September 22, 2019  |  

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

Authors: Wu, Zhigang and Fang, Dongming and Yang, Rui and Gao, Fei and An, Xingyu and Zhuo, Xiaoxuan and Li, Yafei and Yi, Chuandeng and Zhang, Tao and Liang, Chengzhi and others

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.

Journal: Communications biology
DOI: 10.1038/s42003-018-0089-4
Year: 2018

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