Comparative chloroplast genomics of Verbenaceae: structural divergence, adaptive evolution, and phylogenomic insights

The present study established a chloroplast genomic foundation for Verbenaceae phylogenetics and reveals natural selection as the primary force that governs codon usage evolution. Species within Verbenaceae family hold considerable medicinal, economic, and ornamental value, and play critical roles in maintaining ecosystem biodiversity. Despite these multifaceted applications, comprehensive studies on their chloroplast genome characteristics, codon usage patterns, and evolutionary dynamics remain limited. Here, we sequenced and assembled the complete chloroplast genomes of Verbena bonariensis, Glandularia tenera, and Verbena officinalis, and conducted comparative analyses with eight additional Verbenaceae species. All 11 species exhibited the typical quadripartite structure, with genome lengths ranging from 149,869 to 155,079 bp and GC contents varying between 38.23% and 39.25%. Collinearity analysis revealed highly conserved synteny across species. Phylogenetic reconstruction supported a close evolutionary affinity between Verbena and Glandularia. Codon usage bias analysis indicated a preference for A/U-ending codons, with each species exhibiting 29-30 codons with RSCU > 1. Effective number of codons (ENC) analysis suggested weak codon usage bias across all species. Simple sequence repeat (SSR) analysis identified 46-80 SSRs per species, predominantly mononucleotide repeats, primarily located in noncoding regions. ENC-GC3s, parity rule 2 (PR2), and neutrality analyses collectively indicated that natural selection is the predominant force shaping codon usage patterns. Selection pressure analysis further revealed pervasive strong purifying selection (Ka/Ks < 0.5) across most genes. Together, our findings provide an important genomic foundation for phylogenetic reconstruction, molecular evolution, and genetic resource utilization within Verbenaceae.