Integrative chloroplast genomics of Polygonaceae: evolutionary dynamics, codon optimization, and phylogenetic...

Area of Science:

• Plant genomics
• Molecular evolution
• Bioinformatics

Background:

• The Polygonaceae family includes important medicinal plants like Rheum and Fagopyrum.
• Limited comprehensive chloroplast genome analyses exist for this pharmacologically significant family.
• Chloroplast genomes are crucial for plant evolution, phylogeny, and herbal medicine quality control.

Purpose of the Study:

• To conduct a comprehensive analysis of chloroplast genomes across 48 Polygonaceae species.
• To investigate genome architecture, gene content, codon usage, selection pressures, SSRs, and phylogenetic relationships.
• To provide insights into the evolutionary dynamics of Polygonaceae chloroplast genomes.

Main Methods:

• Comparative analysis of 48 Polygonaceae chloroplast genomes.
• Assessment of genome structure, gene composition, and codon usage patterns (RSCU, ENC).
• Evaluation of selection pressures (Ka/Ks), SSR identification, collinearity analysis, and phylogenetic reconstruction.

Main Results:

• Conserved quadripartite chloroplast genome structures with AT enrichment and A/U-ending codon bias.
• Natural selection predominantly influences synonymous codon usage, with six conserved optimal codons.
• High conservation of photosystem-related genes and structural collinearity within genera; 4,593 SSR loci identified.
• Phylogenetic analysis delineated major lineages, correlating codon usage with ecological adaptation.

Conclusions:

• Natural selection plays a key role in codon usage bias within Polygonaceae chloroplast genomes.
• Identified conserved genomic features, SSR resources, and phylogenetic relationships provide a foundation for future research.
• Findings support molecular marker development, quality control of medicinal Polygonaceae species, and evolutionary studies.