A first step in the understanding of the cocoa transcriptome: Analysis of an exhaustive dataset of ESTs on Theobroma cacao generated from various tissues and under various conditions

Argout Xavier, Fouet Olivier, Wincker Patrick, Gramacho Karina Peres, Legavre Thierry, Sabau Xavier, Risterucci Ange-Marie, Da Silva Corinne, Loor Solorzano Rey Gaston, Cascardo Julio Cezar M., Courtois Brigitte, Kuhn David N., Schnell Rey J., Babin Régis, Sounigo Olivier, Ducamp Michel, Verica Joseph, Guiltinan Mark J., Alemanno Laurence, Machado Regina, Phillips Wilbert, Maximova Siela N., Lanaud Claire. 2008. A first step in the understanding of the cocoa transcriptome: Analysis of an exhaustive dataset of ESTs on Theobroma cacao generated from various tissues and under various conditions. In : Abstracts of Plant and Animal Genomes XVIth Conference, San Diego, CA (USA), January 12-16, 2008. s.l. : s.n., Résumé Plant and Animal Genomes Conference. 16, San Diego, États-Unis, 12 January 2008/16 January 2008.

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Abstract : To better understand the cocoa transcriptome and to provide a framework for future investigations on cocoa functional genomics, approximately 175 000 cocoa clones from 52 cDNA libraries were sequenced. These libraries were constructed with RNA isolated from 13 genotypes (mainly from the two genotypes Scavina6 and ISC1) and from various tissues and organs (flowers, seeds, cherels, pod, shoot, root or embryos) under various conditions (fermentation, abiotic and biotic stresses). Suppression subtractive hybridisation (SSH) libraries were also produced under various plant pathogen interactions and from flowers pollinated by self compatible or incompatible pollen. From these cDNA libraries, 149 650 good quality ESTs were generated and analyzed using our "in house" bioinformatics pipeline. The assembly process produced 13837 contigs and 66746 singletons that represent 80583 different potential transcripts. These unigenes were assigned with BLASTX and BLASTN similarities, Gene Ontology annotation and protein domains. A comparison with public ESTs cocoa sequences already already available in public domain indicates that 80% of the unigenes may not have been described in public databases. (Texte intégral)

Mots-clés Agrovoc : Theobroma cacao

Classification Agris : F30 - Plant genetics and breeding

Auteurs et affiliations

  • Argout Xavier, CIRAD-BIOS-UMR DAP (FRA) ORCID: 0000-0002-0100-5511
  • Fouet Olivier, CIRAD-BIOS-UMR DAP (FRA) ORCID: 0000-0001-8547-1474
  • Wincker Patrick, Centre national de séquençage (FRA)
  • Gramacho Karina Peres, CEPLAC (BRA)
  • Legavre Thierry, CIRAD-BIOS-UMR DAP (FRA)
  • Sabau Xavier, CIRAD-BIOS-UMR DAP (FRA)
  • Risterucci Ange-Marie, CIRAD-BIOS-UMR DAP (FRA)
  • Da Silva Corinne, Centre national de séquençage (FRA)
  • Loor Solorzano Rey Gaston, INIAP (ECU)
  • Cascardo Julio Cezar M., UESC (BRA)
  • Courtois Brigitte, CIRAD-BIOS-UMR DAP (FRA) ORCID: 0000-0003-2118-7102
  • Kuhn David N., USDA (USA)
  • Schnell Rey J., USDA (USA)
  • Babin Régis, CIRAD-BIOS-UPR Bioagresseurs de pérennes (CMR) ORCID: 0000-0002-3753-1193
  • Sounigo Olivier, CIRAD-BIOS-UPR Bioagresseurs de pérennes (CMR) ORCID: 0000-0001-6278-8903
  • Ducamp Michel, CIRAD-BIOS-UMR BGPI (FRA)
  • Verica Joseph, Pennsylvania State University (USA)
  • Guiltinan Mark J., Pennsylvania State University (USA)
  • Alemanno Laurence
  • Machado Regina, Masterfoods (BRA)
  • Phillips Wilbert, CATIE (CRI)
  • Maximova Siela N., Pennsylvania State University (USA)
  • Lanaud Claire, CIRAD-BIOS-UMR DAP (FRA) ORCID: 0000-0001-6411-7310

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