[Objectives]: By performing genome assembly, annotation, comparative characterization, and phylogenetic analysis on the complete chloroplast genomes of E. tubulosa and E. japonica—two medicinal plants belonging to the genus Euchresta—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 Fabaceae 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 (E. japonica) and 150,146 bp (E. tubulosa), 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 E. japonica/E. tubulosa, respectively. Leucine was the most frequently encoded amino acid, cysteine the least, and codon usage favored A/U at third positions. Five hypervariable loci—rps19, psbA, trnK, matK, and rps16 (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 Euchresta species, supplying foundational resources for species identification, resource assessment, and conservation planning.

Background: Imidacloprid, a widely used neonicotinoid insecticide, is routinely applied to control pests in Astragalus membranaceus var. mongholicus, a crucial medicinal herb producing Astragali Radix. However, the early short-term transcriptional and metabolic responses of its seedlings under imidacloprid gradient stress remain poorly characterized. Methods: In this study, 80-day seedlings were subjected to three foliar spray treatments: blank control (CK), the recommended imidacloprid concentration (2000-fold dilution, 475 mg·L⁻¹), and an excessively high concentration (500-fold dilution, 1900 mg·L⁻¹). Leaf samples were harvested 24 h post-treatment for untargeted ultra-high-performance liquid chromatography-tandem mass spectrometry (UPLC–MS/MS) metabolomics (6 biological replicates) and RNA-seq transcriptome sequencing (3 biological replicates). Results: The low- and high-dose treatments induced 1076 and 860 differential metabolites and 6818 and 7283 differentially expressed genes, respectively. Flavonoids, saponins, terpenoids, amino acid metabolites, and energy-related pathways were prominently affected. KEGG enrichment indicated activation of flavone/flavonol biosynthesis, phenylpropanoid metabolism, amino acid metabolism, MAPK signaling, cutin/suberin/wax biosynthesis, and ABC transporter pathways, whereas high-dose exposure was associated with stronger changes in genes related to DNA replication and cell wall remodeling. Integrated network analysis highlighted CHS, PAL, MYC2, KCS, and ABCG40 as candidate regulators linking stress signaling, secondary metabolism, and metabolite transport. Conclusions: Seedlings of A. membranaceus var. mongholicus exhibit dose-dependent acute responses to imidacloprid. Moderate pesticide exposure primarily activates defensive secondary metabolism, whereas excessive dosage triggers genome-wide transcriptional reprogramming. This work identifies key metabolic pathways and hub genes, offering candidate molecular markers for investigating pesticide stress adaptation in medicinal Astragalus and guiding standardized pesticide application in cultivation.