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

• Main Authors: Ruiz Manuel, Guiltinan Mark J, Ducamp Michel, Sounigo Olivier, Babin Regis, Loor Gaston, Courtois Brigitte, Verica Joseph, Kuhn David, Allegre Mathilde, Cascardo Julio, Da Silva Corinne, Risterucci Ange, Sabau Xavier, Legavre Thierry, Gramacho Karina, Wincker Patrick, Fouet Olivier, Argout Xavier, Alemanno Laurence, Machado Regina, Phillips Wilberth, Schnell Ray, Gilmour Martin, Rosenquist Eric, Butler David, Maximova Siela, Lanaud Claire
• Format: Article
• Language: English
• Published: BMC 2008-10-01
• Series: BMC Genomics
• Online Access: http://www.biomedcentral.com/1471-2164/9/512

<p>Abstract</p> <p>Background</p> <p><it>Theobroma cacao </it>L., is a tree originated from the tropical rainforest of South America. It is one of the major cash crops for many tropical countries. <it>T. cacao </it>is mainly produced on smallholdings, providing resources for 14 million farmers. Disease resistance and <it>T. cacao </it>quality improvement are two important challenges for all actors of cocoa and chocolate production. <it>T. cacao </it>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.</p> <p>Results</p> <p>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.</p> <p>Gene Ontology (GO) annotation was applied to distribute the ESTs among the main GO categories.</p> <p>A specific information system (ESTtik) was constructed to process, store and manage this EST collection allowing the user to query a database.</p> <p>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 <it>T. cacao </it>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.</p> <p>A large collection of new genetic markers was provided by this ESTs collection.</p> <p>Conclusion</p> <p>This EST collection displays a good representation of the <it>T. cacao </it>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 <it>T. cacao</it>. This EST collection represents a unique and important molecular resource for <it>T. cacao </it>study and improvement, facilitating the discovery of candidate genes for important <it>T. cacao </it>trait variation.</p>