The complete chloroplast genome of <i>Codonopsis javanica</i> (Campanulaceae) from Vietnam: Structure and comparative analysis

<i>Codonopsis javanica</i> (Campanulaceae) is an important medicinal plant in Southeast Asia; however, its taxonomic identification remains challenging due to the high degree of morphological similarity among closely related species. Chloroplast genome analysis is an effective tool for resolving such taxonomic uncertainty. In this study, the complete chloroplast genome of <i>C. javanica</i> from Vietnam was assembled from 2.7 Gb of Illumina paired-end sequencing data. Genome annotation and comparative analyses were conducted to examine structural features, gene content, sequence divergence, and phylogenetic relationships. The chloroplast genome was 177,210 bp in length, with a GC content of 38.64%, and exhibited a typical quadripartite structure. The plastome contained genes associated with photosynthesis, self-replication, and other cellular functions. Comparative analyses revealed that <i>Codonopsis</i> plastomes are highly conserved, with sequence divergence mainly occurring in several non-coding regions (<i>trnT-UGU–rps2, trnY-GUA–trnT-GGU, ndhF–ndhG, rps16–psbI,</i> and <i>cemA–ycf4</i>) and in several coding genes (<i>petN, rpl16, ycf1,</i> and <i>ycf2</i>). Phylogenomic analyses consistently supported the monophyly of <i>Codonopsis</i> and confirmed the phylogenetic position of <i>C. javanica.</i> This study provides the first complete chloroplast genome of <i>C. javanica</i> from Vietnam, offering valuable genomic resources for species identification, phylogenetic analysis, and conservation of this medicinally important genus.