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

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Listed:
  • 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)

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.

Suggested Citation

  • 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 Murta, 2021. "Analysis of the Coptis chinensis genome reveals the diversification of protoberberine-type alkaloids," Nature Communications, Nature, vol. 12(1), pages 1-13, December.
    • Handle: RePEc:nat:natcom:v:12:y:2021:i:1:d:10.1038_s41467-021-23611-0
    DOI: 10.1038/s41467-021-23611-0
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    Cited by:

    1. Liang Leng & Zhichao Xu & Bixia Hong & Binbin Zhao & Ya Tian & Can Wang & Lulu Yang & Zhongmei Zou & Lingyu Li & Ke Liu & Wanjun Peng & Jiangning Liu & Zhoujie An & Yalin Wang & Baozhong Duan & Zhigan, 2024. "Cepharanthine analogs mining and genomes of Stephania accelerate anti-coronavirus drug discovery," Nature Communications, Nature, vol. 15(1), pages 1-16, December.

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