The haplotype-resolved genome assembly of autotetraploid rhubarb Rheum officinale provides insights into its genome evolution and massive accumulation of anthraquinones

Rheum officinale, a member of the Polygonaceae family, is an important medicinal plant used widely in traditional Chinese medicine. Here, we report a 7.68 Gb chromosome-scale assembly of R. officinale with a contig N50 of 3.47 Mb, further clustered into 44 chromosomes across four homologous groups. Comparative genomics analysis revealed that transposable elements contribute significantly to genome evolution, gene copy number variation and gene regulation and expression involved mainly in metabolite biosynthesis, stress resistance and root development of R. officinale. We determined the recently doubled autotetraploid of R. officinale at ∼0.58 Mya and analyzed the genomic features between homologous chromosomes. Although no dominant monoploid genomes were observed at an overall expression level, numerous allele-differential expressed genes, mostly with different transposable elements insertions to their regulatory regions, were identified, suggesting their functional divergence after polyploidization. Combining genomics, transcriptomics and metabolomics, we explored the contributions of gene family amplification and tetraploidization to the abundant production of anthraquinone, and gene expression patterns and the differences in anthraquinone content among tissues of R. officinale. As an autopolyploid genome in herbs, our report offers unprecedented genomic resources for fundamental research of R. officinale and guidance for polyploidy breeding of herbs.