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Article|01 Jun 2021|OPEN
The chromosome-level reference genome of Coptis chinensis provides insights into genomic evolution and berberine biosynthesis
Da-xia Chen1,2,3, Yuan Pan1,2,3, Yu Wang1,2,3, Yan-Ze Cui4, Ying-Jun Zhang4, Rang-yu Mo1,2,3, Xiao-li Wu1,2,3, Jun Tan1,2,3, Jian Zhang1,2,3, Lian-an Guo1,2,3, Xiao Zhao1,2,3, Wenkai Jiang4, Tian-lin Sun4, Xiao-Di Hu4, & Long-yun Li1,
1Chongqing Academy of Chinese Materia Medica, 400065 Chongqing, China
2Chongqing Engineering Research Center for Fine Variety Breeding Techniques of Chinese Materia Medica, 400065 Chongqing, China
3Chongqing Sub-center of National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Science, 400065 Chongqing, China
4Novogene Bioinformatics Institute, Building 301, Zone A10 Jiuxianqiao North 13 Road, Chaoyang District, 100083 Beijing, China

Horticulture Research 8,
Article number: 121 (2021)
doi: 10.1038/hortres.2021.121
Views: 369

Received: 09 Dec 2020
Revised: 03 Mar 2021
Accepted: 14 Mar 2021
Published online: 01 Jun 2021

Abstract

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.