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

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.

PMID: 33083766
PMCID: PMC7509215
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 et al. iScience. 2020.

. 2020 Sep 8;23(9):101538.

doi: 10.1016/j.isci.2020.101538. eCollection 2020 Sep 25.

Authors

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.

PMID: 33083766
PMCID: PMC7509215
DOI: 10.1016/j.isci.2020.101538

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.

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Conflict of interest statement

The authors declare no competing interests.

Figures

**Figure 1**
Comparison of the *P. notoginseng* Genome Assembly with Previous Assemblies (A) The characters of each chromosome of *P. notoginseng*. (B) Comparison of the contig length of our assembly with the published assembly. (C) Comparison of the assembly assessment values among the three assembly versions.

**Figure 2**
Genome Evolution and Disease Resistance (A) Phylogenetic tree and divergence time of two *Panax* species. The events of WGD and WGT were represented by red and green asterisks, respectively. (B) Detection of whole-genome duplication events of two *Panax* species by 4-fold degenerate synonymous sites (4DTv) comparisons. (C) Calculated LTR insertion time of two *Panax* species compared with other related species. (D) The maximum likelihood tree constructed using LTR copia. For simplicity, 1,000 LTR sequences were randomly selected for each species. Blue, green, and red colors represent *P. notoginseng*, *P. ginseng*, and *D. carota*, respectively. (E) Pairwise sequential Markovian coalescent (PSMC) analysis of the historical effective population size of *P. notoginseng*. Global sea level and surface air temperatures are shown in blue and yellow lines, respectively. (F) Comparison of number of R-genes and two transcription factor genes among six species.

**Figure 3**
The Pathway of Ginsenoside Biosynthesis and Several Key Gene Families (A) The ginsenoside synthesis pathway from glycolysis involves terpenoid backbone biosynthesis. (B) Gene tree of DDS genes of two *Panax* species and other species. (C) Protein sequencing: multiple comparisons of DDS among *P. notoginseng*, *P. ginseng,* and other representative plants. Stars represent amino acids conserved in all protein sequences; red circles represent amino acids that are present in *P. notoginseng* and *P. ginseng*, but missing in all other plants. (D) The protein 3D structure of DDS of *P. notoginseng* constructed by the SWISS-MODEL. (E) The partial enlarged view of the protein 3D structure of DDS, and arrows indicate two amino acids specific to *P. notoginseng* and *P. ginseng*. (F) Differentially expressed genes (CYP716, UGT71, and UGT74) among the different tissues and living years.

**Figure 4**
Population Structure and GWAS Analysis of 240 Individuals (A) The SNP tree of 240 individuals. (B) Principal-component analysis results of 240 individuals. (C) The results of GWAS analysis and linkage disequilibrium blocks for the root weight based on SNP data. (D) The results of GWAS analysis and linkage disequilibrium blocks for the stem thickness based on SNP data.

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

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

Authors

Affiliations

Abstract

Conflict of interest statement

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