Identification and Characterization of CCD Gene Family in Rose (Rosa chinensis Jacq. ‘Old Blush’) and Gene Co-Expression Network in Biosynthesis of Flower Scent

Rose (Rosa sp.) is a widely used raw material for essential oil extraction and fragrance production. The carotenoid cleavage dioxygenases pathway is one of the main metabolic pathways for the degradation of carotenoids, which is located downstream of the terpenoids biosynthesis pathway and is closely related to the biosynthesis of volatile compounds. We performed a comprehensive genome-wide analysis of the rose CCD family genes (RcCCDs) in terms of phylogeny, sequence characterization, gene structure, gene duplication events, and transcriptome. Finally, 15 CCD family members were identified from the rose genome, and they were classified into three clades: nine for the CCD clade, four for the NCED clade, and two for the CCD-LIKE clade. The RcCCDs were distributed on chromosomes 1, 4, 5, 6, and 7, and were concentrated on both ends of the chromosomes. RcCCDs did not have paralogous genes or whole genome duplication events (WGD), eleven of them were single-copy genes, and their repetitive sequences were mainly dispersed and tandem. Ten RcCCDs were differentially expressed in the transcriptomes of different flowering stages. The expression of four of them increased and then decreased, which was the same process as the accumulation of volatile compounds, and it was speculated that these genes might be involved in the biosynthesis of volatile compounds. A total of fifteen modules were obtained by weighted gene co-expression network analysis of eighteen volatile compounds-related genes, of which six modules were a highly significant positive correlation with volatile compounds, and 20 hub genes in the modules were predicted. These hub genes all exercised their functions in the early flowering stage with strict temporal specificity. This study provided a theoretical basis for further exploring the biological functions of RcCCDs and hub genes regulating the synthesis and metabolism of volatile compounds in rose.