Chromosome fusion, rearrangement, and polyploidization drive genome evolution in Artemisia

Abstract

Artemisia species possess significant medicinal, ecological, and economic values. However, their taxonomic disputes, complex chromosome variations, insufficient cytogenetic evaluation, and unclear genome evolutionary relationships remain unresolved. Here, we developed nine chromosome-specific oligonucleotide probe libraries for Artemisia based on the Artemisia argyi reference genome. Using chromosome-specific painting and repetitive sequence FISH karyotyping, we anchored the pseudochromosomes of A.ar_QCXA to its actual chromosomes. We first observed at the chromosomal level that chromosome 10 of A. argyi originated from the fusion of chromosomes 8 and 9. We further established comparative chromosome painting karyotypes and homoeologous groups for 21 Artemisia species/accessions, revealing that x = 9 is the ancestral basic chromosome number in Artemisia. These species are likely derived from four core karyotype types that possess 18 ancestral chromosomes, as inferred from chromosomal structural variations. Driven by chromosome fusion, rearrangement, and polyploidization, the core karyotypes further evolved into the 21 Artemisia species/accessions studied here. Mitotic and meiotic chromosome painting verified A. argyi as an autotetraploid, with A. lavandulifolia representing its putative progenitor. Additionally, we created a long-moxa aneuploid A. argyi with 88 chromosomes. Our results revealed that ploidy variation regulates moxa length and metabolite accumulation, and these traits are favorable for the medicinal utilization of A. argyi. Collectively, our findings demonstrate that chromosome fusion, rearrangement, and polyploidization play vital roles in driving genome evolution and karyotype diversification in the genus Artemisia. This study provides a theoretical basis and technical support for the genomic classification of Artemisia species and the improvement of A. argyi varieties.