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

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

doi:10.1038/s41467-021-23611-0

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.

Highlights

Chinese goldthread (Coptis chinensis Franch.), a member of the Ranunculales, represents an important early-diverging eudicot lineage with diverse medicinal applications
We infer that one-round ancient whole-genome duplication (WGD) occur within C. chinensis evolution, and characterize genes from the cytochrome P450 (CYP) family which greatly contribute to the biosynthesis and diversification of protoberberine-type alkaloids in Coptis
Based on the percentage of gene duplications shared by descendant taxa, and comparison to null and positive simulations of WGD, we found one episodic burst of shared gene duplication which was statistically consistent with our positive simulations of WGD at the node shared by the three core eudicot species (MAPS3, Fig. 3g, Supplementary Data 3 and 4)

Summary

Introduction

Chinese goldthread (Coptis chinensis Franch.), a member of the Ranunculales, represents an important early-diverging eudicot lineage with diverse medicinal applications. Genomic analysis of opium poppy has allowed the characterization of BIA gene clusters associated with the biosynthesis of noscapine and morphinan, suggesting potential selection pressure favouring quick formation and evolution of these alkaloids[16]. The evolutionary mechanisms underlying the occurrence of abundant protoberberine-type alkaloids in Coptis belowground rhizomes are still unclear, but this information is critical for our understanding of BIA diversification in plants. We infer that one-round ancient whole-genome duplication (WGD) occur within C. chinensis evolution, and characterize genes from the cytochrome P450 (CYP) family which greatly contribute to the biosynthesis and diversification of protoberberine-type alkaloids in Coptis. The C. chinensis reference genome provides insights into the evolution of eudicots and is valuable for future genetic studies and medicinal applications of Ranunculales

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Conclusion