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Coptis chinensis  Franch, a perennial herb, is mainly distributed in southeastern China. The rhizome of  C. chinensis  has been used as a traditional medicine for more than 2000 years in China and many other Asian countries. The pharmacological activities of  C. chinensis  have been validated by research. Here, we present a de novo high-quality genome of  C. chinensis  with a chromosome-level genome of ~958.20 Mb, a contig N50 of 1.58 Mb, and a scaffold N50 of 4.53 Mb. We found that the relatively large genome size of  C. chinensis  was caused by the amplification of long terminal repeat (LTR) retrotransposons. In addition, a whole-genome duplication event in ancestral Ranunculales was discovered. Comparative genomic analysis revealed that the tyrosine decarboxylase ( TYDC ) and (S)-norcoclaurine synthase ( NCS ) genes were expanded and that the aspartate aminotransferase gene ( ASP5 ) was positively selected in the berberine metabolic pathway. Expression level and HPLC analyses showed that the berberine content was highest in the roots of  C. chinensis  in the third and fourth years. The chromosome-level reference genome of  C. chinensis  provides important genomic data for molecular-assisted breeding and active ingredient biosynthesis.

The chromosome-level reference genome of Coptis chinensis provides insights into genomic evolution and berberine biosynthesis