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

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.

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, Jing-Quan Yu