Genome-wide codon usage pattern analysis reveals the correlation between codon usage bias and gene expression in...

Area of Science:

• Molecular Biology
• Genomics
• Evolutionary Biology

Background:

• The parasitic plant Cuscuta australis exhibits unique adaptations.
• Understanding gene expression and evolution in parasitic plants requires analyzing codon usage patterns.

Purpose of the Study:

• To systematically analyze codon usage patterns in protein-coding sequences and pseudogenes of C. australis.
• To investigate the factors influencing codon bias, including mutation pressure and natural selection.
• To explore the relationship between gene expression levels and codon usage bias.

Main Methods:

• Comparative analysis of codon usage in protein-coding sequences and pseudogenes.
• Application of neutrality plots and effective number of codons analysis.
• Correlation analysis between gene expression levels and codon usage bias.

Main Results:

• Both protein-coding sequences and pseudogenes in C. australis display an A/U bias at the third codon position.
• Protein-coding sequences prefer G/C-ending optimal codons, while pseudogenes prefer A/U-ending optimal codons.
• Natural selection is a stronger driver of codon usage bias than mutation pressure.
• Gene expression levels are positively correlated with codon usage bias; highly expressed genes show greater bias and favor G/C-ending codons.

Conclusions:

• Codon usage patterns in C. australis protein-coding genes and pseudogenes are distinct and shaped by natural selection.
• The observed codon bias is linked to gene expression levels, suggesting optimization for translation efficiency.
• These findings provide insights into the molecular mechanisms underlying gene evolution and adaptation in parasitic plants.