Chromosome-level genome assembly of bunching onion illuminates genome evolution and flavor formation in Allium crops

Nanqiao Liao, Zhongyuan Hu, Jinshan Miao, Xiaodi Hu, Xiaolong Lyu, Haitian Fang, Yi-Mei Zhou, Ahmed Mahmoud, Guancong Deng, Yi-Qing Meng, Kejia Zhang, Yu-Yuan Ma, Yuelin Xia, Meng Zhao, Haiyang Yang, Yong Zhao, Ling Kang, Yiming Wang, Jing-Hua Yang, Yan-Hong Zhou (), Ming-Fang Zhang () and Jing-Quan Yu ()
Additional contact information
Nanqiao Liao: Zhejiang University
Zhongyuan Hu: Zhejiang University
Jinshan Miao: Weifang University of Science and Technology
Xiaodi Hu: Novogene Bioinformatics Institute
Xiaolong Lyu: Zhejiang University
Haitian Fang: Ningxia University
Yi-Mei Zhou: Zhejiang University
Ahmed Mahmoud: Zhejiang University
Guancong Deng: Zhejiang University
Yi-Qing Meng: Zhejiang University
Kejia Zhang: Zhejiang University
Yu-Yuan Ma: Zhejiang University
Yuelin Xia: Zhejiang University
Meng Zhao: Zhejiang University
Haiyang Yang: Zhejiang University
Yong Zhao: Novogene Bioinformatics Institute
Ling Kang: Novogene Bioinformatics Institute
Yiming Wang: Novogene Bioinformatics Institute
Jing-Hua Yang: Zhejiang University
Yan-Hong Zhou: Zhejiang University
Ming-Fang Zhang: Zhejiang University
Jing-Quan Yu: Zhejiang University

Nature Communications, 2022, vol. 13, issue 1, 1-15

Abstract: Abstract The Allium genus is cultivated globally as vegetables, condiments, or medicinal plants and is characterized by large genomes and strong pungency. However, the genome evolution and genomic basis underlying their unique flavor formation remain poorly understood. Herein, we report an 11.27-Gb chromosome-scale genome assembly for bunching onion (A. fistulosum). The uneven bursts of long-terminal repeats contribute to diversity in genome constituents, and dispersed duplication events largely account for gene expansion in Allium genomes. The extensive duplication and differentiation of alliinase and lachrymatory factor synthase manifest as important evolutionary events during flavor formation in Allium crops. Furthermore, differential selective preference for flavor-related genes likely lead to the variations in isoalliin content in bunching onions. Moreover, we reveal that China is the origin and domestication center for bunching onions. Our findings provide insights into Allium genome evolution, flavor formation and domestication history and enable future genome-assisted breeding of important traits in these crops.

Date: 2022
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DOI: 10.1038/s41467-022-34491-3

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