Transcriptome database resource and gene expression atlas for the rose.
Transcriptome database resource and gene expression atlas for the rose.
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DOI：
10.1186/1471-2164-13-638
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发表时间：
2012-11-20
期刊：
影响因子：
4.4
通讯作者：
Bendahmane M
中科院分区：
文献类型：
--
作者：
Dubois A;Carrere S;Raymond O;Pouvreau B;Cottret L;Roccia A;Onesto JP;Sakr S;Atanassova R;Baudino S;Foucher F;Le Bris M;Gouzy J;Bendahmane M
几个世纪以来，人们根据一些特征来选择玫瑰。关于这些性状的遗传和分子基础的信息很少，主要是因为这种重要的观赏植物的表达基因信息很少。在这里，我们结合使用Illumina和454测序技术，利用来自不同组织的RNA，以及对生物和非生物胁迫的反应，生成了Rosa spp转录本的信息。共鉴定了80714个转录本簇，预测了76611个肽，其中20997个聚类到13900个蛋白家族中。在亲缘关系密切的蔷薇科物种中，BLASTp结果显示，草莓和桃子基因组中约有一半的预测肽在蔷薇数据集中具有同源物。利用不同发育阶段和不同应激条件下的器官RNA样本获得数字表达。qPCR验证了23个高表达或低表达基因的数字表达数据。不同组织和器官之间的比较基因表达分析允许识别在给定组织或特定条件下高度富集的簇，证明了数字基因表达分析的有用性。创建了一个网络界面ROSAseq，允许通过BLAST进行数据查询，随后分析DNA簇并访问完整的转录本注释，包括Fragaria vesca， Prunus persica和拟南芥的最佳BLAST匹配。玫瑰肽数据集用于创建ROSAcyc资源途径数据库，该数据库允许访问假定的基因和酶途径。该研究提供了有关Rosa表达基因的有用信息，并对转录本的表达模式进行了全面的注释和概述，具有良好的准确性。
For centuries roses have been selected based on a number of traits. Little information exists on the genetic and molecular basis that contributes to these traits, mainly because information on expressed genes for this economically important ornamental plant is scarce. Here, we used a combination of Illumina and 454 sequencing technologies to generate information on Rosa sp. transcripts using RNA from various tissues and in response to biotic and abiotic stresses. A total of 80714 transcript clusters were identified and 76611 peptides have been predicted among which 20997 have been clustered into 13900 protein families. BLASTp hits in closely related Rosaceae species revealed that about half of the predicted peptides in the strawberry and peach genomes have orthologs in Rosa dataset. Digital expression was obtained using RNA samples from organs at different development stages and under different stress conditions. qPCR validated the digital expression data for a selection of 23 genes with high or low expression levels. Comparative gene expression analyses between the different tissues and organs allowed the identification of clusters that are highly enriched in given tissues or under particular conditions, demonstrating the usefulness of the digital gene expression analysis. A web interface ROSAseq was created that allows data interrogation by BLAST, subsequent analysis of DNA clusters and access to thorough transcript annotation including best BLAST matches on Fragaria vesca, Prunus persica and Arabidopsis. The rose peptides dataset was used to create the ROSAcyc resource pathway database that allows access to the putative genes and enzymatic pathways. The study provides useful information on Rosa expressed genes, with thorough annotation and an overview of expression patterns for transcripts with good accuracy.
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DOI：
10.1093/bioinformatics/btp024
发表时间：
2009-03-01
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Gouzy J;Carrere S;Schiex T
通讯作者：
Schiex T
影响因子：
7.3
作者：
Girault, Tiffanie;Abidi, Farouk;Leduc, Nathalie
通讯作者：
Leduc, Nathalie
影响因子：
3.8
作者：
Huang, Fong-Chin;Horvath, Gyoergyi;Schwab, Wilfried
通讯作者：
Schwab, Wilfried
影响因子：
4.8
作者：
Kaminaga, Yasuhisa;Schnepp, Jennifer;Dudareva, Natalia
通讯作者：
Dudareva, Natalia
影响因子：
6.9
作者：
Borg, Michael;Brownfield, Lynette;Twell, David
通讯作者：
Twell, David