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

• Published in: Horticulture research Vol. 8; no. 1
• Main Authors: Feng, Shijing, Liu, Zhenshan, Cheng, Jian, Li, Zihe, Tian, Lu, Liu, Min, Yang, Tuxi, Liu, Yulin, Liu, Yonghong, Dai, He, Yang, Zujun, Zhang, Qing, Wang, Gang, Zhang, Jisen, Jiang, Huifeng, Wei, Anzhi
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 01.12.2021; Oxford University Press
• Subjects: 631/208/514/2254; 631/449/2667; Agriculture; Anthocyanins; Aroma; Biomedical and Life Sciences; Biosynthesis; Chromosome number; Chromosomes; Divergence; Ecology; Flavor; Gene expression; Genomes; Genomics; Herbal medicine; Heterozygosity; Life Sciences; Medicinal plants; Metabolites; Nucleotide sequence; Plant Breeding/Biotechnology; Plant Genetics and Genomics; Plant Sciences; Reproduction (copying); Secondary metabolites; Sequences; Terpenes; Transposons; Zanthoxylum; Zanthoxylum bungeanum
• ISSN: 2662-6810; 2052-7276; 2052-7276
• DOI: 10.1038/s41438-021-00665-1

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.