Comparative transcriptome analysis provides novel insights into the molecular mechanism of berberine biosynthesis in Coptis chinensis

•Berberine was mainly deposited in xylem of adventitious roots and rhizomes.•The content of total alkaloids of C. chinensis was the highest in rhizomes, among which berberine was the main alkaloids.•RNA-seq technology screened 60 candidate DEGs to be related to biosynthesis of berberine in C. chinensis.•Thirteen genes were identified to be potential key genes involved in berberine biosynthesis of C. chinensis.