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Inversions encounter relaxed genetic constraints and balance birth and death of TPS genes in Curcuma

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  • Xuezhu Liao

    (Chinese Academy of Agricultural Sciences)

  • Dejin Xie

    (Chinese Academy of Agricultural Sciences)

  • Tingting Bao

    (Chinese Academy of Agricultural Sciences)

  • Mengmeng Hou

    (Chinese Academy of Agricultural Sciences)

  • Cheng Li

    (Chinese Academy of Agricultural Sciences)

  • Bao Nie

    (Chinese Academy of Agricultural Sciences)

  • Shichao Sun

    (Chinese Academy of Agricultural Sciences)

  • Dan Peng

    (Chinese Academy of Agricultural Sciences)

  • Haixiao Hu

    (University of California Davis)

  • Hongru Wang

    (Chinese Academy of Agricultural Sciences)

  • Yongfu Tao

    (Chinese Academy of Agricultural Sciences)

  • Yu Zhang

    (Sun Yat-sen University)

  • Wei Li

    (Chinese Academy of Agricultural Sciences)

  • Li Wang

    (Chinese Academy of Agricultural Sciences)

Abstract

Evolutionary dynamics of inversion and its impact on biochemical traits are a puzzling question. Here, we show abundance of inversions in three Curcuma species (turmeric, hidden ginger and Siam tulip). Genes within inversions display higher long terminal repeat content and lower expression level compared with genomic background, suggesting inversions in Curcuma experience relaxed genetic constraints. It is corroborated by depletion of selected SNPs and enrichment of deleterious mutations in inversions detected among 56 Siam tulip cultivars. Functional verification of tandem duplicated terpene synthase (TPS) genes reveals that genes within inversions become pseudogenes, while genes outside retain catalytic function. Our findings suggest that inversions act as a counteracting force against tandem duplication in balancing birth and death of TPS genes and modulating terpenoid contents in Curcuma. This study provides an empirical example that inversions are likely not adaptive but affect biochemical traits.

Suggested Citation

  • Xuezhu Liao & Dejin Xie & Tingting Bao & Mengmeng Hou & Cheng Li & Bao Nie & Shichao Sun & Dan Peng & Haixiao Hu & Hongru Wang & Yongfu Tao & Yu Zhang & Wei Li & Li Wang, 2024. "Inversions encounter relaxed genetic constraints and balance birth and death of TPS genes in Curcuma," Nature Communications, Nature, vol. 15(1), pages 1-15, December.
    • Handle: RePEc:nat:natcom:v:15:y:2024:i:1:d:10.1038_s41467-024-53719-y
    DOI: 10.1038/s41467-024-53719-y
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