title: Transcriptome database resource and gene expression atlas for the rose.
abstract: BACKGROUND
  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.
  
  
  RESULTS
  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.
  
  
  CONCLUSIONS
  The study provides useful information on Rosa expressed genes, with thorough annotation and an overview of expression patterns for transcripts with good accuracy.
authors.affiliation: Reproduction et Développement des Plantes UMR INRA-CNRS- Université Lyon 1-ENSL, Ecole Normale Supérieure, 46 allée d'Italie, Lyon Cedex 07 69364, France.
authors.forename: Annick
authors.initials: A
authors.lastname: Dubois
authors.forename: Sebastien
authors.initials: S
authors.lastname: Carrere
authors.forename: Olivier
authors.initials: O
authors.lastname: Raymond
authors.forename: Benjamin
authors.initials: B
authors.lastname: Pouvreau
authors.forename: Ludovic
authors.initials: L
authors.lastname: Cottret
authors.forename: Aymeric
authors.initials: A
authors.lastname: Roccia
authors.forename: Jean-Paul
authors.initials: JP
authors.lastname: Onesto
authors.forename: Soulaiman
authors.initials: S
authors.lastname: Sakr
authors.forename: Rossitza
authors.initials: R
authors.lastname: Atanassova
authors.forename: Sylvie
authors.initials: S
authors.lastname: Baudino
authors.forename: Fabrice
authors.initials: F
authors.lastname: Foucher
authors.forename: Manuel
authors.initials: M
authors.lastname: Le Bris
authors.forename: Jérôme
authors.initials: J
authors.lastname: Gouzy
authors.forename: Mohammed
authors.initials: M
authors.lastname: Bendahmane
mesh_terms: D030541:Databases, Genetic; D020224:Expressed Sequence Tags; D031985:Fragaria / Q000235:genetics; D015870:Gene Expression; D018506:Gene Expression Regulation, Plant; D018745:Genome, Plant; D059014:High-Throughput Nucleotide Sequencing; D005810:Multigene Family; D010940:Plant Proteins / Q000235:genetics*; D018520:Plant Shoots / Q000235:genetics*; D016133:Polymerase Chain Reaction; D027861:Prunus / Q000235:genetics; D012333:RNA, Messenger / Q000235:genetics*; D027826:Rosa / Q000235:genetics*; D012984:Software; D059467:Transcriptome
chemical_list: D010940:Plant Proteins; D012333:RNA, Messenger