Deciphering the genome structure and paleohistory of Theobroma cacao

Chaparro, Cristian, Murat, Florent, Carlson, John, Guignon, Valentin, Tahi, Mathias, Guiderdoni, Emmanuel, Legavre, Thierry, Fouet, Olivier, Sallet, Erika, Sabau, Xavier, Akaza, Joseph Moroh, Quetier, Francis, Guiltinan, Mark, Poulain, Julie, T., Schiex, Axtell, Michael, Pitollat, Bertrand, Panaud, Olivier, Maximova, Siela, Ruiz, Manuel, Dievart, Anne, Ma, Zhaorong, Gramacho, Karina, Wincker, Patrick, Roguet, Yolande, Kramer, Melissa, Zhang, Yufan, D’Hont, Angélique, Sidibe-Bocs, Stephanie, Lanaud, Claire, Argout, Xavier, Rodier-Goud, Maguy, Gelley, Laura, Brown, Spencer, Brunel, Dominique, Infante, Diogenes, Salse, Jerome, Barbosa-Neto, Jose Fernandes, Sh, Zi, Bourge, Mickael, Golser, Wolfgang, Kebe, Ismael, Aury, Jean Marc, Sabot, Francois, Bérard, Aurélie, Viot, Christopher, Song, Xiang, Costet, Pierre, Droc, Gaetan, Kudrna, Dave, Ammiraju, Jetty Siva, Boccara, Michel, Clement, Didier, Wing, Rod, Gouzy, Jerome, Abrouk, Michael, Schuster, Stephan, Risterucci, Ange Marie, Rivalan, Ronan, McCombie, W Richard, Allegre, Mathilde (2010) Deciphering the genome structure and paleohistory of Theobroma cacao. Nature Precedings. ISSN 1756-0357

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Abstract

We sequenced and assembled the genome of Theobroma cacao, an economically important tropical fruit tree crop that is the source of chocolate. The assembly corresponds to 76% of the estimated genome size and contains almost all previously described genes, with 82% of them anchored on the 10 T. cacao chromosomes. Analysis of this sequence information highlighted specific expansion of some gene families during evolution, for example flavonoid-related genes. It also provides a major source of candidate genes for T. cacao disease resistance and quality improvement. Based on the inferred paleohistory of the T. cacao genome, we propose an evolutionary scenario whereby the ten T. cacao chromosomes were shaped from an ancestor through eleven chromosome fusions. The T. cacao genome can be considered as a simple living relic of higher plant evolution.

Item Type:	Paper
Subjects:	bioinformatics bioinformatics > genomics and proteomics > genetics & nucleic acid processing bioinformatics > genomics and proteomics bioinformatics > genomics and proteomics > genetics & nucleic acid processing > genomes
CSHL Authors:	McCombie, W. Richard
Communities:	CSHL labs > McCombie lab
SWORD Depositor:	CSHL Elements
Depositing User:	CSHL Elements
Date:	2010
Date Deposited:	24 Mar 2026 18:32
Last Modified:	24 Mar 2026 18:32
Related URLs:	Publisher
URI:	https://repository.cshl.edu/id/eprint/42110

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