Open AccessGenome sequencing reveals chromosome fusion and extensive expansion of genes related to secondary metabolism in Artemisia argyi
Author(s) -
Miao Yuhuan,
Luo Dandan,
Zhao Tingting,
Du Hongzhi,
Liu Zhenhua,
Xu Zhongping,
Guo Lanping,
Chen Changjie,
Peng Sainan,
Li Jin Xin,
Ma Lin,
Ning Guogui,
Liu Dahui,
Huang Luqi
Publication year - 2022
Publication title -
plant biotechnology journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.525
H-Index - 115
eISSN - 1467-7652
pISSN - 1467-7644
DOI - 10.1111/pbi.13870
Subject(s) - biology , genome , gene , genetics , gene duplication , comparative genomics , secondary metabolism , synteny , locus (genetics) , genome size , whole genome sequencing , sequence assembly , genomics , transcriptome , gene expression , biosynthesis
Summary Artemisia argyi , as famous as Artemisia annua , is a medicinal plant with huge economic value in the genus of Artemisia and has been widely used in the world for about 3000 years. However, a lack of the reference genome severely hinders the understanding of genetic basis for the active ingredient synthesis of A. argyi . Here, we firstly report a complex chromosome‐level genome assembly of A. argyi with a large size of 8.03 Gb, with features of high heterozygosity (2.36%), high repetitive sequences (73.59%) and a huge number of protein‐coding genes (279 294 in total). The assembly reveals at least three rounds of whole‐genome duplication (WGD) events, including a recent WGD event in the A. argyi genome, and a recent burst of transposable element, which may contribute to its large genome size. The genomic data and karyotype analyses confirmed that A. argyi is an allotetraploid with 34 chromosomes. Intragenome synteny analysis revealed that chromosomes fusion event occurred in the A. argyi genome, which elucidates the changes in basic chromosome numbers in Artemisia genus. Significant expansion of genes related to photosynthesis, DNA replication, stress responses and secondary metabolism were identified in A. argyi , explaining the extensive environmental adaptability and rapid growth characteristics. In addition, we analysed genes involved in the biosynthesis pathways of flavonoids and terpenoids, and found that extensive gene amplification and tandem duplication contributed to the high contents of metabolites in A. argyi . Overall, the reference genome assembly provides scientific support for evolutionary biology, functional genomics and breeding in A. argyi and other Artemisia species.