Allele-aware chromosome-level genome assembly of Artemisia annua reveals the correlation between ADS expansion and artemisinin yield

Baosheng Liao, Xiaofeng Shen, Li Xiang, Shuai Guo, Shiyu Chen, Ying Meng, Yu Liang, Dandan Ding, Junqi Bai, Dong Zhang, Tomasz Czechowski, Yi Li, Hui Yao, Tingyu Ma, Caroline Howard, Chao Sun, Haitao Liu, Jiushi Liu, Jin Pei, Jihai GaoJigang Wang, Xiaohui Qiu, Zhihai Huang, Hongyi Li, Ling Yuan, Jianhe Wei, Ian Graham, Jiang Xu, Boli Zhang, Shilin Chen

Research output: Contribution to journalArticlepeer-review

45 Scopus citations


Artemisia annua is the major natural source of artemisinin, an anti-malarial medicine commonly used worldwide. Here, we present chromosome-level haploid maps for two A. annua strains with different artemisinin contents to explore the relationships between genomic organization and artemisinin production. High-fidelity sequencing, optical mapping, and chromatin conformation capture sequencing were used to assemble the heterogeneous and repetitive genome and resolve the haplotypes of A. annua. Approximately 50,000 genes were annotated for each haplotype genome, and a triplication event that occurred approximately 58.12 million years ago was examined for the first time in this species. A total of 3,903,467–5,193,414 variants (SNPs, indels, and structural variants) were identified in the 1.5-Gb genome during pairwise comparison between haplotypes, consistent with the high heterozygosity of this species. Genomic analyses revealed a correlation between artemisinin concents and the copy number of amorpha-4,11-diene synthase genes. This correlation was further confirmed by resequencing of 36 A. annua samples with varied artemisinin contents. Circular consensus sequencing of transcripts facilitated the detection of paralog expression. Collectively, our study provides chromosome-level allele-aware genome assemblies for two A. annua strains and new insights into the biosynthesis of artemisinin and its regulation, which will contribute to conquering malaria worldwide.

Original languageEnglish
Pages (from-to)1310-1328
Number of pages19
JournalMolecular Plant
Issue number8
StatePublished - Aug 1 2022

Bibliographical note

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  • Artemisia annua
  • amorpha-4,11-diene synthase
  • artemisinin
  • copy number variation
  • haplotype chromosome

ASJC Scopus subject areas

  • Molecular Biology
  • Plant Science


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