Comparative Analysis of Codon Usage Bias in Chloroplast Genomes of eight Argentina Species of Rosaceae and Their Phylogeny

Background The genus Argentina (Rosaceae) represents a taxonomically complex group with significant ethnobotanical value, yet the morphological convergence among genus remains poorly resolved. Codon usage bias (CUB), an important genomic feature has not been systematically investigated in this genus, limiting our understanding of its chloroplast evolution and adaptive mechanisms. Results In this study, we sequenced and annotated the complete chloroplast genomes of three key Argentina species ( A. stenophylla , A. anserina , and A. phanerophlebia ) and reconstructed a phylogeny using 21 taxa (18 Argentina and three Potentilla outgroups). We further conducted a comparative analysis of synonymous codon usage bias in eight representative species. The chloroplast genomes exhibited a typical quadripartite structure with high conservation in size (155,148–155,972 bp), gene order, and content (129 genes). Phylogenetic analysis strongly supported the monophyly of Argentina and identified four major clades. Codon usage analysis revealed a weak overall bias and a consistent preference for A/T-ending codons. Neutrality, ENC-, and PR2-plots indicated that natural selection plays a dominant role in shaping CUB, overriding mutational pressure. We identified 16 optimal codons, only one of which (GGA, encoding Gly) was shared across all species, suggesting lineage-specific codon adaptation. Conclusions This study provides the first comprehensive insight into codon usage patterns in Argentina chloroplast genomes, enhancing our understanding of phylogenetic relationships and molecular evolution in this genus, with implications for future genetic research and codon optimization strategies.