Genes · 2026
Unraveling the Phylogenetic, Structural, and Functional Dynamics of CCO Genes in Citrus sinensis, Olea europaea var. sylvestris, Populus nigra, Prunus dulcis, and Punica granatum: A Comprehensive Bioinformatic Comparative Analysis.
СтатьяСравнительное исследованиеНазвание и аннотация: Перевод в очереди
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Öz Ummahan
Аннотация
BACKGROUND/OBJECTIVES: Citrus sinensis, Olea europaea var. sylvestris, Populus nigra, Prunus dulcis, and Punica granatum are economically and medicinally important perennial plant species. Carotenoid cleavage oxygenase (CCO) genes encode key enzymes involved in carotenoid degradation and play essential roles in plant growth, development, and responses to environmental stresses. In this study, a comprehensive genome-wide comparative analysis of the CCO gene family was conducted in C. sinensis, O. europaea var. sylvestris, P. nigra, P. dulcis, and P. granatum to investigate their structural diversity, evolutionary relationships, and potential biological functions.
METHODS: Chromosomal distribution, phylogenetic relationships, gene structure, conserved protein motifs, homology modeling, subcellular localization, cis-regulatory elements, and miRNA interactions were analyzed.
RESULTS: A total of 12, 23, 22, 11, and 17 CCO genes were identified in C. sinensis, O. europaea var. sylvestris, P. nigra, P. dulcis, and P. granatum, respectively. Most CCO proteins were acidic, and genes were concentrated on specific chromosomes. Phylogenetic analysis grouped CCO genes into three main clades. Gene structure analysis revealed intronless and intron-containing genes of varying lengths. Some CCO proteins possessed all conserved motifs, while others lacked certain motifs or had multiple copies. β-sheets were the predominant secondary structural elements, and CCO proteins were predicted to be localized in chloroplasts, mitochondria, peroxisomes, the cytoplasm, and the nucleus. Stress-related cis-elements and miRNAs were identified.
CONCLUSIONS: These findings provide valuable insights into the diversity and evolutionary characteristics of the CCO gene family and suggest that CCO genes may contribute to plant stress responses and metabolic processes. Overall, this study provides a comprehensive comparative analysis of the CCO gene family in these five perennial plant species and offers a valuable genomic resource for future functional characterization, comparative genomic studies, and molecular breeding applications.
METHODS: Chromosomal distribution, phylogenetic relationships, gene structure, conserved protein motifs, homology modeling, subcellular localization, cis-regulatory elements, and miRNA interactions were analyzed.
RESULTS: A total of 12, 23, 22, 11, and 17 CCO genes were identified in C. sinensis, O. europaea var. sylvestris, P. nigra, P. dulcis, and P. granatum, respectively. Most CCO proteins were acidic, and genes were concentrated on specific chromosomes. Phylogenetic analysis grouped CCO genes into three main clades. Gene structure analysis revealed intronless and intron-containing genes of varying lengths. Some CCO proteins possessed all conserved motifs, while others lacked certain motifs or had multiple copies. β-sheets were the predominant secondary structural elements, and CCO proteins were predicted to be localized in chloroplasts, mitochondria, peroxisomes, the cytoplasm, and the nucleus. Stress-related cis-elements and miRNAs were identified.
CONCLUSIONS: These findings provide valuable insights into the diversity and evolutionary characteristics of the CCO gene family and suggest that CCO genes may contribute to plant stress responses and metabolic processes. Overall, this study provides a comprehensive comparative analysis of the CCO gene family in these five perennial plant species and offers a valuable genomic resource for future functional characterization, comparative genomic studies, and molecular breeding applications.