Exploring the codon patterns between CCD and NCED genes among different plant species

Area of Science:

• Plant molecular biology
• Enzymology
• Bioinformatics

Background:

• Plant Carotenoid Cleavage Oxygenase (CCO) enzymes, including CCD and NCED, are crucial for synthesizing vital apocarotenoid products.
• Understanding the genetic and evolutionary basis of these enzymes is key to optimizing their industrial applications.

Purpose of the Study:

• To conduct a comparative phylogenetic and codon usage analysis of CCD and NCED genes.
• To investigate the evolutionary relationships and codon bias patterns within these important plant enzyme families.

Main Methods:

• Phylogenetic analysis to determine evolutionary relationships.
• Codon usage analysis, including RSCU, ENc, and ENc-GC3S plots.
• Multivariate analysis and correlation analysis of codon adaptation index.

Main Results:

• Phylogenetic analysis revealed a close relationship between CCD and NCED subclasses.
• Both gene families exhibit a preference for the CUC codon and are under mutational pressure.
• NCED genes show a higher codon bias than CCD genes, with variations linked to species-specific roles.

Conclusions:

• CCD and NCED genes display distinct yet related codon usage patterns influenced by mutational pressure and species-specific functions.
• These findings provide insights into optimizing apocarotenoid production for industrial applications.