Comparative analysis of chloroplast genomes reveals molecular evolution and phylogenetic relationships in Styrax (Styracaceae)

Styrax is the most species-rich and economically important genus within Styracaceae, valued for its medicinal, ornamental, and bioactive properties. Chloroplast genomic resources for this genus remain limited. Here, we conducted comparative genomic analyses of 23 newly assembled chloroplast genomes of Styrax to characterize genome architecture and evolutionary patterns, and performed phylogenetic analyses using broader sampling across the genus to resolve infrageneric relationships. All genomes exhibited a typical quadripartite structure with highly conserved IR/SC boundaries and core genes involved in photosynthesis and replication. Six tandem repeat sequences were identified. Codon usage bias indicated a preference for A/U endings, reflecting the interplay of mutation bias and moderate selection. Phylogenetic analyses recovered two well-supported monophyletic clades and revealed that the two sections (Sect. Valvatae and Sect. Styrax) are not monophyletic, whereas all four series recognized by Fritsch (Ser. Styrax, Ser. Valvatae, Ser. Cyrta, and Ser. Benzoin) were recovered as monophyletic. These findings enrich Styracaceae genomic resources, clarify infrageneric relationships, and provide a foundation for DNA barcoding and adaptive evolution studies in Styrax.