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A chromosome-level genome assembly of the wild rice Oryza rufipogon facilitates tracing the origins of Asian cultivated rice

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Abstract

Oryza rufipogon Griff. is a wild progenitor of the Asian cultivated rice Oryza sativa. To better understand the genomic diversity of the wild rice, high-quality reference genomes of O. rufipogon populations are needed, which also facilitate utilization of the wild genetic resources in rice breeding. In this study, we generated a chromosome-level genome assembly of O. rufipogon using a combination of short-read sequencing, single-molecule sequencing, BioNano and Hi-C platforms. The genome sequence (399.8 Mb) was assembled into 46 scaffolds on the 12 chromosomes, with contig N50 and scaffold N50 of 13.2 Mb and 20.3 Mb, respectively. The genome contains 36,520 protein-coding genes, and 49.37% of the genome consists of repetitive elements. The genome has strong synteny with those of the O. sativa subspecies indica and japonica, but containing some large structural variations. Evolutionary analysis unveiled the polyphyletic origins of O. sativa, in which the japonica and indica genome formations involved different divergent O. rufipogon (including O. nivara) lineages, accompanied by introgression of genomic regions between japonica and indica. This high-quality reference genome provides insight on the genome evolution of the wild rice and the origins of the O. sativa subspecies, and valuable information for basic research and rice breeding.

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Acknowledgements

This work was supported by the Key Research Program of Guangzhou Science Technology and Innovation Commission (201904020030), the Major Program of Guangdong Basic and Applied Basic Research (2019B030302006) and the National Natural Science Foundation of China (31701051). We thank IRRI for providing the plant material. We thank Xiangdong Liu for the assistance with growing and maintaining the plants.

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  1. State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China

    Xianrong Xie, Huiwu Tang, Jianian Tang, Xiyu Tan, Weizhi Liu, Tie Li, Zhansheng Lin & Yao-Guang Liu

  2. State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China

    Huilong Du & Chengzhi Liang

  3. Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China

    Xianrong Xie, Weizhi Liu & Yao-Guang Liu

  4. University of Chinese Academy of Sciences, Beijing, 100049, China

    Huilong Du & Chengzhi Liang

  5. College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, China

    Huiwu Tang

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Xie, X., Du, H., Tang, H. et al. A chromosome-level genome assembly of the wild rice Oryza rufipogon facilitates tracing the origins of Asian cultivated rice. Sci. China Life Sci. 64, 282–293 (2021). https://doi.org/10.1007/s11427-020-1738-x

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