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Chloranthus genome provides insights into the early diversification of angiosperms

Author

Listed:
  • Xing Guo

    (State Key Laboratory of Agricultural Genomics, BGI-Shenzhen)

  • Dongming Fang

    (State Key Laboratory of Agricultural Genomics, BGI-Shenzhen)

  • Sunil Kumar Sahu

    (State Key Laboratory of Agricultural Genomics, BGI-Shenzhen)

  • Shuai Yang

    (State Key Laboratory of Agricultural Genomics, BGI-Shenzhen)

  • Xuanmin Guang

    (State Key Laboratory of Agricultural Genomics, BGI-Shenzhen)

  • Ryan Folk

    (Mississippi State University)

  • Stephen A. Smith

    (University of Michigan)

  • Andre S. Chanderbali

    (University of Florida)

  • Sisi Chen

    (State Key Laboratory of Agricultural Genomics, BGI-Shenzhen
    Chinese Academy of Sciences)

  • Min Liu

    (State Key Laboratory of Agricultural Genomics, BGI-Shenzhen)

  • Ting Yang

    (State Key Laboratory of Agricultural Genomics, BGI-Shenzhen)

  • Shouzhou Zhang

    (Chinese Academy of Sciences)

  • Xin Liu

    (State Key Laboratory of Agricultural Genomics, BGI-Shenzhen
    BGI-Fuyang, BGI-Shenzhen)

  • Xun Xu

    (State Key Laboratory of Agricultural Genomics, BGI-Shenzhen
    Guangdong Provincial Key Laboratory of Genome Read and Write, BGI-Shenzhen)

  • Pamela S. Soltis

    (University of Florida)

  • Douglas E. Soltis

    (University of Florida
    University of Florida)

  • Huan Liu

    (State Key Laboratory of Agricultural Genomics, BGI-Shenzhen
    University of Copenhagen)

Abstract

Chloranthales remain the last major mesangiosperm lineage without a nuclear genome assembly. We therefore assemble a high-quality chromosome-level genome of Chloranthus spicatus to resolve enigmatic evolutionary relationships, as well as explore patterns of genome evolution among the major lineages of mesangiosperms (eudicots, monocots, magnoliids, Chloranthales, and Ceratophyllales). We find that synteny is highly conserved between genomic regions of Amborella, Vitis, and Chloranthus. We identify an ancient single whole-genome duplication (WGD) (κ) prior to the divergence of extant Chloranthales. Phylogenetic inference shows Chloranthales as sister to magnoliids. Furthermore, our analyses indicate that ancient hybridization may account for the incongruent phylogenetic placement of Chloranthales + magnoliids relative to monocots and eudicots in nuclear and chloroplast trees. Long genes and long introns are found to be prevalent in both Chloranthales and magnoliids compared to other angiosperms. Overall, our findings provide an improved context for understanding mesangiosperm relationships and evolution and contribute a valuable genomic resource for future investigations.

Suggested Citation

  • Xing Guo & Dongming Fang & Sunil Kumar Sahu & Shuai Yang & Xuanmin Guang & Ryan Folk & Stephen A. Smith & Andre S. Chanderbali & Sisi Chen & Min Liu & Ting Yang & Shouzhou Zhang & Xin Liu & Xun Xu & P, 2021. "Chloranthus genome provides insights into the early diversification of angiosperms," Nature Communications, Nature, vol. 12(1), pages 1-14, December.
  • Handle: RePEc:nat:natcom:v:12:y:2021:i:1:d:10.1038_s41467-021-26922-4
    DOI: 10.1038/s41467-021-26922-4
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    References listed on IDEAS

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    1. Yin-Long Qiu & Jungho Lee & Fabiana Bernasconi-Quadroni & Douglas E. Soltis & Pamela S. Soltis & Michael Zanis & Elizabeth A. Zimmer & Zhiduan Chen & Vincent Savolainen & Mark W. Chase, 1999. "The earliest angiosperms: evidence from mitochondrial, plastid and nuclear genomes," Nature, Nature, vol. 402(6760), pages 404-407, November.
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    Cited by:

    1. Ben Liao & You-Huang Xiang & Yan Li & Kai-Yang Yang & Jun-Xiang Shan & Wang-Wei Ye & Nai-Qian Dong & Yi Kan & Yi-Bing Yang & Huai-Yu Zhao & Hong-Xiao Yu & Zi-Qi Lu & Yan Zhao & Qiang Zhao & Dongling G, 2024. "Dysfunction of duplicated pair rice histone acetyltransferases causes segregation distortion and an interspecific reproductive barrier," Nature Communications, Nature, vol. 15(1), pages 1-18, December.
    2. Xing Guo & Fang Wang & Dongming Fang & Qiongqiong Lin & Sunil Kumar Sahu & Liuming Luo & Jiani Li & Yewen Chen & Shanshan Dong & Sisi Chen & Yang Liu & Shixiao Luo & Yalong Guo & Huan Liu, 2023. "The genome of Acorus deciphers insights into early monocot evolution," Nature Communications, Nature, vol. 14(1), pages 1-15, December.
    3. Liang Ma & Ke-Wei Liu & Zhen Li & Yu-Yun Hsiao & Yiying Qi & Tao Fu & Guang-Da Tang & Diyang Zhang & Wei-Hong Sun & Ding-Kun Liu & Yuanyuan Li & Gui-Zhen Chen & Xue-Die Liu & Xing-Yu Liao & Yu-Ting Ji, 2023. "Diploid and tetraploid genomes of Acorus and the evolution of monocots," Nature Communications, Nature, vol. 14(1), pages 1-18, December.

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