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Zanthoxylum bungeanum  is an important spice and medicinal plant that is unique for its accumulation of abundant secondary metabolites, which create a characteristic aroma and tingling sensation in the mouth. Owing to the high proportion of repetitive sequences, high heterozygosity, and increased chromosome number of  Z. bungeanum , the assembly of its chromosomal pseudomolecules is extremely challenging. Here, we present a genome sequence for  Z. bungeanum , with a dramatically expanded size of 4.23 Gb, assembled into 68 chromosomes. This genome is approximately tenfold larger than that of its close relative  Citrus sinensis . After the divergence of  Zanthoxylum  and  Citrus , the lineage-specific whole-genome duplication event η-WGD approximately 26.8 million years ago (MYA) and the recent transposable element (TE) burst ~6.41 MYA account for the substantial genome expansion in  Z. bungeanum . The independent  Zanthoxylum- specific WGD event was followed by numerous fusion/fission events that shaped the genomic architecture. Integrative genomic and transcriptomic analyses suggested that prominent species-specific gene family expansions and changes in gene expression have shaped the biosynthesis of sanshools, terpenoids, and anthocyanins, which contribute to the special flavor and appearance of  Z. bungeanum . In summary, the reference genome provides a valuable model for studying the impact of WGDs with recent TE activity on gene gain and loss and genome reconstruction and provides resources to accelerate  Zanthoxylum  improvement.

horticulture research

<i>Zanthoxylum-</i>specific whole genome duplication and recent activity of transposable elements in the highly repetitive paleotetraploid <i>Z. bungeanum</i> genome

Zanthoxylum-specific whole genome duplication and recent activity of transposable elements in the highly repetitive paleotetraploid Z. bungeanum genome