Abstract
Physalis minima L. is an herbaceous plant with ethnobotanic importance across many Asian cultures. In this study, we sequenced and assembled the plastid genome (plastome) of a P. minima sample from Malaysia, and conducted intraspecific pairwise and phylogenetic analyses with available data of its relatives. Our sample had a plastome of 156,973 bp in size with a GC content of 37.5%. The genome was circular, consisting of a large single-copy of 87,196 bp, a small single-copy of 18,447 bp and a pair of inverted repeats of 25,665 bp each. A total of 129 genes were annotated, including 84 CDSs, 37 tRNAs and eight rRNAs. Between the China and Malaysia accession, 458 variable sites were identified, and the pairwise distance was 0.003. Phylogenetic analysis was conducted using the complete plastome sequence based on the maximum likelihood and Bayesian inference methods. The findings revealed that our sample was significantly differentiated from the accession from China, and that both P. minima accessions clustered away from P. angulata, the synonym suggested by certain taxonomic authorities. This study facilitates precise taxonomic identification of P. minima within ethnomedicinal frameworks, enabling its distinction from closely related or putatively synonymous species that may exhibit divergent phytochemical compositions. These results provide important insights into the genetic diversity and taxonomic status of P. minima, and support its informed use in future research, conservation, and medicinal applications.