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

被引：281

作者：

Du, Huilong ^{[1
,2
]}

Yu, Ying ^{[1
]}

Ma, Yanfei ^{[1
]}

Gao, Qiang ^{[1
]}

Cao, Yinghao ^{[1
]}

Chen, Zhuo ^{[1
,2
]}

Ma, Bin ^{[1
]}

Qi, Ming ^{[1
]}

Li, Yan ^{[1
]}

Zhao, Xianfeng ^{[1
]}

Wang, Jing ^{[1
]}

Liu, Kunfan ^{[1
]}

Qin, Peng ^{[3
]}

Yang, Xin ^{[1
]}

Zhu, Lihuang ^{[1
]}

Li, Shigui ^{[3
]}

Liang, Chengzhi ^{[1
,2
]}

机构：

[1] Chinese Acad Sci, Inst Genet & Dev Biol, State Key Lab Plant Genom, 1 Beichen West Rd 2, Beijing 100101, Peoples R China

[2] Univ Chinese Acad Sci, Coll Life Sci, Beijing 100049, Peoples R China

[3] Sichuan Agr Univ, Rice Res Inst, Chengdu 611130, Peoples R China

来源：

NATURE COMMUNICATIONS | 2017年 / 8卷

基金：

中国国家自然科学基金;

关键词：

ORYZA-SATIVA; HYBRID STERILITY; POPULATION; DIVERGENCE; GRAIN; DNA;

D O I：

10.1038/ncomms15324

中图分类号：

O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];

学科分类号：

070301 [无机化学]; 070403 [天体物理学]; 070507 [自然资源与国土空间规划学]; 090105 [作物生产系统与生态工程];

摘要：

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 390.3Mb 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.

引用

页数：12

共 41 条

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