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.
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.
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DOI：
10.1186/1471-2164-9-512
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发表时间：
2008-10-30
期刊：
影响因子：
4.4
通讯作者：
Lanaud, Claire
中科院分区：
文献类型：
--
作者：
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
可可，是一种起源于南美洲热带雨林的树。它是许多热带国家的主要经济作物之一。T.可可主要在小块土地上生产，为1 400万农民提供资源。抗病性和T.提高可可质量是可可和巧克力生产所有行为者面临的两个重要挑战。T.可可受到害虫和真菌疾病的严重影响，造成超过40%的产量损失，并且改善质量、营养和感官对消费者也很重要。建立了一个国际合作，以开发可可EST基因组资源数据库。构建了五十六个不同器官、不同基因型和不同环境条件下的cDNA文库。共产生149，650个有效EST序列，对应于48，594个单基因，12，692个重叠群和35，902个单基因。共有29，849个unigenes与其他物种的公共序列具有显著的同源性。基因本体（GO）注释应用于主要GO类别之间的EST分配。建立了一个专门的信息系统（ESTtik）来处理、存储和管理EST收集，允许用户查询数据库。为了检验我们的EST收集的代表性，我们寻找了已知参与两种不同代谢途径的基因，这两种代谢途径在其他植物物种中被广泛研究，并且对T。可可品质：类黄酮和萜烯途径。在其他作物中描述的这两种代谢途径的大多数酶在我们的EST收集中被发现。ESTs收集提供了大量新的遗传标记。这个EST集合显示了T.可可转录组，适用于基于来自这些EST的寡核苷酸微阵列的生化途径分析。它将提供大量的遗传标记，将允许构建一个高密度的基因图谱T。可可。该EST库是T.可可研究和改良，促进重要T.可可性状变异
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.
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影响因子：
30.8
作者：
Buetow, KH;Edmonson, MN;Cassidy, AB
通讯作者：
Cassidy, AB
影响因子：
4.4
作者：
Dreosti, IE
通讯作者：
Dreosti, IE
影响因子：
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作者：
Fu, GK;Stuve, LL
通讯作者：
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影响因子：
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作者：
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通讯作者：
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影响因子：
4.3
作者：
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通讯作者：
Jones, CA