| Summary: | Isoetes japonica A. Braun is a heterosporous quillwort living in low-altitude areas in Japan. In the present study, the complete chloroplast genome of I. japonica was assembled and annotated. This chloroplast genome is a circular structure of 145,517 bp in length, comprising a pair of inverted repeat (IR) regions of 13,204 bp each, a large single copy (LSC) region of 91,868 bp, and a small single copy (SSC) region of 27,241 bp. The chloroplast genome contains 135 genes, including 78 protein-coding genes, 36 tRNA genes, and 8 rRNA genes. Phylogenetic analysis showed that I. japonica is sister to I. sinensis and I. yunguiensis. These results provide additional resources for the future studies on Isoetes species.
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