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The  Coptis chinensis  Franch. is an important medicinal plant from the Ranunculales. We used next generation sequencing technology to determine the complete chloroplast genome of  C. chinensis . This genome is 155,484 bp long with 38.17% GC content. Two 26,758 bp long inverted repeats separated the genome into a typical quadripartite structure. The  C. chinensis  chloroplast genome consists of 128 gene loci, including eight rRNA gene loci, 28 tRNA gene loci, and 92 protein-coding gene loci. Most of the SSRs in  C. chinensis  are poly-A/T. The numbers of mononucleotide SSRs in  C. chinensis  and other Ranunculaceae species are fewer than those in Berberidaceae species, while the number of dinucleotide SSRs is greater than that in the Berberidaceae.  C. chinensis  diverged from other Ranunculaceae species an estimated 81 million years ago (Mya). The divergence between Ranunculaceae and Berberidaceae was ~111 Mya, while the Ranunculales and Magnoliaceae shared a common ancestor during the Jurassic, ~153 Mya. Position 104 of the  C. chinensis ndhG  protein was identified as a positively selected site, indicating possible selection for the photosystem-chlororespiration system in  C. chinensis . In summary, the complete sequencing and annotation of the  C. chinensis  chloroplast genome will facilitate future studies on this important medicinal species.

Complete Chloroplast Genome Sequence of Coptis chinensis Franch. and Its Evolutionary History