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Sequencing and de novo assembly of a near complete indica rice genome

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  • Huilong Du

    (State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences
    College of Life Sciences, University of Chinese Academy of Sciences)

  • Ying Yu

    (State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences)

  • Yanfei Ma

    (State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences)

  • Qiang Gao

    (State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences)

  • Yinghao Cao

    (State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences)

  • Zhuo Chen

    (State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences
    College of Life Sciences, University of Chinese Academy of Sciences)

  • Bin Ma

    (State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences)

  • Ming Qi

    (State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences)

  • Yan Li

    (State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences)

  • Xianfeng Zhao

    (State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences)

  • Jing Wang

    (State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences)

  • Kunfan Liu

    (State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences)

  • Peng Qin

    (Rice Research Institute, Sichuan Agricultural University)

  • Xin Yang

    (State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences)

  • Lihuang Zhu

    (State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences)

  • Shigui Li

    (Rice Research Institute, Sichuan Agricultural University)

  • Chengzhi Liang

    (State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences
    College of Life Sciences, University of Chinese Academy of Sciences)

Abstract

A high-quality reference genome is critical for understanding genome structure, genetic variation and evolution of an organism. Here we report the de novo assembly of an indica rice genome Shuhui498 (R498) through the integration of single-molecule sequencing and mapping data, genetic map and fosmid sequence tags. The 390.3 Mb assembly is estimated to cover more than 99% of the R498 genome and is more continuous than the current reference genomes of japonica rice Nipponbare (MSU7) and Arabidopsis thaliana (TAIR10). We annotate high-quality protein-coding genes in R498 and identify genetic variations between R498 and Nipponbare and presence/absence variations by comparing them to 17 draft genomes in cultivated rice and its closest wild relatives. Our results demonstrate how to de novo assemble a highly contiguous and near-complete plant genome through an integrative strategy. The R498 genome will serve as a reference for the discovery of genes and structural variations in rice.

Suggested Citation

  • Huilong Du & Ying Yu & Yanfei Ma & Qiang Gao & Yinghao Cao & Zhuo Chen & Bin Ma & Ming Qi & Yan Li & Xianfeng Zhao & Jing Wang & Kunfan Liu & Peng Qin & Xin Yang & Lihuang Zhu & Shigui Li & Chengzhi L, 2017. "Sequencing and de novo assembly of a near complete indica rice genome," Nature Communications, Nature, vol. 8(1), pages 1-12, August.
    • Handle: RePEc:nat:natcom:v:8:y:2017:i:1:d:10.1038_ncomms15324
    DOI: 10.1038/ncomms15324
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    Cited by:

    1. Zhe Zhao & Zhi Ding & Jingjing Huang & Hengjun Meng & Zixu Zhang & Xin Gou & Huiwu Tang & Xianrong Xie & Jingyao Ping & Fangming Xiao & Yao-Guang Liu & Yongyao Xie & Letian Chen, 2023. "Copy number variation of the restorer Rf4 underlies human selection of three-line hybrid rice breeding," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
    2. Jingfen Huang & Yilin Zhang & Yapeng Li & Meng Xing & Cailin Lei & Shizhuang Wang & Yamin Nie & Yanyan Wang & Mingchao Zhao & Zhenyun Han & Xianjun Sun & Han Zhou & Yan Wang & Xiaoming Zheng & Xiaoron, 2024. "Haplotype-resolved gapless genome and chromosome segment substitution lines facilitate gene identification in wild rice," Nature Communications, Nature, vol. 15(1), pages 1-15, December.
    3. Kunpeng Li & Peng Xu & Jinpeng Wang & Xin Yi & Yuannian Jiao, 2023. "Identification of errors in draft genome assemblies at single-nucleotide resolution for quality assessment and improvement," Nature Communications, Nature, vol. 14(1), pages 1-12, December.

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