The complete chloroplast genome of <i>Polygala tatarinowii</i> (Polygalaceae)

<i>Polygala tatarinowii</i> (Polygalaceae) is an annual herb with ecological, medicinal, and agricultural potential. Here, we present the inaugural assembly of its chloroplast genome (plastome). The total plastome spans 168,779 bp in length, featuring two expanded inverted repeat (IR) regions measuring 43,427 bp each, flanking a large single-copy (LSC) region of 73,712 bp and a small single-copy (SSC) region of 8213 bp. The plastome exhibits a GC content of 36.8%. Annotation of the plastome revealed a total of 112 unique genes, comprising 78 protein-coding genes, 30 tRNAs and 4 rRNAs. Uncommonly, two copies of the <i>trn</i>Q^UUG gene were identified within the IRs, resulting in the presence of three <i>trn</i>Q^UUG copies in this plastome. Additionally, reductions were observed in the <i>ycf</i>1 and <i>ycf</i>2 genes. Phylogenetic analysis effectively resolves the relationships among sampled Polygalaceae species. Our findings underscore the instrumental role of plastomes in advancing research on the systematics, phylogenetics, and genetic diversity of Polygalaceae.