Genome-Wide Identification and Expression Analysis of the Carotenoid Cleavage Oxygenase Gene Family in Five Rosaceae Species

The carotenoid cleavage oxygenases (CCOs), which include carotenoid cleavage dioxygenases (CCDs) and 9-cis-epoxycarotenoid dioxygenases (NCEDs), are enzymes that are critical to the mediation of the degradation of carotenoids to apocarotenoids. In this study, we identified a total of 12, 20, 11, 8, and 10 CCO genes from Pyrus bretschneideri, Malus domestica, Fragaria vesca, Prunus mume, and Prunus persica, respectively. Phylogenetic analysis showed that these CCO genes clustered into six groups (NCED, CCD1, CCD4, CCD7, CCD8, and CCD-like). Gene structure analysis revealed that CCO genes within the same groups showed similar exon numbers and contained similar motifs. Duplication analysis revealed that tandem duplication played a significant role in the expansion of CCO members in Malus domestica. Purifying selection was involved in the evolution of CCO genes in Pyrus bretschneideri. The transcriptomic data-based expression analysis revealed that the CCO genes exhibited distinct patterns of expression in the roots, leaves, buds, and fruit. The expression patterns based on qRT-PCR showed that there were greater differences on the relative expression levels of PbCCD1 and PbCCD5 between cultivars “Enli” (inflorescence sparsely branched) and “Jinxiangshui” (inflorescence copiously branched) in the three different stages of flower bud morphological differentiation, revealing the possibility of involvement of these genes in the branching of the pear inflorescence. This study provides a valuable resource for further investigations of CCO gene functions in Rosaceae species.