Comparative analysis of the complete chloroplast genomes of Cirsium japonicum from China and Korea

Cirsium japonicum (C. japonicum) is a traditional Chinese medicine belonging to the family Asteraceae. The previous studies have indicated that the chemical compound content of C. japonicum from different places was different. To distinguish C. japonicum from different geographies, the chloroplast genome of C. japonicum from China was sequenced and compared with that from Korea. The total length of this genome is 152,602 bp, similar to that of Korea (152,606 bp). It has a conservative quartile structure which is composed of a large single-copy (LSC) region, a small single-copy (SSC) region and a pair of inverted repeats (IRs) regions, with lengths of 83,487 bp, 18,721 bp, and 25,197 bp, respectively. It encodes 79 protein-coding, 27 transfer RNAs, and 4 ribosomal RNA genes. The overall GC content of the genome is 37.70%. A total of 20 single nucleotide polymorphisms and 6 insertions and deletions were identified between the chloroplast genome of C. japonicum from China and Korea. These results can be applied to develop molecular markers to distinguish C. japonicum from different geographical origins.