G. Tuskan, S. DiFazio, S. Jansson, J. Bohlmann, I. Grigoriev, U. Hellsten, N. Putnam, S. Ralph, S. Rombauts, A. Salamov, J. Schein, L. Sterck, A. Aerts, R. Bhalerao, R. Bhalerao, D. Blaudez, W. Boerjan, A. Brun, A. Brunner, V. Busov, M. Campbell, J. Carlson, M. Chalot, J. Chapman, G.-L. Chen, D. Cooper, P. Coutinho, J. Couturier, S. Covert, Q. Cronk, R. Cunningham, J. Davis, S. Degroeve, A. Déjardin, C. dePamphilis, J. Detter, B. Dirks, I. Dubchak, S. Duplessis, J. Ehlting, B. Ellis, K. Gendler, D. Goodstein, M. Gribskov, J. Grimwood, A. Groover, L. Gunter, B. Hamberger, B. Heinze, Y. Helariutta, B. Henrissat, D. Holligan, R. Holt, W. Huang, N. Islam-Faridi, S. Jones, M. Jones-Rhoades, R. Jørgensen, C. Joshi, J. Kangasjärvi, J. Karlsson, C. Kelleher, R. Kirkpatrick, M. Kirst, A. Kohler, U. Kalluri, F. Larimer, J. Leebens-Mack, J. Leplé, P. LoCascio, Y. Lou, S. Lucas, F. Martin, B. Montanini, C. Napoli, D. Nelson, C. Nelson, K. Nieminen, O. Nilsson, V. Pereda, G. Peter, R. Philippe, G. Pilate, A. Poliakov, J. Razumovskaya, P. Richardson, C. Rinaldi, K. Ritland, P. Rouzé, D. Ryaboy, J. Schmutz, J. Schrader, B. Segerman, H. Shin, A. Siddiqui, F. Sterky, A. Terry, C. Tsai, E. Uberbacher, P. Unneberg, J. Vahala, K. Wall, S. Wessler, G. Yang, T. Yin, C. Douglas, M. Marra, G. Sandberg, Y. Peer, D. Rokhsar (2006)
The Genome of Black Cottonwood, Populus trichocarpa (Torr. & Gray)Science, 313
A. Salmon, Lex Flagel, B. Ying, J. Udall, J. Wendel (2010)
Homoeologous nonreciprocal recombination in polyploid cotton.The New phytologist, 186 1
Chunguang Du, Jason Caronna, Limei He, H. Dooner (2008)
Computational prediction and molecular confirmation of Helitron transposons in the maize genomeBMC Genomics, 9
K. Andreasen, Bruce Baldwin (2001)
Unequal evolutionary rates between annual and perennial lineages of checker mallows (Sidalcea, Malvaceae): evidence from 18S-26S rDNA internal and external transcribed spacers.Molecular biology and evolution, 18 6
S. Raina, Y. Mukai, M. Yamamoto (1998)
In situ hybridization identifies the diploid progenitor species of Coffea arabica (Rubiaceae)Theoretical and Applied Genetics, 97
N. Nassif, J. Penney, S. Pal, W. Engels, G. Gloor (1994)
Efficient copying of nonhomologous sequences from ectopic sites via P-element-induced gap repairMolecular and Cellular Biology, 14
(1975)
Observations sur la conjugaison chromosomique de Coffea arabica L
S. Ossowski, Korbinian Schneeberger, J. Lucas-Lledó, N. Warthmann, Richard Clark, R. Shaw, D. Weigel, M. Lynch (2010)
The Rate and Molecular Spectrum of Spontaneous Mutations in Arabidopsis thalianaScience, 327
A. Hua-Van, A. Rouzic, C. Maisonhaute, P. Capy (2005)
Abundance, distribution and dynamics of retrotransposable elements and transposons: similarities and differencesCytogenetic and Genome Research, 110
Kwangsoo Cho, C. O'Neill, Soo-Jin Kwon, Tae-Jin Yang, A. Smooker, F. Fraser, I. Bancroft (2010)
Sequence-level comparative analysis of the Brassica napus genome around two stearoyl-ACP desaturase loci.The Plant journal : for cell and molecular biology, 61 4
J. Laroche, J. Bousquet (1999)
Evolution of the mitochondrial rps3 intron in perennial and annual angiosperms and homology to nad5 intron 1.Molecular biology and evolution, 16 4
N. Chantret, J. Salse, F. Sabot, A. Bellec, B. Laubin, Ivan Dubois, C. Dossat, P. Sourdille, P. Joudrier, M. Gautier, L. Cattolico, M. Beckert, S. Aubourg, J. Weissenbach, M. Caboche, P. Leroy, M. Bernard, B. Chalhoub (2008)
Contrasted Microcolinearity and Gene Evolution Within a Homoeologous Region of Wheat and Barley SpeciesJournal of Molecular Evolution, 66
P. Musoli, P. Cubry, P. Aluka, C. Billot, M. Dufour, F. Bellis, D. Pot, D. Bieysse, André Charrier, T. Leroy (2009)
Genetic differentiation of wild and cultivated populations: diversity of Coffea canephora Pierre in Uganda.Genome, 52 7
Tree Genet Genomes
The Initiative (2000)
Analysis of the genome sequence of the flowering plant Arabidopsis thalianaNature, 408
T. Bureau, S. Wessler (1994)
Stowaway: a new family of inverted repeat elements associated with the genes of both monocotyledonous and dicotyledonous plants.The Plant cell, 6
R. Riley, V. Chapman (1958)
Genetic Control of the Cytologically Diploid Behaviour of Hexaploid WheatNature, 182
(2012)
Plant Mol Biol
P Lashermes, M Combes, A Ribas, A Cenci, L Mahé, H Etienne (2010)
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, 6
P Musoli, P Cubry, P Aluka, C Billot, M Dufour, F Bellis, D Pot, D Bieyesse, A Charrier, T Leroy (2009)
Genetic differentiation of wild and cultivated populations: diversity of Coffea canephora Pierre in UgandaGenome, 52
GA Tuskan, S DiFazio, S Jansson, J Bohlmann, I Grigoriev, U Hellsten, N Putnam, S Ralph, S Rombauts, A Salamov, J Schein, L Sterck, A Aerts, RR Bhalerao, RP Bhalerao, D Blaudez, W Boerjan, A Brun, A Brunner, V Busov, M Campbell, J Carlson, M Chalot, J Chapman, G Chen, D Cooper, PM Coutinho, J Couturier, S Covert, Q Cronk, R Cunningham, J Davis, S Degroeve, A Dejardin, C dePamphilis, J Detter, B Dirks, I Dubchak, S Duplessis, J Ehlting, B Ellis, K Gendler, D Goodstein, M Gribskov, J Grimwood, A Groover, L Gunter, B Hamberger, B Heinze, Y Helariutta, B Henrissat, D Holligan, R Holt, W Huang, N Islam-Faridi, S Jones, M Jones-Rhoades, R Jorgensen, C Joshi, J Kangasjarvi, J Karlsson, C Kelleher, R Kirkpatrick, M Kirst, A Kohler, U Kalluri, F Larimer, J Leebens-Mack, J Leple, P Locascio, Y Lou, S Lucas, F Martin, B Montanini, C Napoli, DR Nelson, C Nelson, K Nieminen, O Nilsson, V Pereda, G Peter, R Philippe, G Pilate, A Poliakov, J Razumovskaya, P Richardson, C Rinaldi, K Ritland, P Rouze, D Ryaboy, J Schmutz, J Schrader, B Segerman, H Shin, A Siddiqui, F Sterky, A Terry, C Tsai, E Uberbacher, P Unneberg, J Vahala, K Wall, S Wessler, G Yang, T Yin, D Rokhsar (2006)
Douglas C, Marra M, Sandberg G, Van de Peer YScience, 313
A. Zuccolo, A. Sebastian, J. Talag, Yeisoo Yu, Hyeran Kim, K. Collura, D. Kudrna, R. Wing (2007)
Transposable element distribution, abundance and role in genome size variation in the genus OryzaBMC Evolutionary Biology, 7
(2003)
LAGAN and Multi-LAGAN: efficient tools for large-scale multiple alignment of genomic DNA
H. Fu, H. Dooner (2002)
Intraspecific violation of genetic colinearity and its implications in maizeProceedings of the National Academy of Sciences of the United States of America, 99
Quang Le, S. Wright, Z. Yu, T. Bureau (2000)
Transposon diversity in Arabidopsis thaliana.Proceedings of the National Academy of Sciences of the United States of America, 97 13
N. Prakash, M. Combes, S. Dussert, S. Naveen, P. Lashermes (2005)
Analysis of genetic diversity in Indian robusta coffee genepool (Coffea canephora) in comparison with a representative core collection using SSRs and AFLPsGenetic Resources and Crop Evolution, 52
J. Salse, S. Bolot, Michaël Throude, Vincent Jouffe, B. Piégu, U. Quraishi, Thomas Calcagno, R. Cooke, M. Delseny, C. Feuillet (2008)
Identification and Characterization of Shared Duplications between Rice and Wheat Provide New Insight into Grass Genome Evolution[W]The Plant Cell Online, 20
L. Mahé, M. Combes, P. Lashermes (2007)
Comparison between a coffee single copy chromosomal region and Arabidopsis duplicated counterparts evidenced high level synteny between the coffee genome and the ancestral Arabidopsis genomePlant Molecular Biology, 64
J. Szostak, T. Orr-Weaver, R. Rothstein, F. Stahl (1983)
The double-strand-break repair model for recombinationCell, 33
O. Jaillon, J. Aury, Benjamin Noel, A. Policriti, C. Clépet, A. Casagrande, N. Choisne, S. Aubourg, N. Vitulo, Claire Jubin, A. Vezzi, F. Legeai, P. Hugueney, C. Dasilva, D. Horner, E. Mica, D. Jublot, J. Poulain, Clémence Bruyère, A. Billault, Béatrice Segurens, M. Gouyvenoux, Edgardo Ugarte, F. Cattonaro, Véronique Anthouard, V. Vico, Cristian Fabbro, M. Alaux, G. Gaspero, V. Dumas, Nicoletta Felice, S. Paillard, Irena Juman, M. Moroldo, S. Scalabrin, Aurélie Canaguier, I. Clainche, G. Malacrida, E. Durand, G. Pesole, V. Laucou, P. Chatelet, D. Merdinoglu, M. Delledonne, M. Pezzotti, A. Lecharny, C. Scarpelli, F. Artiguenave, M. Pè, G. Valle, M. Morgante, M. Caboche, A. Adam-Blondon, J. Weissenbach, F. Quétier, P. Wincker (2007)
The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phylaNature, 449
P. Lashermes, M. Combes, A. Ribas, A. Cenci, L. Mahé, H. Etienne (2010)
Genetic and physical mapping of the SH3 region that confers resistance to leaf rust in coffee tree (Coffea arabica L.)Tree Genetics & Genomes, 6
Jia-Xing Yue, Jinpeng Li, Dan Wang, H. Araki, Dacheng Tian, Sihai Yang (2010)
Genome-wide investigation reveals high evolutionary rates in annual model plantsBMC Plant Biology, 10
Shaoxing Huang, A. Sirikhachornkit, X. Su, J. Faris, B. Gill, R. Haselkorn, P. Gornicki (2002)
Genes encoding plastid acetyl-CoA carboxylase and 3-phosphoglycerate kinase of the Triticum/Aegilops complex and the evolutionary history of polyploid wheatProceedings of the National Academy of Sciences of the United States of America, 99
P. Lashermes, V. Paczek, P. Trouslot, M. Combes, E. Couturon, A. Charrier (2000)
Single-locus inheritance in the allotetraploid Coffea arabica L. and interspecific hybrid C. arabica x C. canephora.The Journal of heredity, 91 1
C. Gomez, S. Dussert, P. Hamon, S. Hamon, A. Kochko, V. Poncet (2009)
Current genetic differentiation of Coffea canephora Pierre ex A. Froehn in the Guineo-Congolian African zone: cumulative impact of ancient climatic changes and recent human activitiesBMC Evolutionary Biology, 9
Sequence comparison of orthologous regions enables estimation of the divergence between genomes, analysis of their evolution and detection of particular features of the genomes, such as sequence rearrangements and transposable elements. Despite the economic importance of Coffea species, little genomic information is currently available. Coffea is a relatively young genus that includes more than one hundred diploid species and a single tetraploid species. Three Coffea orthologous regions of 470–900 kb were analyzed and compared: both subgenomes of allotetraploid Coffea arabica (contributed by the diploid species Coffea eugenioides and Coffea canephora) and the genome of diploid C. canephora. Sequence divergence was calculated on global alignments or on coding and non-coding sequences separately. A search for transposable elements detected 43 retrotransposons and 198 transposons in the sequences analyzed. Comparative insertion analysis made it possible to locate 165 TE insertions in the phylogenetic tree of the three genomes/subgenomes. In the tetraploid C. arabica, a homoeologous non-reciprocal transposition (HNRT) was detected and characterized: a 50 kb region of the C. eugenioides derived subgenome replaced the C. canephora derived counterpart. Comparative sequence analysis on three Coffea genomes/subgenomes revealed almost perfect gene synteny, low sequence divergence and a high number of shared transposable elements. Compared to the results of similar analysis in other genera (Aegilops/Triticum and Oryza), Coffea genomes/subgenomes appeared to be dramatically less diverged, which is consistent with the relatively recent radiation of the Coffea genus. Based on nucleotide substitution frequency, the HNRT was dated at 10,000–50,000 years BP, which is also the most recent estimation of the origin of C. arabica.
Plant Molecular Biology – Springer Journals
Published: Nov 16, 2011
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