A chromosome-scale genome assembly of Artemisia argyi reveals unbiased subgenome evolution and key contributions of gene duplication to volatile terpenoid diversity

Artemisia argyi Le ' vl. et Vant., a perennial Artemisia herb with an intense fragrance, is widely used in tradi-tional medicine in China and many other Asian countries. Here, we present a chromosome-scale genome as-sembly of A. argyi comprising 3.89 Gb assembled into 17 pseudochromosomes. Phylogenetic and compar-ative genomic analyses revealed that A. argyi underwent a recent lineage-specific whole-genome duplication (WGD) event after divergence from Artemisia annua, resulting in two subgenomes. We deciphered the diploid ancestral genome of A. argyi, and unbiased subgenome evolution was observed. The recent WGD led to a large number of duplicated genes in the A. argyi genome. Expansion of the terpene synthase (TPS) gene fam-ily through various types of gene duplication may have greatly contributed to the diversity of volatile terpe-noids in A. argyi. In particular, we identified a typical germacrene D synthase gene cluster within the expanded TPS gene family. The entire biosynthetic pathways of germacrenes, (+)-borneol, and (+)-camphor were elucidated in A. argyi. In addition, partial deletion of the amorpha-4,11-diene synthase (ADS) gene and loss of function of ADS homologs may have resulted in the lack of artemisinin production in A. argyi. Our study provides new insights into the genome evolution of Artemisia and lays a foundation for further improve-ment of the quality of this important medicinal plant.