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

Author

Listed:
  • 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
    Ministry of Agriculture and Rural Affairs
    Hainan Institute of Zhejiang University, Yazhou Bay Science and Technology City)

  • 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
    Ministry of Agriculture and Rural Affairs
    Hainan Institute of Zhejiang University, Yazhou Bay Science and Technology City)

  • Yan-Hong Zhou

    (Zhejiang University
    Ministry of Agriculture and Rural Affairs)

  • Ming-Fang Zhang

    (Zhejiang University
    Ministry of Agriculture and Rural Affairs
    Hainan Institute of Zhejiang University, Yazhou Bay Science and Technology City)

  • Jing-Quan Yu

    (Zhejiang University
    Ministry of Agriculture and Rural Affairs)

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.

Suggested Citation

  • 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 & , 2022. "Chromosome-level genome assembly of bunching onion illuminates genome evolution and flavor formation in Allium crops," Nature Communications, Nature, vol. 13(1), pages 1-15, December.
  • Handle: RePEc:nat:natcom:v:13:y:2022:i:1:d:10.1038_s41467-022-34491-3
    DOI: 10.1038/s41467-022-34491-3
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    1. Justine K. Kitony & Kelly Colt & Bradley W. Abramson & Nolan T. Hartwick & Semar Petrus & Emadeldin H. E. Konozy & Nisa Karimi & Levi Yant & Todd P. Michael, 2024. "Chromosome-level baobab genome illuminates its evolutionary trajectory and environmental adaptation," Nature Communications, Nature, vol. 15(1), pages 1-14, December.
    2. Xiao-Xiao Wang & Chien-Hsun Huang & Diego F. Morales-Briones & Xiang-Yu Wang & Ying Hu & Na Zhang & Pu-Guang Zhao & Xiao-Mei Wei & Kun-Hua Wei & Xinya Hemu & Ning-Hua Tan & Qing-Feng Wang & Ling-Yun C, 2024. "Phylotranscriptomics reveals the phylogeny of Asparagales and the evolution of allium flavor biosynthesis," Nature Communications, Nature, vol. 15(1), pages 1-14, December.

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