title: 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.
abstract: BACKGROUND
  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.
  
  
  RESULTS
  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.
  
  
  CONCLUSIONS
  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.
authors.affiliation: Biological Systems Department, UMR DAP TA 40/03, CIRAD, Montpellier, France. xavier.argout@cirad.fr
authors.forename: Xavier
authors.initials: X
authors.lastname: Argout
authors.forename: Olivier
authors.initials: O
authors.lastname: Fouet
authors.forename: Patrick
authors.initials: P
authors.lastname: Wincker
authors.forename: Karina
authors.initials: K
authors.lastname: Gramacho
authors.forename: Thierry
authors.initials: T
authors.lastname: Legavre
authors.forename: Xavier
authors.initials: X
authors.lastname: Sabau
authors.forename: Ange Marie
authors.initials: AM
authors.lastname: Risterucci
authors.forename: Corinne
authors.initials: C
authors.lastname: Da Silva
authors.forename: Julio
authors.initials: J
authors.lastname: Cascardo
authors.forename: Mathilde
authors.initials: M
authors.lastname: Allegre
authors.forename: David
authors.initials: D
authors.lastname: Kuhn
authors.forename: Joseph
authors.initials: J
authors.lastname: Verica
authors.forename: Brigitte
authors.initials: B
authors.lastname: Courtois
authors.forename: Gaston
authors.initials: G
authors.lastname: Loor
authors.forename: Regis
authors.initials: R
authors.lastname: Babin
authors.forename: Olivier
authors.initials: O
authors.lastname: Sounigo
authors.forename: Michel
authors.initials: M
authors.lastname: Ducamp
authors.forename: Mark J
authors.initials: MJ
authors.lastname: Guiltinan
authors.forename: Manuel
authors.initials: M
authors.lastname: Ruiz
authors.forename: Laurence
authors.initials: L
authors.lastname: Alemanno
authors.forename: Regina
authors.initials: R
authors.lastname: Machado
authors.forename: Wilberth
authors.initials: W
authors.lastname: Phillips
authors.forename: Ray
authors.initials: R
authors.lastname: Schnell
authors.forename: Martin
authors.initials: M
authors.lastname: Gilmour
authors.forename: Eric
authors.initials: E
authors.lastname: Rosenquist
authors.forename: David
authors.initials: D
authors.lastname: Butler
authors.forename: Siela
authors.initials: S
authors.lastname: Maximova
authors.forename: Claire
authors.initials: C
authors.lastname: Lanaud
mesh_terms: D002099:Cacao / Q000235:genetics*; D030561:Databases, Nucleic Acid; D020224:Expressed Sequence Tags; D020869:Gene Expression Profiling; D015723:Gene Library; D017343:Genes, Plant; D018745:Genome, Plant; D005838:Genotype; D020411:Oligonucleotide Array Sequence Analysis; D018749:RNA, Plant / Q000235:genetics; D017422:Sequence Analysis, DNA
chemical_list: D018749:RNA, Plant