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

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 ~777 Mb de novo assembled genome sequence of Oryza granulata . Recent bursts of long-terminal repeat retrotransposons, espec...

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Published in:Communications biology 2018-06, Vol.1 (1), p.84-84, Article 84
Main Authors: Wu, Zhigang, Fang, Dongming, Yang, Rui, Gao, Fei, An, Xingyu, Zhuo, Xiaoxuan, Li, Yafei, Yi, Chuandeng, Zhang, Tao, Liang, Chengzhi, Cui, Peng, Cheng, Zhukuan, Luo, Qiong
Format: Article
Language:English
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631/1647/334/2244/1791
631/181/735
631/208/212/2304
631/449/2669
Biology
Biomedical and Life Sciences
Centromeres
Copy number
Evolution
Evolution & development
Genomes
Life Sciences
Long terminal repeat
Nucleotide sequence
Oryza granulata
Photosynthesis
Positive selection
Speciation
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Summary: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 ~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 . Zhigang Wu, Dongming Fang, Rui Yang, et al. present the genome assembly of a wild rice species Oryza granulata , revealing critical insights about the rapid genome expansion and evolution observed in the Oryza genus. They find that recent bursts of LTR retrotransposons have led to the rapid increase in O. granulate genome size following speciation.
ISSN:2399-3642
2399-3642
DOI:10.1038/s42003-018-0089-4