De novo genome assembly of Oryza granulata reveals rapid genome expansion and adaptive evolution

被引：20

作者：

Wu, Zhigang ^{[1
]}

Fang, Dongming ^{[2
]}

Yang, Rui ^{[1
]}

Gao, Fei ^{[2
]}

An, Xingyu ^{[1
]}

Zhuo, Xiaoxuan ^{[1
]}

Li, Yafei ^{[3
]}

Yi, Chuandeng ^{[4
]}

Zhang, Tao ^{[4
]}

Liang, Chengzhi ^{[3
]}

Cui, Peng ^{[2
]}

Cheng, Zhukuan ^{[3
]}

Luo, Qiong ^{[1
]}

机构：

[1] Yunnan Agr Univ, State Key Lab Conservat & Utilizat Bioresources Y, Key Lab Agr Biodivers Plant Dis Management, Minist Educ, Kunming 650201, Yunnan, Peoples R China

[2] Chinese Acad Agr Sci, Agr Genom Inst Shenzhen, Shenzhen 518120, Guangdong, Peoples R China

[3] Chinese Acad Sci, Inst Genet & Dev Biol, State Key Lab Plant Genom, Beijing 100101, Peoples R China

[4] Yangzhou Univ, Agr Coll, Yangzhou 225009, Jiangsu, Peoples R China

来源：

COMMUNICATIONS BIOLOGY | 2018年 / 1卷

基金：

中国国家自然科学基金;

关键词：

PHYLOGENETIC ANALYSIS; SATELLITE REPEAT; CENTROMERIC DNA; RICE; IDENTIFICATION; PROGRAM; SEQUENCE; SIZE; TOOL; CONSTRUCTION;

D O I：

10.1038/s42003-018-0089-4

中图分类号：

Q [生物科学];

学科分类号：

07 ; 0710 ; 09 ;

摘要：

The wild relatives of rice have adapted to different ecological environments and constitute a useful reservoir of agronomic traits for genetic improvement. Here we present the similar to 777 Mb de novo assembled genome sequence of Oryza granulata. Recent bursts of long-terminal repeat retrotransposons, especially RIRE2, led to a rapid twofold increase in genome size after O. granulata speciation. Universal centromeric tandem repeats are absent within its centromeres, while gypsy-type LTRs constitute the main centromere-specific repetitive elements. A total of 40,116 protein-coding genes were predicted in O. granulata, which is close to that of Oryza sativa. Both the copy number and function of genes involved in photosynthesis and energy production have undergone positive selection during the evolution of O. granulata, which might have facilitated its adaptation to the low light habitats. Together, our findings reveal the rapid genome expansion, distinctive centromere organization, and adaptive evolution of O. granulata.

引用

页数：10

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