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

Viola vaginata, a perennial herb in subsection Stolonosae, 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 V. vaginata in a clade with subsection Biobatae species and some Patellares species, while other Patellares species formed a distinct clade, contrasting with previous nuclear ITS results. These findings highlight the phylogenetic complexity within Viola.鞘柄堇菜（Viola vaginata）为匍匐茎亚组（Stolonosae）下的多年生草本植物，特产于日本日本海沿岸的雪山区域。其完整叶绿体基因组（chloroplast genome）长度为156056 bp，由一个大单拷贝区（large single-copy region，86407 bp）、一个小单拷贝区（small single-copy region，17301 bp）以及两个反向重复区（inverted repeat region，各长27174 bp）组成。该基因组共包含111个独特基因，其中包括77个蛋白质编码基因（protein-coding genes）、30个转运RNA（transfer RNA）基因以及4个核糖体RNA（ribosomal RNA）基因。系统发育分析（phylogenetic analysis）结果显示，鞘柄堇菜与Biobatae亚组（Biobatae）物种及部分Patellares组（Patellares）物种聚为同一演化支（clade）；而其余Patellares组物种则形成独立演化支，这与此前基于细胞核内转录间隔区（Internal Transcribed Spacer, ITS）的研究结果相悖。上述研究结果凸显了堇菜属（Viola）内系统发育关系的复杂性。