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

iScience. 2020 Sep 8;23(9):101538. doi: 10.1016/j.isci.2020.101538. eCollection 2020 Sep 25.

Authors

Guangyi Fan^{1

2

3

4}, Xiaochuan Liu², Shuai Sun^{2

5}, Chengcheng Shi², Xiao Du², Kai Han², Binrui Yang¹, Yuanyuan Fu², Minghua Liu⁶, Inge Seim^{7

8}, He Zhang², Qiwu Xu², Jiahao Wang², Xiaoshan Su², Libin Shao², Yuanfang Zhu², Yunchang Shao⁹, Yunpeng Zhao¹⁰, Andrew Kc Wong⁵, Dennis Zhuang⁵, Wenbin Chen⁹, Gengyun Zhang³, Huanming Yang^{9

11}, Xun Xu^{9

12}, Stephen Kwok-Wing Tsui⁶, Xin Liu^{2

9

3

13}, Simon Ming-Yue Lee¹

Affiliations

¹ State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao 999078, China.
² BGI-QingDao, BGI-Shenzhen, Qingdao 266555, China.
³ State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, China.
⁴ Qingdao-Europe Advanced Institute for Life Sciences, BGI-Shenzhen, Qingdao 266555, China.
⁵ System Design Engineering, University of Waterloo, Ontario, N2L 3G1 Canada.
⁶ School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, China.
⁷ Integrative Biology Laboratory, College of Life Sciences, Nanjing Normal University, Nanjing 210046, China.
⁸ Comparative and Endocrine Biology Laboratory, Translational Research Institute-Institute of Health and Biomedical Innovation, School of Biomedical Sciences, Queensland University of Technology, Brisbane 4102, Australia.
⁹ BGI-Shenzhen, Shenzhen 518083, China.
¹⁰ The Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, College of Life Sciences, Zhejiang University, Hangzhou 310058, China.
¹¹ Guangdong Provincial Academician Workstation of BGI Synthetic Genomics, BGI-Shenzhen, Shenzhen 518120, China.
¹² Guangdong Provincial Key Laboratory of Genome Read and Write, BGI-Shenzhen, Shenzhen 518120, China.
¹³ BGI-Fuyang, BGI-Shenzhen, Fuyang 236009, China.

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.