Chloroplast Genome Features and Phylogeny of Two Nationally Protected Medicinal Plants, Euchresta tubulosa and Euchresta japonica: Molecular Resources for Identification and Conservation

[Objectives]: By performing genome assembly, annotation, comparative characterization, and phylogenetic analysis on the complete chloroplast genomes of <i>E. tubulosa</i> and <i>E. japonica</i>-two medicinal plants belonging to the genus <i>Euchresta</i>-this study aims to identify their differential genes, thereby providing fundamental research for screening candidate genes as DNA barcodes for species identification and facilitating the conservation of these endangered species. [Methods]: Illumina PE150 sequencing was performed. Chloroplast genomes (plastomes) were assembled and annotated with GetOrganelle/SPAdes. Comparative analyses assessed gene content, IR/LSC/SSC structure, repeat profiles, and codon-usage bias. Using related <i>Fabaceae</i> as references, we conducted mVISTA alignments and sliding-window nucleotide diversity (Pi) analyses to identify candidate DNA barcodes. Phylogenies from whole-plastome sequences were inferred with Maximum Likelihood, Bayesian Inference, and Maximum Parsimony. [Results]: The plastomes measured 153,960 bp (<i>E. japonica</i>) and 150,146 bp (<i>E. tubulosa</i>), with GC contents of 36.30% and 36.20%, respectively, each exhibiting a typical quadripartite structure. IR/SC boundaries were highly conserved without evident expansion or contraction. Repeat statistics were 20/30 palindromic repeats, 57/64 tandem repeats, and 156/159 simple sequence repeats (SSRs) in <i>E. japonica/E. tubulosa</i>, respectively. Leucine was the most frequently encoded amino acid, cysteine the least, and codon usage favored A/U at third positions. Five hypervariable loci-<i>rps19</i>, <i>psbA</i>, <i>trnK</i>, <i>matK</i>, and <i>rps16</i> (Pi > 0.03)-were identified as candidate DNA barcodes. All trees consistently placed both species within Papilionoideae (Fabaceae) and recovered the closest relationship to Sophora macrocarpa. [Conclusions]: This study provides, for the first time, complete plastomes and candidate barcoding regions for two protected <i>Euchresta</i> species, supplying foundational resources for species identification, resource assessment, and conservation planning.