The Citrus clementina (citrus) plant produces various phytohormones due to the significant involvement of the carotenoid cleavage oxygenase (CCO) gene family in its growth and development. CCO genes can be divided into two main categories: NCED (9-cis-epoxy carotenoid dioxygenase), responsible for abscisic acid (ABA) production, and CCD (carotenoid cleavage dioxygenase), involved in pigment and strigolactone formation. To better understand the roles and positions of CcCCO gene members in relation to these hormones, researchers analyzed the clementine genome. To identify their structural features, they employed phylogenetic analysis, protein interactions, localization, structure, miRNA targets, evolutionary analysis, and transcriptome studies. The study revealed the presence of 15 CcCCO genes, including 11 NCED and 4 CCD genes, scattered across various chromosomes, with the majority located in chloroplasts. Promoter sequencing analysis indicated the presence of different cis-regulatory elements that likely interacted with phytohormones, such as auxin and abscisic acid among others. Notably, two genes, CcNCED1 and CcNCED3, were significantly expressed among the CCO genes, and these were found to be expressed during stress and played a crucial role in enabling optimal plant development. Furthermore, a comprehensive genome-wide comparison of CCO genes in C. Clementine and Arabidopsis thaliana models was conducted to understand their functional characteristics. This research provides a solid foundation for further exploration of the unique attributes of the C. clementina plant, contributing to a deeper understanding of its growth and development processes.

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