Transcriptome-sequencing analyses reveal putative genes related to flower color variation in Chinese Rosa rugosa

Rosa rugosa is an excellent landscaping plant famous for its fragrance and primarily red flower. In this study, transcriptome sequencing on R. rugosa ‘Red Zizhi’ and its bud mutations R. rugosa ‘Pink Zizhi’ and R. rugosa ‘White Zizhi’ were conducted using the Illumina HiSeq™ 2000 platform. In total, 103,446 assembled contigs and 51,332 unigenes were obtained with average lengths of 359 and 735 bp, respectively. A total of 40,018 (77.96%) unigenes were functionally annotated; 20,054 (39.07%) of which were annotated in 128 Kyoto Encyclopedia of Genes and Genomes database pathways. Moreover, 316 (1.58%) unigenes were annotated to phenylalanine synthetic pathways related to coloration, 191 (0.95%) to flavonoid synthetic pathways and 15 (0.07%) to anthocyanin synthetic pathways. Analysis of differential gene expression profiles showed that ‘White Zizhi’ and ‘Pink Zizhi’ differed by 431 unigenes, ‘Red Zizhi’, and ‘Pink Zizhi’ by 1319 unigenes, and ‘Red Zizhi’ and ‘White Zizhi’ by 1324 unigenes. Five candidate genes were possibly highly related to the biosynthesis of rose flower pigments; they were selected by applying the differentially expressed gene method. Analyses were conducted to confirm the expression patterns of selected genes and changes and contents of flower pigments in petals of the three rose varieties in different flower development stages. Finally, by analyzing the relationship between gene expression and flower pigment synthesis, we discovered that the 4-coumarate:CoA ligase gene is possibly related to the formation of pink flowers, and low dihydroflavonol 4-reductase gene expression levels may be related to color formation in ‘White Zizhi’.