Analysis of the Coptis chinensis genome reveals the diversification of protoberberine-type alkaloids

Yifei Liu (), Bo Wang, Shaohua Shu, Zheng Li, Chi Song, Di Liu, Yan Niu, Jinxin Liu, Jingjing Zhang, Heping Liu, Zhigang Hu, Bisheng Huang, Xiuyu Liu, Wei Liu, Liping Jiang, Mohammad Murtaza Alami, Yuxin Zhou, Yutao Ma, Xiangxiang He, Yicheng Yang, Tianyuan Zhang, Hui Hu, Michael S. Barker, Shilin Chen (), Xuekui Wang () and Jing Nie ()
Additional contact information
Yifei Liu: Hubei University of Chinese Medicine
Bo Wang: Hubei Institute for Drug Control
Shaohua Shu: Huazhong Agricultural University
Zheng Li: University of Arizona
Chi Song: Wuhan Benagen Tech Solutions Company Limited
Di Liu: Hubei University of Chinese Medicine
Yan Niu: Wuhan Benagen Tech Solutions Company Limited
Jinxin Liu: Huazhong Agricultural University
Jingjing Zhang: Hubei University of Chinese Medicine
Heping Liu: Huazhong Agricultural University
Zhigang Hu: Hubei University of Chinese Medicine
Bisheng Huang: Hubei University of Chinese Medicine
Xiuyu Liu: China Academy of Chinese Medical Sciences
Wei Liu: Hubei University of Chinese Medicine
Liping Jiang: Hubei University of Chinese Medicine
Mohammad Murtaza Alami: Huazhong Agricultural University
Yuxin Zhou: Hubei Institute for Drug Control
Yutao Ma: Huazhong Agricultural University
Xiangxiang He: Wuhan Benagen Tech Solutions Company Limited
Yicheng Yang: Wuhan Benagen Tech Solutions Company Limited
Tianyuan Zhang: Wuhan Benagen Tech Solutions Company Limited
Hui Hu: Jing Brand Chizhengtang Pharmaceutical Company Limited
Michael S. Barker: University of Arizona
Shilin Chen: Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences
Xuekui Wang: Huazhong Agricultural University
Jing Nie: Hubei Institute for Drug Control

Nature Communications, 2021, vol. 12, issue 1, 1-13

Abstract: Abstract Chinese goldthread (Coptis chinensis Franch.), a member of the Ranunculales, represents an important early-diverging eudicot lineage with diverse medicinal applications. Here, we present a high-quality chromosome-scale genome assembly and annotation of C. chinensis. Phylogenetic and comparative genomic analyses reveal the phylogenetic placement of this species and identify a single round of ancient whole-genome duplication (WGD) shared by the Ranunculaceae. We characterize genes involved in the biosynthesis of protoberberine-type alkaloids in C. chinensis. In particular, local genomic tandem duplications contribute to member amplification of a Ranunculales clade-specific gene family of the cytochrome P450 (CYP) 719. The functional versatility of a key CYP719 gene that encodes the (S)-canadine synthase enzyme involved in the berberine biosynthesis pathway may play critical roles in the diversification of other berberine-related alkaloids in C. chinensis. Our study provides insights into the genomic landscape of early-diverging eudicots and provides a valuable model genome for genetic and applied studies of Ranunculales.

Date: 2021
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DOI: 10.1038/s41467-021-23611-0

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