Figure S1 Read coverage of the assembled genome. The paired-end (PE) reads were remapped to the assembled genome. The number aligned bases and the polymorphic sites were counted from the mapping result. Figure S2 Phylogenetic tree of 69 plant species. The tree was calculated from the connected sequence of the 38 orthologous proteins. Figure S3 Edited sites on ycf4. The sequence of ycf4 from three Vigna species, which have this gene in their cp genomes, and P. vulgaris are aligned and three edited sites are marked with pink bars. Table S1 Orthologous genes calculated from the chloroplast genome of twelve legume species with OrthoFinder program.