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

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 and Li Wang ()
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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

Nature Communications, 2024, vol. 15, issue 1, 1-15

Abstract: 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.

Date: 2024
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DOI: 10.1038/s41467-024-53719-y

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