Milk thistle (Silybum marianum Gaertn.) is a well-known medicinal plant which has been used for more than 2,000 years around the world. It produces silymarin, which cures the liver from hepatitis and toxin damages. In this study, a selfed and purified breeding line of the milk thistle from the Korean environment was used as a source of chloroplast genome construction. It showed high concentration of silybin B (3.50 mg/g) in its dried seeds. The complete chloroplast genome of S. marianum acc. ‘912036’ is 152,556 bp in length and G+C content is 37.69%. A total of 87 protein coding genes with 104 exons were annotated. Chloroplast genomes of five accessions from different countries were compared with that of ‘912036’, and no sequence polymorphism among them was identified. Thus, the chloroplast genome from this study can be used to develop S. marianum-specific DNA markers when compared with other diverse S. marianum accessions and Asteraceae species.

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