Chromosome-level genome assembly of Aralia cordata unveils evolution history and genomic landscape diversification in Aralia-Panax

Aralia and Panax , two neighboring medicinal plant genera, underwent diverse genomic evolution, including genome expansion and polyploidization. Their variable genome sizes, ploidy levels, and metabolite compositions make these genera valuable genomic resources for elucidating genome evolution. However, the lack of genomic data for the Aralia genus has hindered the full exploration of genomic features and evolution in this genus. Here, we assembled a high-quality chromosome-level genome of Aralia cordata with a length of 1.06 Gbp for 24 chromosomes. Candidate gene mining suggested that the gene loss and tandem gene duplication might be associated with the species-specific secondary metabolite compositions. Comprehensive genomic analyses with related species revealed their divergence history. Ancestral karyotype reconstruction suggested the modern chromosome evolution scenario of Araliaceae. Despite being tetraploid, A. cordata had a comparable genome size to the diploid A. elata , which has species-specific LTR expansions. We also inspected the distribution of the Araliaceae family-wide common 160 bp centromeric tandem repeat (TR160). The TR160s were identified in each chromosome of the Aralia and Eleutherococcus genera but not significantly in the Panax genus. The genomic analyses in this study provided valuable insight into chromosome evolution, polyploidization, and secondary metabolite diversification in the Araliaceae family.