Transcriptome database resource and gene expression atlas for the rose

BMC Genomics

Research Article

Ludovic Cottret¹  Sebastien Carrere¹  Jérôme Gouzy¹  Jean-Paul Onesto²  Manuel Le Bris³  Soulaiman Sakr⁴  Fabrice Foucher⁴  Sylvie Baudino⁵  Annick Dubois⁶  Olivier Raymond⁶  Benjamin Pouvreau⁶  Mohammed Bendahmane⁶  Aymeric Roccia⁷  Rossitza Atanassova⁸ 

[1] INRA, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR441, F-31326, Castanet-Tolosan, France;CNRS, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR2594, F-31326, Castanet-Tolosan, France;INRA, Unité de Recherches Intégrées en Horticulture, 400 route des Chappes BP 167, 06903, Sophia Antipolis, Cedex, France;Institut Méditerranéen de Biodiversité et d’Ecologie marine et continentale, UMR Université d'Aix-Marseille- CNRS 7263, Université d’Aix-Marseille, IRD 237, Université d’Avignon, Avenue Escadrille Normandie-Niemen, F-13397, Marseille, France;Institut de Recherche en Horticulture et Semences (INRA, Agrocacmpus-Ouest, Université d’Angers), SFR 149 QUASAV, BP 60057-49071, Beaucouzé, cedex, France;Laboratoire BVpam, EA2061, Université de Saint-Etienne, Université de Lyon, rue du Dr Michelon, F-42023, Saint-Etienne, France;Reproduction et Développement des Plantes UMR INRA-CNRS- Université Lyon 1-ENSL, Ecole Normale Supérieure, 46 allée d'Italie, 69364, Lyon, Cedex 07, France;Reproduction et Développement des Plantes UMR INRA-CNRS- Université Lyon 1-ENSL, Ecole Normale Supérieure, 46 allée d'Italie, 69364, Lyon, Cedex 07, France;Laboratoire BVpam, EA2061, Université de Saint-Etienne, Université de Lyon, rue du Dr Michelon, F-42023, Saint-Etienne, France;Université de Poitiers, UMR CNRS 7267 Écologie et Biologie des Interactions, 40 Av. du Recteur Pineau, 86022, Poitiers, Cedex, France;

关键词: Rose;    Transcriptome;    Gene expression atlas;   

DOI  :  10.1186/1471-2164-13-638

 received in 2012-07-25, accepted in 2012-11-06,  发布年份 2012

来源: Springer

【 摘 要 】

BackgroundFor 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.ResultsHere, 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.ConclusionsThe study provides useful information on Rosa expressed genes, with thorough annotation and an overview of expression patterns for transcripts with good accuracy.

【 授权许可】

Unknown   
© Dubois et al.; licensee BioMed Central Ltd. 2012. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.