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Chromosome conformation capture resolved near complete genome assembly of broomcorn millet

Author

Listed:
  • Junpeng Shi

    (China Agricultural University)

  • Xuxu Ma

    (China Agricultural University)

  • Jihong Zhang

    (China Agricultural University)

  • Yingsi Zhou

    (China Agricultural University)

  • Minxuan Liu

    (Chinese Academy of Agricultural Sciences)

  • Liangliang Huang

    (China Agricultural University)

  • Silong Sun

    (China Agricultural University)

  • Xiangbo Zhang

    (China Agricultural University)

  • Xiang Gao

    (China Agricultural University)

  • Wei Zhan

    (Annoroad Gene Technology (Beijing) Co., Ltd)

  • Pinghua Li

    (Shandong Agricultural University)

  • Lun Wang

    (Shanxi Academy of Agricultural Sciences)

  • Ping Lu

    (Chinese Academy of Agricultural Sciences)

  • Haiming Zhao

    (China Agricultural University)

  • Weibin Song

    (China Agricultural University)

  • Jinsheng Lai

    (China Agricultural University
    China Agricultural University)

Abstract

Broomcorn millet (Panicum miliaceum L.) has strong tolerance to abiotic stresses, and is probably one of the oldest crops, with its earliest cultivation that dated back to ca. ~10,000 years. We report here its genome assembly through a combination of PacBio sequencing, BioNano, and Hi-C (in vivo) mapping. The 18 super scaffolds cover ~95.6% of the estimated genome (~887.8 Mb). There are 63,671 protein-coding genes annotated in this tetraploid genome. About ~86.2% of the syntenic genes in foxtail millet have two homologous copies in broomcorn millet, indicating rare gene loss after tetraploidization in broomcorn millet. Phylogenetic analysis reveals that broomcorn millet and foxtail millet diverged around ~13.1 Million years ago (Mya), while the lineage specific tetraploidization of broomcorn millet may be happened within ~5.91 million years. The genome is not only beneficial for the genome assisted breeding of broomcorn millet, but also an important resource for other Panicum species.

Suggested Citation

  • Junpeng Shi & Xuxu Ma & Jihong Zhang & Yingsi Zhou & Minxuan Liu & Liangliang Huang & Silong Sun & Xiangbo Zhang & Xiang Gao & Wei Zhan & Pinghua Li & Lun Wang & Ping Lu & Haiming Zhao & Weibin Song &, 2019. "Chromosome conformation capture resolved near complete genome assembly of broomcorn millet," Nature Communications, Nature, vol. 10(1), pages 1-9, December.
    • Handle: RePEc:nat:natcom:v:10:y:2019:i:1:d:10.1038_s41467-018-07876-6
    DOI: 10.1038/s41467-018-07876-6
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    Cited by:

    1. Taikui Zhang & Weichen Huang & Lin Zhang & De-Zhu Li & Ji Qi & Hong Ma, 2024. "Phylogenomic profiles of whole-genome duplications in Poaceae and landscape of differential duplicate retention and losses among major Poaceae lineages," Nature Communications, Nature, vol. 15(1), pages 1-27, December.
    2. Aiping Song & Jiangshuo Su & Haibin Wang & Zhongren Zhang & Xingtan Zhang & Yves Peer & Fei Chen & Weimin Fang & Zhiyong Guan & Fei Zhang & Zhenxing Wang & Likai Wang & Baoqing Ding & Shuang Zhao & Li, 2023. "Analyses of a chromosome-scale genome assembly reveal the origin and evolution of cultivated chrysanthemum," Nature Communications, Nature, vol. 14(1), pages 1-15, December.

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