Codon Bias and Phylogenesis Analysis of Chloroplast Genome in Medicinal Plants of Elsholtzia

Abstract Objective: To investigate the phylogenetic relationships based on chloroplast genomes, patterns of codon usage bias (CUB), and the underlying influencing factors in medicinal plants of the genus Elsholtzia . Materials and Methods: Chloroplast genomic features of five Elsholtzia species were analyzed using MISA, IRscope, and mVISTA. CUB and phylogenetic analyses were performed using CodonW 1.4.2, CUSP, chiplot, and MEGA. Results: The coding regions of the chloroplast genomes among the five Elsholtzia species were highly conserved, with relatively stable boundary regions and only minor structural variations. The average GC content of the coding regions (GCall) was below 40%, indicating a preferential use of A/U-ending codons. The most frequent optimal codon across all five species was AAU. The effective number of codons (ENC) ranged from 35.88 to 61.00, suggesting a weak CUB. Combined analyses including ENC-plot, neutrality plot, and PR2-bias plot indicated that CUB in these chloroplast genomes is influenced by both mutation pressure and natural selection, with natural selection being the dominant factor. Phylogenetic analysis revealed the closest genetic relationship between Elsholtzia splendens and Elsholtzia rugulosa . Conclusions: This study provides a foundation for understanding the genetic structure and diversity within the genus Elsholtzia and offers a theoretical basis for chloroplast genetic engineering and enhancing the expression of exogenous genes.