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. Conclusion: 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.
| Original language | English (US) |
|---|---|
| Article number | 512 |
| Journal | BMC genomics |
| Volume | 9 |
| DOIs | |
| State | Published - Oct 30 2008 |
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All Science Journal Classification (ASJC) codes
- Biotechnology
- Genetics
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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; Legavre, Thierry; Sabau, Xavier; Risterucci, Ange Marie; Da Silva, Corinne; Cascardo, Julio; Allegre, Mathilde; Kuhn, David; Verica, Joseph; Courtois, Brigitte; Loor, Gaston; Babin, Regis; Sounigo, Olivier; Ducamp, Michel; Guiltinan, Mark J.; Ruiz, Manuel; Alemanno, Laurence; Machado, Regina; Phillips, Wilberth; Schnell, Ray; Gilmour, Martin; Rosenquist, Eric; Butler, David; Maximova, Siela; Lanaud, Claire.
In: BMC genomics, Vol. 9, 512, 30.10.2008.Research output: Contribution to journal › Article
TY - JOUR
T1 - Towards the understanding of the cocoa transcriptome
T2 - Production and analysis of an exhaustive dataset of ESTs of Theobroma cacao L. generated from various tissues and under various conditions
AU - Argout, Xavier
AU - Fouet, Olivier
AU - Wincker, Patrick
AU - Gramacho, Karina
AU - Legavre, Thierry
AU - Sabau, Xavier
AU - Risterucci, Ange Marie
AU - Da Silva, Corinne
AU - Cascardo, Julio
AU - Allegre, Mathilde
AU - Kuhn, David
AU - Verica, Joseph
AU - Courtois, Brigitte
AU - Loor, Gaston
AU - Babin, Regis
AU - Sounigo, Olivier
AU - Ducamp, Michel
AU - Guiltinan, Mark J.
AU - Ruiz, Manuel
AU - Alemanno, Laurence
AU - Machado, Regina
AU - Phillips, Wilberth
AU - Schnell, Ray
AU - Gilmour, Martin
AU - Rosenquist, Eric
AU - Butler, David
AU - Maximova, Siela
AU - Lanaud, Claire
PY - 2008/10/30
Y1 - 2008/10/30
N2 - 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. Conclusion: 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.
AB - 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. Conclusion: 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.
UR - http://www.scopus.com/inward/record.url?scp=60549092591&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=60549092591&partnerID=8YFLogxK
U2 - 10.1186/1471-2164-9-512
DO - 10.1186/1471-2164-9-512
M3 - Article
C2 - 18973681
AN - SCOPUS:60549092591
VL - 9
JO - BMC Genomics
JF - BMC Genomics
SN - 1471-2164
M1 - 512
ER -