iScience (Sep 2020)
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
Affiliations
- Guangyi Fan
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao 999078, China; BGI-QingDao, BGI-Shenzhen, Qingdao 266555, China; State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, China; Qingdao-Europe Advanced Institute for Life Sciences, BGI-Shenzhen, Qingdao 266555, China
- Xiaochuan Liu
- BGI-QingDao, BGI-Shenzhen, Qingdao 266555, China
- Shuai Sun
- BGI-QingDao, BGI-Shenzhen, Qingdao 266555, China; System Design Engineering, University of Waterloo, Ontario, N2L 3G1 Canada
- Chengcheng Shi
- BGI-QingDao, BGI-Shenzhen, Qingdao 266555, China
- Xiao Du
- BGI-QingDao, BGI-Shenzhen, Qingdao 266555, China
- Kai Han
- BGI-QingDao, BGI-Shenzhen, Qingdao 266555, China
- Binrui Yang
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao 999078, China
- Yuanyuan Fu
- BGI-QingDao, BGI-Shenzhen, Qingdao 266555, China
- Minghua Liu
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, China
- Inge Seim
- Integrative Biology Laboratory, College of Life Sciences, Nanjing Normal University, Nanjing 210046, China; 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
- He Zhang
- BGI-QingDao, BGI-Shenzhen, Qingdao 266555, China
- Qiwu Xu
- BGI-QingDao, BGI-Shenzhen, Qingdao 266555, China
- Jiahao Wang
- BGI-QingDao, BGI-Shenzhen, Qingdao 266555, China
- Xiaoshan Su
- BGI-QingDao, BGI-Shenzhen, Qingdao 266555, China
- Libin Shao
- BGI-QingDao, BGI-Shenzhen, Qingdao 266555, China
- Yuanfang Zhu
- BGI-QingDao, BGI-Shenzhen, Qingdao 266555, China
- Yunchang Shao
- BGI-Shenzhen, Shenzhen 518083, China
- Yunpeng Zhao
- The Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
- Andrew KC. Wong
- System Design Engineering, University of Waterloo, Ontario, N2L 3G1 Canada
- Dennis Zhuang
- System Design Engineering, University of Waterloo, Ontario, N2L 3G1 Canada
- Wenbin Chen
- BGI-Shenzhen, Shenzhen 518083, China
- Gengyun Zhang
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, China
- Huanming Yang
- BGI-Shenzhen, Shenzhen 518083, China; Guangdong Provincial Academician Workstation of BGI Synthetic Genomics, BGI-Shenzhen, Shenzhen 518120, China
- Xun Xu
- BGI-Shenzhen, Shenzhen 518083, China; Guangdong Provincial Key Laboratory of Genome Read and Write, BGI-Shenzhen, Shenzhen 518120, China
- Stephen Kwok-Wing Tsui
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, China; Corresponding author
- Xin Liu
- BGI-QingDao, BGI-Shenzhen, Qingdao 266555, China; BGI-Shenzhen, Shenzhen 518083, China; State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, China; BGI-Fuyang, BGI-Shenzhen, Fuyang 236009, China; Corresponding author
- Simon Ming-Yue Lee
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao 999078, China; Corresponding author
- Journal volume & issue
-
Vol. 23,
no. 9
p. 101538
Abstract
Summary: 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.
