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Genome-wide analysis of Dongxiang wild rice (Oryza rufipogon Griff.) to investigate lost/acquired genes during rice domestication

文献类型： 外文期刊

作者： Zhang, Fantao 1 ; Xu, Tao 2 ; Mao, Linyong 3 ; Yan, Shuangyong 4 ; Chen, Xiwen 5 ; Wu, Zhenfeng 6 ; Chen, Rui 7 ; Luo, Xi 1 ;

作者机构： 1.Jiangxi Normal Univ, Coll Life Sci, Nanchang 330022, Jiangxi, Peoples R China

2.Shanxi Agr Univ, Coll Anim Sci & Vet Med, Taigu 030801, Shanxi, Peoples R China

3.Howard Univ, Dept Biochem & Mol Biol, Coll Med, Washington, DC 20059 USA

4.Tianjin Acad Agr Sci, Tianjin Inst Crop Res, Tianjin 300381, Peoples R China

5.Nankai Univ, Coll Life Sci, Tianjin 300071, Peoples R China

6.Nankai Univ, Sch Math Sci, Tianjin 300071, Peoples R China

7.Tianjin Acad Agr Sci, Tianjin Inst Agr Qual Stand & Testing Technol, Tianjin 300381, Peoples R China

关键词： Dongxiang wild rice;Whole genome sequencing;Transcriptome;Comparative genomics analysis;Structural variation

期刊名称：BMC PLANT BIOLOGY （ 影响因子：4.215； 五年影响因子：4.96 ）

ISSN： 1471-2229

年卷期： 2016 年 16 卷

页码：

收录情况： SCI

摘要： Background: It is widely accepted that cultivated rice (Oryza sativa L.) was domesticated from common wild rice (Oryza rufipogon Griff.). Compared to other studies which concentrate on rice origin, this study is to genetically elucidate the substantially phenotypic and physiological changes from wild rice to cultivated rice at the whole genome level. Results: Instead of comparing two assembled genomes, this study directly compared the Dongxiang wild rice (DXWR) Illumina sequencing reads with the Nipponbare (O. sativa) complete genome without assembly of the DXWR genome. Based on the results from the comparative genomics analysis, structural variations (SVs) between DXWR and Nipponbare were determined to locate deleted genes which could have been acquired by Nipponbare during rice domestication. To overcome the limit of the SV detection, the DXWR transcriptome was also sequenced and compared with the Nipponbare transcriptome to discover the genes which could have been lost in DXWR during domestication. Both 1591 Nipponbare-acquired genes and 206 DXWR-lost transcripts were further analyzed using annotations from multiple sources. The NGS data are available in the NCBI SRA database with ID SRP070627. Conclusions: These results help better understanding the domestication from wild rice to cultivated rice at the whole genome level and provide a genomic data resource for rice genetic research or breeding. One finding confirmed transposable elements contribute greatly to the genome evolution from wild rice to cultivated rice. Another finding suggested the photophosphorylation and oxidative phosphorylation system in cultivated rice could have adapted to environmental changes simultaneously during domestication.

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