It is likely that the sequences of these genes have diverged far enough to render the annotation difficult. These highly divergent genes may have evolved functions that are be specific to the Rosa genus or Rosaceae family and are therefore of particular interest. We harvested six pools of samples corresponding to different flower development stages in compared the transcriptome in successive stages. We found three distinct groups with common genes. These groups corresponded to early, mid and late floral development. To validate and evaluate the accuracy of the microarray data, we performed quantitative real-time PCR. Twenty four genes were selected from the microarray transcriptomics comparisons based on previous bibliographic reports and/or deregulation levels, then, using qPCR, we further characterized the expression profiles. The correlation between the microarray results and those obtained by qPCR was assessed by calculating the Pearson��s product moment correlation coefficient. Pearson��s correlation coefficient was Tubacin calculated between each pair of fold change as estimated by microarray and qPCR experiments. The statistical significance of each Pearson��s correlation coefficient was assessed using the cor.test routine in R. A global correlation coefficient of 0.858 calculated by the average of every gene was observed. These results indicate that our microarrays are able to detect consistently both low and high foldchanges with high accuracy in different experimental conditions. Sequences corresponding to 401 genes were detected as differentially regulated between stages 5 and VP. Among these genes, 233 were down-regulated and 168 were up-regulated. Genes that exhibit strong similarities to genes involved in carotene, flavonoid and anthocyanin biosynthesis are up-regulated between stages 5 and VP. Among these genes, Afatinib clinical trial putative phytoene synthase, zeta carotene desaturase, lycopene betacyclase are likely to be involved in carotenoid biosynthesis. The expression of UDP-glucose anthocyanidin-oglucosyltransferase, previously involved in anthocyanin synthesis, was strongly up-regulated. A similar strong up-regulation was observed for genes encoding putative phenylalanine ammonia-lyase, chalcone synthase, flavonol synthase and anthocyanidin synthase. Altogether, these genes are likely good candidates involved in anthocyanins biosynthesis in rose petals. Interestingly, genes predicted to encode five putative cyclins and a putative cyclin dependent kinase are strongly down-regulated during floral organ morphogenesis. This downregulation may reflect the transition from mitotic growth to postmitotic growth where floral organs grow through cell expansion.