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Chromosome-level and haplotype-resolved genome provides insight into the tetraploid hybrid origin of patchouli

Author

Listed:
  • Yanting Shen

    (Guangzhou University of Chinese Medicine
    Chinese Academy of Sciences)

  • Wanying Li

    (Guangzhou University of Chinese Medicine)

  • Ying Zeng

    (Guangzhou University of Chinese Medicine)

  • Zhipeng Li

    (Guangzhou University of Chinese Medicine)

  • Yiqiong Chen

    (Guangzhou University of Chinese Medicine)

  • Jixiang Zhang

    (Chinese Academy of Sciences)

  • Hong Zhao

    (Beijing Academy of Agriculture and Forestry Sciences)

  • Lingfang Feng

    (Key Laboratory of Chinese Medicinal Resource from Lingnan (Guangzhou University of Chinese Medicine), Ministry of Education)

  • Dongming Ma

    (Key Laboratory of Chinese Medicinal Resource from Lingnan (Guangzhou University of Chinese Medicine), Ministry of Education)

  • Xiaolu Mo

    (Guangdong Food and Drug Vocational College)

  • Puyue Ouyang

    (Guangdong Food and Drug Vocational College)

  • Lili Huang

    (Guangzhou University of Chinese Medicine)

  • Zheng Wang

    (Beijing Academy of Agriculture and Forestry Sciences)

  • Yuannian Jiao

    (Chinese Academy of Sciences
    University of Chinese Academy of Sciences)

  • Hong-bin Wang

    (Guangzhou University of Chinese Medicine
    Key Laboratory of Chinese Medicinal Resource from Lingnan (Guangzhou University of Chinese Medicine), Ministry of Education
    Guangzhou University of Chinese Medicine)

Abstract

Patchouli (Pogostemon cablin (Blanco) Benth.), a member of the Lamiaceae family, is an important aromatic plant that has been widely used in medicine and perfumery. Here, we report a 1.94 Gb chromosome-scale assembly of the patchouli genome (contig N50 = 7.97 Mb). The gene annotation reveals that tandem duplication of sesquiterpene biosynthetic genes may be a major contributor to the biosynthesis of patchouli bioactivity components. We further phase the genome into two distinct subgenomes (A and B), and identify a chromosome substitution event that have occurred between them. Further investigations show that a burst of universal LTR-RTs in the A subgenome lead to the divergence between two subgenomes. However, no significant subgenome dominance is detected. Finally, we track the evolutionary scenario of patchouli including whole genome tetraploidization, subgenome divergency, hybridization, and chromosome substitution, which are the key forces to determine the complexity of patchouli genome. Our work sheds light on the evolutionary history of patchouli and offers unprecedented genomic resources for fundamental patchouli research and elite germplasm development.

Suggested Citation

  • Yanting Shen & Wanying Li & Ying Zeng & Zhipeng Li & Yiqiong Chen & Jixiang Zhang & Hong Zhao & Lingfang Feng & Dongming Ma & Xiaolu Mo & Puyue Ouyang & Lili Huang & Zheng Wang & Yuannian Jiao & Hong-, 2022. "Chromosome-level and haplotype-resolved genome provides insight into the tetraploid hybrid origin of patchouli," Nature Communications, Nature, vol. 13(1), pages 1-15, December.
  • Handle: RePEc:nat:natcom:v:13:y:2022:i:1:d:10.1038_s41467-022-31121-w
    DOI: 10.1038/s41467-022-31121-w
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    References listed on IDEAS

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    1. Therese Mitros & Adam M. Session & Brandon T. James & Guohong Albert Wu & Mohammad B. Belaffif & Lindsay V. Clark & Shengqiang Shu & Hongxu Dong & Adam Barling & Jessica R. Holmes & Jessica E. Mattick, 2020. "Genome biology of the paleotetraploid perennial biomass crop Miscanthus," Nature Communications, Nature, vol. 11(1), pages 1-11, December.
    2. Haitao Chen & Yan Zeng & Yongzhi Yang & Lingli Huang & Bolin Tang & He Zhang & Fei Hao & Wei Liu & Youhan Li & Yanbin Liu & Xiaoshuang Zhang & Ru Zhang & Yesheng Zhang & Yongxin Li & Kun Wang & Hua He, 2020. "Allele-aware chromosome-level genome assembly and efficient transgene-free genome editing for the autotetraploid cultivated alfalfa," Nature Communications, Nature, vol. 11(1), pages 1-11, December.
    3. Adam M. Session & Yoshinobu Uno & Taejoon Kwon & Jarrod A. Chapman & Atsushi Toyoda & Shuji Takahashi & Akimasa Fukui & Akira Hikosaka & Atsushi Suzuki & Mariko Kondo & Simon J. van Heeringen & Ian Qu, 2016. "Genome evolution in the allotetraploid frog Xenopus laevis," Nature, Nature, vol. 538(7625), pages 336-343, October.
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    Cited by:

    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.

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