Carotenoids are key metabolites in goji (Lycium), a traditional Chinese medicine plant; however, the carotenoid content varies in fruits of different goji species, and the mechanism of this variation is not clear. Carotenoids participate in signal transduction and photosynthesis, and function as colorants and photoprotectors. Members of the carotenoid cleavage oxygenase (CCO) gene family are involved in the regulation of phytohormones, pigments, and aromatic substances, such as abscisic acid (ABA), β-carotenoid, and α-ionone, by degrading carotenoids. Some CCO genes are also related to an abiotic stress response. Here, a total of 12 LbCCO genes were identified and analyzed from the L. barbarum genome. CCO genes were divided into six subfamilies based on the constructed phylogenetic tree, including LbNCEDs, LbCCD1, LbCCD3, LbCCD4, LbCCD7, and LbCCD8. Among them, CCD3 was reported for the first time. The gene structure and motif analysis revealed the conservation of CCO subfamilies. Pseudogene generation and the importance of each subfamily in CCOs were revealed by collinearity analysis. The spatiotemporal transcriptomes of L. barbarum and L. ruthenicum were compared, suggesting that CCD4-1 may dominate carotenoid degradation in goji fruits. Cis-acting elements prediction and environment responsive gene expression analyses indicated that salt-alkali stress and photothermal conditions might influence the expression of CCOs in goji. The results of this study enhance our understanding of the carotenoid degradation pathway, and the functions and responses of CCOs in goji species.

Lycium barbarum, a nutrient-rich fruit known for its resilience to drought and high salinity, presents an opportunity to explore stress tolerance at the molecular level. This study explores the molecular mechanisms underlying stress tolerance and fruit development in L. barbarum by characterizing its Dof transcription factor family. Through genomic analysis, 39 LbDof genes were identified, with their structural, phylogenetic, and physicochemical properties systematically examined. Cis-acting regulatory element analysis revealed motifs associated with growth, stress, light, and hormone responses, while expression profiling demonstrated organ-specific patterns and significant upregulation under drought and saline–alkaline stress. Additionally, dynamic expression changes were observed across fruit development stages, suggesting regulatory roles in maturation. Phylogenetic classification grouped LbDof genes into ten subgroups, with chromosomal mapping indicating segmental duplications as a key evolutionary driver. Furthermore, the study offers a comprehensive genomic and functional analysis of LbDof genes, highlighting their potential roles in stress adaptation and fruit maturation. The findings provide a theoretical basis for breeding stress-resistant crops and insights into enhancing plant resilience.