De novo assembly of a Chinese soybean genome

被引：125

作者：

Shen, Yanting ^{[1
,5
]}

Liu, Jing ^{[2
]}

Geng, Haiying ^{[3
]}

Zhang, Jixiang ^{[1
,5
]}

Liu, Yucheng ^{[1
,5
]}

Zhang, Haikuan ^{[4
]}

Xing, Shilai ^{[4
]}

Du, Jianchang ^{[2
]}

Ma, Shisong ^{[3
]}

Tian, Zhixi ^{[1
,5
]}

机构：

[1] Chinese Acad Sci, Inst Genet & Dev Biol, State Key Lab Plant Cell & Chromosome Engn, Beijing 100101, Peoples R China

[2] Jiangsu Acad Agr Sci, Inst Crop Germplasm & Biotechnol, Prov Key Lab Agrobiol, Nanjing 210014, Jiangsu, Peoples R China

[3] Univ Sci & Technol China, Sch Life Sci, Hefei 230027, Anhui, Peoples R China

[4] Berry Genom Corp, Beijing 100015, Peoples R China

[5] Univ Chinese Acad Sci, Beijing 100039, Peoples R China

来源：

SCIENCE CHINA-LIFE SCIENCES | 2018年 / 61卷 / 08期

基金：

中国国家自然科学基金;

关键词：

de novo soybean genome; Zhonghuang; 13; Gmax_ZH13; structure variation; gene co-expression; QUANTITATIVE TRAIT LOCI; MAX L.-MERR; RNA-SEQ DATA; GLYCINE-MAX; FLOWERING TIME; AGRONOMIC TRAITS; TRANSPOSABLE ELEMENTS; GENETIC DIVERSITY; MATURITY LOCUS; QTL ANALYSIS;

D O I：

10.1007/s11427-018-9360-0

中图分类号：

Q [生物科学];

学科分类号：

07 ; 0710 ; 09 ;

摘要：

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.

引用

页码：871 / 884

页数：14

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