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.

中文翻译：

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花椒特异性全基因组复制和高度重复的古四倍体花椒基因组中转座元件的最新活性

花椒是一种重要的香料和药用植物，其独特之处在于积累了丰富的次生代谢产物，在口腔中产生特有的香气和刺痛感。由于重复序列比例高、杂合度高、染色体数目增多白花椒，其染色体假分子的组装极具挑战性。在这里，我们展示了基因组序列白花椒，大小显着扩大到 4.23 Gb，组装成 68 条染色体。该基因组比其近亲基因组大大约十倍柑橘。分歧之后花椒属和柑橘类，大约 2680 万年前的谱系特异性全基因组复制事件 η-WGD (MYA) 和最近的转座元件 (TE) 爆发 ~6.41 MYA 解释了白花椒。独立花椒-特定的 WGD 事件之后是许多塑造基因组结构的融合/裂变事件。综合基因组和转录组分析表明，显着的物种特异性基因家族扩展和基因表达的变化塑造了山椒素、萜类化合物和花青素的生物合成，这有助于形成山椒的特殊风味和外观。白花椒。总之，参考基因组为研究近期 TE 活动的 WGD 对基因获得和丢失以及基因组重建的影响提供了有价值的模型，并为加速提供资源花椒属改进。