Open Access Highly Accessed Research article

Towards the understanding of the cocoa transcriptome: Production and analysis of an exhaustive dataset of ESTs of Theobroma cacao L. generated from various tissues and under various conditions

Xavier Argout1*, Olivier Fouet1, Patrick Wincker2, Karina Gramacho3, Thierry Legavre1, Xavier Sabau1, Ange Marie Risterucci1, Corinne Da Silva2, Julio Cascardo4, Mathilde Allegre1, David Kuhn5, Joseph Verica6, Brigitte Courtois1, Gaston Loor7, Regis Babin89, Olivier Sounigo89, Michel Ducamp10, Mark J Guiltinan6, Manuel Ruiz1, Laurence Alemanno11, Regina Machado12, Wilberth Phillips13, Ray Schnell5, Martin Gilmour14, Eric Rosenquist15, David Butler16, Siela Maximova6 and Claire Lanaud1

Author Affiliations

1 Biological Systems Department – UMR DAP TA 40/03, CIRAD, Montpellier, France

2 GENOSCOPE, 2 rue Gaston Crémieux, 91057 Evry, France

3 CEPLAC, Km 22 Rod. Ilheus Itabuna, Cx. postal 07, Itabuna 45600-00, Bahia, Brazil

4 Laboratório de Genômica e Expressão GênicaRodovia Ilhéus-Itabuna, UESC, Km 16, Ilhéus, Brazil

5 USDA-ARS, 13601 Old Cutler Rd. Miami, Florida, USA

6 Department of Horticulture, The Pennsylvania State University, 422 Life Sciences Building, University Park, PA, 16802, USA

7 EET-Pichilingue, INIAP, Código Postal 24 Km 5 vía Quevedo El Empalme, Ecuador

8 IRAD, Nkolbisson, BP 2067, Yaoundé, Cameroon

9 UPR 31 TA 80/02, CIRAD, Montpellier, France

10 UMR BGPI TA41/K, CIRAD- 34398 Montpellier France

11 UMR BEPC TA 80/03, CIRAD, Montpellier, France

12 MASTERFOODS, Almirante, Brazil

13 CATIE, P.O.Box 7170, Turrialba, Costa Rica

14 Mars Inc., Dundee Road, Slough, SL1 4JX, UK

15 National Program Staff, USDA-ARS, Beltsville, Maryland 20705, USA

16 Cocoa Research Unit, The University of the West Indies, St. Augustine, Trinidad and Tobago

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BMC Genomics 2008, 9:512  doi:10.1186/1471-2164-9-512

Published: 30 October 2008



Theobroma cacao L., is a tree originated from the tropical rainforest of South America. It is one of the major cash crops for many tropical countries. T. cacao is mainly produced on smallholdings, providing resources for 14 million farmers. Disease resistance and T. cacao quality improvement are two important challenges for all actors of cocoa and chocolate production. T. cacao is seriously affected by pests and fungal diseases, responsible for more than 40% yield losses and quality improvement, nutritional and organoleptic, is also important for consumers. An international collaboration was formed to develop an EST genomic resource database for cacao.


Fifty-six cDNA libraries were constructed from different organs, different genotypes and different environmental conditions. A total of 149,650 valid EST sequences were generated corresponding to 48,594 unigenes, 12,692 contigs and 35,902 singletons. A total of 29,849 unigenes shared significant homology with public sequences from other species.

Gene Ontology (GO) annotation was applied to distribute the ESTs among the main GO categories.

A specific information system (ESTtik) was constructed to process, store and manage this EST collection allowing the user to query a database.

To check the representativeness of our EST collection, we looked for the genes known to be involved in two different metabolic pathways extensively studied in other plant species and important for T. cacao qualities: the flavonoid and the terpene pathways. Most of the enzymes described in other crops for these two metabolic pathways were found in our EST collection.

A large collection of new genetic markers was provided by this ESTs collection.


This EST collection displays a good representation of the T. cacao transcriptome, suitable for analysis of biochemical pathways based on oligonucleotide microarrays derived from these ESTs. It will provide numerous genetic markers that will allow the construction of a high density gene map of T. cacao. This EST collection represents a unique and important molecular resource for T. cacao study and improvement, facilitating the discovery of candidate genes for important T. cacao trait variation.