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Two telomere-to-telomere gapless genomes reveal insights into Capsicum evolution and capsaicinoid biosynthesis

Author

Listed:
  • Weikai Chen

    (Shandong Laboratory of Advanced Agricultural Sciences in Weifang)

  • Xiangfeng Wang

    (Shandong Laboratory of Advanced Agricultural Sciences in Weifang)

  • Jie Sun

    (Shandong Laboratory of Advanced Agricultural Sciences in Weifang)

  • Xinrui Wang

    (Shandong Laboratory of Advanced Agricultural Sciences in Weifang)

  • Zhangsheng Zhu

    (Shandong Laboratory of Advanced Agricultural Sciences in Weifang
    South China Agricultural University)

  • Dilay Hazal Ayhan

    (Shandong Laboratory of Advanced Agricultural Sciences in Weifang)

  • Shu Yi

    (Shandong Laboratory of Advanced Agricultural Sciences in Weifang)

  • Ming Yan

    (Shandong Laboratory of Advanced Agricultural Sciences in Weifang)

  • Lili Zhang

    (Shandong Laboratory of Advanced Agricultural Sciences in Weifang
    Weifang Institute of Technology)

  • Tan Meng

    (Shandong Laboratory of Advanced Agricultural Sciences in Weifang)

  • Yu Mu

    (Shandong Laboratory of Advanced Agricultural Sciences in Weifang)

  • Jun Li

    (Shandong Laboratory of Advanced Agricultural Sciences in Weifang)

  • Dian Meng

    (Shandong Laboratory of Advanced Agricultural Sciences in Weifang)

  • Jianxin Bian

    (Shandong Laboratory of Advanced Agricultural Sciences in Weifang)

  • Ke Wang

    (Shandong Laboratory of Advanced Agricultural Sciences in Weifang
    Shandong Agricultural University)

  • Lu Wang

    (Shandong Laboratory of Advanced Agricultural Sciences in Weifang)

  • Shaoying Chen

    (Shandong Laboratory of Advanced Agricultural Sciences in Weifang)

  • Ruidong Chen

    (Shandong Laboratory of Advanced Agricultural Sciences in Weifang)

  • Jingyun Jin

    (Shandong Laboratory of Advanced Agricultural Sciences in Weifang)

  • Bosheng Li

    (Shandong Laboratory of Advanced Agricultural Sciences in Weifang)

  • Xingping Zhang

    (Shandong Laboratory of Advanced Agricultural Sciences in Weifang)

  • Xing Wang Deng

    (Shandong Laboratory of Advanced Agricultural Sciences in Weifang
    Peking University)

  • Hang He

    (Shandong Laboratory of Advanced Agricultural Sciences in Weifang
    Peking University)

  • Li Guo

    (Shandong Laboratory of Advanced Agricultural Sciences in Weifang)

Abstract

Chili pepper (Capsicum) is known for its unique fruit pungency due to the presence of capsaicinoids. The evolutionary history of capsaicinoid biosynthesis and the mechanism of their tissue specificity remain obscure due to the lack of high-quality Capsicum genomes. Here, we report two telomere-to-telomere (T2T) gap-free genomes of C. annuum and its wild nonpungent relative C. rhomboideum to investigate the evolution of fruit pungency in chili peppers. We precisely delineate Capsicum centromeres, which lack high-copy tandem repeats but are extensively invaded by CRM retrotransposons. Through phylogenomic analyses, we estimate the evolutionary timing of capsaicinoid biosynthesis. We reveal disrupted coding and regulatory regions of key biosynthesis genes in nonpungent species. We also find conserved placenta-specific accessible chromatin regions, which likely allow for tissue-specific biosynthetic gene coregulation and capsaicinoid accumulation. These T2T genomic resources will accelerate chili pepper genetic improvement and help to understand Capsicum genome evolution.

Suggested Citation

  • Weikai Chen & Xiangfeng Wang & Jie Sun & Xinrui Wang & Zhangsheng Zhu & Dilay Hazal Ayhan & Shu Yi & Ming Yan & Lili Zhang & Tan Meng & Yu Mu & Jun Li & Dian Meng & Jianxin Bian & Ke Wang & Lu Wang & , 2024. "Two telomere-to-telomere gapless genomes reveal insights into Capsicum evolution and capsaicinoid biosynthesis," Nature Communications, Nature, vol. 15(1), pages 1-14, December.
    • Handle: RePEc:nat:natcom:v:15:y:2024:i:1:d:10.1038_s41467-024-48643-0
    DOI: 10.1038/s41467-024-48643-0
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    References listed on IDEAS

    as
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