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Prunus persica f.versicolor (Sieb.) Voss is one of the main varieties of ornamental peach,which is characterized by the presence of red and white flowers on the same branch.Since chimera of flower pigmentation occurred within the same genotype,such plants are desirable system to study the genetic mechanisms triggering the formation of chimera of flower colors.To gain a global view of the genes differentially expressed between the red and white flower petals and to develop a database for further studies,we performed a large-scale transcriptome sequencing of petals with different flower colors which were separately collected within one tree.Totally,1,556,597 high quality reads were obtained,with an average length of 445bp and a total length of 694Mb.The ESTs were assembled into 16,530 contigs,and 42,050 singletons.These unigenes were further functionally annotated by comparing their sequences to different proteins and functional domain databases and assigned with Gene Ontology (GO) terms.A biochemical pathway database containing 229 predicted pathways was also created based on the annotations of the unigenes.Digital expression analysis identified 513 differentially expressed genes between the red and white flower petals.We specifically examined the expression of flavonoid structural genes,and detected 4 differentially expressed genes,which were all highly expressed in red flower.In addition,we also detected 11 transcription factors differentially expressed between red and white flowers.Among which 9 were highly expressed in red flower and 2 were highly expressed in white flower.These genes were worthy of special notification in future studies.Furthermore,the transcriptome dataset obtained in this study will provide new insights to study the gene function and serve as a valuable public resource to the peach research community.