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De novo assembly of a Chinese soybean genome

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Abstract

Soybean was domesticated in China and has become one of the most important oilseed crops. Due to bottlenecks in their introduction and dissemination, soybeans from different geographic areas exhibit extensive genetic diversity. Asia is the largest soybean market; therefore, a high–quality soybean reference genome from this area is critical for soybean research and breeding. Here, we report the de novo assembly and sequence analysis of a Chinese soybean genome for “Zhonghuang 13” by a combination of SMRT, Hi–C and optical mapping data. The assembled genome size is 1.025 Gb with a contig N50 of 3.46 Mb and a scaffold N50 of 51.87 Mb. Comparisons between this genome and the previously reported reference genome (cv. Williams 82) uncovered more than 250,000 structure variations. A total of 52,051 protein coding genes and 36,429 transposable elements were annotated for this genome, and a gene co–expression network including 39,967 genes was also established. This high quality Chinese soybean genome and its sequence analysis will provide valuable information for soybean improvement in the future.

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Acknowledgements

This work was supported by the National Natural Science Foundation of China (91531304, 31525018, 31370266, and 31788103), the “Strategic Priority Research Program” of the Chinese Academy of Sciences (XDA08000000), and the State Key Laboratory of Plant Cell and Chromosome Engineering (PCCE–KF–2017–03).

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Authors and Affiliations

  1. State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China

    Yanting Shen, Jixiang Zhang, Yucheng Liu & Zhixi Tian

  2. Provincial Key Laboratory of Agrobiology, Institute of Crop Germplasm and Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China

    Jing Liu & Jianchang Du

  3. School of Life Sciences, University of Science and Technology of China, Hefei, 230027, China

    Haiying Geng & Shisong Ma

  4. Berry Genomics Corporation, Beijing, 100015, China

    Haikuan Zhang & Shilai Xing

  5. University of Chinese Academy of Sciences, Beijing, 100039, China

    Yanting Shen, Jixiang Zhang, Yucheng Liu & Zhixi Tian

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  1. Yanting Shen
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Shen, Y., Liu, J., Geng, H. et al. De novo assembly of a Chinese soybean genome. Sci. China Life Sci. 61, 871–884 (2018). https://doi.org/10.1007/s11427-018-9360-0

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