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The allotetraploid horseradish genome provides insights into subgenome diversification and formation of critical traits

Author

Listed:
  • Fei Shen

    (Beijing Academy of Agriculture and Forestry Sciences)

  • Shixiao Xu

    (Tobacco College, Henan Agricultural University)

  • Qi Shen

    (Genome Research Center, Leeuwenhoek Biotechnology Inc.
    Shangji Biotechnology Inc.
    Nanjing Agricultural University)

  • Changwei Bi

    (Nanjing Forestry University)

  • Martin A. Lysak

    (Masaryk University)

Abstract

Polyploidization can provide a wealth of genetic variation for adaptive evolution and speciation, but understanding the mechanisms of subgenome evolution as well as its dynamics and ultimate consequences remains elusive. Here, we report the telomere-to-telomere (T2T) gap-free reference genome of allotetraploid horseradish (Armoracia rusticana) sequenced using a comprehensive strategy. The (epi)genomic architecture and 3D chromatin structure of the A and B subgenomes differ significantly, suggesting that both the dynamics of the dominant long terminal repeat retrotransposons and DNA methylation have played critical roles in subgenome diversification. Investigation of the genetic basis of biosynthesis of glucosinolates (GSLs) and horseradish peroxidases reveals both the important role of polyploidization and subgenome differentiation in shaping the key traits. Continuous duplication and divergence of essential genes of GSL biosynthesis (e.g., FMOGS-OX, IGMT, and GH1 gene family) contribute to the broad GSL profile in horseradish. Overall, the T2T assembly of the allotetraploid horseradish genome expands our understanding of polyploid genome evolution and provides a fundamental genetic resource for breeding and genetic improvement of horseradish.

Suggested Citation

  • Fei Shen & Shixiao Xu & Qi Shen & Changwei Bi & Martin A. Lysak, 2023. "The allotetraploid horseradish genome provides insights into subgenome diversification and formation of critical traits," Nature Communications, Nature, vol. 14(1), pages 1-19, December.
    • Handle: RePEc:nat:natcom:v:14:y:2023:i:1:d:10.1038_s41467-023-39800-y
    DOI: 10.1038/s41467-023-39800-y
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    1. Shengnan Li & Dexing Lin & Yunwei Zhang & Min Deng & Yongxing Chen & Bin Lv & Boshu Li & Yuan Lei & Yanpeng Wang & Long Zhao & Yueting Liang & Jinxing Liu & Kunling Chen & Zhiyong Liu & Jun Xiao & Jin, 2022. "Genome-edited powdery mildew resistance in wheat without growth penalties," Nature, Nature, vol. 602(7897), pages 455-460, February.
    2. Yuannian Jiao & Norman J. Wickett & Saravanaraj Ayyampalayam & André S. Chanderbali & Lena Landherr & Paula E. Ralph & Lynn P. Tomsho & Yi Hu & Haiying Liang & Pamela S. Soltis & Douglas E. Soltis & S, 2011. "Ancestral polyploidy in seed plants and angiosperms," Nature, Nature, vol. 473(7345), pages 97-100, May.
    3. Murukarthick Jayakodi & Agnieszka A. Golicz & Jonathan Kreplak & Lavinia I. Fechete & Deepti Angra & Petr Bednář & Elesandro Bornhofen & Hailin Zhang & Raphaël Boussageon & Sukhjiwan Kaur & Kwok Cheun, 2023. "The giant diploid faba genome unlocks variation in a global protein crop," Nature, Nature, vol. 615(7953), pages 652-659, March.
    4. Shengyi Liu & Yumei Liu & Xinhua Yang & Chaobo Tong & David Edwards & Isobel A. P. Parkin & Meixia Zhao & Jianxin Ma & Jingyin Yu & Shunmou Huang & Xiyin Wang & Junyi Wang & Kun Lu & Zhiyuan Fang & Ia, 2014. "The Brassica oleracea genome reveals the asymmetrical evolution of polyploid genomes," Nature Communications, Nature, vol. 5(1), pages 1-11, September.
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