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Sci China Life Sci. 2018 Aug;61(8):871-884. doi: 10.1007/s11427-018-9360-0. Epub 2018 Jul 27.

De novo assembly of a Chinese soybean genome.

Author information

1
State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China.
2
University of Chinese Academy of Sciences, Beijing, 100039, China.
3
Provincial Key Laboratory of Agrobiology, Institute of Crop Germplasm and Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China.
4
School of Life Sciences, University of Science and Technology of China, Hefei, 230027, China.
5
Berry Genomics Corporation, Beijing, 100015, China.
6
Provincial Key Laboratory of Agrobiology, Institute of Crop Germplasm and Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China. dujianchang@hotmail.com.
7
School of Life Sciences, University of Science and Technology of China, Hefei, 230027, China. sma@ustc.edu.cn.
8
State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China. zxtian@genetics.ac.cn.
9
University of Chinese Academy of Sciences, Beijing, 100039, China. zxtian@genetics.ac.cn.

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.

KEYWORDS:

Gmax_ZH13; Zhonghuang 13; de novo soybean genome; gene co–expression network; structure variation

PMID:
30062469
DOI:
10.1007/s11427-018-9360-0
[Indexed for MEDLINE]

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