Comprehensive analysis of chloroplast codon usage patterns in the important medicinal genus Panax

Area of Science:

• * Botany
• * Molecular Biology
• * Genomics

Background:

• * The genus Panax includes valuable medicinal plants.
• * Chloroplast codon usage patterns in Panax are not well understood.
• * Understanding these patterns is crucial for genetic studies.

Purpose of the Study:

• * To investigate chloroplast codon usage bias (CUB) across nine Panax species.
• * To identify factors influencing CUB in Panax chloroplast genomes.
• * To provide a basis for future chloroplast genetic engineering in Panax.

Main Methods:

• * Analysis of coding sequences from nine Panax chloroplast genomes.
• * Assessment of nucleotide composition, codon usage, and optimal codons.
• * Application of ENC-plot, PR2-plot, neutrality-plot, and correspondence analyses.

Main Results:

• * Moderate and conserved CUB observed across Panax species, with a preference for A/T-ending codons.
• * GC content at the third codon position ranged from 30.15% to 30.52%.
• * Multiple factors, not just GC-related mutational pressure, shape Panax chloroplast CUB.

Conclusions:

• * The conserved A/T-ending codon preference serves as a reference for Panax chloroplast genome evolution.
• * Findings offer a resource for chloroplast genetic engineering studies in Panax.
• * Analytical approaches are indirect; optimal codons require experimental validation.