Open Access Highly Accessed Research article

Transcriptome database resource and gene expression atlas for the rose

Annick Dubois1, Sebastien Carrere23, Olivier Raymond1, Benjamin Pouvreau1, Ludovic Cottret23, Aymeric Roccia14, Jean-Paul Onesto5, Soulaiman Sakr6, Rossitza Atanassova7, Sylvie Baudino4, Fabrice Foucher6, Manuel Le Bris8, Jérôme Gouzy23 and Mohammed Bendahmane1*

Author Affiliations

1 Reproduction et Développement des Plantes UMR INRA-CNRS- Université Lyon 1-ENSL, Ecole Normale Supérieure, 46 allée d'Italie, Lyon Cedex 07, 69364, France

2 INRA, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR441, Castanet-Tolosan, F-31326, France

3 CNRS, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR2594, Castanet-Tolosan, F-31326, France

4 Laboratoire BVpam, EA2061, Université de Saint-Etienne, Université de Lyon, rue du Dr Michelon, Saint-Etienne, F-42023, France

5 INRA, Unité de Recherches Intégrées en Horticulture, 400 route des Chappes BP 167, Sophia Antipolis Cedex, 06903, France

6 Institut de Recherche en Horticulture et Semences (INRA, Agrocacmpus-Ouest, Université d’Angers), SFR 149 QUASAV, Beaucouzé cedex, BP 60057-49071, France

7 Université de Poitiers, UMR CNRS 7267 Écologie et Biologie des Interactions, 40 Av. du Recteur Pineau, Poitiers Cedex, 86022, France

8 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, Marseille, F-13397, France

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BMC Genomics 2012, 13:638  doi:10.1186/1471-2164-13-638

Published: 20 November 2012



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.

Rose; Transcriptome; Gene expression atlas