Objective High-throughput sequencing of Rehmannia chrysantha L.was performed to elucidate the structure of its chloroplast genome and its phylogenetic relationship with related species. Methods Codon preference analysis of chloroplasts of R. chrysantha was performed using CodonW v1.3 software. The codon usage bias was analyzed by using CodonW v1.3 software. Then, the obtained data were imported into IRscope and mVISTA to clarify sequence variations between R. chrysantha and related species. This study constructed a phylogenetic tree of the genus Rehmannia and its related genera on MEGA11 software. Results The chloroplast genome of R. chrysantha was a typical circular double-stranded molecule with a quadripartite structure and a total length of 153 789 bp. It has 28 high-frequency codons. Neutral plot analysis, ENC-plot analysis, and PR2-plot analysis all indicated that natural selection was the main cause of codon usage bias in R. chrysantha. It was also found that there were varying degrees of variation in the inverted repeat (IR) boundaries of the Rehmannia genus, and these changes were mainly concentrated in JLA and JLB. The genes rpl2, psbI, petN, psbZ, ycf1, and ndhB were identified as potential DNA barcodes for distinguishing closely related genus Rehmannia. In addition, phylogenetic analysis revealed a close evolutionary relationship between R. chrysantha and R. glutinosa L. Conclusion Protein-coding genes in the chloroplast genomes of genus Rehmannia exhibited a preferential use of codons ending in A/U, with natural selection being the primary factor influencing this codon usage bias. These findings will provide a foundation for future studies on molecular evolution, phylogeny, and chloroplast genetic engineering within this genus.

Rehmannia chrysantha L.  /  chloroplast genome  /  codon preference  /  sequence variation  /  phylogeny