Abstract
Capparis spinosa L. and Capparis decidua Forsk. belong to the Capparaceae family. The two species are important medicinal plants uses in treatment of various ailments. In this study, we present the complete chloroplast genomes of the two species. The complete plastome genomes of the two species have a circular structure and a length of 157,728 bp in Capparis spinosa and 157,573 bp in Capparis decidua and GC content of 35.91, 35.96% respectively. The chloroplast genome of C. spinosa and C. decidua is divided into four regions: LSC of 86,732 and 85,950 bp respectively, SSC from 18,322 to 18,621 bp and a pair of inverted repeats 26,337 and 26,501 bp each. Both of the chloroplast genomes contained 115 different genes, including 80 protein coding genes, 31 tRNA genes and four rRNA genes. A phylogenetic analysis demonstrated that C. spinosa is sister to Capparis urophylla. The two species are sister to C. decidua.