Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2021 Feb;64(2):282-293.
doi: 10.1007/s11427-020-1738-x. Epub 2020 Jul 28.

A chromosome-level genome assembly of the wild rice Oryza rufipogon facilitates tracing the origins of Asian cultivated rice

Xianrong Xie #  1   2 , Huilong Du #  3   4 , Huiwu Tang  1   5 , Jianian Tang  1 , Xiyu Tan  1 , Weizhi Liu  1   2 , Tie Li  1 , Zhansheng Lin  1 , Chengzhi Liang  6   7 , Yao-Guang Liu  8   9
Affiliations

A chromosome-level genome assembly of the wild rice Oryza rufipogon facilitates tracing the origins of Asian cultivated rice

Xianrong Xie et al. Sci China Life Sci. 2021 Feb.

Abstract

Oryza rufipogon Griff. is a wild progenitor of the Asian cultivated rice Oryza sativa. To better understand the genomic diversity of the wild rice, high-quality reference genomes of O. rufipogon populations are needed, which also facilitate utilization of the wild genetic resources in rice breeding. In this study, we generated a chromosome-level genome assembly of O. rufipogon using a combination of short-read sequencing, single-molecule sequencing, BioNano and Hi-C platforms. The genome sequence (399.8 Mb) was assembled into 46 scaffolds on the 12 chromosomes, with contig N50 and scaffold N50 of 13.2 Mb and 20.3 Mb, respectively. The genome contains 36,520 protein-coding genes, and 49.37% of the genome consists of repetitive elements. The genome has strong synteny with those of the O. sativa subspecies indica and japonica, but containing some large structural variations. Evolutionary analysis unveiled the polyphyletic origins of O. sativa, in which the japonica and indica genome formations involved different divergent O. rufipogon (including O. nivara) lineages, accompanied by introgression of genomic regions between japonica and indica. This high-quality reference genome provides insight on the genome evolution of the wild rice and the origins of the O. sativa subspecies, and valuable information for basic research and rice breeding.

Keywords: Oryza rufipogon; evolution; genome; genome sequencing; rice.

PubMed Disclaimer

References

    1. Alexander, D.H., Novembre, J., and Lange, K. (2009). Fast model-based estimation of ancestry in unrelated individuals. Genome Res 19, 1655–1664. - PubMed - PMC
    1. Atwell, B.J., Wang, H., and Scafaro, A.P. (2014). Could abiotic stress tolerance in wild relatives of rice be used to improve Oryza sativa? Plant Sci 215–216, 48–58. - PubMed
    1. Ammiraju, J.S., Luo, M., Goicoechea, J.L., Wang, W., Kudrna, D., Mueller, C., Talag, J., Kim, H.R., Sisneros, N.B., Blackmon, B., et al. (2006). The Oryza bacterial artificial chromosome library resource: Construction and analysis of 12 deep-coverage large-insert BAC libraries that represent the 10 genome types of the genus Oryza. Genome Res 16, 140–147. - PubMed - PMC
    1. Bao, W., Kojima, K.K., and Kohany, O. (2015). Repbase Update, a database of repetitive elements in eukaryotic genomes. Mob DNA 6, 11. - PubMed - PMC
    1. Benson, G. (1999). Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res 27, 573–580. - PubMed - PMC

LinkOut - more resources