The complete chloroplast genome of <i>Viola vaginata</i> (Violaceae), an endemic species of the snowy region in Japan

<i>Viola vaginata</i>, a perennial herb in subsection <i>Stolonosae</i>, is endemic to the snowy mountainous regions on the Sea of Japan side of Japan. Its complete chloroplast genome was 156,056 bp in length, comprising one large single-copy region (86,407 bp), one small single-copy region (17,301 bp), and two inverted repeat regions (27,174 bp each). It contained 111 unique genes, including 77 protein-coding genes, 30 transfer RNA genes, and 4 ribosomal RNA genes. Phylogenetic analysis placed <i>V. vaginata</i> in a clade with subsection <i>Biobatae</i> species and some <i>Patellares</i> species, while other <i>Patellares</i> species formed a distinct clade, contrasting with previous nuclear ITS results. These findings highlight the phylogenetic complexity within <i>Viola.</i>