The complete chloroplast genome sequence and phylogenetic position of Causonis japonica (Thunb.) Raf. (Vitaceae)

Causonis japonica (Thunb.) Raf. (Vitaceae), the type species of the genus Causonis, holds notable medicinal and systematic value. In this study, we present the complete chloroplast genome of C. japonica (158,414 bp), which exhibits the conserved four-part structure typical of angiosperms—comprising a large single-copy (LSC, 87,629 bp) region, a small single-copy (SSC, 19,101 bp) region, and two inverted repeats (IRa/IRb, 25,842 bp each). The plastome contains 139 annotated genes, including 92 protein-coding genes, 39 tRNA genes, and 8 rRNA genes, with an overall GC proportion of 37%. Among these, 11 genes possess introns (9 single-intron genes, and clpP1 and pafI each with two). The rps12 gene is trans-spliced across three exons, and the inverted repeat segments replicate 8 protein-coding genes, 3 tRNAs, and 4 rRNAs. Phylogenomic inference based on complete chloroplast sequences of Vitaceae confirms C. japonica as an independent evolutionary lineage, distinct from Cissus and Tetrastigma, thereby offering robust molecular evidence for the evolutionary separation and taxonomic integrity of Causonis.