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
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.
Main Authors: | , , , , , , , , , , , , , , , , , , , , , , , , , , , |
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Subjects: | F30 - Génétique et amélioration des plantes, H20 - Maladies des plantes, Theobroma cacao, adn, séquence nucléotidique, transcription, collection de matériel génétique, expression des gènes, génie génétique, résistance aux maladies, marqueur génétique, http://aims.fao.org/aos/agrovoc/c_7713, http://aims.fao.org/aos/agrovoc/c_2347, http://aims.fao.org/aos/agrovoc/c_27583, http://aims.fao.org/aos/agrovoc/c_35126, http://aims.fao.org/aos/agrovoc/c_36739, http://aims.fao.org/aos/agrovoc/c_27527, http://aims.fao.org/aos/agrovoc/c_15974, http://aims.fao.org/aos/agrovoc/c_2328, http://aims.fao.org/aos/agrovoc/c_24030, |
Online Access: | http://agritrop.cirad.fr/548501/ http://agritrop.cirad.fr/548501/1/document_548501.pdf |
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F30 - Génétique et amélioration des plantes H20 - Maladies des plantes Theobroma cacao adn séquence nucléotidique transcription collection de matériel génétique expression des gènes génie génétique résistance aux maladies marqueur génétique http://aims.fao.org/aos/agrovoc/c_7713 http://aims.fao.org/aos/agrovoc/c_2347 http://aims.fao.org/aos/agrovoc/c_27583 http://aims.fao.org/aos/agrovoc/c_35126 http://aims.fao.org/aos/agrovoc/c_36739 http://aims.fao.org/aos/agrovoc/c_27527 http://aims.fao.org/aos/agrovoc/c_15974 http://aims.fao.org/aos/agrovoc/c_2328 http://aims.fao.org/aos/agrovoc/c_24030 F30 - Génétique et amélioration des plantes H20 - Maladies des plantes Theobroma cacao adn séquence nucléotidique transcription collection de matériel génétique expression des gènes génie génétique résistance aux maladies marqueur génétique http://aims.fao.org/aos/agrovoc/c_7713 http://aims.fao.org/aos/agrovoc/c_2347 http://aims.fao.org/aos/agrovoc/c_27583 http://aims.fao.org/aos/agrovoc/c_35126 http://aims.fao.org/aos/agrovoc/c_36739 http://aims.fao.org/aos/agrovoc/c_27527 http://aims.fao.org/aos/agrovoc/c_15974 http://aims.fao.org/aos/agrovoc/c_2328 http://aims.fao.org/aos/agrovoc/c_24030 |
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F30 - Génétique et amélioration des plantes H20 - Maladies des plantes Theobroma cacao adn séquence nucléotidique transcription collection de matériel génétique expression des gènes génie génétique résistance aux maladies marqueur génétique http://aims.fao.org/aos/agrovoc/c_7713 http://aims.fao.org/aos/agrovoc/c_2347 http://aims.fao.org/aos/agrovoc/c_27583 http://aims.fao.org/aos/agrovoc/c_35126 http://aims.fao.org/aos/agrovoc/c_36739 http://aims.fao.org/aos/agrovoc/c_27527 http://aims.fao.org/aos/agrovoc/c_15974 http://aims.fao.org/aos/agrovoc/c_2328 http://aims.fao.org/aos/agrovoc/c_24030 F30 - Génétique et amélioration des plantes H20 - Maladies des plantes Theobroma cacao adn séquence nucléotidique transcription collection de matériel génétique expression des gènes génie génétique résistance aux maladies marqueur génétique http://aims.fao.org/aos/agrovoc/c_7713 http://aims.fao.org/aos/agrovoc/c_2347 http://aims.fao.org/aos/agrovoc/c_27583 http://aims.fao.org/aos/agrovoc/c_35126 http://aims.fao.org/aos/agrovoc/c_36739 http://aims.fao.org/aos/agrovoc/c_27527 http://aims.fao.org/aos/agrovoc/c_15974 http://aims.fao.org/aos/agrovoc/c_2328 http://aims.fao.org/aos/agrovoc/c_24030 Argout, Xavier Fouet, Olivier Wincker, Patrick Gramacho, Karina Peres Legavre, Thierry Sabau, Xavier Risterucci, Ange-Marie Da Silva, Corinne Cascardo, Julio Cezar M. Allègre, Mathilde Kuhn, David N. Verica, Joseph Courtois, Brigitte Loor, Rey Gaston Babin, Régis Sounigo, Olivier Ducamp, Michel Guiltinan, Mark J. Ruiz, Manuel Alemanno, Laurence Machado, Regina Phillips, Wilbert Schnell, Raymond J. Gilmour, Martin Rosenquist, Eric Butler, David R. Maximova, Siela N. Lanaud, Claire 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 |
description |
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. |
format |
article |
topic_facet |
F30 - Génétique et amélioration des plantes H20 - Maladies des plantes Theobroma cacao adn séquence nucléotidique transcription collection de matériel génétique expression des gènes génie génétique résistance aux maladies marqueur génétique http://aims.fao.org/aos/agrovoc/c_7713 http://aims.fao.org/aos/agrovoc/c_2347 http://aims.fao.org/aos/agrovoc/c_27583 http://aims.fao.org/aos/agrovoc/c_35126 http://aims.fao.org/aos/agrovoc/c_36739 http://aims.fao.org/aos/agrovoc/c_27527 http://aims.fao.org/aos/agrovoc/c_15974 http://aims.fao.org/aos/agrovoc/c_2328 http://aims.fao.org/aos/agrovoc/c_24030 |
author |
Argout, Xavier Fouet, Olivier Wincker, Patrick Gramacho, Karina Peres Legavre, Thierry Sabau, Xavier Risterucci, Ange-Marie Da Silva, Corinne Cascardo, Julio Cezar M. Allègre, Mathilde Kuhn, David N. Verica, Joseph Courtois, Brigitte Loor, Rey Gaston Babin, Régis Sounigo, Olivier Ducamp, Michel Guiltinan, Mark J. Ruiz, Manuel Alemanno, Laurence Machado, Regina Phillips, Wilbert Schnell, Raymond J. Gilmour, Martin Rosenquist, Eric Butler, David R. Maximova, Siela N. Lanaud, Claire |
author_facet |
Argout, Xavier Fouet, Olivier Wincker, Patrick Gramacho, Karina Peres Legavre, Thierry Sabau, Xavier Risterucci, Ange-Marie Da Silva, Corinne Cascardo, Julio Cezar M. Allègre, Mathilde Kuhn, David N. Verica, Joseph Courtois, Brigitte Loor, Rey Gaston Babin, Régis Sounigo, Olivier Ducamp, Michel Guiltinan, Mark J. Ruiz, Manuel Alemanno, Laurence Machado, Regina Phillips, Wilbert Schnell, Raymond J. Gilmour, Martin Rosenquist, Eric Butler, David R. Maximova, Siela N. Lanaud, Claire |
author_sort |
Argout, Xavier |
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 |
title_short |
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 |
title_full |
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 |
title_fullStr |
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 |
title_full_unstemmed |
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 |
title_sort |
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 |
url |
http://agritrop.cirad.fr/548501/ http://agritrop.cirad.fr/548501/1/document_548501.pdf |
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dig-cirad-fr-5485012024-01-28T16:53:33Z http://agritrop.cirad.fr/548501/ http://agritrop.cirad.fr/548501/ 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. Argout Xavier, Fouet Olivier, Wincker Patrick, Gramacho Karina Peres, Legavre Thierry, Sabau Xavier, Risterucci Ange-Marie, Da Silva Corinne, Cascardo Julio Cezar M., Allègre Mathilde, Kuhn David N., Verica Joseph, Courtois Brigitte, Loor Rey Gaston, Babin Régis, Sounigo Olivier, Ducamp Michel, Guiltinan Mark J., Ruiz Manuel, Alemanno Laurence, Machado Regina, Phillips Wilbert, Schnell Raymond J., Gilmour Martin, Rosenquist Eric, Butler David R., Maximova Siela N., Lanaud Claire. 2008. BMC Genomics, 9 (512), 19 p.https://doi.org/10.1186/1471-2164-9-512 <https://doi.org/10.1186/1471-2164-9-512> 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 Argout, Xavier Fouet, Olivier Wincker, Patrick Gramacho, Karina Peres Legavre, Thierry Sabau, Xavier Risterucci, Ange-Marie Da Silva, Corinne Cascardo, Julio Cezar M. Allègre, Mathilde Kuhn, David N. Verica, Joseph Courtois, Brigitte Loor, Rey Gaston Babin, Régis Sounigo, Olivier Ducamp, Michel Guiltinan, Mark J. Ruiz, Manuel Alemanno, Laurence Machado, Regina Phillips, Wilbert Schnell, Raymond J. Gilmour, Martin Rosenquist, Eric Butler, David R. Maximova, Siela N. Lanaud, Claire eng 2008 BMC Genomics F30 - Génétique et amélioration des plantes H20 - Maladies des plantes Theobroma cacao adn séquence nucléotidique transcription collection de matériel génétique expression des gènes génie génétique résistance aux maladies marqueur génétique http://aims.fao.org/aos/agrovoc/c_7713 http://aims.fao.org/aos/agrovoc/c_2347 http://aims.fao.org/aos/agrovoc/c_27583 http://aims.fao.org/aos/agrovoc/c_35126 http://aims.fao.org/aos/agrovoc/c_36739 http://aims.fao.org/aos/agrovoc/c_27527 http://aims.fao.org/aos/agrovoc/c_15974 http://aims.fao.org/aos/agrovoc/c_2328 http://aims.fao.org/aos/agrovoc/c_24030 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. article info:eu-repo/semantics/article Journal Article info:eu-repo/semantics/publishedVersion http://agritrop.cirad.fr/548501/1/document_548501.pdf application/pdf Cirad license info:eu-repo/semantics/openAccess https://agritrop.cirad.fr/mention_legale.html https://doi.org/10.1186/1471-2164-9-512 10.1186/1471-2164-9-512 info:eu-repo/semantics/altIdentifier/doi/10.1186/1471-2164-9-512 info:eu-repo/semantics/altIdentifier/purl/https://doi.org/10.1186/1471-2164-9-512 info:eu-repo/semantics/reference/purl/http://www.biomedcentral.com/1471-2164/9/512 |