Abstract
Systems-wide understanding of gene expression profile regulating flower colour formation in Rhododendron simsii Planchon is insufficient. In this research, integration analysis of ribonucleic acid (RNA)omics and microRNAome were performed to reveal the molecular mechanism of flower colour formation in three R. simsii varieties with red, pink and crimson flowers, respectively. Totally, 3129, 5755 and 5295 differentially expressed gene (DEG)s were identified through comparative transcriptome analysis between 'Red variety' and 'Pink variety' (1507 up-regulated and 1622 down-regulated), 'Red variety' and 'Crimson variety' (2148 up-regulated 3607 down-regulated), as well as 'Pink variety' and 'Crimson variety' (2089 up-regulated and 3206 down-regulated), which were involved in processes of 'catalytic activity', 'binding', 'metabolic process' and 'cellular process', as well as pathways of 'metabolic pathways', 'biosynthesis of secondary metabolites', 'plant-pathogen interaction' and 'phenylpropanoid biosynthesis'. A total of 215 miRNAs, containing 153 known miRNAs belonging to 57 families and 62 novel miRNA, were involved in flower colour formation. In particular, 55 miRNAs were significantly differently expressed. Based on miRNA-mRNA regulatory network, ath-miR5658 could affect the synthesis of pelargonidin, cyanidin and delphinidin through downregulating accumulation of anthocyanidin 3-O-glucosyltransferase; ath-miR868-3p could regulate isoflavonoid biosynthesis through downregulating expression of CYP81E1/E7; ath-miR156g regulated the expression of flavonoid 3',5'-hydroxylase; and ath-miR829-5p regulated flavonol synthasein flavonoid biosynthesis process. This research will provide important roles in breeding new varieties with rich flower colour.