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Phylotranscriptomics reveals the phylogeny of Asparagales and the evolution of allium flavor biosynthesis

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  • Xiao-Xiao Wang

    (China Pharmaceutical University
    Guangxi Botanical Garden of Medicinal Plants)

  • Chien-Hsun Huang

    (Inner Mongolia University
    Fudan University)

  • Diego F. Morales-Briones

    (Ludwig-Maximilians-Universität München)

  • Xiang-Yu Wang

    (China Pharmaceutical University)

  • Ying Hu

    (Guangxi Botanical Garden of Medicinal Plants)

  • Na Zhang

    (China Pharmaceutical University)

  • Pu-Guang Zhao

    (China Pharmaceutical University)

  • Xiao-Mei Wei

    (Guangxi Botanical Garden of Medicinal Plants)

  • Kun-Hua Wei

    (Guangxi Botanical Garden of Medicinal Plants
    Guangdong Pharmaceutical University)

  • Xinya Hemu

    (China Pharmaceutical University)

  • Ning-Hua Tan

    (China Pharmaceutical University)

  • Qing-Feng Wang

    (Chinese Academy of Sciences)

  • Ling-Yun Chen

    (China Pharmaceutical University)

Abstract

Asparagales, the largest monocot order, is renowned for its ecological, economic, and medicinal significance. Here, we leverage transcriptome data from 455 Asparagales species to explore the phylogeny of Asparagales. Moreover, we investigate the evolutionary patterns of the genes involved in allium flavor formation. We not only establish a robust bifurcating phylogeny of Asparagales but also explore their reticulate relationships. Notably, we find that eight genes involved in the biosynthesis of allium flavor compounds underwent expansion in Allium species. Furthermore, we observe Allium-specific mutations in one amino acid within alliinase and three within lachrymatory factor synthase. Overall, our findings highlight the role of gene expansion, increased expression, and amino acid mutations in driving the evolution of Allium-specific compounds. These insights not only deepen our understanding of the phylogeny of Asparagales but also illuminate the genetic mechanisms underpinning specialized compounds.

Suggested Citation

  • 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.
  • Handle: RePEc:nat:natcom:v:15:y:2024:i:1:d:10.1038_s41467-024-53943-6
    DOI: 10.1038/s41467-024-53943-6
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    References listed on IDEAS

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    1. 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.
    2. Alexandre R. Zuntini & Tom Carruthers & Olivier Maurin & Paul C. Bailey & Kevin Leempoel & Grace E. Brewer & Niroshini Epitawalage & Elaine Françoso & Berta Gallego-Paramo & Catherine McGinnie & Raque, 2024. "Phylogenomics and the rise of the angiosperms," Nature, Nature, vol. 629(8013), pages 843-850, May.
    3. Bastien Christ & Chengchao Xu & Menglong Xu & Fu-Shuang Li & Naoki Wada & Andrew J. Mitchell & Xiu-Lin Han & Meng-Liang Wen & Makoto Fujita & Jing-Ke Weng, 2019. "Repeated evolution of cytochrome P450-mediated spiroketal steroid biosynthesis in plants," Nature Communications, Nature, vol. 10(1), pages 1-11, December.
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