The complete chloroplast genome of Polygala subopposita, an endemic milkwort in China

Polygala subopposita is an endemic milkwort species in China. In this study, we present the assembly of its chloroplast genome (plastome) for the first time. The total plastome size is 164,784 bp in length, consisting of a large single-copy (LSC) region of 83,235 bp, a small single-copy (SSC) region of 8,037 bp, and two inverted repeat (IR) regions of 36,756 bp that have expanded approximately 10 kb into the SSC region. A total of 111 unique genes were identified in the plastome, including 77 protein-coding, 30 tRNA, and four rRNA genes. Interestingly, the trnQUUG gene was found to have two additional copies in the IRs, and the clpP gene lost its entire intron 2. Phylogenetic analysis suggests a close relationship between P. subopposita and P. crotalarioides. These findings provide valuable genomic resources for further research on the phylogenetic and evolutionary studies of Polygalaceae.