Codon usage patterns in Chinese bayberry (Myrica rubra) based on RNA-Seq data

Area of Science:

• Genomics
• Molecular Biology
• Evolutionary Biology

Background:

• Codon usage analysis is crucial for understanding evolution, translation, and gene discovery.
• Species-specific codon usage studies are necessary but often limited to model organisms.
• RNA-Sequencing (RNA-Seq) enables codon usage studies in non-model species.

Purpose of the Study:

• To investigate codon usage bias and codon pair bias in Chinese bayberry using RNA-Seq data.
• To analyze codon usage patterns at the plant kingdom, organism, and gene levels.
• To explore the evolutionary significance of codon usage and its impact on gene function.

Main Methods:

• RNA-Seq data analysis of Chinese bayberry.
• Identification of high and low frequency codons and codon pairs.
• Analysis of relative synonymous codon usage (RSCU) and GC content of 3rd synonymous codons (GC3s).
• Assessment of codon adaptation index (CAI) and gene ontology (GO) categories.

Main Results:

• Identified high-frequency codons (e.g., AGG, GCU) and low-frequency codons (e.g., NCG, NUA).
• Discovered 397 high-frequency codon pairs, including 26 preferred and 141 avoided neighboring codon pairs.
• Observed significant codon usage pattern changes during plant evolution, more so than GC3s.
• Found differential influence of CAI and GC3s on nine GO categories, particularly 'Molecular function'.
• Noted an increase in average CAI within genes from the start codon.

Conclusions:

• Established a comprehensive codon usage table and identified high-frequency codon pairs.
• Proposed that codon bias aids in avoiding DNA mutation, enhancing protein production, and regulating synthesis rate.
• Highlighted the significance of codon usage patterns in plant evolution, gene function classification, and translation start site prediction.
• Promoted codon biology research and provided a reference for RNA-Seq data analysis in other non-model species.