iScience (2020-09-01)

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

Journal volume & issue
Vol. 23, no. 9
p. 101538

Abstract

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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.

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