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Article|03 Sep 2021|OPEN
Zanthoxylum-specific whole genome duplication and recent activity of transposable elements in the highly repetitive paleotetraploid Z. bungeanum genome
Shijing Feng1,2, Zhenshan Liu3, Jian Cheng4, Zihe Li5, Lu Tian1,2, Min Liu6, Tuxi Yang1,2, Yulin Liu1,2, Yonghong Liu1,2, He Dai6, Zujun Yang7, Qing Zhang8, Gang Wang8, Anzhi Wei1,2,, Jisen Zhang8, & Huifeng Jiang4,
1College of Forestry, Northwest A&F University, Yangling, Shaanxi, China
2Research Centre for Engineering and Technology of Zanthoxylum State Forestry Administration, Yangling, Shaanxi, China
3College of Life Science, Northwest A&F University, Yangling, Shaanxi, China
4Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
5School of Ecology and Environment, Northwestern Polytechnical University, Xi’an, Shanxi, China
6Biomarker Technologies Corporation, Beijing, China
7Center for Information in Biology, College of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, China
8Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China

Horticulture Research 8,
Article number: 205 (2021)
doi: 10.1038/hortres.2021.205
Views: 68

Received: 15 Jun 2021
Revised: 29 Jul 2021
Accepted: 30 Jul 2021
Published online: 03 Sep 2021


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.