The Chromosome Level Genome and Genome-wide Association Study for the Agronomic Traits of Panax Notoginseng

Guangyi Fan; Xiaochuan Liu; Shuai Sun; Chengcheng Shi; Xiao Du; Kai Han; Binrui Yang; Yuanyuan Fu; Minghua Liu; Inge Seim; He Zhang; Qiwu Xu; Jiahao Wang; Xiaoshan Su; Libin Shao; Yuanfang Zhu; Yunchang Shao; Yunpeng Zhao; Andrew KC Wong; Dennis Zhuang; Wenbin Chen; Gengyun Zhang; Huanming Yang; Xun Xu; Stephen Kwok Wing Tsui; Xin Liu; Simon Ming Yue Lee

doi:10.1016/j.isci.2020.101538

The Chromosome Level Genome and Genome-wide Association Study for the Agronomic Traits of Panax Notoginseng

Guangyi Fan
, Xiaochuan Liu
, Shuai Sun
, Chengcheng Shi
, Xiao Du
, Kai Han
, Binrui Yang
, Yuanyuan Fu
, Minghua Liu
, Inge Seim
, He Zhang
, Qiwu Xu
, Jiahao Wang
, Xiaoshan Su
, Libin Shao
, Yuanfang Zhu
, Yunchang Shao
, Yunpeng Zhao
, Andrew KC Wong
, Dennis Zhuang

Wenbin Chen, Gengyun Zhang, Huanming Yang, Xun Xu, Stephen Kwok Wing Tsui, Xin Liu, Simon Ming Yue Lee

University of Macau
BGI-Shenzhen
University of Waterloo
Chinese University of Hong Kong
Nanjing Normal University
Queensland University of Technology
Zhejiang University
BGI Research-Shenzhen

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

49 Scopus citations

Abstract

The Chinese ginseng Panax notoginseng is a domesticated herb with significant medicinal and economic value. Here we report a chromosome-level P. notoginseng genome assembly with a high (∼79%) repetitive sequence content. The juxtaposition with the widely distributed, closely related Korean ginseng (Panax ginseng) genome revealed contraction of plant defense genes (in particular R-genes) in the P. notoginseng genome. We also investigated the reasons for the larger genome size of Panax species, revealing contributions from two Panax-specific whole-genome duplication events and transposable element expansion. Transcriptome data and comparative genome analysis revealed the candidate genes involved in the ginsenoside synthesis pathway. We also performed a genome-wide association study on 240 cultivated P. notoginseng individuals and identified the associated genes with dry root weight (63 genes) and stem thickness (168 genes). The P. notoginseng genome represents a critical step toward harnessing the full potential of an economically important and enigmatic plant.

Original language	English
Article number	101538
Journal	iScience
Volume	23
Issue number	9
DOIs	https://doi.org/10.1016/j.isci.2020.101538
State	Published - 25 Sep 2020
Externally published	Yes

Keywords

Biological Sciences
Genomics
Plant Biology
Transcriptomics

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10.1016/j.isci.2020.101538

Cite this

Fan, G., Liu, X., Sun, S., Shi, C., Du, X., Han, K., Yang, B., Fu, Y., Liu, M., Seim, I., Zhang, H., Xu, Q., Wang, J., Su, X., Shao, L., Zhu, Y., Shao, Y., Zhao, Y., Wong, A. KC., ... Lee, S. M. Y. (2020). The Chromosome Level Genome and Genome-wide Association Study for the Agronomic Traits of Panax Notoginseng. iScience, 23(9), Article 101538. https://doi.org/10.1016/j.isci.2020.101538

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title = "The Chromosome Level Genome and Genome-wide Association Study for the Agronomic Traits of Panax Notoginseng",

abstract = "The Chinese ginseng Panax notoginseng is a domesticated herb with significant medicinal and economic value. Here we report a chromosome-level P. notoginseng genome assembly with a high (∼79\%) repetitive sequence content. The juxtaposition with the widely distributed, closely related Korean ginseng (Panax ginseng) genome revealed contraction of plant defense genes (in particular R-genes) in the P. notoginseng genome. We also investigated the reasons for the larger genome size of Panax species, revealing contributions from two Panax-specific whole-genome duplication events and transposable element expansion. Transcriptome data and comparative genome analysis revealed the candidate genes involved in the ginsenoside synthesis pathway. We also performed a genome-wide association study on 240 cultivated P. notoginseng individuals and identified the associated genes with dry root weight (63 genes) and stem thickness (168 genes). The P. notoginseng genome represents a critical step toward harnessing the full potential of an economically important and enigmatic plant.",

keywords = "Biological Sciences, Genomics, Plant Biology, Transcriptomics",

author = "Guangyi Fan and Xiaochuan Liu and Shuai Sun and Chengcheng Shi and Xiao Du and Kai Han and Binrui Yang and Yuanyuan Fu and Minghua Liu and Inge Seim and He Zhang and Qiwu Xu and Jiahao Wang and Xiaoshan Su and Libin Shao and Yuanfang Zhu and Yunchang Shao and Yunpeng Zhao and Wong, \{Andrew KC\} and Dennis Zhuang and Wenbin Chen and Gengyun Zhang and Huanming Yang and Xun Xu and Tsui, \{Stephen Kwok Wing\} and Xin Liu and Lee, \{Simon Ming Yue\}",

note = "Publisher Copyright: {\textcopyright} 2020 The Author(s)",

year = "2020",

month = sep,

day = "25",

doi = "10.1016/j.isci.2020.101538",

language = "英语",

volume = "23",

journal = "iScience",

issn = "2589-0042",

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Fan, G, Liu, X, Sun, S, Shi, C, Du, X, Han, K, Yang, B, Fu, Y, Liu, M, Seim, I, Zhang, H, Xu, Q, Wang, J, Su, X, Shao, L, Zhu, Y, Shao, Y, Zhao, Y, Wong, AKC, Zhuang, D, Chen, W, Zhang, G, Yang, H, Xu, X, Tsui, SKW, Liu, X & Lee, SMY 2020, 'The Chromosome Level Genome and Genome-wide Association Study for the Agronomic Traits of Panax Notoginseng', iScience, vol. 23, no. 9, 101538. https://doi.org/10.1016/j.isci.2020.101538

TY - JOUR

T1 - The Chromosome Level Genome and Genome-wide Association Study for the Agronomic Traits of Panax Notoginseng

AU - Fan, Guangyi

AU - Liu, Xiaochuan

AU - Sun, Shuai

AU - Shi, Chengcheng

AU - Du, Xiao

AU - Han, Kai

AU - Yang, Binrui

AU - Fu, Yuanyuan

AU - Liu, Minghua

AU - Seim, Inge

AU - Zhang, He

AU - Xu, Qiwu

AU - Wang, Jiahao

AU - Su, Xiaoshan

AU - Shao, Libin

AU - Zhu, Yuanfang

AU - Shao, Yunchang

AU - Zhao, Yunpeng

AU - Wong, Andrew KC

AU - Zhuang, Dennis

AU - Chen, Wenbin

AU - Zhang, Gengyun

AU - Yang, Huanming

AU - Xu, Xun

AU - Tsui, Stephen Kwok Wing

AU - Liu, Xin

AU - Lee, Simon Ming Yue

PY - 2020/9/25

Y1 - 2020/9/25

N2 - The Chinese ginseng Panax notoginseng is a domesticated herb with significant medicinal and economic value. Here we report a chromosome-level P. notoginseng genome assembly with a high (∼79%) repetitive sequence content. The juxtaposition with the widely distributed, closely related Korean ginseng (Panax ginseng) genome revealed contraction of plant defense genes (in particular R-genes) in the P. notoginseng genome. We also investigated the reasons for the larger genome size of Panax species, revealing contributions from two Panax-specific whole-genome duplication events and transposable element expansion. Transcriptome data and comparative genome analysis revealed the candidate genes involved in the ginsenoside synthesis pathway. We also performed a genome-wide association study on 240 cultivated P. notoginseng individuals and identified the associated genes with dry root weight (63 genes) and stem thickness (168 genes). The P. notoginseng genome represents a critical step toward harnessing the full potential of an economically important and enigmatic plant.

AB - The Chinese ginseng Panax notoginseng is a domesticated herb with significant medicinal and economic value. Here we report a chromosome-level P. notoginseng genome assembly with a high (∼79%) repetitive sequence content. The juxtaposition with the widely distributed, closely related Korean ginseng (Panax ginseng) genome revealed contraction of plant defense genes (in particular R-genes) in the P. notoginseng genome. We also investigated the reasons for the larger genome size of Panax species, revealing contributions from two Panax-specific whole-genome duplication events and transposable element expansion. Transcriptome data and comparative genome analysis revealed the candidate genes involved in the ginsenoside synthesis pathway. We also performed a genome-wide association study on 240 cultivated P. notoginseng individuals and identified the associated genes with dry root weight (63 genes) and stem thickness (168 genes). The P. notoginseng genome represents a critical step toward harnessing the full potential of an economically important and enigmatic plant.

KW - Biological Sciences

KW - Genomics

KW - Plant Biology

KW - Transcriptomics

UR - https://www.scopus.com/pages/publications/85091236156

U2 - 10.1016/j.isci.2020.101538

DO - 10.1016/j.isci.2020.101538

M3 - 文章

AN - SCOPUS:85091236156

SN - 2589-0042

VL - 23

JO - iScience

JF - iScience

IS - 9

M1 - 101538

ER -

The Chromosome Level Genome and Genome-wide Association Study for the Agronomic Traits of Panax Notoginseng

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Keywords

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