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

Liu, Yifei; Wang, Bo; Shu, Shaohua; Li, Zheng; Song, Chi; Liu, Di; Niu, Yan; Liu, Jinxin; Zhang, Jingjing; Liu, Heping; Hu, Zhigang; Huang, Bisheng; Liu, Xiuyu; Liu, Wei; Jiang, Liping; Alami, Mohammad Murtaza; Zhou, Yuxin; Ma, Yutao; He, Xiangxiang; Yang, Yicheng

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.

GENOMICS; GENETIC models; GENOMES; BERBERINE; GENE families; CYTOCHROME P-450; ALKALOIDS

Nature Communications, 2021, Vol 12, Issue 1, p1

2041-1723

Academic Journal

10.1038/s41467-021-23611-0