Journal Article

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

Hu, Zhigang, He, Xiangxiang, Song, Chi, Yang, Yicheng, Barker, Michael S., Wang, Xuekui, Liu, Xiuyu, Alami, Mohammad Murtaza, Zhang, Tianyuan, Ma, Yutao, Chen, Shilin, Zhang, Jingjing, Huang, Bisheng, Liu, Di, Liu, Heping, Li, Zheng, Liu, Yifei, Liu, Wei, Zhou, Yuxin, Nie, Jing, Liu, Jinxin, Wang, Bo, Niu, Yan, Hu, Hui, Jiang, Liping, Shu, Shaohua

2021

Overview

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. Coptis chinensis represents an early-diverging eudicot lineage with diverse medicinal applications. Here, the authors report its chromosome-scale genome assembly, infer a single ancient whole-genome duplication, and characterize the function of CYP719 in diversification of protoberberine-type alkaloids.

• Publisher: Nature Publishing Group UK,Nature Publishing Group,Nature Portfolio
• Subject: 38/23 / 38/39 / 38/91 / 45 / 631/208/212/2304 / 631/208/514/2254 / 631/449/2667 / 631/449/2669 / Alkaloids / Annotations / Assembly / Berberine / Berberine Alkaloids - metabolism / Biosynthesis / Biosynthetic Pathways - genetics / Chromosomes / Coptis - chemistry / Coptis - genetics / Coptis - metabolism / Coptis chinensis / Cytochrome P-450 Enzyme System - genetics / Cytochrome P-450 Enzyme System - metabolism / Cytochrome P450 / Cytochromes P450 / Diversification / Drugs, Chinese Herbal / Gene Duplication / Gene Expression Regulation, Plant / Gene Ontology / Genome, Plant / Genomes / Genomic analysis / Genomics / Humanities and Social Sciences / Medicinal plants / Molecular Sequence Annotation / multidisciplinary / Phylogenetics / Phylogeny / Plant Proteins - genetics / Plant Proteins - metabolism / Plants, Medicinal / Ranunculales / Reproduction (copying) / Science / Science (multidisciplinary)