Comparative Chloroplast Genomics, Codon Usage Bias, and Phylogenetic Placement of Euonymus alatus

Euonymus alatus is a species of medicinal and ornamental value, yet high-quality chloroplast genome resources for this taxon remain scarce. The complete chloroplast genome of E. alatus was assembled and compared with 15 congeneric species to investigate genomic structure and evolutionary dynamics. The genome is 157,416 bp with a GC content of 37.3%, containing 131 genes and 156 repeats (67 tandem repeats, 49 dispersed repeats, and 40 SSRs). Divergence was concentrated in non-coding regions, with 14 hypervariable regions identified as potential markers. IR expansion occurred independently in E. fortunei and E. japonicus, while no genome-wide inversions were detected. 11 protein-coding genes were identified under positive selection, among which clpP exhibited the strongest signal, suggesting a possible role in adaptive evolution. Codon usage bias analysis revealed that both mutation pressure and natural selection shape codon usage patterns, with the latter playing a relatively prominent role; 17 optimal codons were identified. Phylogenetic analysis strongly supported E. alatus as sister to E. phellomanus. This study provides a valuable genomic resource for species authentication, phylogenetic revision, and breeding in this genus.