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; Jing Nie

doi:10.1038/s41467-021-23611-0

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 YangTianyuan Zhang, Hui Hu, Michael S. Barker, Shilin Chen, Xuekui Wang, Jing Nie

Research output: Contribution to journal › Article › peer-review

12 Scopus citations

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.

Original language	English (US)
Article number	3276
Journal	Nature communications
Volume	12
Issue number	1
DOIs	https://doi.org/10.1038/s41467-021-23611-0
State	Published - Dec 2021
Externally published	Yes

ASJC Scopus subject areas

Chemistry(all)
Biochemistry, Genetics and Molecular Biology(all)
Physics and Astronomy(all)

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10.1038/s41467-021-23611-0

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Liu, Y., Wang, B., Shu, S., Li, Z., Song, C., Liu, D., Niu, Y., Liu, J., Zhang, J., Liu, H., Hu, Z., Huang, B., Liu, X., Liu, W., Jiang, L., Alami, M. M., Zhou, Y., Ma, Y., He, X., ... Nie, J. (2021). Analysis of the Coptis chinensis genome reveals the diversification of protoberberine-type alkaloids. Nature communications, 12(1), [3276]. https://doi.org/10.1038/s41467-021-23611-0

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; Zhang, Tianyuan; Hu, Hui; Barker, Michael S.; Chen, Shilin; Wang, Xuekui; Nie, Jing.

In: Nature communications, Vol. 12, No. 1, 3276, 12.2021.

Research output: Contribution to journal › Article › peer-review

Liu, Y, Wang, B, Shu, S, Li, Z, Song, C, Liu, D, Niu, Y, Liu, J, Zhang, J, Liu, H, Hu, Z, Huang, B, Liu, X, Liu, W, Jiang, L, Alami, MM, Zhou, Y, Ma, Y, He, X, Yang, Y, Zhang, T, Hu, H, Barker, MS, Chen, S, Wang, X & Nie, J 2021, 'Analysis of the Coptis chinensis genome reveals the diversification of protoberberine-type alkaloids', Nature communications, vol. 12, no. 1, 3276. https://doi.org/10.1038/s41467-021-23611-0

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 ; Zhang, Tianyuan ; Hu, Hui ; Barker, Michael S. ; Chen, Shilin ; Wang, Xuekui ; Nie, Jing. / Analysis of the Coptis chinensis genome reveals the diversification of protoberberine-type alkaloids. In: Nature communications. 2021 ; Vol. 12, No. 1.

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title = "Analysis of the Coptis chinensis genome reveals the diversification of protoberberine-type alkaloids",

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.",

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

note = "Funding Information: We thank Shuibing Wang for assistant of some bioinformatic analyses, Juan Guo for biochemical assays, and Xu Wang and Xin Hu for helping with figures. This work was supported by the National Key Research & Development Program of China (2019YFC1711100, 2017YFC1700700, and 2017YFC1701000), National Natural Science Foundation of China (31870198, 81973429, 31961133007, and 82011530137), the Central Government Guides Local Science and Technology Development Fund in Hubei Province (2019ZYYD063), Hubei Science Foundation for Distinguished Young Scholars (2019CFA097), and Technological Innovation Project of Hubei Province (2018ACA125). Publisher Copyright: {\textcopyright} 2021, The Author(s).",

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doi = "10.1038/s41467-021-23611-0",

language = "English (US)",

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AU - Liu, Yifei

AU - Wang, Bo

AU - Shu, Shaohua

AU - Li, Zheng

AU - Song, Chi

AU - Liu, Di

AU - Niu, Yan

AU - Liu, Jinxin

AU - Zhang, Jingjing

AU - Liu, Heping

AU - Hu, Zhigang

AU - Huang, Bisheng

AU - Liu, Xiuyu

AU - Liu, Wei

AU - Jiang, Liping

AU - Alami, Mohammad Murtaza

AU - Zhou, Yuxin

AU - Ma, Yutao

AU - He, Xiangxiang

AU - Yang, Yicheng

AU - Zhang, Tianyuan

AU - Hu, Hui

AU - Barker, Michael S.

AU - Chen, Shilin

AU - Wang, Xuekui

AU - Nie, Jing

N1 - Funding Information: We thank Shuibing Wang for assistant of some bioinformatic analyses, Juan Guo for biochemical assays, and Xu Wang and Xin Hu for helping with figures. This work was supported by the National Key Research & Development Program of China (2019YFC1711100, 2017YFC1700700, and 2017YFC1701000), National Natural Science Foundation of China (31870198, 81973429, 31961133007, and 82011530137), the Central Government Guides Local Science and Technology Development Fund in Hubei Province (2019ZYYD063), Hubei Science Foundation for Distinguished Young Scholars (2019CFA097), and Technological Innovation Project of Hubei Province (2018ACA125). Publisher Copyright: © 2021, The Author(s).

PY - 2021/12

Y1 - 2021/12

N2 - 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.

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

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