Analysis of Codon Usage Patterns in Herbaceous Peony (Paeonia lactiflora Pall.) Based on Transcriptome Data

Area of Science:

• Genomics
• Molecular Evolution
• Bioinformatics

Background:

• Codon usage bias influences gene expression and evolution.
• Herbaceous peony (Paeonia lactiflora) is a culturally significant plant with limited genomic data.
• Understanding codon usage provides insights into plant genome evolution.

Purpose of the Study:

• To analyze synonymous codon usage patterns in Paeonia lactiflora.
• To identify the primary drivers of codon usage bias in this species.
• To provide a foundation for future research on P. lactiflora gene expression and evolution.

Main Methods:

• Analysis of 24,216 reconstructed genes from the P. lactiflora transcriptome.
• Calculation of nucleotide content (GC content) and GC content at the third codon position (GC3).
• Effective number of codons (ENC) and Parity Rule 2 (PR2) analyses were performed.

Main Results:

• P. lactiflora genes exhibit a mean GC content of 44.4%, indicating an AT-rich genome.
• A wide distribution of GC3 was observed, with a correlation between GC12 and GC3.
• Mutational bias, particularly nucleotide composition bias, and translational selection were identified as key factors influencing codon usage.

Conclusions:

• Mutational bias is a major determinant of codon usage bias in P. lactiflora.
• Nucleotide composition and translational selection jointly shape codon usage patterns.
• These findings are crucial for understanding P. lactiflora evolutionary mechanisms and heterologous protein expression.