Pan-Chloroplast Genomes Reveal the Accession-Specific Marker for f. .

rhizomes have been applied as traditional medicinal materials for thousands of years. In China, f. (red flower and stem, Ge), f. (green, Gv), and f. (black, Gg) represent the primary cultivars in artificial cultivation. Although the annual output of amounts to 150,000 tons, only 20% is Gg. The long production period, low yield, and high quality of Gg led to its extremely high market prices. However, an effective method to identify this crude drug based solely on its morphological or chemical characteristics is lacking. In this study, the complete chloroplast genomes of three variants were sequenced using the Illumina HiSeq 2500 platform. Another 21 chloroplast genomes from species, which have published in previous reports, were combined and analyzed together. Our results showed that larger genomic sizes, fewer long tandem repeats, and more simple sequence repeats were the major features of the Gg chloroplast genomes. Phylogenetic analysis showed that the Gg samples were separately clustered in a subclade. Moreover, an accession-specific marker was successfully developed and validated for distinguishing additional rhizome samples. Our study provides investigations of the taxonomic relationships of species. The molecular marker will be useful for differentiating products on the market.