Biomaterial Database

The chromosome-level reference genome of Coptis chinensis provides insights into genomic evolution and berberine biosynthesis. 2021

Da-Xia Chen, and Yuan Pan, and Yu Wang, and Yan-Ze Cui, and Ying-Jun Zhang, and Rang-Yu Mo, and Xiao-Li Wu, and Jun Tan, and Jian Zhang, and Lian-An Guo, and Xiao Zhao, and Wenkai Jiang, and Tian-Lin Sun, and Xiao-Di Hu, and Long-Yun Li

Chongqing Academy of Chinese Materia Medica, 400065, Chongqing, China.

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.