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

Shijing Feng; Zhenshan Liu; Jian Cheng; Zihe Li; Lu Tian; Min Liu; Tuxi Yang; Yulin Liu; Yonghong Liu; He Dai; Zujun Yang; Qing Zhang; Gang Wang; Jisen Zhang; Huifeng Jiang; Anzhi Wei

doi:10.1038/s41438-021-00665-1

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

Hortic Res. 2021 Sep 3;8(1):205. doi: 10.1038/s41438-021-00665-1.

Authors

Shijing Feng^#^{1

2}, Zhenshan Liu^#³, Jian Cheng^#⁴, Zihe Li^#⁵, Lu Tian^{1

2}, Min Liu⁶, Tuxi Yang^{1

2}, Yulin Liu^{1

2}, Yonghong Liu^{1

2}, He Dai⁶, Zujun Yang⁷, Qing Zhang⁸, Gang Wang⁸, Jisen Zhang⁹, Huifeng Jiang¹⁰, Anzhi Wei^{11

12}

Affiliations

¹ College of Forestry, Northwest A&F University, Yangling, Shaanxi, China.
² Research Centre for Engineering and Technology of Zanthoxylum State Forestry Administration, Yangling, Shaanxi, China.
³ College of Life Science, Northwest A&F University, Yangling, Shaanxi, China.
⁴ Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China.
⁵ School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, Shanxi, China.
⁶ Biomarker Technologies Corporation, Beijing, China.
⁷ Center for Information in Biology, College of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, China.
⁸ Center 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.
⁹ Center 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. zjisen@126.com.
¹⁰ Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China. jiang_hf@tib.cas.cn.
¹¹ College of Forestry, Northwest A&F University, Yangling, Shaanxi, China. weianzhi@126.com.
¹² Research Centre for Engineering and Technology of Zanthoxylum State Forestry Administration, Yangling, Shaanxi, China. weianzhi@126.com.

^# Contributed equally.

Abstract

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.