Features and Phylogenetic Analysis of the Chloroplast Genome of the Medicinal Plant Euchresta tubulosa

Background: Euchresta tubulosa is a medicinal plant in the Fabaceae family, traditionally used in Chinese herbal medicine for treating ailments such as sore throat and esophageal cancer. Despite its pharmacological importance and endangered status, no complete chloroplast genome data had been reported for this species or its genus prior to this study. Chloroplast genomes, being highly conserved and maternally inherited, serve as powerful tools for species identification, phylogenetic inference and genetic diversity assessment in plants. Methods: Fresh leaves of E. tubulosa were collected and genomic DNA was extracted using the cetyltrimethylammonium bromide (CTAB) method. High-throughput sequencing was carried out on the Illumina NovaSeq6000 platform. Clean reads were assembled into a complete chloroplast genome using NovoPlasty, with a related species as the seed reference. Genome annotation was performed using DOGMA and validated manually. Codon usage patterns were analyzed using RSCU values and simple sequence repeats (SSRs) were identified with MISA software. A maximum likelihood phylogenetic tree was constructed using PhyML, based on complete chloroplast genome sequences from 14 related species. Result: The assembled chloroplast genome of E. tubulosa measured 153,960 bp and exhibited a typical quadripartite structure, comprising a large single-copy region (LSC), a small single-copy region (SSC) and two inverted repeats (IRs). The overall GC content was 36.3%. A total of 127 genes were identified, including 44 related to photosynthesis, 72 involved in self-replication, 5 with other biological roles and 6 hypothetical or unknown genes. Codon usage analysis revealed 31 codons with RSCU greater than 1, showing a strong bias toward A/U-ending codons. A total of 109 SSR loci were detected, the majority of which were located in intergenic spacer regions. Phylogenetic analysis clearly positioned E. tubulosa as an independent lineage within the Fabaceae, supported by high bootstrap values. The genomic information provided by this study lays a foundation for future research in molecular taxonomy, phylogenetics and conservation of this endangered medicinal plant.